1
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Pomogaeva AV, Lisovenko AS, Timoshkin AY. Structures and stability of I 2 and ICl complexes with pyridine: Ab initio and DFT study. J Comput Chem 2024; 45:903-914. [PMID: 38165152 DOI: 10.1002/jcc.27300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 01/03/2024]
Abstract
Theoretical investigation of thermodynamic stability and bonding features of possible isomers of the molecular and ionic complexes of pyridine with molecular iodine and iodine monochloride IX (X = I,Cl) is presented. M06-2X DFT functional is found to provide bond distances and dissociation energies which are close to those obtained at high-level ab initio CCSD(T)/aug-cc-pvtz//CCSD/aug-cc-pvtz benchmark computations for the most stable isomers, formed via donation of a lone pair of nitrogen atom of pyridine to the iodine atom. These isomers are by 23-33 kJ mol-1 (in case of I2) and by 39-56 kJ mol-1 (in case of ICl) more stable than other molecular complexes. T-shaped π-σ* bonded isomers turn out to be energetically comparable with van der Waals bound compounds. Among the ionic isomers, structures featuring [IPy2]+ cation with I3 - or ICl2 - counterions are more stable. Oligomerization favors ionic isomers starting from the tetrameric clusters of the composition (IX)4Py4.
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Affiliation(s)
- Anna V Pomogaeva
- Institute of Chemistry, Saint Petersburg State University, St. Petersburg, Russia
| | - Anna S Lisovenko
- Institute of Chemistry, Saint Petersburg State University, St. Petersburg, Russia
| | - Alexey Y Timoshkin
- Institute of Chemistry, Saint Petersburg State University, St. Petersburg, Russia
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2
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Wang L, Bohmer MJ, Wang J, Nardella F, Calla J, Laureano De Souza M, Schindler KA, Montejo L, Mittal N, Rocamora F, Treat M, Charlton JT, Tumwebaze PK, Rosenthal PJ, Cooper RA, Chakrabarti R, Winzeler EA, Chakrabarti D, Gray NS. Discovery of Potent Antimalarial Type II Kinase Inhibitors with Selectivity over Human Kinases. J Med Chem 2024; 67:1460-1480. [PMID: 38214254 PMCID: PMC10950204 DOI: 10.1021/acs.jmedchem.3c02046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
While progress has been made in the effort to eradicate malaria, the disease remains a significant threat to global health. Acquired resistance to frontline treatments is emerging in Africa, urging a need for the development of novel antimalarial agents. Repurposing human kinase inhibitors provides a potential expedited route given the availability of a diverse array of kinase-targeting drugs that are approved or in clinical trials. Phenotypic screening of a library of type II human kinase inhibitors identified compound 1 as a lead antimalarial, which was initially developed to target human ephrin type A receptor 2 (EphA2). Here, we report a structure-activity relationship study and lead optimization of compound 1, which led to compound 33, with improved antimalarial activity and selectivity.
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Affiliation(s)
- Lushun Wang
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Monica J Bohmer
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Jinhua Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Flore Nardella
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Jaeson Calla
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Mariana Laureano De Souza
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Lukas Montejo
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Nimisha Mittal
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Frances Rocamora
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Mayland Treat
- School of Public Health, University of California, Berkeley California 94704, United States
| | - Jordan T Charlton
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California 94901, United States
| | | | - Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, California 94110, United States
| | - Roland A Cooper
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California 94901, United States
| | - Ratna Chakrabarti
- Division of Cancer Research, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Debopam Chakrabarti
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
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3
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Peluso P, Chankvetadze B. Recent developments in molecular modeling tools and applications related to pharmaceutical and biomedical research. J Pharm Biomed Anal 2024; 238:115836. [PMID: 37939549 DOI: 10.1016/j.jpba.2023.115836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/21/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
In modern pharmaceutical and biomedical research, molecular modeling represents a useful tool to explore processes and their mechanistic bases at the molecular level. Integrating experimental and virtual analysis is a fruitful approach to study ligand-receptor interaction in chemical, biochemical and biological environments. In these fields, molecular docking and molecular dynamics are considered privileged techniques for modeling (bio)macromolecules and related complexes. This review aims to present the current landscape of molecular modeling in pharmaceutical and biomedical research by examining selected representative applications published in the last years and highlighting current topics and trends of this field. Thus, a systematic compilation of all published literature has not been attempted herein. After a brief overview of the main theoretical and computational tools used to investigate mechanisms at molecular level, recent applications of molecular modeling in drug discovery, ligand binding and for studying protein conformation and function will be discussed. Furthermore, specific sections will be devoted to the application of molecular modeling for unravelling enantioselective mechanisms underlying the enantioseparation of chiral compounds of pharmaceutical and biomedical interest as well as for studying new forms of noncovalent interactivity identified in biochemical and biological environments. The general aim of this review is to provide the reader with a modern overview of the topic, highlighting advancements and outlooks as well as drawbacks and pitfalls still affecting the applicability of theoretical and computational methods in the field of pharmaceutical and biomedical research.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB-CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy.
