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Manchev YT, Popelier PLA. FFLUX molecular simulations driven by atomic Gaussian process regression models. J Comput Chem 2024; 45:1235-1246. [PMID: 38345165 DOI: 10.1002/jcc.27323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 04/19/2024]
Abstract
Machine learning (ML) force fields are revolutionizing molecular dynamics (MD) simulations as they bypass the computational cost associated with ab initio methods but do not sacrifice accuracy in the process. In this work, the GPyTorch library is used to create Gaussian process regression (GPR) models that are interfaced with the next-generation ML force field FFLUX. These models predict atomic properties of different molecular configurations that appear in a progressing MD simulation. An improved kernel function is utilized to correctly capture the periodicity of the input descriptors. The first FFLUX molecular simulations of ammonia, methanol, and malondialdehyde with the updated kernel are performed. Geometry optimizations with the GPR models result in highly accurate final structures with a maximum root-mean-squared deviation of 0.064 Å and sub-kJ mol-1 total energy predictions. Additionally, the models are tested in 298 K MD simulations with FFLUX to benchmark for robustness. The resulting energy and force predictions throughout the simulation are in excellent agreement with ab initio data for ammonia and methanol but decrease in quality for malondialdehyde due to the increased system complexity. GPR model improvements are discussed, which will ensure the future scalability to larger systems.
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Affiliation(s)
- Yulian T Manchev
- Department of Chemistry, The University of Manchester, Manchester, Great Britain
| | - Paul L A Popelier
- Department of Chemistry, The University of Manchester, Manchester, Great Britain
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El Bakri Y, Ahmad B, Saravanan K, Ahmad I, Bakhite EA, Younis O, Al-Waleedy SAH, Ibrahim OF, Nafady A, Mague JT, Mohamed SK. Insight into crystal structures and identification of potential styrylthieno[2,3- b]pyridine-2-carboxamidederivatives against COVID-19 Mpro through structure-guided modeling and simulation approach. J Biomol Struct Dyn 2024; 42:4325-4343. [PMID: 37318002 DOI: 10.1080/07391102.2023.2220799] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/28/2023] [Indexed: 06/16/2023]
Abstract
Anti-SARS-CoV-2 drugs are urgently needed to prevent the pandemic and for immunization. Their protease inhibitor treatment for COVID-19 has been used in clinical trials. In Calu-3 and THP1 cells, 3CL SARS-CoV-2 Mpro protease is required for viral expression, replication, and the activation of the cytokines IL-1, IL-6, and TNF-. The Mpro structure was chosen for this investigation because of its activity as a chymotrypsin-like enzyme and the presence of a cysteine-containing catalytic domain. Thienopyridine derivatives increase the release of nitric oxide from coronary endothelial cells, which is an important cell signaling molecule with antibacterial activity against bacteria, protozoa, and some viruses. Using DFT calculations, global descriptors are computed from HOMO-LUMO orbitals; the molecular reactivity sites are analyzed from an electrostatic potential map. NLO properties are calculated, and topological analysis is also part of the QTAIM studies. Both compounds 1 and 2 were designed from the precursor molecule pyrimidine and exhibited binding energies (-14.6708 kcal/mol and -16.4521 kcal/mol). The binding mechanisms of molecule 1 towards SARS-COV-2 3CL Mpro exhibited strong hydrogen bonding as well as Vdw interaction. In contrast, derivative 2 was bound to the active site protein's active studied that several residues and positions, including (His41, Cys44, Asp48, Met49, Pro52, Tyr54, Phe140, Leu141, Ser144, His163, Ser144, Cys145, His164, Met165, Glu166, Leu167, Asp187, Gln189, Thr190, and GLn192) are critical for the maintenance of inhibitors inside the active pocket. Molecular docking and 100 ns MD simulation analysis revealed that Both compounds 1 and 2 with higher binding affinity and stability toward the SARS-COV-2 3CL Mpro protein. Binding free energy calculations and other MD parameters support the finding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | - Basharat Ahmad
- Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | | | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, Maharashtra, India
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Etify A Bakhite
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
| | - Osama Younis
- Chemistry Department, Faculty of Science, the New Valley University, El-Kharja, Egypt
| | | | - Omaima F Ibrahim
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
| | - Ayman Nafady
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Shaaban K Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester, England
- Chemistry Department, Faculty of Science, Minia University, El-Minia, Egypt
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Karnamkkott HS, Das S, Mondal T, Mondal KC. Small molecule activation by sila/germa boryne species. J Comput Chem 2024; 45:804-819. [PMID: 38135467 DOI: 10.1002/jcc.27275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
The inability of p-block elements to participate in π-backbonding restricts them from activating small molecules like CO, H2 , and so forth. However, the development of the main group metallomimetics became a new pathway, where the main-group elements like boron can bind and activate small molecules like CO and H2 . The concept of the frustrated Lewis pair, Boron-Boron multiple bonds, and borylene are previously illustrated. Some of these reported classes of boron species can mimic the jobs of the metal complexes. Hence, we have theoretically studied the binding of CO/N2 molecules at B-center of elusive species like sila/germa boryne stabilized by donor base ligands (cAAC)BE(Me)(L), where E Si, L cAACMe , NHCMe , PMe3 , E Ge, L cAACMe and (NHCMe )BE(Me)(cAACMe )). The substitutional analogues of (cAACR )BSiR1 (cAAC) and E P, L cAACMe ) have been studied by density functional theory (DFT), natural bond orbital, QTAIM calculations and energy decomposition analysis (EDA) coupled with natural orbital for chemical valence (NOCV) analyses. The computed bond dissociation energy and inner stability analyses by the EDA-NOCV method showed that the CO molecule can bind at the B-center of the above-mentioned species due to stronger σ-donor ability while binding of N2 has been theoretically predicted to be weak. The energy barrier for the CO binding is estimated to be 13-14 kcal/mol by transition state calculation. The change of partial triple bond character to single bond nature of the BSi bond and the bending of CBSi bond angle of sila-boryne species are the reason for the activation energy. Our study reveals the ability of such species to bind and activate the CO molecule to mimic the transition metal-containing complexes. We have additionally shown that binding of Fe(CO)4 and Ni(CO)3 is feasible at Si-center after binding of CO at the B-center.
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Affiliation(s)
| | - Sujit Das
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, India
| | - Totan Mondal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
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Esquivel RO, Carrera E. The separability problem in molecular quantum systems: Information-Theoretic framework for Atoms in Molecules. Chemphyschem 2024:e202400030. [PMID: 38646938 DOI: 10.1002/cphc.202400030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
Even though molecules are fundamentally quantum entities, the concept of a molecule retains certain classical attributes concerning its constituents. This includes the empirical separability of a molecule into its three-dimensional, rigid structure in Euclidean space, a framework often obtained through experimental methods like X-Ray crystallography. In this work, we delve into the mathematical implications of partitioning a molecule into its constituent parts using the widely recognized Atoms-In-Molecules (AIM) schemes, aiming to establish their validity within the framework of Information Theory concepts. We have uncovered information-theoretical justifications for employing some of the most prevalent AIM schemes in the field of Chemistry, including Hirshfeld (stockholder partitioning), Bader's (topological dissection), and the quantum approach (Hilbert's space definition). In the first approach we have applied the generalized principle of minimum relative entropy derived from Sharma-Mittal relative entropy, avoiding the need for an arbitrary selection of reference promolecular atoms. Within the realm of topological-information partitioning, we have demonstrated that the Fisher information of Bader's atoms conform to a comprehensive theory based on the Principle of Extreme Physical Information. For the quantum approach we have presented information-theoretic justifications for conducting Löwdin symmetric transformations on the density matrix to form atomic Hilbert spaces.
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Affiliation(s)
- Rodolfo O Esquivel
- Universidad Autonoma Metropolitana Iztapalapa Division of Basic Sciences and Engineering, CHEMISTRY, San Rafael Atlixco 186, Col Vicentina, 09340, MEXICO CITY, MEXICO
| | - Edmundo Carrera
- Universidad Autonoma Metropolitana Iztapalapa Division of Basic Sciences and Engineering, chemistry, MEXICO
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Barbosa WG, Santos-Jr CV, Andrade RB, Lucena JR, Moura RT. Bond analysis in meta- and para-substituted thiophenols: overlap descriptors, local mode analysis, and QTAIM. J Mol Model 2024; 30:139. [PMID: 38639900 DOI: 10.1007/s00894-024-05932-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/07/2024] [Indexed: 04/20/2024]
Abstract
CONTEXT This study delves into the chemical nuances of thiophenols and their derivatives through a comprehensive computational analysis, moving beyond traditional energetic perspectives such as bond dissociation enthalpy and S-H dissociation dynamics. By employing the overlap model along with its topological descriptors (OP/TOP), quantum theory of atoms in molecules (QTAIM), and local vibrational mode (LVM) theories, the research provides a deeper understanding of the S-H and C-S bonding scenarios in substituted thiophenols. The investigation follows the electron-donating capacity of S-H substituent variation with the nature and positioning of other ring substituents. Energy profile analyses indicate distinct stability differences in the cis and trans conformations of meta- and para-PhSH systems, influenced by the electron-donating strength of these substituents. The study also uncovers significant variations in S-H bond distances and descriptor values, particularly in para-substituted PhSH, reflecting the influence of electron-donating or withdrawing substituents. In contrast, alterations at the meta-position show minimal effects on C-S bond descriptors, while para-substitutions markedly influence C-S bond characteristics, demonstrating a clear correlation with the electron-donating or withdrawing capabilities of the substituents. This research sheds light on the intricate bond dynamics in aromatic systems with diverse substituents, highlighting the complex interaction between electronic effects and molecular conformation. METHODS The study employs the ω B97X-D/Def2TZVP level of theory for molecular geometries, ensuring accurate characterization of structures as true minima via analytical harmonic frequency determination. The electronic properties of S-H and C-S bonds in variously substituted thiophenols were analyzed using OP/TOP, QTAIM, and LVM methodologies. Computational processes, including conformational scans, geometry optimizations, and vibrational frequency calculations, were conducted using Gaussian 09, with ultra-fine integration grids and tight convergence criteria for the SCF procedure. Bond descriptors were computed utilizing ChemBOS, Multiwfn, and LModeA software, providing a robust and detailed examination of bond properties.
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Affiliation(s)
- Willis G Barbosa
- Department of Chemistry, State University of Paraiba, Campina Grande, 58429-500, PB, Brazil
| | - Carlos V Santos-Jr
- Department of Chemistry, Federal University of Paraiba, João Pessoa, 58051-970, PB, Brazil
| | - Railton B Andrade
- Department of Chemistry, State University of Paraiba, Campina Grande, 58429-500, PB, Brazil
| | - Juracy R Lucena
- Department of Chemistry, State University of Paraiba, Campina Grande, 58429-500, PB, Brazil
| | - Renaldo T Moura
- Department of Chemistry and Physics, Center of Agrarian Sciences, Federal University of Paraiba, Areia, 58397-000, PB, Brazil.
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, 75275, USA.
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Taylor LJ, Lawson EE, Cordes DB, Athukorala Arachchige KS, Slawin AMZ, Chalmers BA, Kilian P. Synthesis and Structural Studies of peri-Substituted Acenaphthenes with Tertiary Phosphine and Stibine Groups. Molecules 2024; 29:1841. [PMID: 38675660 DOI: 10.3390/molecules29081841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Two mixed peri-substituted phosphine-chlorostibines, Acenap(PiPr2)(SbPhCl) and Acenap(PiPr2)(SbCl2) (Acenap = acenaphthene-5,6-diyl) reacted cleanly with Grignard reagents or nBuLi to give the corresponding tertiary phosphine-stibines Acenap(PiPr2)(SbRR') (R, R' = Me, iPr, nBu, Ph). In addition, the Pt(II) complex of the tertiary phosphine-stibine Acenap(PiPr2)(SbPh2) as well as the Mo(0) complex of Acenap(PiPr2)(SbMePh) were synthesised and characterised. Two of the phosphine-stibines and the two metal complexes were characterised by single-crystal X-ray diffraction. The peri-substituted species act as bidentate ligands through both P and Sb atoms, forming rather short Sb-metal bonds. The tertiary phosphine-stibines display through-space J(CP) couplings between the phosphorus atom and carbon atoms bonded directly to the Sb atom of up to 40 Hz. The sequestration of the P and Sb lone pairs results in much smaller corresponding J(CP) being observed in the metal complexes. QTAIM (Quantum Theory of Atoms in Molecules) and EDA-NOCV (Energy Decomposition Analysis employing Naturalised Orbitals for Chemical Valence) computational techniques were used to provide additional insight into a weak n(P)→σ*(Sb-C) intramolecular bonding interaction (pnictogen bond) in the phosphine-stibines.
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Affiliation(s)
- Laurence J Taylor
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Emma E Lawson
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - David B Cordes
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | | | - Alexandra M Z Slawin
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Brian A Chalmers
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Petr Kilian
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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Paul BK. Blue- and Red-Shifting C-H×××O Hydrogen Bonds of Cyclic Ethers with Haloforms: Effect of Ring-Size and Consistency with Bent's Rule. Chemphyschem 2024:e202400263. [PMID: 38590027 DOI: 10.1002/cphc.202400263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
A DFT-based computational study is carried out to delve into the interplay between hyperconjugation and rehybridization effects underlying the formation of blue- or red-shifting H-bonds (HBs) in 1:1 complexes of cyclic ethers (HB acceptor) of varying ring-size with haloforms, CHF3 and CHCl3 (HB donor). The calculations reveal that with decreasing angular strain (increasing ring-size) of the cyclic ethers, the extent of blue-shift increases for 1:1 complexes with CHF3, while a reverse sequence is observed with CHCl3, eventually leading to a red-shifting HB in the oxepane:CHCl3 complex. It is noted that the trend in the shift of C-H stretching fundamental is not mirrored by the C-H bond length or interaction energies for both the systems studied, that is, the low sensitivity of the changes on the strain on the O-atom of HB acceptor (cyclic ethers) is to be emphasized.
