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Kumar A, Anand VJ, Kumar P. Nitrous Acid (HONO) Dissociation on the Water and Ice Surface: An Ab Initio Molecular Dynamics Study. J Phys Chem A 2024. [PMID: 38850256 DOI: 10.1021/acs.jpca.4c02815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Abstract
In the atmosphere, the photodissociation of HONO is a significant source of OH radicals after ozone. In the present study, using Born-Oppenheimer molecular dynamics, we showed that HONO can dissociate on ice and water surfaces without light. In addition, the dissociation time of HONO is found to be much less on the ice surface compared to the same time on the water droplets.
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Affiliation(s)
- Amit Kumar
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur 302017, India
| | - Vishva Jeet Anand
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur 302017, India
| | - Pradeep Kumar
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur 302017, India
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2
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Sen S, Sinha A, Banerjee S, Debnath S, Ghosh A, Chakraborty J, Gangopadhyay J. Noncovalent and Covalent O-H···O Interactions in PPh 3O Cocrystals: A Correlation Study Involving QTAIM, SAPT, NBO, and IBSI Methods. ACS OMEGA 2024; 9:22476-22487. [PMID: 38799333 PMCID: PMC11112592 DOI: 10.1021/acsomega.4c02658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024]
Abstract
PPh3O.hemihydrate polymorphs and 11 assorted PPh3O cocrystals collectively constitute a reliable stock to pursue a systematic analysis aiming to investigate the impacts of some vital issues on the TPPO.H-bond donor aggregates. The issues highlighted herein are (i) effect of varying acidity of H-bond donors on the degeneracy of lone pairs of the H-bond acceptor (PPh3O), (ii) effectiveness of the |V(r)|/G(r) and H(r)/ρ(r) parameters as a covalency metric, (iii) 3c-4e bonding in the covalent PPh3O.nitric acid cocrystal, (iv) salient features of H-bond interaction energy and an interplay of its components, (v) an intrinsic bond strength scale for the PPh3O cocrystals, and (vi) reliable empirical relations between several bond descriptors for a quick estimation of interaction energy. To be specific about point (vi), we have propounded two promising avenues for a fast semiquantitative calculation of interaction energy from an endearing nonenergetic parameter, viz., bond length: dO-H···O → ρBCP (MAPE = 2.36%) → ESAPT0 (MAPE = 9.26%), and dO-H···O → IBSI (MAPE = 1.87%) → ESAPT0 (MAPE = 9.66%). All the aforesaid issues have been explored in detail through the QTAIM, NBO, and IBSI analyses (M06-2X-D3/def2-TZVP level), as well as by the SAPT study at the SAPT0/aug-cc-pVDZ platform. The statistically valid correlation studies can be particularly conducive for practical purposes as a transformative extension of the established facts into postulates for the unknown cocrystals.
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Affiliation(s)
- Suphal Sen
- School
of Applied Material Sciences, Central University
of Gujarat, Gandhinagar, Gujarat 382030, India
| | - Ankita Sinha
- Department
of Chemistry, St. Paul’s Cathedral Mission College, University of Calcutta, 33/1 Raja Rammohan Roy Sarani, Kolkata 700009, India
| | - Suparna Banerjee
- Department
of Chemistry, Uluberia College, University
of Calcutta, Howrah 711315, India
| | - Snehasish Debnath
- Analytical
& Environmental Science Division and Centralized Instrument Facility, CSIR-CSMCRI, Bhavnagar, Gujarat 364002, India
| | - Aniruddha Ghosh
- Department
of Chemistry, St. Paul’s Cathedral Mission College, University of Calcutta, 33/1 Raja Rammohan Roy Sarani, Kolkata 700009, India
| | - Jishnunil Chakraborty
- Department
of Chemistry, St. Paul’s Cathedral Mission College, University of Calcutta, 33/1 Raja Rammohan Roy Sarani, Kolkata 700009, India
| | - Jaydip Gangopadhyay
- Department
of Chemistry, St. Paul’s Cathedral Mission College, University of Calcutta, 33/1 Raja Rammohan Roy Sarani, Kolkata 700009, India
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3
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Moppel I, Elliott B, Chen S. Intermolecular hydrogen bonding behavior of amino acid radical cations. Org Biomol Chem 2024; 22:3966-3978. [PMID: 38690804 DOI: 10.1039/d4ob00301b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Amino acid and peptide radicals are of broad interest due to their roles in biochemical oxidative damage, pathogenesis and protein radical catalysis, among others. Using density functional theory (DFT) calculations at the ωB97X-D/def2-QZVPPD//ωB97X-D/def2-TZVPP level of theory, we systematically investigated the hydrogen bonding between water and fourteen α-amino acids (Ala, Asn, Cys, Gln, Gly, His, Met, Phe, Pro, Sel, Ser, Thr, Trp, and Tyr) in both neutral and radical cation forms. For all amino acids surveyed, stronger hydrogen-bonding interactions with water were observed upon single-electron oxidation, with the greatest increases in hydrogen-bonding strength occurring in Gly, Ala and His. We demonstrate that the side chain has a significant impact on the most favorable hydrogen-bonding modes experienced by amino acid radical cations. Our computations also explored the fragmentation of amino acid radical cations through the loss of a COOH radical facilitated by hydrogen bonding. The most favorable pathways provided stabilization of the resulting cationic fragments through hydrogen bonding, resulting in more favorable thermodynamics for the fragmentation process. These results indicate that non-covalent interactions with the environment have a profound impact on the structure and chemical fate of oxidized amino acids.