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, 0179 Tbilisi, Georgia
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4
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Adeniyi E, Odubo FE, Zeller M, Torubaev YV, Rosokha SV. Halogen Bonding and/or Covalent Bond: Analogy of 3c-4e N···I···X (X = Cl, Br, I, and N) Interactions in Neutral, Cationic, and Anionic Complexes. Inorg Chem 2023; 62:18239-18247. [PMID: 37870922 DOI: 10.1021/acs.inorgchem.3c02843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
X-ray structural measurements and computational analysis demonstrated the similarity of the geometries and electronic structures of the X-I···N (X = Cl, Br, I, and N) bonding in strong halogen-bonded (HaB) complexes and in the anionic or cationic halonium ions. In particular, I···N bond lengths in the solid-state associations formed by strong HaB donors (e.g., I2, IBr, ICl, and N-iodosuccinimide) and acceptors (e.g., quinuclidine or pyridines) were in the same range of 2.3 ± 0.1 Å as those in the halonium ions [e.g., the bis(quinuclidine)iodonium cation or the 1,1'-iodanylbis(pyrrolidine-2,5-dione) anion]. In all cases, bond lengths were much closer to those of the N-I covalent bond than to the van der Waals separations of these atoms. The strong N···I bonding in the HaB complexes led to a substantial charge transfer, lengthening and weakening of the I···X bonds, and polarization of the HaB donors. As a result, the central iodine atoms in the strong HaB complexes bear partial positive charges akin to those in the halonium ions. The energies and Mayer bond orders for both N···I and I···X bonds in such associations are also comparable to those in the halonium ions. The similarity of the bonding in such complexes and in halonium ions was further supported by the analysis of electron densities and energies at bond critical (3, -1) points in the framework of the quantum theory of atoms in molecules and by the density overlap region indicator. Overall, all these data point out the analogy of the symmetric N···I···N bonding in the halonium ions and the asymmetric X···I···N bonding in the strong HaB complexes, as well as the weakly covalent character of these 3c-4e interactions.
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Affiliation(s)
- Emmanuel Adeniyi
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Favour E Odubo
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Matthias Zeller
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yury V Torubaev
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Sergiy V Rosokha
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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5
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Tyagi R, Zen A, Voora VK. Quantifying the Impact of Halogenation on Intermolecular Interactions and Binding Modes of Aromatic Molecules. J Phys Chem A 2023. [PMID: 37406194 DOI: 10.1021/acs.jpca.3c02291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Halogenation of aromatic molecules is frequently used to modulate intermolecular interactions with ramifications for optoelectronic and mechanical properties. In this work, we accurately quantify and understand the nature of intermolecular interactions in perhalogenated benzene (PHB) clusters. Using benchmark binding energies from the fixed-node diffusion Monte Carlo (FN-DMC) method, we show that generalized Kohn-Sham semicanonical projected random phase approximation (GKS-spRPA) plus approximate exchange kernel (AKX) provides reliable interaction energies with mean absolute error (MAE) of 0.23 kcal/mol. Using the GKS-spRPA+AXK method, we quantify the interaction energies of several binding modes of PHB clusters ((C6X6)n; X = F, Cl, Br, I; n = 2, 3). For a given binding mode, the interaction energies increase 3-4 times from X = F to X = I; the X-X binding modes have energies in the range of 2-4 kcal/mol, while the π-π binding mode has interaction energies in the range of 4-12 kcal/mol. SAPT-DFT-based energy decomposition analysis is then used to show that the equilibrium geometries are dictated primarily by the dispersion and exchange interactions. Finally, we test the accuracy of several dispersion-corrected density functional approximations and show that only the r2SCAN-D4 method has a low MAE and correct long-range behavior, which makes it suitable for large-scale simulations and for developing structure-function relationships of halogenated aromatic systems.
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Affiliation(s)
- Ritaj Tyagi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Andrea Zen
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
| | - Vamsee K Voora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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6
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Sherard M, Dang QM, Reiff SC, Simpson JH, Leopold MC. On-Site Detection of Neonicotinoid Pesticides Using Functionalized Gold Nanoparticles and Halogen Bonding. ACS APPLIED NANO MATERIALS 2023; 6:8367-8381. [PMID: 37260915 PMCID: PMC10227770 DOI: 10.1021/acsanm.3c00618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/10/2023] [Indexed: 06/02/2023]
Abstract
Neonicotinoid (NN) pesticides have emerged globally as one of the most widely used agricultural tools for protecting crops from pest damage and boosting food production. Unfortunately, some NN compounds, such as extensively employed imidacloprid-based pesticides, have also been identified as likely endangering critical pollinating insects like honey bees. To this end, NN pesticides pose a potential threat to world food supplies. As more countries restrict or prohibit the use of NN pesticides, tools are needed to effectively and quickly identify the presence of NN compounds like imidacloprid on site (e.g., in storage areas on farms or pesticide distribution warehouses). This study represents a proof-of-concept where the colloidal properties of specifically modified gold nanoparticles (Au-NPs) able to engage in the rare intermolecular interaction of halogen bonding (XB) can result in the detection of certain NN compounds. Density functional theory and diffusion-ordered NMR spectroscopy (DOSY NMR) are used to explore the fundamental XB interactions between strong XB-donor structures and NN compounds, with the latter found to possess multiple XB-acceptor binding sites. A fundamental understanding of these XB interactions allows for the functionalization of alkanethiolate-stabilized Au-NPs, known as monolayer-protected gold clusters (MPCs), with XB-donor capability (f-MPCs). In the presence of certain NN compounds such as imidacloprid, the f-MPCs subsequently exhibit visual XB-induced aggregation that is also measured with absorption (UV-vis) spectroscopy and verified with transmission electron microscopy (TEM) imaging. The demonstrated f-MPC-aggregation detection scheme has a number of favorable attributes, including quickly reporting the presence of the NN target, requiring only micrograms of suspect material, and being highly selective for imidacloprid, the most prevalent and most important NN insecticide compound. Requiring no instrumentation, the presented methodology can be envisioned as a simple screening test in which dipping a cotton swab of an unknown powder from a surface in a f-MPC solution causes f-MPCs to aggregate and yield a preliminary indication of imidacloprid presence.