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Affiliation(s)
- Bijan K Paul
- West Bengal State University, Chemistry, 700120, Kolkata, INDIA
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Tumakuru Nagarajappa L, Chikkappaiahnayaka S, Benedict Leoma M, Isamura BK, Venkatesh K, Singh KR, Sindogi K, Mandayam Anandalwar S, P Sadashiva M. Unraveling the crystal structure, stability and drug likeness of 1,3,4-oxadiazole derivatives against Myelofibrosis: a combined experimental and computational investigation. J Biomol Struct Dyn 2024:1-15. [PMID: 38555733 DOI: 10.1080/07391102.2024.2330013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/20/2024] [Indexed: 04/02/2024]
Abstract
Herein, we report the synthesis and characterization of novel 1,3,4-oxadiazole derivatives, 2-methoxybenzyl 5-(4-chlorophenyl)-1,3,4-oxadiazole-2-carboxylate (C1) 2-methoxybenzyl 5-(2-chlorophenyl)-1,3,4-oxadiazole-2-carboxylate (C2), and methoxybenzyl 5-(3-chlorophenyl)-1,3,4-oxadiazole-2-carboxylate (C3) obtained through desulfurative cyclization reaction. The compound C2 was crystallized, and its crystal structure was elucidated using single-crystal X-ray diffraction technique. The Hirshfeld surface analysis was carried out to analyze, visualize and globally appreciate the weak interactions involved in crystal packing. These analyses were complemented by Quantum Theory of Atoms In Molecules (QTAIM) and Reduced Density Gradient (RDG), which allowed us to decipher the nature and types of attractive forces that contribute to maintain the crystal structure of the titled compound. Moreover, the ADME profile of the compound was predicted to assess its drug likeness. Finally, in silico studies were performed to explore the binding affinity of the compounds (C1-3) against Myelofibrosis through molecular docking and molecular dynamic simulations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lohith Tumakuru Nagarajappa
- Department of Physics, The National Institute of Engineering, Mysuru, India
- Department of Studies in Physics, University of Mysore, Mysuru, Karnataka, India
| | | | | | | | - Karthik Venkatesh
- Department of Studies in Physics, University of Mysore, Mysuru, Karnataka, India
| | - Krishna Ravi Singh
- Department of Studies in Chemistry, University of Mysore, Mysuru, Karnataka, India
| | - Kishorkumar Sindogi
- Solid state and Structural Chemistry Unit (SSCU), Indian Institute of Science (IISc), Bangalore, India
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Chérif I, Gassoumi B, Ayachi H, Echabaane M, Caccamo MT, Magazù S, Said AH, Taoufik B, Ayachi S. A theoretical and electrochemical impedance spectroscopy study of the adsorption and sensing of selected metal ions by 4-morpholino-7-nitrobenzofuran. Heliyon 2024; 10:e26709. [PMID: 38439845 PMCID: PMC10909671 DOI: 10.1016/j.heliyon.2024.e26709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
The selectivity of a novel chemosensor, based on a modified nitrobenzofurazan referred to as NBD-Morph, has been investigated for the detection of heavy metal cations (Co2+, Pb2+, Mg2+, Ag+, Cu2+, Hg2+, Ni2+, and Zn2+). The ligand, 4-morpholino-7-nitrobenzofurazan (NBD-Morph), was characterized using spectroscopic techniques including FT-IR and 1H NMR. Vibrational frequencies obtained from FT-IR and proton NMR (1H) chemical shifts were accurately predicted employing the density functional theory (DFT) at the B3LYP level of theory. Furthermore, an examination of the structural, electronic, and quantum chemical properties was conducted and discussed. DFT calculations were employed to explore the complex formation ability of the NBD-Morph ligand with Co2+, Pb2+, Mg2+, Ag+, Cu2+, Hg2+, Ni2+, and Zn2+ metal cations. The comparison of adsorption energies for all possible conformations reveals that NBD-Morph exhibits sensitivity and selectivity towards metal ions, including Pb2+, Cu2+, Ag+, and Ni2+. However, an assessment of their reactivity using QTAIM topological parameters demonstrated the ligand's greater complexation ability toward Cu2+ or Ni2+ than those formed by Pb2+ or Ag+. Additionally, molecular electrostatic potential (MEP), Hirshfeld surfaces, and their associated 2D-fingerprint plots were applied to a detailed study of the inter-molecular interactions in NBD-Morph-X (X = Pb2+, Cu2+, Ag+, Ni2+) complexes. The electron localization function (ELF) and the localized-orbital locator (LOL) were generated to investigate the charge transfer and donor-acceptor interactions within the complexes. Electrochemical analysis further corroborates the theoretical findings, supporting the prediction of NBD-Morph's sensory ability towards Ni2+ metal cations. In conclusion, NBD-Morph stands out as a promising sensor for Ni2+.
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Affiliation(s)
- Imen Chérif
- Laboratory of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, Avenue of the Environment 5019 Monastir, University of Monastir, Tunisia
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università di Messina, Viale Ferdinando Stagno D'Alcontres No. 31, S. Agata, 98166, Messina, Italy
| | - Bouzid Gassoumi
- Laboratoire Interfaces et Matériaux Avancés (LIMA), Faculté des Sciences, Université de Monastir, Avenue de l’Environnement, 5019, Monastir, Tunisia
| | - Hajer Ayachi
- Laboratoire de Chimie Hétérocyclique, Produits Naturels et Réactivité (LR11ES39), Faculté des Sciences, Université de Monastir, Avenue de l’Environnement, 5019, Monastir, Tunisia
| | - Mosaab Echabaane
- CRMN, Centre de Recherche en Microélectronique et Nanotechnologie de Sousse, Nanomisene, LR16CRMN01, 4054, Sousse, Tunisie
| | - Maria Teresa Caccamo
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università di Messina, Viale Ferdinando Stagno D'Alcontres No. 31, S. Agata, 98166, Messina, Italy
| | - Salvatore Magazù
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università di Messina, Viale Ferdinando Stagno D'Alcontres No. 31, S. Agata, 98166, Messina, Italy
| | - Ayoub Haj Said
- Laboratoire Interfaces et Matériaux Avancés (LIMA), Faculté des Sciences, Université de Monastir, Avenue de l’Environnement, 5019, Monastir, Tunisia
| | - Boubaker Taoufik
- Laboratoire de Chimie Hétérocyclique, Produits Naturels et Réactivité (LR11ES39), Faculté des Sciences, Université de Monastir, Avenue de l’Environnement, 5019, Monastir, Tunisia
| | - Sahbi Ayachi
- Laboratory of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, Avenue of the Environment 5019 Monastir, University of Monastir, Tunisia
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Devi R, Sharma K, Ghule VD, Dharavath S. Bistriazolotriazole-tetramine: commendable energetic moiety and cation. J Mol Model 2024; 30:98. [PMID: 38461222 DOI: 10.1007/s00894-024-05892-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
CONTEXT Various 7H,7'H-[6,6'-bi[1,2,4]triazolo[4,3-b][1,2,4]triazole]-3,3',7,7'-tetramine (A) based nitrogen-rich energetic salts were designed and their properties explored. All energetic salts possess relatively high nitrogen content (> 48%), positive heats of formation (> 429 kJ/mol) and stability owing to a significant contribution from fused backbone. The cationic component shows a very high heat of formation (2516 kJ/mol); therefore, it is highly suitable for enthalpy enhancement in new energetic salts. The cation was paired with the energetic anions nitrate (NO3-), perchlorate (ClO4-), dinitromethanide (CH(NO2)2-), trinitromethanide (C(NO2)3-), nitroamide (NHNO2-), and dinitroamide (N(NO2)2-) to improve oxygen balance and detonation performance. Designed salts show moderate detonation velocities (7.9-8.7 km/s) and pressures (23.8 - 33.1 GPa). The distribution of frontier molecular orbitals, molecular electrostatic surface potentials, QTAIM topological properties, and noncovalent interactions of designed salts were simulated to understand the electronic structures, charge distribution in molecules, hydrogen bonding, and other nonbond interactions. The predicted safety factor (SF) and impact sensitivity (H50) of designed salts suggest their insensitivity to mechanical stimuli. This work explored the 7H,7'H-[6,6'-bi[1,2,4]triazolo[4,3-b][1,2,4]triazole]-3,3',7,7'-tetramine as a suitable cationic component which could be promising and serve exemplarily in energetic materials. METHODS The optimization and energy calculations of all the designed compounds were carried out at the B3LYP/6-311 + + G(d,p) and M06-2X/def2-TZVPP levels, utilizing the Gaussian software package. The molecular surface electrostatic potential, quantum theory of atoms in molecules (QTAIM), reduced density gradient (RDG), and noncovalent interaction (NCI) analysis were performed by employing Multiwfn software. The EXPLO5 (v 7.01) thermochemical code and PILEM web application were used to predict the detonation properties.
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Affiliation(s)
- Rimpi Devi
- Department of Chemistry, National Institute of Technology Kurukshetra, Kurukshetra, 136119, Haryana, India
| | - Kalpana Sharma
- Department of Chemistry, National Institute of Technology Kurukshetra, Kurukshetra, 136119, Haryana, India
| | - Vikas D Ghule
- Department of Chemistry, National Institute of Technology Kurukshetra, Kurukshetra, 136119, Haryana, India.
| | - Srinivas Dharavath
- Energetic Materials Laboratory, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, Uttar Pradesh, India
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Falcioni F, Bennett S, Stroer-Jarvis P, Popelier PLA. Probing Non-Covalent Interactions through Molecular Balances: A REG-IQA Study. Molecules 2024; 29:1043. [PMID: 38474554 DOI: 10.3390/molecules29051043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
The interaction energies of two series of molecular balances (1-X with X = H, Me, OMe, NMe2 and 2-Y with Y = H, CN, NO2, OMe, NMe2) designed to probe carbonyl…carbonyl interactions were analysed at the B3LYP/6-311++G(d,p)-D3 level of theory using the energy partitioning method of Interacting Quantum Atoms/Fragments (IQA/IQF). The partitioned energies are analysed by the Relative Energy Gradient (REG) method, which calculates the correlation between these energies and the total energy of a system, thereby explaining the role atoms have in the energetic behaviour of the total system. The traditional "back-of-the-envelope" open and closed conformations of molecular balances do not correspond to those of the lowest energy. Hence, more care needs to be taken when considering which geometries to use for comparison with the experiment. The REG-IQA method shows that the 1-H and 1-OMe balances behave differently to the 1-Me and 1-NMe2 balances because the latter show more prominent electrostatics between carbonyl groups and undergoes a larger dihedral rotation due to the bulkiness of the functional groups. For the 2-Y balance, REG-IQA shows the same behaviour across the series as the 1-H and 1-OMe balances. From an atomistic point of view, the formation of the closed conformer is favoured by polarisation and charge-transfer effects on the amide bond across all balances and is counterbalanced by a de-pyramidalisation of the amide nitrogen. Moreover, focusing on the oxygen of the amide carbonyl and the α-carbon of the remaining carbonyl group, electrostatics have a major role in the formation of the closed conformer, which goes against the well-known n-π* interaction orbital overlap concept. However, REG-IQF shows that exchange-correlation energies overtake electrostatics for all the 2-Y balances when working with fragments around the carbonyl groups, while they act on par with electrostatics for the 1-OMe and 1-NMe2. REG-IQF also shows that exchange-correlation energies in the 2-Y balance are correlated to the inductive electron-donating and -withdrawing trends on aromatic groups. We demonstrate that methods such as REG-IQA/IQF can help with the fine-tuning of molecular balances prior to the experiment and that the energies that govern the probed interactions are highly dependent on the atoms and functional groups involved.
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Affiliation(s)
- Fabio Falcioni
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Sophie Bennett
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Pallas Stroer-Jarvis
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Paul L A Popelier
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
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Bento-Oliveira A, Moita MLCJ, de Almeida RFM, Starosta R. Unraveling environmental effects in the absorption and fluorescence spectra of p-methoxyphenylpiperazine derivatives. Spectrochim Acta A Mol Biomol Spectrosc 2024; 306:123583. [PMID: 37913739 DOI: 10.1016/j.saa.2023.123583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023]
Abstract
The p-methoxyphenylpiperazine motif can be found in many biologically active molecules, including approved drugs. It is characterized by a relatively weak fluorescence, which can be employed in different types of studies involving molecules with this motif. In this work, a thorough analysis of the absorption, excitation and emission spectra of the diphenyl(aminomethyl)phosphine and tris(aminomethyl)phosphine derivatives of p-methoxyphenylpiperazine, supported by the DFT calculations (ωB97XD/6-311++G(d,p)) with NBO and QTAIM analysis also for different model molecules (e.g. 1-(4-methoxyphenyl)-4-methylpiperazine) enabled determination of the mechanisms underlying beneath the electronic transitions and allowed to rationalize mixed solvent effects observed in electronic spectra of the studied compounds. Electronic transition from the ground state to the first excited state can be regarded as the n,π → π* transition with no solvatochromic effects, however the hydrogen bonds between the HBD solvent molecules and the nitrogen atom bound directly to the aromatic ring (N(4)) are shifting strongly the 1st absorption or excitation band maxima to the higher energies. Fluorescence band, as a result of the electron transition from the equilibrated 1st excited state to the ground state, can be described as the π*→π with positive solvatochromism. N(4) in the excited states adopts a sp2 hybridization and is no longer able to form HBs. On the other hand, increased electron density on the aromatic ring makes the emission processes vulnerable to its direct environment.