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7
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Theoretical and experimental study of new deep eutectic solvents for extraction of perfluorinated iodoalkanes. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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8
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Assessing How Residual Errors of Scoring Functions Correlate to Ligand Structural Features. Int J Mol Sci 2022; 23:ijms232315018. [PMID: 36499344 PMCID: PMC9739603 DOI: 10.3390/ijms232315018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
Scoring functions (SFs) are ubiquitous tools for early stage drug discovery. However, their accuracy currently remains quite moderate. Despite a number of successful target-specific SFs appearing recently, up until now, no ideas on how to systematically improve the general scope of SFs have been formulated. In this work, we hypothesized that the specific features of ligands, corresponding to interactions well appreciated by medicinal chemists (e.g., hydrogen bonds, hydrophobic and aromatic interactions), might be responsible, in part, for the remaining SF errors. The latter provides direction to efforts aimed at the rational and systematic improvement of SF accuracy. In this proof-of-concept work, we took a CASF-2016 coreset of 285 ligands as a basis for comparison and calculated the values of scores for a representative panel of SFs (including AutoDock 4.2, AutoDock Vina, X-Score, NNScore2.0, ΔVina RF20, and DSX). The residual error of linear correlation of each SF value, with the experimental values of affinity and activity, was then analyzed in terms of its correlation with the presence of the fragments responsible for certain medicinal chemistry defined interactions. We showed that, despite the fact that SFs generally perform reasonably, there is room for improvement in terms of better parameterization of interactions involving certain fragments in ligands. Thus, this approach opens a potential way for the systematic improvement of SFs without their significant complication. However, the straightforward application of the proposed approach is limited by the scarcity of reliable available data for ligand-receptor complexes, which is a common problem in the field.
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9
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Mo Y, Danovich D, Shaik S. The roles of charge transfer and polarization in non-covalent interactions: a perspective from ab initio valence bond methods. J Mol Model 2022; 28:274. [PMID: 36006511 DOI: 10.1007/s00894-022-05187-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions are ubiquitous and have been well recognized in chemistry, biology and material science. Yet, there are still recurring controversies over their natures, due to the wide range of noncovalent interaction terms. In this Essay, we employed the Valence Bond (VB) methods to address two types of interactions which recently have drawn intensive attention, i.e., the halogen bonding and the CH‧‧‧HC dihydrogen bonding. The VB methods have the advantage of interpreting molecular structures and properties in the term of electron-localized Lewis (resonance) states (structures), which thereby shed specific light on the alteration of the bonding patterns. Due to the electron localization nature of Lewis states, it is possible to define individually and measure both polarization and charge transfer effects which have different physical origins. We demonstrated that both the ab initio VB method and the block-localized wavefunction (BLW) method can provide consistent pictures for halogen bonding systems, where strong Lewis bases NH3, H2O and NMe3 partake as the halogen bond acceptors, and the halogen bond donors include dihalogen molecules and XNO2 (X = Cl, Br, I). Based on the structural, spectral, and energetic changes, we confirm the remarkable roles of charge transfer in these halogen bonding complexes. Although the weak C-H∙∙∙H-C interactions in alkane dimers and graphene sheets are thought to involve dispersion only, we show that this term embeds delicate yet important charge transfer, bond reorganization and polarization interactions.
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Affiliation(s)
- Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC, 27401, USA.
| | - David Danovich
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel.
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10
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Zhao X, Xiong D, Luo S, Duan L. Molecular investigation of the dual inhibition mechanism for targeted P53 regulator MDM2/MDMX inhibitors. Phys Chem Chem Phys 2022; 24:16799-16815. [PMID: 35775962 DOI: 10.1039/d2cp01780f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Inhibitors that competitively bind MDM2/MDMX can block the inhibition of P53 by MDM2/MDMX and restart its tumor-suppressive effect. Molecular studies targeting MDM2/MDMX inhibitors have always been a hot topic in anticancer drug design. Although numerous inhibitors have been designed previously against MDM2/MDMX, their dual inhibition efficacy has not been demonstrated, and few studies assessed the general causes affecting the dual inhibition of MDM2/MDMX by these inhibitors. Here, molecular dynamics simulations and alanine scanning combined with the interaction entropy method were employed to precisely investigate whether 16 inhibitors could dually inhibit MDM2/MDMX and the similarities and differences in the interaction modes. Thereby addressing the key residue sites affecting dual inhibition. Residues L54/M53, I61/60, M62/61, Y67/66, and V93/92 of MDM2/MDMX, which are in corresponding positions in both protein structures, provide significant conditions for these inhibitors to bind to MDM2/MDMX tightly. In addition, most of these inhibitors prefer to bind MDM2 than MDMX, and residues H96 and I99 in MDM2 are attractive targets for inhibitors, resulting in inhibitors binding to MDM2/MDMX with different affinity. These key residues should be considered in the development of dual inhibitors. For these 16 inhibitors, most have dual inhibitory potential for MDM2/MDMX based on the binding affinity of the complexes. Still, it is questionable whether they can exert excellent dual inhibition considering the assessment of the hot-spots. At least their binding affinity for MDMX is not superior to that for MDM2 due to the difference in energy of the van der Waals interactions at the key sites. Furthermore, based on the analysis of three representative inhibitors (TUZ/HRH and HRQ with different binding preferences for MDM2/MDMX), 3-chloropyridine in TUZ leads to the differential binding affinity between the inhibitor and MDM2/MDMX. It readily forms hydrophobic interactions with the surrounding residues H96 and I99. But this phenomenon does not occur in the TUZ-MDMX system, implying the critical role of residues H96/P95 and I99/L98. And the completely different binding mechanism of HRQ binding to MDM2/MDMX explains its inability to inhibit MDM2 well. Thus, we are cautious about its dual inhibitory ability. Besides, HRH is more prone to strong van der Waals interactions with MDM2 than MDMX whereas its 2-chlorofluorobenzene is detrimental to this. We hope that these findings will provide reliable molecular insights for the screening and optimization of targeting MDM2/MDMX dual inhibitors.