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Affiliation(s)
- Andreia Bento-Oliveira
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Maria-Luísa C J Moita
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Rodrigo F M de Almeida
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Radosław Starosta
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland.
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Vishwakarma K, Ravi S, Mittal S. Ab initio Modeling of Hydrogen Bonding of Remdesivir and Adenosine with Uridine. Chemphyschem 2024; 25:e202300552. [PMID: 37983746 DOI: 10.1002/cphc.202300552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/18/2023] [Accepted: 11/19/2023] [Indexed: 11/22/2023]
Abstract
Remdesivir (RDV) emerged as an effective drug against the SARS-CoV-2 virus pandemic. One of the crucial steps in the mechanism of action of RDV is its incorporation into the growing RNA strand. RDV, an adenosine analogue, forms Watson-Crick (WC) type hydrogen bonds with uridine in the complementary strand and the strength of this interaction will control efficacy of RDV. While there is a plethora of structural and energetic information available about WC H-bonds in natural base pairs, the interaction of RDV with uridine has not been studied yet at the atomic level. In this article, we aim to bridge this gap, to understand RDV and its hydrogen bonding interactions, by employing density functional theory (DFT) at the M06-2X/cc-pVDZ level. The interaction energy, QTAIM analysis, NBO and SAPT2 are performed for RDV, adenosine, and their complex with uridine to gain insights into the nature of hydrogen bonding. The computations show that RDV has similar geometry, energetic, molecular orbitals, and aromaticity as adenosine, suggesting that RDV is an effective adenosine analogue. The important geometrical parameters, such as bond distances and red-shift in the stretching vibrational modes of adenosine, RDV and uridine identify two WC-type H-bonds. The relative strength of these two H-bonds is computed using QTAIM parameters and the computed hydrogen bond energy. Finally, the SAPT2 study is performed at the minima and at non-equilibrium base pair distances to understand the dominant intermolecular physical force. This study, based on a thorough analysis of a variety of computations, suggests that both adenosine and RDV have similar structure, energetic, and hydrogen bonding behaviour.
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Affiliation(s)
- Kamini Vishwakarma
- School of Advance Science and Languages, VIT Bhopal University, Kothrikalan, Sehore, Madhya, Pradesh, 466114, India
| | - Satyam Ravi
- School of Advance Science and Languages, VIT Bhopal University, Kothrikalan, Sehore, Madhya, Pradesh, 466114, India
| | - Sumit Mittal
- School of Advance Science and Languages, VIT Bhopal University, Kothrikalan, Sehore, Madhya, Pradesh, 466114, India
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14
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Duraisamy PD, S PMP, Gopalan P, Angamuthu A. Enhanced hydrogen storage of alkaline earth metal-decorated B n (n = 3-14) nanoclusters: a DFT study. J Mol Model 2024; 30:55. [PMID: 38291281 DOI: 10.1007/s00894-024-05847-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/16/2024] [Indexed: 02/01/2024]
Abstract
CONTEXT Boron-based nanostructures hold significant promise for revolutionizing hydrogen storage technologies due to their exceptional properties and potential in efficiently accommodating and interacting with hydrogen molecules. In this paper, boron-based Bn (n = 3-14) nanoclusters decorated with alkaline earth metals (AEM = Ca and Be) were investigated for hydrogen storage applications based on density function theory (DFT) calculations. To evaluate H2 adsorption capability, the adsorption energies, frontier molecular orbitals (FMOs), natural bond orbital (NBO), and quantum theory of atoms in molecule (QTAIM) analysis are performed. The primary aim of this research work is to achieve targeted value of 5.5 wt% set by the US Department of Energy (DOE) for the year 2025. The results revealed that B5Ca2, B6Ca2, and B10Ca2 structures have the ability to hold up to 12H2 molecules with gravimetric capacities of 15.20, 14.21, and 8.60 wt%, respectively, when compared to other boron structures decorated with calcium. Similarly, for Be-decorated structure, B3Be2 structure can accommodate 3H2 molecules with gravimetric capacity of 10.59 wt%. The result of this study indicates that AEM-decorated Bn nanoclusters hold great promise as potential materials for hydrogen storage. METHODS Density functional theory (DFT) approach at ωB97XD/6-311++G(d,p) level of theory is employed to investigate the possibility of storing H2 molecules on alkaline earth metal (AEM = Ca and Be)-decorated Bn (n = 3-14) nanoclusters. All DFT computations were performed using Gaussian 09 software. To calculate frontier molecular orbitals (FMOs) and quantum theory of atoms in molecule (QTAIM) analysis, we have used GaussView and Multiwfn software, respectively.
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Affiliation(s)
- Parimala Devi Duraisamy
- Department of Physical Sciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, 641114, India
| | - Prince Makarios Paul S
- Department of Physical Sciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, 641114, India
| | - Praveena Gopalan
- Department of Physics, PSGR Krishnammal College for Women, Coimbatore, Tamil Nadu, 641004, India
| | - Abiram Angamuthu
- Department of Physical Sciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, 641114, India.
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Kégl TR, Kégl T. Comparative Analysis of Nickel-Phosphine Complexes with Cumulated Double Bond Ligands: Structural Insights and Electronic Interactions via ETS-NOCV and QTAIM Approaches. Molecules 2024; 29:324. [PMID: 38257236 DOI: 10.3390/molecules29020324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
This study presents a comprehensive analysis of nickel-phosphine complexes, specifically Ni(PH3)2(OCCH2), Ni(PH3)2(H2CCO), Ni(PH3)2(H2CCCH2), Ni(PH3)2(NNCH2), and Ni(PH3)2(η1-H2CNN). Utilizing ETS-NOCV analysis, we explored orbital energy decomposition and the Hirshfeld charges of the ligands, providing insights into the electronic structures and donor-acceptor interactions within these complexes. The interactions in the ketene and allene complexes exhibit similar deformation densities and NOCV orbital shapes to those calculated for Ni(PH3)2(NNCH2), indicating consistent interaction characteristics across these complexes. The total interaction energy for all η2 complexes is observed to be over 60 kcal/mol, slightly exceeding that of the analogous carbon dioxide complex reported earlier. Furthermore, the study highlights the stronger back-donation as compared to donor interactions across all η2 complexes. This is further corroborated by Hirshfeld analysis, revealing the charge distribution dynamics within the ligand fragments. The research offers new perspectives on the electron distribution and interaction energies in nickel-phosphine complexes, contributing to a deeper understanding of their catalytic and reactive behaviors.
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Affiliation(s)
- Tímea R Kégl
- National Laboratory of Renewable Energy, University of Pécs, H-7624 Pécs, Hungary
| | - Tamás Kégl
- Department of General and Inorganic Chemistry and HUN-REN Research Group for Selective Chemical Syntheses, Hungary, University of Pécs, H-7624 Pécs, Hungary
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16
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Daboe M, Parlak C, Direm A, Alver Ö, Ramasami P. Interaction between escitalopram and ibuprofen or paracetamol: DFT and molecular docking on the drug-drug interactions. J Biomol Struct Dyn 2024; 42:672-686. [PMID: 37042928 DOI: 10.1080/07391102.2023.2195004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/17/2023] [Indexed: 04/13/2023]
Abstract
A large number of drugs are introduced each year to treat different diseases. Most of the time, patients suffer from more than one health problem which makes it necessary to take multiple drugs. When drugs are combined, the problem of drug-drug interaction becomes relevant. In this work, we studied the drug-drug interaction between escitalopram and ibuprofen or paracetamol using density functional theory and quantum theory of atoms in molecules. The results suggest that following the interactions, the activity of drugs changes according to site of interaction. Most reactive and most stable interactions would be preferable for the purpose of use. The in silico drug-likeness studies show that escitalopram and paracetamol couple is more bioavailable than escitalopram and ibuprofen couple. Moreover, in order to gain additional insights into the mentioned drugs' interactions, the drugs were docked separately and jointly against the potential targets for antidepressants and NSAIDs, namely 6HIS and 2PXX. The molecular docking results showed a potential improvement of the effectiveness of the drugs after combining by forming hydrogen bonds, hydrophobic contacts and π…π stacking.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Musa Daboe
- Department of Physics, Science Faculty, Ege University, Izmir, Turkey
| | - Cemal Parlak
- Department of Physics, Science Faculty, Ege University, Izmir, Turkey
| | - Amani Direm
- Department of Matter Sciences, Faculty of Sciences and Technology, Abbes Laghrour University, Khenchela, Algeria
- Laboratory of Structures, Properties and Interatomic Interactions LASPI2A, Faculty of Sciences and Technology, Abbes Laghrour University, Khenchela, Algeria
| | - Özgür Alver
- Department of Physics, Science Faculty, Eskişehir Technical University, Eskişehir, Turkey
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit, Mauritius
- Department of Chemistry College of Science, Engineering and Technology, University of South Africa, Pretoria, South Africa
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17
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Afonin AV, Rusinska-Roszak D. Quantification of hydrogen bond energy based on equations using spectroscopic, structural, QTAIM-based, and NBO-based descriptors which calibrated by the molecular tailoring approach. J Mol Model 2023; 30:18. [PMID: 38159168 PMCID: PMC10757697 DOI: 10.1007/s00894-023-05811-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
CONTEXT Hydrogen bonds critically influence the structure and properties of both organic molecules and biomolecules, as well as supramolecular assemblies. For this reason, the development and elaboration of methods for quantitative assessment of hydrogen bond energy is an urgent challenge. In this study, using a large series of hydroxycarbonyl aliphatic compounds with the O‒H···O = C intramolecular hydrogen bond, a bank of hydrogen bond descriptors was created, including spectroscopic, structural, QTAIM-based, and NBO-based parameters. It was shown that the O‒H vibration frequency, OH chemical shift as the spectroscopic descriptors, the O···H hydrogen bond length, O···O distance, and O‒H covalent bond length as the structural descriptors, the electron density and its Laplacian, electron potential energy density in the hydrogen bond critical point, the electron density at the ring critical point as the QTAIM-based descriptors change in a correlated manner. The same correlation is found in change of the charge transfer energy through a hydrogen bond, the occupancy of the O‒H bond antibonding orbital, the Wiberg indices of the O···H hydrogen bond, and the O‒H covalent bond, as well as the polarization of the O‒H bond, which are the NBO-based descriptors. It was also recognized that the specified descriptors from the spectroscopic, structural, QTAIM-based, and NBO-based categories are functionally related to the values of intramolecular hydrogen bond energy, quantified via the molecular tailoring approach. This allowed one to obtain a system of equations for quantitative estimation of intramolecular hydrogen bond energy based on the spectroscopic, structural, QTAIM, and NBO descriptors, which makes such quantification more dependable and reliable. METHODS To obtain the spectroscopic descriptors, the vibrational spectra and shielding constants were calculated using the GIAO method. Structural descriptors were obtained for the equilibrium geometry of molecules, calculated at the MP2(FC)/6-311 + + (2d,2p) level using the Gaussian 09 program. The QTAIM-based descriptors were calculated using the AIMAll program within the framework of the quantum theory "Atoms in Molecules." The NBO-based descriptors were calculated using the NBO 3.1 program implemented into Gaussian 09. To quantify the energy of intramolecular hydrogen bonds, molecular fragmentation was used within the molecular tailoring approach.
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Affiliation(s)
- Andrei V Afonin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of Russian Academy of Sciences, Irkutsk, Russia
| | - Danuta Rusinska-Roszak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Poznan, Poland.
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18
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Zahid MN, Kosar N, Sajid H, Ibrahim KE, Gatasheh MK, Mahmood T. Unveiling the Potential of B 3O 3 Nanoflake as Effective Transporter for the Antiviral Drug Favipiravir: Density Functional Theory Analysis. Molecules 2023; 28:8092. [PMID: 38138581 PMCID: PMC10746011 DOI: 10.3390/molecules28248092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
In this study, for the first time, boron oxide nanoflake is analyzed as drug carrier for favipiravir using computational studies. The thermodynamic stability of the boron oxide and favipiravir justifies the strong interaction between both species. Four orientations are investigated for the interaction between the favipiravir and the B3O3 nanoflake. The Eint of the most stable orientation is -26.98 kcal/mol, whereas the counterpoise-corrected energy is -22.59 kcal/mol. Noncovalent interaction index (NCI) and quantum theory of atoms in molecules (QTAIM) analyses are performed to obtain insights about the behavior and the types of interactions that occur between B3O3 nanoflake and favipiravir. The results indicate the presence of hydrogen bonding between the hydrogen in the favipiravir and the oxygen in the B3O3 nanoflake in the most stable complex (FAV@B3O3-C1). The electronic properties are investigated through frontier molecular orbital analysis, dipole moments and chemical reactivity descriptors. These parameters showed the significant activity of B3O3 for favipiravir. NBO charge analysis transfer illustrated the charge transfer between the two species, and UV-VIS analysis confirmed the electronic excitation. Our work suggested a suitable drug carrier system for the antiviral drug favipiravir, which can be considered by the experimentalist for better drug delivery systems.