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Affiliation(s)
- Xiaoyu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Danyang Xiong
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Song Luo
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
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11
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Howe D, Wilson J, Rosokha SV. Solvent and Ionic Atmosphere Effects in Anion-π Interactions: Complexes of Halide Anions with p-Benzoquinones. J Phys Chem A 2022; 126:4255-4263. [PMID: 35737724 DOI: 10.1021/acs.jpca.2c03491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interplay between the solvent polarity and ionic atmosphere in anion-π association was evaluated via an experimental and a computational study of the BQ·X- complexes between benzoquinones (BQ) and halide anions (X-). The UV-Vis spectral measurements showed that these complexes are characterized by the strong absorption bands in the 300-450 nm range and their effective formation constants, Keff, measured in dichloromethane in the absence (or at low concentrations) of the supporting electrolyte, Bu4NPF6, were higher than those in acetonitrile. The experimental data were consistent with the results of the computations, which showed that magnitudes of the interaction energy, ΔE, between BQ and X- decreased considerably with the increase in the polarity of the media. The addition of auxiliary electrolytes (e.g., Bu4NPF6) led to a decrease in the concentration of the BQ·X- complexes. These changes were related to the competing associations of the π-acceptors with halides and PF6- anions (since the interaction energies between BQ acceptors and common non-halide anions, e.g., PF6-, BF4-, and NO3-, were comparable to those in the BQ·X- complexes) and to the increased ionic strength of the solutions. The variations in strength of anion-π interactions with the solvent polarity and ionic atmosphere were related to the higher effective ionic radii of the complexes. Due to the larger effects of the auxiliary electrolytes in dichloromethane, the formation constants for the BQ·X- complexes measured at high ionic strength in this solvent were lower than those in more polar acetonitrile or propylene carbonate. Such a combination of the effects of the solvent and ionic atmosphere should be taken into account when comparing experimental data with the results of the calculations and in design of the systems for molecular recognition and catalysis.
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Affiliation(s)
- Devin Howe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Joshua Wilson
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Sergiy V Rosokha
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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12
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Shulga DA, Tserkovnikova NA, Tarasov DN, Tovbin DG. Investigation of the tight binding mechanism of a new anticoagulant DD217 to factor Xa by means of molecular docking and molecular dynamics. J Biomol Struct Dyn 2022:1-12. [PMID: 35532097 DOI: 10.1080/07391102.2022.2072387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A new promising drug candidate DD217 has been proposed recently as a potent anticoagulant acting on factor Xa (fXa) target. It exhibits the lowest concentration of doubling the prothrombin time among the known anticoagulants. In order to explain the efficacy of DD217 in terms of molecular interactions with its target we studied the hypothesis of the tight binding mechanism by means of molecular dynamics simulations and statistical analysis of the trajectory. The conducted analysis confirms the significant contributions to the MM/GBSA estimated binding free energy of the S4 pocket residues as well the crucial role of establishing the hydrogen bonds between the ligand and the backbone amides of Gly216 and Gly218 of the target. The simulation results support the hypothesis of the tight binding mechanism of DD217 to fXa.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dmitry A Shulga
- Department of Chemistry, Moscow State University, Moscow, Russia
| | - Natalia A Tserkovnikova
- Department of Kinetics and Catalysis, Institute of Chemical Physics of Russian, Academy of Sciences, Moscow, Russia
| | - Dmitry N Tarasov
- Department of Kinetics and Catalysis, Institute of Chemical Physics of Russian, Academy of Sciences, Moscow, Russia.,PharmaDiall LLC, Moscow, Russia
| | - Dmitry G Tovbin
- Department of Kinetics and Catalysis, Institute of Chemical Physics of Russian, Academy of Sciences, Moscow, Russia.,PharmaDiall LLC, Moscow, Russia
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13
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Zhang ZL, Chen C, Qu SY, Ding Q, Xu Q. Unexpected Dynamic Binding May Rescue the Binding Affinity of Rivaroxaban in a Mutant of Coagulation Factor X. Front Mol Biosci 2022; 9:877170. [PMID: 35601826 PMCID: PMC9117642 DOI: 10.3389/fmolb.2022.877170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
A novel coagulation factor X (FX) Tyr319Cys mutation (Y99C as chymotrypsin numbering) was identified in a patient with severe bleeding. Unlike the earlier reported Y99A mutant, this mutant can bind and cleave its specific chromogenetic substrate at a normal level, suggesting an intact binding pocket. Here, using molecular dynamics simulations and MM-PBSA calculations on a FX-rivaroxaban (RIV) complex, we confirmed a much stronger binding of RIV in Y99C than in Y99A on a molecular level, which is actually the average result of multiple binding poses in dynamics. Detailed structural analyses also indicated the moderate flexibility of the 99-loop and the importance of the flexible side chain of Trp215 in the different binding poses. This case again emphasizes that binding of ligands may not only be a dynamic process but also a dynamic state, which is often neglected in drug design and screening based on static X-ray structures. In addition, the computational results somewhat confirmed our hypothesis on the activated Tyr319Cys FX (Y99C FXa) with an impaired procoagulant function to bind inhibitors of FXa and to be developed into a potential reversal agent for novel oral anticoagulants (NOAC).