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Affiliation(s)
- Muhammad Nauman Zahid
- Department of Biology, College of Science, University of Bahrain, Sakhir P.O. Box 32038, Bahrain;
| | - Naveen Kosar
- Department of Chemistry, University of Management and Technology (UMT), C-11, Johar Town Lahore, Lahore 54770, Pakistan;
| | - Hasnain Sajid
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK;
| | - Khalid Elfaki Ibrahim
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Mansour K. Gatasheh
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Tariq Mahmood
- Department of Chemistry, COMSATS University, Abbottabad Campus, Abbottabad 22060, Pakistan
- Department of Chemistry, College of Science, University of Bahrain, Sakhir P.O. Box 32038, Bahrain
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Radael GN, Oliveira GG, Pontes RM. A DFT study of ethanol interaction with the bimetallic clusters of PtSn and its implications on reactivity. J Mol Graph Model 2023; 125:108621. [PMID: 37689026 DOI: 10.1016/j.jmgm.2023.108621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023]
Abstract
The comprehension of the factors affecting the adsorption of ethanol over metals and metal alloys is a crucial step for the rational development of new catalysts for hydrogen production through ethanol reforming. In this work, we analyze the effect of combining Pt and Sn on a metal cluster on the complexation energy and reactivity for OH dehydrogenation of ethanol. Metal clusters of Pt10, Sn10 and Pt5Sn5 had their putative minimum located with the help of the artificial bee colony algorithm. Whereas the isolated Pt cluster shows a high degree of polarization (ESP surface), the Sn cluster shows a quite uniform electron density surface. The PtSn cluster is strongly polarized, with Pt atoms withdrawing electron density of Sn atoms. Complexation occurs with the oxygen atom of ethanol directed towards the point of highest electron potential in the ESP surface. Pt presents the highest complexation energy, -20.90 kcal/mol, against only -7.83 kcal/mol (at the B97-3c level). For the PtSn cluster, the value is intermediate, namely -12.39 kcal/mol. The more malleable electron density of Pt and its electron affinity are responsible for its highest complexation energy. These characteristics are partially transferred to the PtSn cluster. QTAIM results show that, for the PtSn cluster, the O-H bond in ethanol is somewhat weaker than for pure Pt and Sn. As a consequence, the energy barrier for the O-H dehydrogenation has its lowest value for the PtSn cluster, which shows that the alloying of two metals can lead to quite quite unexpected results opening the perspective for a more rational fine tuning of catalysts properties.
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Affiliation(s)
- Graziela N Radael
- Departamento de Química, Universidade Estadual de Maringá, Av. Colombo, 5790, Maringá, Paraná, CEP 87900-020, Brazil
| | - Gabriel G Oliveira
- Departamento de Química, Universidade Estadual de Maringá, Av. Colombo, 5790, Maringá, Paraná, CEP 87900-020, Brazil
| | - Rodrigo M Pontes
- Departamento de Química, Universidade Estadual de Maringá, Av. Colombo, 5790, Maringá, Paraná, CEP 87900-020, Brazil.
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Pembere AMS, Louis H, Wu H. Mechanism and dynamics of Baeyer-Villiger oxidation of furfural to maleic anhydride in presence of H 2O 2 and Au clusters. J Mol Model 2023; 29:359. [PMID: 37924368 DOI: 10.1007/s00894-023-05764-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023]
Abstract
CONTEXT The increasing demand for fuels and chemicals in the world has prompted the exploration of various forms of renewable energy resources. Using C5-based furfural as the platform to replace the fossil energy resources is greatly attractive because of its abundance and environmental friendliness. Here we study the activity, selectivity, and possible reaction pathways for the Baeyer-Villiger oxidation of furfural over small Au clusters using hydrogen peroxide as oxidant. Furfural reacts with hydrogen peroxide in the presence of the catalysts with 93% selectivity towards maleic anhydride. Natural population analysis, frontier molecular orbital analysis, and spectroscopic analysis are used to illustrate the interaction mechanism between C5H4O2, H2O2, and Au. Reaction pathways leading to the formation of maleic anhydride are also explored. The reaction of C5H4O2 with H2O2 in the absence of a catalyst bears a relatively high transition state energy barrier of 2.98 eV for the first step involving absorption of H atom of H2O2 on the -OH group of C5H4O2. This is in agreement with the blank experiment where there were rare oxidation products observed in the absence of the metal cluster catalysts. On the other hand, transition state energies in the presence of the Au metal clusters are lower and the most feasible pathway is where the substrate and H2O2 co-bind on the Au catalyst and H2O2 molecule transfers an oxygen to the substrate, leading to the cleavage of the O-O bond. METHODS DFT calculations were done with B3PW91 functional. 6-311G(df, p) basis set was used for C, O, and H and aug-cc-pVDZ-PP was used for gold atoms. Gaussian 09 software was used for the calculations. Multiwfn 3.7 dev was used for the quantum theory of atoms-in-molecules (QTAIM) investigations.
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Affiliation(s)
- Anthony M S Pembere
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O Box 210, Bondo, 40601, Kenya.
| | - Hitler Louis
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, 1115, Nigeria
- Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education,, Kelambakkam, Tamil Nadu 603103, India
| | - Haiming Wu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.
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Chahkandi B, Chahkandi M. An accurate DFT study within conformational survey of the D-form serine-alanine protected dipeptide. BMC Chem 2023; 17:138. [PMID: 37828563 PMCID: PMC10571400 DOI: 10.1186/s13065-023-01051-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
The conformational analysis of N-formyl-D-serine-D-alanine-NH2 dipeptide was studied using density functional theory methods at B3LYP, B3LYP‒D3, and M06‒2X levels using 6‒311 + G (d,p) basis set in the gas and water phases. 87 conformers of 243 stable ones were located and the rest of them were migrated to the more stable geometries. Migration pattern suggests the more stable dipeptide model bears serine in βL, γD, γL and the alanine in γL and γD configurations. The investigation of side‒chain‒backbone interactions revealed that the most stable conformer, γD-γL, is in the β‒turn region of Ramachandran map; therefore, serine-alanine dipeptide model should be adopted with a β‒turn conformation. Intramolecular hydrogen bonding in β‒turns consideration by QTAIM disclosed γD-γL includes three hydrogen bonds. The computed UV‒Vis spectrum alongside of NBO calculation showed the five main electronic transition bands derived of n → n* of intra‒ligand alanine moiety of dipeptide structure.
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Affiliation(s)
- Behzad Chahkandi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
| | - Mohammad Chahkandi
- Department of Chemistry, Hakim Sabzevari University, Sabzevar, 96179-76487, Iran
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22
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S V N, B S C, Mahesha, K N CP, M K H, N K L. In-silico investigation of 4-nitro-N-1H-pyrazol-3-ylbenzamide towards its potential use against SARS-CoV-2: a DFT, molecular docking and molecular dynamics study. J Biomol Struct Dyn 2023:1-21. [PMID: 37771166 DOI: 10.1080/07391102.2023.2262597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/17/2023] [Indexed: 09/30/2023]
Abstract
In the present research work, we report the synthesis and characterization of novel pyrazole derivative obtained by the condensation reaction of 4-nitro benzaldehyde group with one equivalent of the 2-amino pyrazole yielding 4-nitro-N-1H-pyrazol-3-ylbenzamide with high yield. The two symmetry-independent molecules (molecule A and molecule B) differ about the central C-N bond, with the dihedral angles between the pyrazole ring system and the nitrobenzene ring being 13.90° and 18.64°, respectively. By optimizing the symmetry-independent dimer molecules, the rotational barrier between the conformers is found to be within the 2.5-5.5 kcal/mol range. QTAIM and RDG based NCI isosurface revealed the presence of strong N-H…N and C-H…O hydrogen bonds which stabilize the two independent centrosymmetric inversion-related dimers. Further, weak and short directional interactions such as C-H…N, H…H and C-H…π were also analyzed systematically using various topological parameters. The compound is found to adhere to the Lipinski's rule of five and exhibit good pharmacokinetic properties. The results of molecular docking studies performed against SARS-CoV-2 virus main protease (PDB IDs: 6LU7, 6W9C and 6WQF) revealed that the compound showed better docking scores. Molecular docking studies verified the inhibition activity of the synthesized novel compound. Finally, the binding free energy and contributed energies were calculated using MM-GBSA method. The 6LU7-ligand complex showed highest binding free energy and among all other interactions, the contributions of the covalent binding and van der Waals energy are found to be significant.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Niranjana S V
- Department of Studies in Physics, University of Mysore, Mysuru, India
- Department of Studies in Physics, Karnataka State Open University, Mysuru, India
| | - Chethan B S
- Department of Studies in Physics, University of Mysore, Mysuru, India
| | - Mahesha
- Department of Studies in Physics, University of Mysore, Mysuru, India
- Department of Physics, SJCE, JSS Science and Technology University, Mysuru, India
| | - Chethan Prathap K N
- Department of Physics, University College of Science, Tumkur University, Tumakuru, India
| | - Hema M K
- Department of Studies in Physics, University of Mysore, Mysuru, India
| | - Lokanath N K
- Department of Studies in Physics, University of Mysore, Mysuru, India
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23
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Kononov LO, Fukase K, Bunkin NF. Editorial: Chemical reactivity and solution structure. Front Chem 2023; 11:1293697. [PMID: 37822774 PMCID: PMC10562685 DOI: 10.3389/fchem.2023.1293697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Affiliation(s)
- Leonid O Kononov
- Laboratory of GlycoChemistry, N. D. Zelinsky Institute of Organic Chemistry, Moscow, Russia
| | - Koichi Fukase
- Department of Chemistry, Osaka University, Osaka, Japan
| | - Nikolai F Bunkin
- Department of Fundamental Sciences, Bauman Moscow State Technical University, Moscow, Russia
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24
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Hadi H, Bouzid G, Nasr S, Ghalla H, Ben Chaabane R, Ayachi S. Design, synthesis, and density functional theory studies of a new selective chemosensor for Pb 2. Heliyon 2023; 9:e20206. [PMID: 37809941 PMCID: PMC10559993 DOI: 10.1016/j.heliyon.2023.e20206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/24/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Herein, we have focused on a new colorimetric ligand synthesized from the reaction of 2-hydroxy-5-methylbenzene-1,3-dialdehyde with 2-amino-thiophenol, and investigated its activity as a sensor. In this regard, the sensory activity of the ligand towards different ions (Mn2+, Cu2+, Co2+, Fe2+, Fe3+, Zn2+, Ni2+, Cd2+, Ag+, Na+, Cs+, Mg2+, Al3+, Ba2+, K+, and Pb2+) was studied. The specificity of ion bindings is discussed through UV-Vis analysis. The ligand that was synthesized showed remarkable sensitivity, with a detection limit of 0.001 ppb. Additionally, the presence of Pb2+ ions can be visually detected through a color change from colorless to yellow. In the last part of this work, we seek to predict the available experimental measurements. Density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM) are employed to examine the bonding between the ligand and the Pb2+ ion. The effect of water solvent was thoroughly examined for all the steps via the conductor-like Polarizable Continuum Model (CPCM). The theoretical findings revealed that electronic properties, including energy gap, adsorption energy, charge/energy transfer, and optical characteristics, undergo significant changes when Pb2+ cations are present. Hence, it can be inferred that the newly synthesized chemosensor (NC) is highly efficient in detecting Pb2+.