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Affiliation(s)
- Zhi-Li Zhang
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Si-Ying Qu
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Qiulan Ding, ; Qin Xu,
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Qiulan Ding, ; Qin Xu,
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14
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Miller DK, Chernyshov IY, Torubaev YV, Rosokha SV. From weak to strong interactions: structural and electron topology analysis of the continuum from the supramolecular chalcogen bonding to covalent bonds. Phys Chem Chem Phys 2022; 24:8251-8259. [PMID: 35320823 DOI: 10.1039/d1cp05441d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The relationship between covalent and supramolecular bonding, and the criteria of the assignments of different interactions were explored via the review of selenium and tellurium containing structures in the Cambridge Structural Database and their computational analysis using Quantum Theory of Atoms in Molecules (QTAIM). This combined study revealed continuums of the interatomic Se⋯Br and Te⋯I distances, dCh⋯X, in the series of associations from the sums of the van der Waals radii of these atoms (rCh + rX) to their covalent bond lengths. The electron densities, ρ(r), at Bond Critical Points (BCPs) along the chalcogen bond paths increased gradually from about 0.01 a.u. common for the non-covalent interactions to about 0.1 a.u. typical for the covalent bonds. The log ρ(r) values fell on the same linear trend line when plotted against normalized interatomic distances, RXY = dCh⋯X/(rCh + rX). The transition from the positive to negative values of the energy densities, H(r), at the BCPs (related to a changeover of essentially non-covalent into partially covalent interactions) were observed at RXY ≈ 0.80. Synchronous changes of bonding characteristics with RXY (similar to that found earlier in the halogen-bonded systems) designated normalized interatomic separation as a critical factor determining the nature of these bondings. The uninterrupted continuums of Te⋯I and Se⋯Br bond lengths and BCPs' characteristics signified an intrinsic link between limiting types of bonding involving chalcogen atoms and between covalent and supramolecular bonding in general.
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Affiliation(s)
- Daniel K Miller
- Chemistry Department, Ball State University, Muncie, IN, 47306, USA.
| | - Ivan Yu Chernyshov
- TheoMat group, ChemBio Cluster, ITMO University, Lomonosova 9, St. Petersburg, 191002, Russia
| | - Yury V Torubaev
- N.S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, GSP-1, L eninsky prospect, 31, Moscow, 119991, Russia
| | - Sergiy V Rosokha
- Chemistry Department, Ball State University, Muncie, IN, 47306, USA.
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15
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Dang QM, Simpson JH, Parish CA, Leopold MC. Evaluating Halogen-Bond Strength as a Function of Molecular Structure Using Nuclear Magnetic Resonance Spectroscopy and Computational Analysis. J Phys Chem A 2021; 125:9377-9393. [PMID: 34661411 DOI: 10.1021/acs.jpca.1c07554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Halogen bonding (XB) is a highly directional, non-covalent intermolecular interaction between a molecule (XB donor) presenting a halogen with an electron-deficient region or sigma hole (σ-hole) and an electron-rich or Lewis-base molecule (XB acceptor). A systematic, experimental, and theoretical study of solution-phase XB strength as a function of the molecular structure for both XB donor and acceptor molecules is presented. The impact of specific structural features is assessed using 19F and 1H nuclear magnetic resonance (NMR) titrations to determine association constants, density functional theory calculations for interaction energies and bond lengths, as well as 19F-1H HOESY NMR measurements of intermolecular cross-relaxation between the interacting XB donor-acceptor adducts. For XB donor molecules (perfluoro-halogenated benzenes), results indicate the critical importance of iodine coupled with electron-withdrawing entities. Prominent structural components of XB acceptor molecules include a central atom working in conjunction with a Lewis-base atom to present high electron density directed at the σ-hole (e.g., tributylphosphine oxide). Additionally, larger surrounding aliphatic R groups (e.g., butyl and octyl) were found to significantly stabilize strong XB, particularly in solvents that promote the interaction. With a more thorough understanding of structure-optimized XB, one can envision harnessing XB interactions more strategically for specific design of optimal materials and chemical applications.
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Affiliation(s)
- Quang Minh Dang
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23173, United States
| | - Jeffrey H Simpson
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23173, United States
| | - Carol A Parish
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23173, United States
| | - Michael C Leopold
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23173, United States
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16
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Tarannam N, Shukla R, Kozuch S. Yet another perspective on hole interactions. Phys Chem Chem Phys 2021; 23:19948-19963. [PMID: 34514473 DOI: 10.1039/d1cp03533a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hole interactions are known by different names depending on the key atom of the bond (halogen bond, chalcogen bond, hydrogen bond, etc.), and the geometry of the interaction (σ if in line, π if perpendicular to the Lewis acid plane). However, its origin starts with the creation of a Lewis acid by an underlying covalent bond, which forms an electrostatic depletion and a virtual antibonding orbital, which can create non-covalent interactions with Lewis bases. In this (maybe subjective) perspective, we will claim that hole interactions must be defined via the molecular orbital origin of the molecule. Under this premise we can better explore the richness of such bonding patterns. For that, we will study old, recent and new systems, trying to pinpoint some misinterpretations that are often associated with them. We will use as exemplars the triel bonds, a couple of metal complexes, a discussion on convergent σ-holes, and many cases of anti-electrostatic hole interactions.