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Affiliation(s)
- Hamid Hadi
- Department of Chemistry, Physical Chemistry group, Lorestan University, Khorramabad, Iran
| | - Gassoumi Bouzid
- Laboratory of Advanced Materials and Interfaces (LIMA), Faculty of Sciences, University of Monastir, 5019 Monastir, Tunisia
| | - Samia Nasr
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Chemistry Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Houcine Ghalla
- Quantum and Statistical Physics Laboratory, Faculty of Sciences, University of Monastir, 5019 Monastir, Tunisia
| | - Rafik Ben Chaabane
- Laboratory of Advanced Materials and Interfaces (LIMA), Faculty of Sciences, University of Monastir, 5019 Monastir, Tunisia
| | - Sahbi Ayachi
- Laboratory of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, University of Monastir, 5019 Monastir, Tunisia
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25
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Jabłoński M. Bader's Topological Bond Path Does Not Necessarily Indicate Stabilizing Interaction-Proof Studies Based on the Ng@[3 n]cyclophane Endohedral Complexes. Molecules 2023; 28:6353. [PMID: 37687183 PMCID: PMC10490063 DOI: 10.3390/molecules28176353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
According to Bader's quantum theory of atoms in molecules (QTAIM), the simultaneous presence of a bond path and the corresponding bond critical point between any two atoms is both a necessary and sufficient condition for the atoms to be bonded to one another. In principle, this means that this pair of atoms should make a stabilizing contribution to the molecular system. However, the multitude of so-called counterintuitive bond paths strongly suggests that this statement is not necessarily true. Particularly 'troublesome' are endohedral complexes, in which encapsulation-enforced proximity between the trapped guest (e.g., an atom) and the host's cage system usually 'produces' many counterintuitive bond paths. In the author's opinion, the best evidence to demonstrate the repulsive nature of the intra-cage guest⋯host interaction is the use of some trapping systems containing small escape channels and then showing that the initially trapped entity spontaneously escapes outside the host's cage during geometry optimization of the initially built guest@host endohedral complex. For this purpose, a group of 24 Ng@[3n]cyclophane (3≤n≤6) endohedral complexes is used. As a result, arguments are presented showing that Bader's topological bond path does not necessarily indicate a stabilizing interaction.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100 Toruń, Poland
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26
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Smirnov AS, Katlenok EA, Mikherdov AS, Kryukova MA, Bokach NA, Kukushkin VY. Halogen Bonding Involving Isomeric Isocyanide/Nitrile Groups. Int J Mol Sci 2023; 24:13324. [PMID: 37686131 PMCID: PMC10487382 DOI: 10.3390/ijms241713324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
2,3,5,6-Tetramethyl-1,4-diisocyanobenzene (1), 1,4-diisocyanobenzene (2), and 1,4-dicyanobenzene (3) were co-crystallized with 1,3,5-triiodotrifluorobenzene (1,3,5-FIB) to give three cocrystals, 1·1,3,5-FIB, 2·2(1,3,5-FIB), and 3·2(1,3,5-FIB), which were studied by X-ray diffraction. A common feature of the three structures is the presence of I···Cisocyanide or I···Nnitrile halogen bonds (HaBs), which occurs between an iodine σ-hole and the isocyanide C-(or the nitrile N-) atom. The diisocyanide and dinitrile cocrystals 2·2(1,3,5-FIB) and 3·2(1,3,5-FIB) are isostructural, thus providing a basis for accurate comparison of the two types of noncovalent linkages of C≡N/N≡C groups in the composition of structurally similar entities and in one crystal environment. The bonding situation was studied by a set of theoretical methods. Diisocyanides are more nucleophilic than the dinitrile and they exhibit stronger binding to 1,3,5-FIB. In all structures, the HaBs are mostly determined by the electrostatic interactions, but the dispersion and induction components also provide a noticeable contribution and make the HaBs attractive. Charge transfer has a small contribution (<5%) to the HaB and it is higher for the diisocyanide than for the dinitrile systems. At the same time, diisocyanide and dinitrile structures exhibit typical electron-donor and π-acceptor properties in relation to the HaB donor.
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Affiliation(s)
- Andrey S. Smirnov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia; (A.S.S.); (E.A.K.); (A.S.M.); (M.A.K.); (N.A.B.)
| | - Eugene A. Katlenok
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia; (A.S.S.); (E.A.K.); (A.S.M.); (M.A.K.); (N.A.B.)
| | - Alexander S. Mikherdov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia; (A.S.S.); (E.A.K.); (A.S.M.); (M.A.K.); (N.A.B.)
| | - Mariya A. Kryukova
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia; (A.S.S.); (E.A.K.); (A.S.M.); (M.A.K.); (N.A.B.)
| | - Nadezhda A. Bokach
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia; (A.S.S.); (E.A.K.); (A.S.M.); (M.A.K.); (N.A.B.)
| | - Vadim Yu. Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russia; (A.S.S.); (E.A.K.); (A.S.M.); (M.A.K.); (N.A.B.)
- Laboratory of Crystal Engineering of Functional Materials, South Ural State University, 76, Lenin Av., 454080 Chelyabinsk, Russia
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27
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Dakkouri M. A Theoretical Investigation of Novel Sila- and Germa-Spirocyclic Imines and Their Relevance for Electron-Transporting Materials and Drug Discovery. Molecules 2023; 28:6298. [PMID: 37687127 PMCID: PMC10489060 DOI: 10.3390/molecules28176298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
A new class of spirocyclic imines (SCIs) has been theoretically investigated by applying a variety of quantum chemical methods and basis sets. The uniqueness of these compounds is depicted by various peculiarities, e.g., the incidence of planar six-membered rings each with two imine groups (two π bonds) and the incorporation of the isosteres carbon, silicon, or germanium spiro centers. Additional peculiarities of these novel SCIs are mirrored by their three-dimensionality, the simultaneous occurrence of nucleophilic and electrophilic centers, and the cross-hyperconjugative (spiro-conjugation) interactions, which provoke charge mobility along the spirocyclic scaffold. Substitution of SCIs with strong electron-withdrawing substituents, like the cyano group or fluorine, enhances their docking capability and impacts their reactivity and charge mobility. To gain thorough knowledge about the molecular properties of these SCIs, their structures have been optimized and various quantum chemical concepts and models were applied, e.g., full NBO analysis and the frontier molecular orbitals (FMOs) theory (HOMO-LUMO energy gap) and the chemical reactivity descriptors derived from them. For the assessment of the charge density distribution along the SCI framework, additional complementary quantum chemical methods were used, e.g., molecular electrostatic potential (MESP) and Bader's QTAIM. Additionally, using the aromaticity index NICS (nuclear independent chemical shift) and other criteria, it could be shown that the investigated cross-hyperconjugated sila and germa SCIs are spiro-aromatics of the Heilbronner Craig-type Möbius aromaticity.
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Affiliation(s)
- Marwan Dakkouri
- Department of Electrochemistry, University of Ulm, D-89069 Ulm, Germany
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28
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Buikin P, Vologzhanina A, Novikov R, Dorovatovskii P, Korlyukov A. Abiraterone Acetate Complexes with Biometals: Synthesis, Characterization in Solid and Solution, and the Nature of Chemical Bonding. Pharmaceutics 2023; 15:2180. [PMID: 37765151 PMCID: PMC10535913 DOI: 10.3390/pharmaceutics15092180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Abiraterone acetate (AbirAc) is the most used steroidal therapeutic agent for treatment of prostate cancer. The mainly hydrophobic molecular surface of AbirAc results in its poor solubility and plays an important role for retention of abiraterone in the cavity of the receptor formed by peptide chains and heme fragments. In order to evaluate the hydrolytic stability of AbirAc, to modify its solubility by formation of new solid forms and to model bonding of this medication with the heme, a series of d-metal complexes with AbirAc was obtained. AbirAc remains stable in water, acetonitrile, tetrahydrofuran, and ethanol, and readily interacts with dications as a terminal ligand to create discrete complexes, including [FePC(AbirAc)2] and [ZnTPP(AbirAc)] (H2PC = phthalocyanine and H2TPP = 5,10,15,20-tetraphenylporphyrine) models for ligand-receptor bonding. In reactions with silver(I) nitrate, AbirAc acts as a bridge ligand. Energies of chemical bonding between AbirAc and these cations vary from 97 to 235 kJ mol-1 and exceed those between metal atoms and water molecules. This can be indicative of the ability of abiraterone to replace solvent molecules in the coordination sphere of biometals in living cells, although the model [ZnTPP] complex remains stable in CDCl3, CD2Cl2, and 1,1,2,2-tetrachloroethane-d2 solvents and decomposes in polar dimethylsulfoxide-d6 and methanol-d4 solvents, as follows from the 1H DOSY spectra. Dynamics of its behavior in 1,1,2,2-tetrachloroethane-d2 were studied by ROESY and NMR spectra.
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Affiliation(s)
- Petr Buikin
- A. N. Nesmeyanov Institute of Organoelement Compounds, RAS, 119334 Moscow, Russia;
- N. S. Kurnakov Institute of General and Inorganic Chemistry, RAS, 119991 Moscow, Russia
| | - Anna Vologzhanina
- A. N. Nesmeyanov Institute of Organoelement Compounds, RAS, 119334 Moscow, Russia;
| | - Roman Novikov
- N. D. Zelinsky Institute of Organic Chemistry, RAS, 119991 Moscow, Russia;
| | | | - Alexander Korlyukov
- A. N. Nesmeyanov Institute of Organoelement Compounds, RAS, 119334 Moscow, Russia;
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29
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Percino MJ, Udayakumar M, Cerón M, Pérez-Gutiérrez E, Venkatesan P, Thamotharan S. Weak noncovalent interactions in two positional isomers of acrylonitrile derivatives: inputs from PIXEL energy, Hirshfeld surface and QTAIM analyses. Front Chem 2023; 11:1209428. [PMID: 37448855 PMCID: PMC10338114 DOI: 10.3389/fchem.2023.1209428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
A single crystal X-ray diffraction analysis was performed on two positional isomers (m-tolyl and p-tolyl) of acrylonitrile derivatives, namely, (Z)-3-(4-(pyridin-2-yl) phenyl)-2-(m-tolyl) acrylonitrile (1) and (Z)-3-(4-(pyridin-2-yl)phenyl)-2-(p-tolyl) acrylonitrile (2). Compound 1 crystallized in the monoclinic P21/n space group with two crystallographically independent molecules. Compound 2 also possesses two crystallographically independent molecules and crystallized in the triclinic P-1 space group. The Hirshfeld surface analysis revealed that, in both isomers, intermolecular H⋅⋅⋅H/C/N contacts contribute significantly to the crystal packing. More than 40% of the contribution arises from intermolecular C-H⋅⋅⋅C(π) contacts. In both compounds, the relative contribution of these contacts is comparable, indicating that the positional isomeric effects are marginal. The structures in which these isomers are arranged in the solid state are very similar, and the lattice energies are also comparable between the isomers. The Coulomb-London-Pauli-PIXEL (CLP-PIXEL) energy analysis identified the energetically significant dimers. The strength of the intra- and intermolecular interactions was evaluated using the quantum theory of atoms in molecules approach. The UV-Vis absorbance in three different solvents (chloroform, ethanol, and ethyl acetate) for isomers 1 and 2 are very similar. This result is in good agreement with the time-dependent density-functional theory (TD-DFT) calculations.
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Affiliation(s)
- M. Judith Percino
- Instituto de Ciencias, Unidad de Polímeros y Electrónica Orgánica, Benemérita Universidad Autónoma de Puebla, Val3-Ecocampus Valsequillo, Puebla, CP, Mexico
| | - Mani Udayakumar
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Margarita Cerón
- Instituto de Ciencias, Unidad de Polímeros y Electrónica Orgánica, Benemérita Universidad Autónoma de Puebla, Val3-Ecocampus Valsequillo, Puebla, CP, Mexico
| | - Enrique Pérez-Gutiérrez
- Instituto de Ciencias, Unidad de Polímeros y Electrónica Orgánica, Benemérita Universidad Autónoma de Puebla, Val3-Ecocampus Valsequillo, Puebla, CP, Mexico
| | - Perumal Venkatesan
- Department of Chemistry, Srimad Andavan Arts and Science College (Autonomous), Tiruchirappalli, India
| | - Subbiah Thamotharan
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
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30
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Lemos Silva RA, Barbosa MR, Martins CR, Scalabrini Machado DF, Ribeiro L, de Oliveira HCB, da Silva Filho DA. (Ro)vibrational Spectroscopic Constants, Lifetime and QTAIM Evaluation of Fullerene Dimers Stability. Molecules 2023; 28:5023. [PMID: 37446684 DOI: 10.3390/molecules28135023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 07/15/2023] Open
Abstract
The iconic caged shape of fullerenes gives rise to a series of unique chemical and physical properties; hence a deeper understanding of the attractive and repulsive forces between two buckyballs can bring detrimental information about the structural stability of such complexes, providing significant data applicable for several studies. The potential energy curves for the interaction of multiple van der Waals buckyball complexes with increasing mass were theoretically obtained within the DFT framework at ωB97xD/6-31G(d) compound model. These potential energy curves were employed to estimate the spectroscopic constants and the lifetime of the fullerene complexes with the Discrete Variable Representation and with the Dunham approaches. It was revealed that both methods are compatible in determining the rovibrational structure of the dimers and that they are genuinely stable, i.e., long-lived complexes. To further inquire into the nature of such interaction, Bader's QTAIM approach was applied. QTAIM descriptors indicate that the interactions of these closed-shell systems are dominated by weak van der Waals forces. This non-covalent interaction character was confirmed by the RDG analysis scheme. Indirectly, QTAIM also allowed us to confirm the stability of the non-covalent bonded fullerene dimers. Our lifetime calculations have shown that the studied dimers are stable for more than 1 ps, which increases accordingly with the number of carbon atoms.