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Affiliation(s)
- Naziha Tarannam
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Rahul Shukla
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
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17
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Miller D, Loy C, Rosokha SV. Examining a Transition from Supramolecular Halogen Bonding to Covalent Bonds: Topological Analysis of Electron Densities and Energies in the Complexes of Bromosubstituted Electrophiles. ACS OMEGA 2021; 6:23588-23597. [PMID: 34549156 PMCID: PMC8444318 DOI: 10.1021/acsomega.1c03779] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
The transition from weak (noncovalent) interactions to fully developed covalent bonds is examined using the quantum theory of atoms in molecules in a series of halogen-bonded (XB) complexes of bromosubstituted electrophiles, RBr, with 1,4-diazabicyclo[2.2.2]octane (DABCO) and Cl- and Br- anions. The gradual decrease in the XB lengths in these associations, d Br···Y (where Y = Cl-, Br-, or N), was accompanied by the exponential increase in the binding energies and charge transfer, as well as electron densities and magnitudes of the kinetic and potential energy densities at the bond critical points (BCPs) on the Br···Y bond path. These indices, as well as characteristics of the adjacent bonds in the XB donor, followed remarkably close trend lines when plotted against the normalized XB length R BrY = d Br···Y/(r Br + r Y) (where r Br and r Y are the van der Waals radii) regardless of the methods [MP2/6-311+G(d,p) or M062X/6-311+G(d,p)], media (gas phase or dichloromethane), and nucleophiles (Cl-, Br-, or DABCO). In the systems with an R BrY higher than about 0.78, the energy densities H(r) at BCPs at the Br···Y bond path were small and positive, and XBs did not substantially affect the characteristics of the adjacent R-Br covalent bond in the XB donor. Accordingly, the XB can be identified as noncovalent in this range. In the complexes with R BrY values between about 0.67 and 0.78, energy densities H(r) at Br···Y BCPs were negative, and their magnitudes increased with the decrease in the Br···Y separation. In this range, formation of XBs was accompanied by the increase in the R-Br bond length in the XB donor and the decrease in the magnitude of the (negative) H(r) values at the BCPs of the R-Br bonds. XBs can be classified as partially covalent in this R BrY range. At an R BrY less than about 0.67, electron densities were larger, and energy densities were more negative at BCPs of the Br···Y bond than those at BCPs of the R-Br bond in the XB donor. This indicates that Br···Y bonds were stronger than R-Br bonds, and these (Br···Y) XBs can be regarded as essentially covalent. The synchronous change of a variety of (R-Br and Br···Y) bonding characteristics with R BrY suggests that the normalized XB bond length can be used as a basic parameter in the identification of the type of intermolecular interaction. A continuity of these characteristics suggests an inherent relationship between limiting (covalent and noncovalent) types of XBs and thus an onset of molecular-orbital interactions in the weaker bonds.
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18
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Tribedi S, Kitaura K, Nakajima T, Sunoj RB. On the question of steric repulsion versus noncovalent attractive interactions in chiral phosphoric acid catalyzed asymmetric reactions. Phys Chem Chem Phys 2021; 23:18936-18950. [PMID: 34612433 DOI: 10.1039/d1cp02499j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The origin of enantioselectivity in asymmetric catalysis is often built around the differential steric interaction in the enantiocontrolling transition states (TSs). A closer perusal of enantiocontrolling TSs in an increasingly diverse range of reactions has revealed that the cumulative effect of weak noncovalent interactions could even outweigh the steric effects. While enunciating this balance is conspicuously important, quantification of such intramolecular forces within a TS continues to remain scarce and challenging. Herein, we demonstrate the utility of the fragment molecular orbital method in establishing the relative contributions of various attractive and repulsive contributions in the total interaction energy between the suitably chosen fragments in enantiocontrolling TSs. Three types of reactions of high contemporary importance, namely, axially chiral phosphoric acid (CPA) catalyzed kinetic resolution of rac-α-methyl-γ-hydroxy ester (reaction I), asymmetric dearomative amination of β-naphthols by dimethyl azodicarboxylate (IIa and IIb), and intramolecular desymmetrization of β,β-disubstituted methyl oxetanes (IIIa) and hydroxyl oxetane (IIIb), bearing a tethered alcohol (-OCH2CH2OH or -(CH2)2CH2OH), are considered. In all the five reactions, the differences in the stabilizing contributions arising due to electrostatic, charge-transfer, and dispersion interactions between the catalyst and the reacting partners in the enantiocontrolling transition states are weighed against the destabilizing exchange interaction. The balancing interactions are found to be between dispersion and exchange repulsion in reaction I, a combination of charge transfer and dispersion energies offsets the repulsive energy in reaction IIb involving the electron rich anthryl groups in the catalyst, whereas the -(CF3)2C6H4 3,3'-substituent in the catalyst (reaction IIa) leads to a trade-off between dispersion and exchange energies. In reactions IIIa and IIIb, however, electrostatic and dispersion energies help compensate the repulsive interactions. These quantitative insights on the intramolecular interactions in the stereocontrolling TSs could help in the rational design of asymmetric catalysis.
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Affiliation(s)
- Soumi Tribedi
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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19
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Oliveira VP, Marcial BL, Machado FBC, Kraka E. Relating Bond Strength and Nature to the Thermodynamic Stability of Hypervalent Togni-Type Iodine Compounds. Chempluschem 2021; 86:1199-1210. [PMID: 34437775 DOI: 10.1002/cplu.202100285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/09/2021] [Indexed: 11/08/2022]
Abstract
The bond strength and nature of a set of 32 Togni-like reagents have been investigated at the M062X/def2-TZVP(D) level of theory in acetonitrile described with the SMD continuum solvent model, to rationalize the main factors responsible for their thermodynamic stability in different conformations, and trifluoromethylation capabilities. For the assessment of bond strength, we utilized local stretching force constants and associated bond strength orders, complemented with local features of the electron density to access the nature of the bonds. Bond dissociation energies varied from 31.6 to 79.9 kcal/mol depending on the polarizing power of the ligand trans to CF3 . Based on the analysis of the Laplacian of the density, we propose that the charge-shift bond character plays an important role in the stability of the molecules studied, especially for those containing I-O bonds. New insights on the trans influence and on possible ways to fine-tune the stability of these reagents are provided.
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Affiliation(s)
- Vytor Pinheiro Oliveira
- Instituto Tecnológico de Aeronáutica (ITA), Departamento de Química, São José dos Campos, 12228-900, São Paulo, Brazil
| | - Bruna Luana Marcial
- Instituto Federal Goiano (IF Goiano), Núcleo de Química, Campus Morrinhos, Goiás, Brazil
| | - Francisco B C Machado
- Instituto Tecnológico de Aeronáutica (ITA), Departamento de Química, São José dos Campos, 12228-900, São Paulo, Brazil
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas, 75275-0314, USA
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20
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Baykov SV, Geyl KK, Ivanov DM, Gomila RM, Frontera A, Kukushkin VY. Azine Steric Hindrances Switch Halogen Bonding to N-Arylation upon Interplay with σ-Hole Donating Haloarenenitriles. Chem Asian J 2021; 16:1445-1455. [PMID: 33844884 DOI: 10.1002/asia.202100282] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/11/2021] [Indexed: 12/24/2022]
Abstract
An interplay between 4-bromo- and 4-iodo-5-nitrophthalonitriles (XNPN, X=Br or I) and any one of the azines (pyridine 1, 4-dimethylaminopyridine 2, isoquinoline 3, 4-cyanopyridine 4, 2-methylpyridine 5, 2-aminopyridine 6, quinoline 7, 1-methylisoquinoline 8, and 2,2'-bipyridine 9) proceeds differently depending on steric and electronic effects of the heterocycles. Sterically unhindered azines 1-3 underwent N-arylation to give the corresponding azinium salts (characterized by 1 H and 13 C{H} NMR and high-resolution ESI-MS). In contrast, azines 4-9 with sterically hindered N atoms or bearing an electron-withdrawing substituent, form stable co-crystals with XNPN, where two interacting molecules are bound by halogen bonding. In all obtained co-crystals, X⋅⋅⋅N structure-directed halogen bonds were recognized and theoretically evaluated including DFT calculations (PBE0-D3/def2-TZVP level of theory), QTAIM analysis, molecular electrostatic potential surfaces, and noncovalent interaction plot index. Estimated energies of halogen bonding vary from -7.6 kcal/mol (for 6 ⋅ INPN) to -11.4 kcal/mol (5 ⋅ INPN).
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Affiliation(s)
- Sergey V Baykov
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., Saint Petersburg, 199034, Russian Federation
| | - Kirill K Geyl
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., Saint Petersburg, 199034, Russian Federation
| | - Daniil M Ivanov
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., Saint Petersburg, 199034, Russian Federation
| | - Rosa M Gomila
- Serveis Científico-Tècnics, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), Spain
| | - Vadim Y Kukushkin
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., Saint Petersburg, 199034, Russian Federation.,Laboratory of Crystal Engineering of Functional Materials, South Ural State University, 76 Lenin Av., Chelyabinsk, 454080, Russian Federation
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21
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Wysokiński R, Zierkiewicz W, Michalczyk M, Scheiner S. Crystallographic and Theoretical Evidences of Anion⋅⋅⋅Anion Interaction. Chemphyschem 2021; 22:818-821. [PMID: 33719162 DOI: 10.1002/cphc.202100132] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/08/2021] [Indexed: 11/10/2022]
Abstract
Planar (HgCl3 )- anions are stacked fairly closely together in a slipped parallel arrangement within several crystal structures. Quantum chemical analysis shows evidence of strong noncovalent spodium bonds between the Hg π-hole of one unit and the Cl atom of an adjacent unit. Anion⋅⋅⋅anion spodium bonds work in tandem with crystal packing forces.
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Affiliation(s)
- Rafał Wysokiński
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah, 84322-0300, United States
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22
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Anion-Anion Interactions in Aerogen-Bonded Complexes. Influence of Solvent Environment. Molecules 2021; 26:molecules26082116. [PMID: 33917030 PMCID: PMC8067769 DOI: 10.3390/molecules26082116] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/17/2022] Open
Abstract
Ab initio calculations are applied to the question as to whether a AeX5- anion (Ae = Kr, Xe) can engage in a stable complex with another anion: F-, Cl-, or CN-. The latter approaches the central Ae atom from above the molecular plane, along its C5 axis. While the electrostatic repulsion between the two anions prevents their association in the gas phase, immersion of the system in a polar medium allows dimerization to proceed. The aerogen bond is a weak one, with binding energies less than 2 kcal/mol, even in highly polar aqueous solvent. The complexes are metastable in the less polar solvents THF and DMF, with dissociation opposed by a small energy barrier.
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23
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Inscoe B, Rathnayake H, Mo Y. Role of Charge Transfer in Halogen Bonding. J Phys Chem A 2021; 125:2944-2953. [PMID: 33797922 DOI: 10.1021/acs.jpca.1c01412] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Halogen bonding has received intensive attention recently for its applications in the construction of supramolecular assemblies and crystal engineering and its implications and potentials in chemical and biological processes and rational drug design. Peculiarly, in intermolecular interactions, halogen atoms are known as electron-donating groups carrying partial negative charges in molecules due to its high electronegativity, but they can counterintuitively act as Lewis acids and bind with Lewis bases in the form of a halogen bond. The unsettling issue regarding the nature of the halogen bonding is whether the electrostatics or charge transfer interaction dominates. The recently proposed σ-hole concept nicely reinforces the role of electrostatic attraction. Also, good correlations between the halogen bonding strength and the interaction energy from the simple point-charge model have been found. This leads to the claim that there is no need to invoke the charge transfer concept in the halogen bond. But there is alternative evidence supporting the importance of charge transfer interaction. Here, we visited a series of prominent halogen bonded complexes of the types Y3C-X···Z (X = Br, I; Y = F, Cl, Br; Z = F-, Cl-, Br-, I-, NMe3) with the block-localized wave function (BLW) method at the M06-2X-D3/6-311+G(d,p) (def2-SVP for iodine) level of theory. As the simplest variant of ab initio valence bond (VB) theory, the BLW method is unique in the strict localization of electrons within interacting moieties, allowing for quantitative evaluation of the charge transfer effect on geometries, spectral properties, and energetics in halogen bonding complexes. By comparing the halogen bonding complexes with and without the charge transfer interaction, we proved that the charge transfer interaction significantly shortens the X···Z bonding distance and stretches the C-X bonds. But the shortening of the halogen bonding results in the less favorable steric effect, which is composed of Pauli repulsion, electrostatics, and electron correlation. There are approximate linear correlations between the charge transfer effect and binding energy and between bonding distance and binding energy. These correlations may lead to the illusion that the charge transfer interaction is unimportant or irrelevant, but further analyses showed that the inclusion of charge transfer is critical for the proper description of the halogen bonding, as considering only electrostatics and polarization leads to only about 45-60% of the binding strengths and much elongated bonding distances.