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Affiliation(s)
- Rodrigo A Lemos Silva
- Instituto Federal de Educação, Ciência e Tecnologia de Goiás (IFG), Câmpus Jataí, Jataí 75804-714, GO, Brazil
- Grupo de Química Teórica e Estrutural de Anápolis (GQTEA), Campus Central Anápolis de Ciências Exatas e Tecnológicas Henrique Santillo, Universidade Estadual de Goiás, CP 459, Anápolis 75132-903, GO, Brazil
| | - Mateus R Barbosa
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular (LEEDMOL), Instituto de Química, Universidade Federal de Goiás, CP 131, Goiânia 74001-970, GO, Brazil
| | - Caio R Martins
- Grupo de Química Teórica e Estrutural de Anápolis (GQTEA), Campus Central Anápolis de Ciências Exatas e Tecnológicas Henrique Santillo, Universidade Estadual de Goiás, CP 459, Anápolis 75132-903, GO, Brazil
| | - Daniel F Scalabrini Machado
- Laboratório de Modelagem Molecular de Sistemas Complexos (LMSC), Instituto de Química, Universidade de Brasília, CP 4478, Brasília 70919-970, DF, Brazil
| | - Luciano Ribeiro
- Grupo de Química Teórica e Estrutural de Anápolis (GQTEA), Campus Central Anápolis de Ciências Exatas e Tecnológicas Henrique Santillo, Universidade Estadual de Goiás, CP 459, Anápolis 75132-903, GO, Brazil
| | - Heibbe C B de Oliveira
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular (LEEDMOL), Instituto de Química, Universidade Federal de Goiás, CP 131, Goiânia 74001-970, GO, Brazil
| | - Demétrio A da Silva Filho
- Grupo de Semicondutores Orgânicos, Instituto de Física, Campus Darcy Ribeiro, Universidade de Brasília, CP 4478, Brasília 70919-970, DF, Brazil
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31
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Chérif I, Raissi H, Abiedh K, Gassoumi B, Caccamo MT, Magazu S, Said AH, Hassen F, Boubaker T, Ayachi S. Exploration of intramolecular charge transfer in para-substituted nitrobenzofurazan: Experimental and theoretical analyses. Spectrochim Acta A Mol Biomol Spectrosc 2023; 301:122939. [PMID: 37285745 DOI: 10.1016/j.saa.2023.122939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/09/2023]
Abstract
The present work aims at exploring the high electrophilic character of 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) toward the morpholine group by an SNAr reaction in acetonitrile or water (thereafter referred to as NBD-Morph). The electron-donating ability of the morpholine causes intra-molecular charge transfer (ICT). In this report, we present a comprehensive study on the optical characteristics using UV-Vis, photoluminescence (cw-PL) and its time-resolved (TR-PL) to determine the properties of the emissive intramolecular charge transfer (ICT) in the NBD-Morph donor-acceptor system. An exhaustive theoretical investigation utilizing the density functional theory (DFT) and its extension TD-DFT methods is an essential complement of experiments to rationalize and understand the molecular structure and related properties. The findings from QTAIM, ELF, and RDG analyses establish that the bonding between morpholine and NBD moieties is of the electrostatic or hydrogen bond type. In addition, the Hirshfeld surfaces have been established to explore the types of interactions. Further, the non-linear optical (NLO) responses of the compound have been examined. The structure-property relationships obtained through the combined experimental and theoretical offer valuable insights for designing efficient NLO material.
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Affiliation(s)
- Imen Chérif
- Laboratory of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, University of Monastir, Avenue of the environment, 5019 Monastir, Tunisia
| | - Hanen Raissi
- Laboratoire de Chimie Hétérocyclique, Produits Naturels et Réactivité (LR11ES39), Faculté des Sciences, Université de Monastir, Avenue de l'Environnement, 5019 Monastir, Tunisia
| | - Khouloud Abiedh
- Laboratoire de Micro-Optoélectronique et Nanostructures (LR99/ES29), Faculté des Sciences, Université de Monastir, Monastir, Tunisia
| | - Bouzid Gassoumi
- Laboratoire Interfaces et Matériaux Avancés (LIMA), Faculté des Sciences, Université de Monastir, Avenue de l'Environnement, 5019 Monastir, Tunisia
| | - Maria Teresa Caccamo
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra Università di Messina Viale Ferdinando Stagno D', Alcontres n°31, S. Agata, 98166 Messina Italy
| | - Salvatore Magazu
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra Università di Messina Viale Ferdinando Stagno D', Alcontres n°31, S. Agata, 98166 Messina Italy
| | - Ayoub Haj Said
- Laboratoire Interfaces et Matériaux Avancés (LIMA), Faculté des Sciences, Université de Monastir, Avenue de l'Environnement, 5019 Monastir, Tunisia; Centre de Recherche en Microélectronique et Nanotechnologie, Technopôle de Sousse, BP 334, Sahloul, 4054 Sousse, Tunisia
| | - Fredj Hassen
- Laboratoire de Micro-Optoélectronique et Nanostructures (LR99/ES29), Faculté des Sciences, Université de Monastir, Monastir, Tunisia
| | - Taoufik Boubaker
- Laboratoire de Chimie Hétérocyclique, Produits Naturels et Réactivité (LR11ES39), Faculté des Sciences, Université de Monastir, Avenue de l'Environnement, 5019 Monastir, Tunisia
| | - Sahbi Ayachi
- Laboratory of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, University of Monastir, Avenue of the environment, 5019 Monastir, Tunisia.
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32
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Das S, Devi K, Suthar S, Mondal KC. Bonding and stability of elusive silaboryne (SiB) and germaboryne (GeB) with donor base ligands. J Comput Chem 2023. [PMID: 37177883 DOI: 10.1002/jcc.27118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 03/28/2023] [Accepted: 04/06/2023] [Indexed: 05/15/2023]
Abstract
Stabilizing the exotic chemical species possessing multiple bonds is often extremely challenging due to insufficient orbital overlap, especially involving one heavier element. Bulky aryl groups and/or carbene as ligand have previously stabilized the SiSi, GeGe, and BB triple bonds. Herein, theoretical calculations have been carried out to shed light on the stability and bonding of elusive silaboryne/germaboryne (Si/GeB triple bond) stabilized by donor base ligands ((cAAC)BE(Me)(L); E = Si, L = cAACMe , NHCMe , PMe3 ; E = Ge, L = cAACMe ). The heavier analogues (Sn, Pb) have been further studied for comparison. Additionally, the effects of bulky substituents at the Si and N atoms on the structural parameters and stability of those species have been investigated. Energy decomposition analysis coupled with natural orbital for chemical valence (EDA-NOCV; for Si) showed that cAAC/NHC ligands could stabilize the exotic BSi-Me species more efficiently than PMe3 ligands. The BSi partial triple bond of the corresponding species possesses a mixture of one covalent electron sharing BSi σ-bond and two dative π-bonds (B ← Si, B → Si).
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Affiliation(s)
- Sujit Das
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, India
| | - Kavita Devi
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, India
| | - Sonam Suthar
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, India
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33
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Sohail U, Ullah F, Binti Zainal Arfan NH, Abdul Hamid MHS, Mahmood T, Sheikh NS, Ayub K. Transition Metal Sensing with Nitrogenated Holey Graphene: A First-Principles Investigation. Molecules 2023; 28:molecules28104060. [PMID: 37241800 DOI: 10.3390/molecules28104060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The toxicity of transition metals, including copper(II), manganese(II), iron(II), zinc(II), hexavalent chromium, and cobalt(II), at elevated concentrations presents a significant threat to living organisms. Thus, the development of efficient sensors capable of detecting these metals is of utmost importance. This study explores the utilization of two-dimensional nitrogenated holey graphene (C2N) nanosheet as a sensor for toxic transition metals. The C2N nanosheet's periodic shape and standard pore size render it well suited for adsorbing transition metals. The interaction energies between transition metals and C2N nanosheets were calculated in both gas and solvent phases and were found to primarily result from physisorption, except for manganese and iron which exhibited chemisorption. To assess the interactions, we employed NCI, SAPT0, and QTAIM analyses, as well as FMO and NBO analysis, to examine the electronic properties of the TM@C2N system. Our results indicated that the adsorption of copper and chromium significantly reduced the HOMO-LUMO energy gap of C2N and significantly increased its electrical conductivity, confirming the high sensitivity of C2N towards copper and chromium. The sensitivity test further confirmed the superior sensitivity and selectivity of C2N towards copper. These findings offer valuable insight into the design and development of sensors for the detection of toxic transition metals.
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Affiliation(s)
- Uroosa Sohail
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Faizan Ullah
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | | | | | - Tariq Mahmood
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
- Department of Chemistry, College of Science, University of Bahrain, Isa Town 32038, Bahrain
| | - Nadeem S Sheikh
- Chemical Sciences, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
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34
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Michalczyk M, Wojtkowiak K, Panek JJ, Jezierska A, Zierkiewicz W. Static and Dynamical Quantum Studies of CX 3-AlX 2 and CSiX 3-BX 2 (X = F, Cl, Br) Complexes with Hydrocyanic Acid: Unusual Behavior of Strong π-Hole at Triel Center. Int J Mol Sci 2023; 24:ijms24097881. [PMID: 37175586 PMCID: PMC10177972 DOI: 10.3390/ijms24097881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
The set of TX3-TrX2 (T = C, Si, Ge; Tr = B, Al, Ga; X = F, Cl, Br) molecules offers a rather unique opportunity to study both σ-hole and π-hole dimerization on the tetrel and triel ends, respectively. According to the molecular electrostatic potential (MEP) distribution, the π-hole extrema (acidic sites) were more intense than their σ-hole counterparts. The molecules owning the most (CX3-AlX2) and least (SiX3-BX2) intense π-holes were chosen to evaluate their capacities to attract one and two HCN molecules (Lewis bases). We discovered that the energetic characteristics of π-hole dimers severely conflict with the monomers MEP pattern since the weakest π-hole monomer forms a dimer characterized by interaction energy compared to those created by the monomers with noticeably greater power in the π-hole region. This outcome is due to the deformation of the weakest π-hole donor. Furthermore, the MEP analysis for monomers in the geometry of respective dimers revealed a "residual π-hole" site that was able to drive second ligand attachment, giving rise to the two "unusual trimers" examined further by the NCI and QTAIM analyses. Apart from them, the π-hole/π-hole and σ-hole/π-hole trimers have also been obtained throughout this study and described using energetic and geometric parameters. The SAPT approach revealed details of the bonding in one of the "unusual trimers". Finally, Born-Oppenheimer Molecular Dynamics (BOMD) simulations were carried out to investigate the time evolution of the interatomic distances of the studied complexes as well as their stability.
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Affiliation(s)
- Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Kamil Wojtkowiak
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Jarosław J Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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35
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Wojtkowiak K, Jezierska A. Role of Non-Covalent Interactions in Carbonic Anhydrase I-Topiramate Complex Based on QM/MM Approach. Pharmaceuticals (Basel) 2023; 16:ph16040479. [PMID: 37111236 PMCID: PMC10146004 DOI: 10.3390/ph16040479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 04/29/2023] Open
Abstract
Carbonic anhydrase (CA) I with a Topiramate (TPM) complex was investigated on the basis of a Quantum Mechanics/Molecular Mechanics (QM/MM) approach. The QM part was treated using Density Functional Theory (DFT) while the MM was simulated using Amberff14SB and GAFF force fields. In addition, the TIP3P model was applied to reproduce the polar environment influence on the studied complex. Next, three snapshots (after 5 ps, 10 ps, and 15 ps of the simulation time) were taken from the obtained trajectory to provide an insight into the non-covalent interactions present between the ligand and binding pocket of the protein. Our special attention was devoted to the binding site rearrangement, which is known in the literature concerning the complex. This part of the computations was performed using ωB97X functional with Grimme D3 dispersion corrections as well as a Becke-Johnson damping function (D3-BJ). Two basis sets were applied: def2-SVP (for larger models) and def2-TZVPD (for smaller models), respectively. In order to detect and describe non-covalent interactions between amino acids of the binding pocket and the ligand, Independent Gradient Model based on Hirshfeld partitioning (IGMH), Interaction Region Indicator (IRI), Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbitals (NBO) methods were employed. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was applied for energy decomposition between the ligand and protein. It was found that during the simulation time, the ligand position in the binding site was preserved. Nonetheless, amino acids interacting with TPM were exchanging during the simulation, thus showing the binding site reorganization. The energy partitioning revealed that dispersion and electrostatics are decisive factors that are responsible for the complex stability.
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Affiliation(s)
- Kamil Wojtkowiak
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
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36
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Chevreau H, Pilmé J. Promising insights in parallel grid-based algorithms for quantum chemical topology. J Comput Chem 2023; 44:1505-1516. [PMID: 36932729 DOI: 10.1002/jcc.27105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023]
Abstract
Some straightforward improvements designed to make grid-based quantum chemical topology more efficient and faster are presented. The strategy focuses on both the evaluation of the scalar function over three-dimensional discrete grids and the algorithms aimed to follow and integrate gradient trajectories over the basin volumes together. Beyond the density analysis, we show that the scheme is quite suitable for the electron localization function and its complex topology. With this speed-up of the parallelized process used to generate 3d-grids, this new scheme is several orders of magnitude faster than the original grid-based method implemented in our laboratory (TopMod09). The efficiency of our implementation (TopChem2) was also compared with well-known grid-based algorithms designed to assign the grid points to basins. The performances, speed versus accuracy have been discussed on the basis of results obtained from selected illustrative examples.
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Affiliation(s)
- Hilaire Chevreau
- Laboratoire de Chimie Théorique, CNRS, Sorbonne Université, 75252, Paris, Cedex 05, France
| | - Julien Pilmé
- Laboratoire de Chimie Théorique, CNRS, Sorbonne Université, 75252, Paris, Cedex 05, France
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37
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Ondar EE, Polynski MV, Ananikov VP. Predicting 195 Pt NMR Chemical Shifts in Water-Soluble Inorganic/Organometallic Complexes with a Fast and Simple Protocol Combining Semiempirical Modeling and Machine Learning. Chemphyschem 2023:e202200940. [PMID: 36806426 DOI: 10.1002/cphc.202200940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
Water-soluble Pt complexes are the key components in medicinal chemistry and catalysis. The well-known cisplatin family of anticancer drugs and industrial hydrosylilation catalysts are two leading examples. On the molecular level, the activity mechanisms of such complexes mostly involve changes in the Pt coordination sphere. Using 195 Pt NMR spectroscopy for operando monitoring would be a valuable tool for uncovering the activity mechanisms; however, reliable approaches for the rapid correlation of Pt complex structure with 195 Pt chemical shifts are very challenging and not available for everyday research practice. While NMR shielding is a response property, molecular 3D structure determines NMR spectra, as widely known, which allows us to build up 3D structure to 195 Pt chemical shift correlations. Accordingly, we present a new workflow for the determination of lowest-energy configurational/conformational isomers based on the GFN2-xTB semiempirical method and prediction of corresponding chemical shifts with a Machine Learning (ML) model tuned for Pt complexes. The workflow was designed for the prediction of 195 Pt chemical shifts of water-soluble Pt(II) and Pt(IV) anionic, neutral, and cationic complexes with halide, NO2 - , (di)amino, and (di)carboxylate ligands with chemical shift values ranging from -6293 to 7090 ppm. The model offered an accuracy (normalized root-mean-square deviation/RMSD) of 1.08 %/145.02 ppm on the held-out test set.