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Affiliation(s)
- Brandon Inscoe
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
| | - Hemali Rathnayake
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
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24
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Scheiner S. Relative Strengths of a Pnicogen and a Tetrel Bond and Their Mutual Effects upon One Another. J Phys Chem A 2021; 125:2631-2641. [PMID: 33734698 DOI: 10.1021/acs.jpca.1c01211] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability of the T and Z atoms of TR3ZR2 to engage in a noncovalent interaction with NH3 is assessed by DFT calculations, where the T atom refers to C, Si, and Ge; Z = As, Sb, and P; and substituents R = H and F. In most instances, the tetrel bond (TB) is both stronger and shorter than the pnicogen bond (ZB). These two bond strengths can be equalized, or preference shifted to the ZB, if F substituents are placed on the Z and H on the T atoms. Employing C as the T atom results in a very weak TB, with the ZB clearly favored energetically. The simultaneous formation of both TB and ZB weakens both, particularly the latter, but both bonds survive intact. Geometric and spectroscopic perturbations of the subunits reflect the two types of noncovalent bonds.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University†Logan, Utah 84322-0300, United States
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25
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Saidykhan A, Fenwick NW, Bowen RD, Telford R, Seaton CC. Isostructurality of quinoxaline crystal phases: the interplay of weak hydrogen bonds and halogen bonding. CrystEngComm 2021. [DOI: 10.1039/d1ce00878a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Creation of isostructural systems is a balance between thermodynamic and kinetic factors, shown by a set of substituted quinoxalines, where the lighter halogens form a set of metastable isostructural crystals, different to the heavy substitutions.
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Affiliation(s)
- Amie Saidykhan
- School of Chemistry and Biosciences, University of Bradford, Bradford, Richmond Road, Bradford BD7 1DP, UK
| | - Nathan W. Fenwick
- School of Chemistry and Biosciences, University of Bradford, Bradford, Richmond Road, Bradford BD7 1DP, UK
| | - Richard D. Bowen
- School of Chemistry and Biosciences, University of Bradford, Bradford, Richmond Road, Bradford BD7 1DP, UK
| | - Richard Telford
- School of Chemistry and Biosciences, University of Bradford, Bradford, Richmond Road, Bradford BD7 1DP, UK
| | - Colin C. Seaton
- School of Chemistry and Biosciences, University of Bradford, Bradford, Richmond Road, Bradford BD7 1DP, UK
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26
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Alipour M, Fallahzadeh P. On the role of steric and exchange–correlation effects in halogenated complexes. NEW J CHEM 2021. [DOI: 10.1039/d1nj02581c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Density functional theory formalisms of energy partitioning schemes are utilized to find out what energetic components govern interactions in halogenated complexes.
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Affiliation(s)
- Mojtaba Alipour
- Department of Chemistry, School of Science, Shiraz University, Shiraz 71946-84795, Iran
| | - Parisa Fallahzadeh
- Department of Chemistry, School of Science, Shiraz University, Shiraz 71946-84795, Iran
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27
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Nemec V, Lisac K, Bedeković N, Fotović L, Stilinović V, Cinčić D. Crystal engineering strategies towards halogen-bonded metal–organic multi-component solids: salts, cocrystals and salt cocrystals. CrystEngComm 2021. [DOI: 10.1039/d1ce00158b] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This highlight presents an overview of the current advances in the preparation of halogen bonded metal–organic multi-component solids, including salts and cocrystals comprising neutral and ionic constituents.
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Affiliation(s)
- Vinko Nemec
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Katarina Lisac
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Nikola Bedeković
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Luka Fotović
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Vladimir Stilinović
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Dominik Cinčić
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
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28
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Scheiner S. Competition between a Tetrel and Halogen Bond to a Common Lewis Acid. J Phys Chem A 2020; 125:308-316. [DOI: 10.1021/acs.jpca.0c10060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Halogen Bonding in the Complexes of Brominated Electrophiles with Chloride Anions: From a Weak Supramolecular Interaction to a Covalent Br–Cl Bond. CRYSTALS 2020. [DOI: 10.3390/cryst10121075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The wide-range variation of the strength of halogen bonds (XB) not only facilitates a variety of applications of this interaction, but it also allows examining the relation (and interconversion) between supramolecular and covalent bonding. Herein, the Br…Cl halogen bonding in a series of complexes of bromosubstituted electrophiles (R-Br) with chloride anions were examined via X-ray crystallographic and computational methods. Six co-crystals showing such bonding were prepared by evaporation of solutions of R-Br and tetra-n-propylammonium chloride or using Cl− anions released in the nucleophilic reaction of 1,4-diazabicyclo[2.2.2]octane with dichloromethane in the presence of R-Br. The co-crystal comprised networks formed by 3:3 or 2:2 halogen bonding between R-Br and Cl−, with the XB lengths varying from 3.0 Å to 3.25 Å. Analysis of the crystallographic database revealed examples of associations with substantially longer and shorter Br…Cl separations. DFT computations of an extended series of R–Br…Cl− complexes confirmed that the judicious choice of brominated electrophile allows varying halogen Br…Cl bond strength and length gradually from the values common for the weak intermolecular complexes to that approaching a fully developed covalent bond. This continuity of halogen bond strength in the experimental (solid-state) and calculated associations indicates a fundamental link between the covalent and supramolecular bonding.
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Study on the halogen bond and π-π stacking interaction between fluoro substituted iodobenzene and pyrazine. J Mol Model 2020; 26:333. [DOI: 10.1007/s00894-020-04586-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/22/2020] [Indexed: 10/23/2022]
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