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Affiliation(s)
- Evgeniia E Ondar
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russia
| | - Mikhail V Polynski
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russia.,Scientific Technological Center of Organic and Pharmaceutical Chemistry, National Academy of Sciences, 26 Azatutyan Ave, 0014, Yerevan, Armenia
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russia
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38
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Klyukin IN, Kolbunova AV, Novikov AS, Nelyubin AV, Zhdanov AP, Kubasov AS, Selivanov NA, Bykov AY, Zhizhin KY, Kuznetsov NT. Synthesis of Disubstituted Carboxonium Derivatives of Closo-Decaborate Anion [2,6-B 10H 8O 2CC 6H 5] -: Theoretical and Experimental Study. Molecules 2023; 28:molecules28041757. [PMID: 36838745 PMCID: PMC9966448 DOI: 10.3390/molecules28041757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
A comprehensive study focused on the preparation of disubstituted carboxonium derivatives of closo-decaborate anion [2,6-B10H8O2CC6H5]- was carried out. The proposed synthesis of the target product was based on the interaction between the anion [B10H11]- and benzoic acid C6H5COOH. It was shown that the formation of this product proceeds stepwise through the formation of a mono-substituted product [B10H9OC(OH)C6H5]-. In addition, an alternative one-step approach for obtaining the target derivative is postulated. The structure of tetrabutylammonium salts of carboxonium derivative ((C4H9)4N)[2,6-B10H8O2CC6H5] was established with the help of X-ray structure analysis. The reaction pathway for the formation of [2,6-B10H8O2CC6H5]- was investigated with the help of density functional theory (DFT) calculations. This process has an electrophile induced nucleophilic substitution (EINS) mechanism, and intermediate anionic species play a key role. Such intermediates have a structure in which one boron atom coordinates two hydrogen atoms. The regioselectivity for the process of formation for the 2,6-isomer was also proved by theoretical calculations. Generally, in the experimental part, the simple and available approach for producing disubstituted carboxonium derivative was introduced, and the mechanism of this process was investigated with the help of theoretical calculations. The proposed approach can be applicable for the preparation of a wide range of disubstituted derivatives of closo-borate anions.
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Affiliation(s)
- Ilya N. Klyukin
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
- Correspondence: (I.N.K.); (A.S.N.)
| | - Anastasia V. Kolbunova
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Alexander S. Novikov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia
- Research Institute of Chemistry, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya St. 6, 117198 Moscow, Russia
- Correspondence: (I.N.K.); (A.S.N.)
| | - Alexey V. Nelyubin
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Andrey P. Zhdanov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Alexey S. Kubasov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Nikita A. Selivanov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Alexander Yu. Bykov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Konstantin Yu. Zhizhin
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Nikolay T. Kuznetsov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
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Gribben J, Wilson TR, Eberhart ME. Unicorns, Rhinoceroses and Chemical Bonds. Molecules 2023; 28:molecules28041746. [PMID: 36838734 PMCID: PMC9967439 DOI: 10.3390/molecules28041746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
The nascent field of computationally aided molecular design will be built around the ability to make computation useful to synthetic chemists who draw on their empirically based chemical intuition to synthesize new and useful molecules. This fact poses a dilemma, as much of existing chemical intuition is framed in the language of chemical bonds, which are pictured as possessing physical properties. Unfortunately, it has been posited that calculating these bond properties is impossible because chemical bonds do not exist. For much of the computationalchemistry community, bonds are seen as mythical-the unicorns of the chemical world. Here, we show that this is not the case. Using the same formalism and concepts that illuminated the atoms in molecules, we shine light on the bonds that connect them. The real space analogue of the chemical bond becomes the bond bundle in an extended quantum theory of atoms in molecules (QTAIM). We show that bond bundles possess all the properties typically associated with chemical bonds, including an energy and electron count. In addition, bond bundles are characterized by a number of nontraditional attributes, including, significantly, a boundary. We show, with examples drawn from solid state and molecular chemistry, that the calculated properties of bond bundles are consistent with those that nourish chemical intuition. We go further, however, and show that bond bundles provide new and quantifiable insights into the structure and properties of molecules and materials.
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Affiliation(s)
- Jordan Gribben
- Chemistry Department, Loras College, 1450 Alta Vista Street, Dubuque, IA 52001, USA
| | - Timothy R. Wilson
- Chemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401, USA
| | - Mark E. Eberhart
- Chemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401, USA
- Correspondence:
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40
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Scheiner S. Competition Between the Two σ-Holes in the Formation of a Chalcogen Bond. Chemphyschem 2023; 24:e202200936. [PMID: 36744997 DOI: 10.1002/cphc.202200936] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/07/2023]
Abstract
A chalcogen atom Y contains two separate σ-holes when in a R1 YR2 molecular bonding pattern. Quantum chemical calculations consider competition between these two σ-holes to engage in a chalcogen bond (ChB) with a NH3 base. R groups considered include F, Br, I, and tert-butyl (tBu). Also examined is the situation where the Y lies within a chalcogenazole ring, where its neighbors are C and N. Both electron-withdrawing substituents R1 and R2 act cooperatively to deepen the two σ-holes, but the deeper of the two holes consistently lies opposite to the more electron-withdrawing group, and is also favored to form a stronger ChB. The formation of two simultaneous ChBs in a triad requires the Y atom to act as double electron acceptor, and so anti-cooperativity weakens each bond relative to the simple dyad. This effect is such that some of the shallower σ-holes are unable to form a ChB at all when a base occupies the other site.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, 84322-0300, Logan, Utah, USA
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41
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Garcia MR, Iribarren I, Rozas I, Trujillo C. Simultaneous Hydrogen Bonds with Different Binding Modes: The Acceptor "Rules" but the Donor "Chooses". Chemistry 2023; 29:e202203577. [PMID: 36701250 DOI: 10.1002/chem.202203577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/26/2023] [Accepted: 01/26/2023] [Indexed: 01/27/2023]
Abstract
This computational work studies the different hydrogen bond (HB) binding modes that can be established between neighbouring HB donors and acceptors in structures with relevance in catalysis and biology. To analyse the electronic effect on the σ-hole, unsubstituted HB donors and ones with two different substituents, an electron withdrawing (EWG), and an electron donating (EDG) group, were studied. Upon complexation, three different binding modes were observed: bifurcated, parallel, and zigzag. It was found that, as a general trend, HBs within a parallel pattern are the strongest followed by those within bifurcated and zigzag binding modes, leading to a "competition" between the last two. Similar patterns and trends have been found in experimental structures found in a search within the CSD. In conclusion, even though the HB acceptors "rule" the pattern and strength of the HB interactions within the dimers, when there is an option for different binding modes within a particular dimer, the HB donors "choose" the type of binding established.
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Affiliation(s)
- Marianne Rica Garcia
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, D02 R590, Dublin, Ireland
| | - Iñigo Iribarren
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, D02 R590, Dublin, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, D02 R590, Dublin, Ireland
| | - Cristina Trujillo
- School of Chemistry, Trinity College Dublin, The University of Dublin, 154-160 Pearse Street, D02 R590, Dublin, Ireland.,Department of Chemistry, The University of Manchester, Oxford Road, M13 9PL, Manchester, UK
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42
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Moreno-Velarde F, Martín EI, Hidalgo Toledo J, Sánchez-Coronilla A. DFT Study on the Enhancement of Isobaric Specific Heat of GaN and InN Nanosheets for Use as Nanofluids in Solar Energy Plants. Materials (Basel) 2023; 16:915. [PMID: 36769922 PMCID: PMC9917575 DOI: 10.3390/ma16030915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/13/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
In this work, GaN and InN nanosheets with dodecylamine (DDA) as surfactant have been studied as nanofluids to be used in solar plants. The interactions between the sheets and the surfactants have been performed using density functional theory. The most favorable interaction site on the surface corresponds to the metallic atom of the sheet with the N atom of the surfactant. In this interaction, the pair of electrons of N from the surfactant with the metal atom of the sheet play a stabilizing role, which is corroborated by electron localization function (ELF), quantum theory of atoms in molecules (QTAIM), and density of states (DOS) analysis. The isobaric specific heat values for the most favorable interaction were obtained in the presence of water, ethylene glycol, and diphenyl oxide as solvents for the first time. The highest value corresponds to systems with diphenyl oxide, being the values obtained of 0.644 J/gK and 0.363 J/gK for GaN-DDA and InN-DDA systems, respectively. These results open the possibilities of using GaN-DDA and InN-DDA systems in solar energy applications.
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Affiliation(s)
- Francisco Moreno-Velarde
- Departamento de Química Física, Facultad de Farmacia, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - Elisa I. Martín
- Departamento de Ingeniería Química, Facultad de Química, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - José Hidalgo Toledo
- Departamento de Química Física, Facultad de Farmacia, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - Antonio Sánchez-Coronilla
- Departamento de Química Física, Facultad de Farmacia, Universidad de Sevilla, E-41012 Sevilla, Spain
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43
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Pouye SF, Bernès S, Yaffa L, Diallo W, Cissé I, Diop CAK, Sidibé M, Diop L. Synthesis and topology analysis of chlorido-triphen-yl(triphenyl phosphate-κ O)tin(IV). Acta Crystallogr E Crystallogr Commun 2023; 79:99-102. [PMID: 36793403 PMCID: PMC9912461 DOI: 10.1107/s2056989023000270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
The title SnIV complex, [Sn(C6H5)3Cl(C18H15O4P)], is a formal adduct between triphenyl phosphate (PhO)3P=O and the stannane derivative chlorido-tri-phenyl-tin, SnPh3Cl. The structure refinement reveals that this mol-ecule displays the largest Sn-O bond length for compounds including the X=O→SnPh3Cl fragment (X = P, S, C, or V), 2.6644 (17) Å. However, an AIM topology analysis based on the wavefunction calculated from the refined X-ray structure shows the presence of a bond critical point (3,-1), lying on the inter-basin surface separating the coordinated phosphate O atom and the Sn atom. This study thus shows that an actual polar covalent bond is formed between (PhO)3P=O and SnPh3Cl moieties.
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Affiliation(s)
- Serigne Fallou Pouye
- Département de Sciences Appliquées et Technologies Emergentes, Ecole Supérieure des Sciences et Techniques de l’Ingénieur, Université Amadou Mahtar Mbow, BP 45927 Dakar NAFA VDN, Dakar, Senegal,Correspondence e-mail: ,
| | - Sylvain Bernès
- Instituto de Física, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y 18 Sur, 72570 Puebla, Pue., Mexico,Correspondence e-mail: ,
| | - Lamine Yaffa
- Laboratoire de Chimie Minérale et Analytique (LACHIMIA), Département de Chimie, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Waly Diallo
- Laboratoire de Chimie Minérale et Analytique (LACHIMIA), Département de Chimie, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Ibrahima Cissé
- Département de Sciences Appliquées et Technologies Emergentes, Ecole Supérieure des Sciences et Techniques de l’Ingénieur, Université Amadou Mahtar Mbow, BP 45927 Dakar NAFA VDN, Dakar, Senegal
| | - Cheikh Abdoul Khadir Diop
- Laboratoire de Chimie Minérale et Analytique (LACHIMIA), Département de Chimie, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Mamadou Sidibé
- Laboratoire de Chimie Minérale et Analytique (LACHIMIA), Département de Chimie, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Libasse Diop
- Laboratoire de Chimie Minérale et Analytique (LACHIMIA), Département de Chimie, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
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Kenouche S, Bachir N, Martínez-Araya JI. Explaining the High Catalytic Activity in Bis(indenyl)methyl Zirconium Cation Using Combined EDA-NOCV/ QTAIM Approach. Chemphyschem 2023; 24:e202200488. [PMID: 36161688 DOI: 10.1002/cphc.202200488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/24/2022] [Indexed: 01/20/2023]
Abstract
The main purpose of this study is to elucidate some discrepancies already observed in the catalytic activity values of some zirconocene methyl cations. The EDA-NOCV scheme was employed for a theoretical description of the interactions between an ethylene molecule and five catalysts of zirconocene methyl cation. The nature of the chemical interactions has been elucidated through the QTAIM topological analysis. The steric hindrance due to the ligands was evaluated qualitatively by means of an IRI-based analysis and quantitively through Fisher information. The findings prove that the indenyl ligand seems to favor the orbital interaction between the ethylene molecule and the metal centre of zirconocene methyl cation. Both electrostatic and orbital contributions play a crucial role in stabilising the studied complexes. Based on the NOCV deformation density contributions, the strongest orbital interaction is reached with the bis(indenyl)methyl zirconium cation, which is the only one exhibiting covalent interactions. Especially, the strong contribution of π-back donation (occurring from the occupied orbitals of the zirconium atom to the π* anti-bonding orbital of ethylene) may be a key to understand why this catalyst has a higher polymerisation yield than the other studied catalysts. This work suggests a perspective for predicting values of catalytic activity when theoretically designing novel catalysts of zirconocene type.
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Affiliation(s)
- Samir Kenouche
- Group of Modeling of Chemical Systems using Quantum Calculations, Applied Chemistry Laboratory (LCA)., University of M. Khider of Biskra, BP 145 RP, 07000, Biskra, Algeria
| | - Nassima Bachir
- Group of Modeling of Chemical Systems using Quantum Calculations, Applied Chemistry Laboratory (LCA)., University of M. Khider of Biskra, BP 145 RP, 07000, Biskra, Algeria
| | - Jorge I Martínez-Araya
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello (UNAB), Av. República 275, 8370146, Santiago, Chile
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Majerz I, Krawczyk MS. Crystal Structure and Chemical Bonds in [Cu II2(Tolf) 4(MeOH) 2]∙2MeOH. Int J Mol Sci 2023; 24:ijms24021745. [PMID: 36675260 PMCID: PMC9864235 DOI: 10.3390/ijms24021745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/02/2023] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
A new coordination compound of copper(II) with a tolfenamate ligand of the paddle-wheel-like structure [CuII2(Tolf)4(MeOH)2]∙2MeOH was obtained and structurally characterized. Chemical bonds of Cu(II)∙∙∙Cu(II) and Cu(II)-O were theoretically analyzed and compared with the results for selected similar structures from the CSD database. QTAIM analysis showed that the Cu(II)∙∙∙Cu(II) interaction has a strength comparable to a hydrogen bond, as indicated by the electron density at a critical point. The remaining QTAIM parameters indicate stability of the Cu(II)∙∙∙Cu(II) interaction. Other methods, such as NCI and NBO, also indicate a significant strength of this interaction. Thus, the Cu(II)∙∙∙Cu(II) interaction can be treated as one of the noncovalent interactions that affects the structure of the coordination compound, the packing of molecules in the crystal, and the general properties of the compound.
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Kizior B, Michalczyk M, Panek JJ, Zierkiewicz W, Jezierska A. Unraveling the Nature of Hydrogen Bonds of "Proton Sponges" Based on Car-Parrinello and Metadynamics Approaches. Int J Mol Sci 2023; 24. [PMID: 36675059 DOI: 10.3390/ijms24021542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/26/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023] Open
Abstract
The nature of intra- and intermolecular non-covalent interactions was studied in four naphthalene derivatives commonly referred to as "proton sponges". Special attention was paid to an intramolecular hydrogen bond present in the protonated form of the compounds. The unsubstituted "proton sponge" served as a reference structure to study the substituent influence on the hydrogen bond (HB) properties. We selected three compounds substituted by methoxy, amino, and nitro groups. The presence of the substituents either retained the parent symmetry or rendered the compounds asymmetric. In order to reveal the non-covalent interaction properties, the Hirshfeld surface (HS) was computed for the crystal structures of the studied compounds. Next, quantum-chemical simulations were performed in vacuo and in the crystalline phase. Car-Parrinello molecular dynamics (CPMD), Path Integral Molecular Dynamics (PIMD), and metadynamics were employed to investigate the time-evolution changes of metric parameters and free energy profile in both phases. Additionally, for selected snapshots obtained from the CPMD trajectories, non-covalent interactions and electronic structure were studied. Quantum theory of atoms in molecules (QTAIM) and the Density Overlap Regions Indicator (DORI) were applied for this purpose. It was found based on Hirshfeld surfaces that, besides intramolecular hydrogen bonds, other non-covalent interactions are present and have a strong impact on the crystal structure organization. The CPMD results obtained in both phases showed frequent proton transfer phenomena. The proton was strongly delocalized in the applied time-scale and temperature, especially in the PIMD framework. The use of metadynamics allowed for tracing the free energy profiles and confirming that the hydrogen bonds present in "proton sponges" are Low-Barrier Hydrogen Bonds (LBHBs). The electronic and topological analysis quantitatively described the temperature dependence and time-evolution changes of the electronic structure. The covalency of the hydrogen bonds was estimated based on QTAIM analysis. It was found that strong hydrogen bonds show greater covalency, which is additionally determined by the proton position in the hydrogen bridge.
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Das S, Chakraborty A. Non-covalent interactions in the monohydrated complexes of 1,2,3,4-tetrahydroisoquinoline. J Mol Model 2023; 29:37. [PMID: 36629924 DOI: 10.1007/s00894-022-05438-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
The eleven monohydrates of 1, 2, 3, 4-tetrahydroisoquinoline (THIQ) are analyzed through natural bond orbital (NBO) analysis and QTAIM methods employing M06-2X functional in DFT and MP2 methods. Here, the role of OH bonds as an acceptor and donor is critically analyzed. The role of lone pairs of O is critically monitored in two of the complexes, where N-H···O hydrogen bonds are present. The relative contributions of rehybridisation and hyperconjugation are compared in detail. Popelier criteria are satisfied in all the complexes barring a few exceptions involving weak hydrogen bonds. At the bond critical points (BCP), four monohydrates show higher values of electron density (ρC) and negative values of total electron energy density (HC), while Laplacian [Formula: see text] remains positive. These complexes satisfy the criteria of partial covalency. All these are O-H⋅⋅⋅N-type bonds. Remaining h-bonds are weaker in nature. These are also confirmed by the smaller values of ρC at the respective BCP. The variation of potential energy density (VC) among the complexes seems to be the most important factor in determining the nature of non-covalent interactions.
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Affiliation(s)
- Santu Das
- Department of Physics, Government General Degree College, Hooghly, Singur, 712409, India
- Department of Physics, The University of Burdwan, Golapbag Campus, Burdwan, 713104, West Bengal, India
| | - Abhijit Chakraborty
- Department of Physics, The University of Burdwan, Golapbag Campus, Burdwan, 713104, West Bengal, India.
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Feitosa LF, Campos RB, Richter WE. Energetics and electronics of polar Diels-Alder reactions at the atomic level: QTAIM and IQA analyses of complete IRC paths. J Mol Graph Model 2023; 118:108326. [PMID: 36166996 DOI: 10.1016/j.jmgm.2022.108326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/28/2022]
Abstract
The mechanism of Diels-Alder reactions between cyclopentadiene and several cyanoethylenes was studied by means of Density Functional Theory calculations using QTAIM and IQA (Interacting Quantum Atoms) analyses along complete IRC paths. Each geometry from the IRC had its wavefunction computed and the topology of the electronic density for it was then evaluated. By means of IQA, the global energetic profile was partitioned among the various atoms in the molecule, providing insight into what atoms are the main ones responsible for the magnitude of the energy barriers. The (a)synchronicity of the reaction mechanisms featuring non-symmetrically substituted dienophiles was characterized, from QTAIM, by the electron densities and Laplacians over the LCP's as well as by the different atomic energy barriers obtained from IQA. The magnitude of the atomic barrier nicely explains the (a)synchronicity of the reaction mechanisms, and the degree of (a)synchronicity is nicely revealed by the difference between the earlier and later bond breaking and bond formations. The main conclusion is that important energetic and electronic changes are occurring before and after the position of the transition state structure, mainly for those asynchronous mechanisms, and although these provide essential insight into the reaction mechanism, most studies cannot assess this kind of information because they are focusing solely on reactants, transition states, and products. We advocate that the additional computational effort required for such analyses is more than compensated by the great amount of useful information it provides.
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Affiliation(s)
- Lucas Freitas Feitosa
- Department of Chemistry and Biology, Federal University of Technology - Paraná [UTFPR], 81.280-340, Curitiba PR, Brazil
| | - Renan Borsoi Campos
- Department of Chemistry and Biology, Federal University of Technology - Paraná [UTFPR], 81.280-340, Curitiba PR, Brazil
| | - Wagner Eduardo Richter
- Department of Chemistry, Federal University of Technology - Paraná [UTFPR], 84.017-220, Ponta Grossa PR, Brazil.
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Szymańska M, Majerz I. Prototropy, Intramolecular Interactions, Electron Delocalization, and Physicochemical Properties of 1,8-dihydroxy-9-anthrone-DFT-D3 Study of Substituent Effects. Molecules 2023; 28:molecules28010344. [PMID: 36615539 PMCID: PMC9822037 DOI: 10.3390/molecules28010344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023]
Abstract
1,8-dihydroxy-9-anthrone are tricyclic compounds with a ketone group in the middle ring and two hydroxyl groups substituted in the side-aromatic rings what results in formation of two intramolecular hydrogen bonds in which the oxygen atom from the ketone group is the proton acceptor. 1,8-dihydroxy-9-anthrones in which intramolecular proton transfer between C10 and CO in the middle ring occurs, can exist in a tautomeric keto-enol equilibrium. For anthralin, the most important representative of this group, this equilibrium has been studied previously, but it has not been studied for its derivatives. Substituents in the middle ring change the geometry of 1,8-dihydroxy-9-anthrones so they are also expected to affect the keto-enol equilibrium. It is also important to study the effect of intramolecular hydrogen bonds on the structure of both tautomeric forms. It was found that the nature of the substituent in the middle ring could affect the antioxidant properties of the investigated compound.
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50
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Gassoumi B, Dlala NA, Echabaane M, Karayel A, Özkınalı S, Castro M, Melendez F, Ghalla H, Nouar L, Madi F, Chaabane RB. Stability, spectroscopic, electrochemistry and QTAIM analysis of Cu-Zn n-1O n clusters for glucose sensing application: A study on theoretical and experimental insights. Heliyon 2022; 8:e12387. [PMID: 36582723 PMCID: PMC9793285 DOI: 10.1016/j.heliyon.2022.e12387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/17/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Clusters of (ZnO)n (n = 2-4) have been shown to play a central role in the detection of glucose entity based on the existence of photo-induced electrons (PE), which facilitates the interaction between (ZnO)n clusters and glucose entity guests. The electrochemistry experiment has confirmed the detection of glucose by the title clusters. The optimization, energetic parameters, and vibrational frequency calculations have indicated that the Cu-Znn-1On-glucose are more stable than the (ZnO)n-glucose complexes. It has been demonstrated that the Cu doping enhanced the chemical behavior of the clusters and formed a high intramolecular charge transfer (ICT) in the system. The glucose sensing by all the forms of Cu-Znn-1On clusters showed that the Cu-Zn3O4, Cu-Wurtzite, and Cu-Rocksalt clusters are the most suitable for adsorbing the glucose guest. The HOMO/LUMO iso-surfaces of the complexes showed that the electron concentrations are localized in the d orbitals and mainly in the form of the d10 orbitals around Zn atoms. The molecular electrostatic potential (MEP) has clearly indicated that a high charge transfer occurs between the copper and the oxygen atoms, which facilitate the adsorption of glucose. The reactivity parameters also indicated that the Wurtzite-glucose complex has a high electrophilicity index (ω), which means a good acceptor behavior to interact with glucose. Additionally, the bond between the (ZnO)n clusters and the glucose polar element has been studied in detail by using QTAIM theory. Finally, the theoretical and experimental studies prove that the Cu-Znn-1On clusters are very suitable and competent compounds for detecting glucose.
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Affiliation(s)
- B. Gassoumi
- Laboratory of Advanced Materials and Interfaces (LIMA), University of Monastir, Faculty of Science of Monastir, Avenue of Environment, 5000 Monastir, Tunisia
- Corresponding author.
| | - N. Aouled Dlala
- Quantum and Statistical Physics Laboratory, Faculty of Sciences, University of Monastir, 5079 Monastir, Tunisia
| | - M. Echabaane
- Laboratory of Advanced Materials and Interfaces (LIMA), University of Monastir, Faculty of Science of Monastir, Avenue of Environment, 5000 Monastir, Tunisia
- NANOMISENE Lab, LR16CRMN01, Centre for Research on Microelectronics and Nanotechnology CRMN of Technopark of Sousse, B.P. 334, Sahloul, 4034 Sousse, Tunisia
| | - A. Karayel
- Department of Physics, Faculty of Arts and Sciences, Hitit University, Çorum, Turkey
- Corresponding author.
| | - S. Özkınalı
- Department of Chemistry, Faculty of Arts and Sciences, Hitit University, Çorum, Turkey
| | - M.E. Castro
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, 18 sur y Av. San, Claudio, Col. San Manuel Puebla C. P. 72570, Mexico
| | - F.J. Melendez
- Lab. de Química Teórica, Centro de Investigación, Depto. de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Edif. FCQ10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, C.P 72570, Puebla, Mexico
| | - H. Ghalla
- Quantum and Statistical Physics Laboratory, Faculty of Sciences, University of Monastir, 5079 Monastir, Tunisia
| | - L. Nouar
- Laboratory of Computational Chemistry and Nanostructures, Department of Material Sciences, Faculty of Mathematical, Informatics and Material Sciences, University of 8 May 1945, Guelma, Algeria
| | - F. Madi
- Laboratory of Computational Chemistry and Nanostructures, Department of Material Sciences, Faculty of Mathematical, Informatics and Material Sciences, University of 8 May 1945, Guelma, Algeria
| | - R. Ben. Chaabane
- Laboratory of Advanced Materials and Interfaces (LIMA), University of Monastir, Faculty of Science of Monastir, Avenue of Environment, 5000 Monastir, Tunisia
- Corresponding author.
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