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Affiliation(s)
- Isabella Moppel
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA.
| | - BarbaraAnn Elliott
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA.
| | - Shuming Chen
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA.
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Chávez BY, Paz JL, Gonzalez-Paz LA, Alvarado YJ, Contreras JS, Loroño-González MA. Theoretical Study of Cyanidin-Resveratrol Copigmentation by the Functional Density Theory. Molecules 2024; 29:2064. [PMID: 38731555 PMCID: PMC11085293 DOI: 10.3390/molecules29092064] [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: 03/03/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 05/13/2024] Open
Abstract
Anthocyanins are colored water-soluble plant pigments. Upon consumption, anthocyanins are quickly absorbed and can penetrate the blood-brain barrier (BBB). Research based on population studies suggests that including anthocyanin-rich sources in the diet lowers the risk of neurodegenerative diseases. The copigmentation caused by copigments is considered an effective way to stabilize anthocyanins against adverse environmental conditions. This is attributed to the covalent and noncovalent interactions between colored forms of anthocyanins (flavylium ions and quinoidal bases) and colorless or pale-yellow organic molecules (copigments). The present work carried out a theoretical study of the copigmentation process between cyanidin and resveratrol (CINRES). We used three levels of density functional theory: M06-2x/6-31g+(d,p) (d3bj); ωB97X-D/6-31+(d,p); APFD/6-31+(d,p), implemented in the Gaussian16W package. In a vacuum, the CINRES was found at a copigmentation distance of 3.54 Å between cyanidin and resveratrol. In water, a binding free energy ∆G was calculated, rendering -3.31, -1.68, and -6.91 kcal/mol, at M06-2x/6-31g+(d,p) (d3bj), ωB97X-D/6-31+(d,p), and APFD/6-31+(d,p) levels of theory, respectively. A time-dependent density functional theory (TD-DFT) was used to calculate the UV spectra of the complexes and then compared to its parent molecules, resulting in a lower energy gap at forming complexes. Excited states' properties were analyzed with the ωB97X-D functional. Finally, Shannon aromaticity indices were calculated and isosurfaces of non-covalent interactions were evaluated.
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Affiliation(s)
- Breyson Yaranga Chávez
- Departamento Académico de Fisicoquímica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - José L. Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Lenin A. Gonzalez-Paz
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Biocomputación (LB), Maracaibo 4001, Zulia, República Bolivariana de Venezuela
| | - Ysaias J. Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Biofísica Teórica y Experimental (LQBTE), Maracaibo 4001, Zulia, República Bolivariana de Venezuela
| | - Julio Santiago Contreras
- Departamento Académico de Química Orgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Marcos A. Loroño-González
- Departamento Académico de Fisicoquímica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
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Badri Z, Foroutan-Nejad C. Classical versus Collective Interactions in Asymmetric Trigonal Bipyramidal Alkaline Metal-Boron Halide Complexes. Chemistry 2024:e202400156. [PMID: 38642012 DOI: 10.1002/chem.202400156] [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: 01/13/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
Collective interactions are a novel type of chemical bond formed between metals and electron-rich substituents around an electron-poor central atom. So far only a limited number of candidates for having collective interactions are reported. In this work, we extend the newly introduced concept of collective bonding to a series of neutral boron complexes with the general formula M2BX3 (M=Li, Na, and K; X=F, Cl, and Br). Our state-of-the-art ab initio computations suggest that these complexes form trigonal bipyramidal structures with a D3h to C3v distortion along the C3 axis of symmetry. The BX3 unit in the complexes distorts from planar to pyramidal akin to a sp3 hybridized atom. Interestingly, the interaction of the metals with the pyramidal side of BX3, where the lone pair in a hypothetical [BX3]2- should be located, is weaker than the interactions of metals with the inverted side, i. e., the middle of three halogen atoms. The origin of this stronger interaction can be explained by the formation of collective interactions between metals and halogen atoms as we explored via energy decomposition within the context of the theory of interacting quantum atoms, IQA.
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Affiliation(s)
- Zahra Badri
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Cina Foroutan-Nejad
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
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6
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Kumar A, Kumar P. Dissociation of H 2O 2 on water surfaces (ice and water droplets). Phys Chem Chem Phys 2024; 26:11331-11339. [PMID: 38563356 DOI: 10.1039/d3cp04107g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
OH radicals are an important constituent of the atmosphere. Therefore, all reactions that act as a source of OH radicals are important. It is known that photo-dissociation of H2O2 is an important source of OH radicals in the atmosphere. In the present study, using Born-Oppenheimer molecular dynamics simulations, we have shown that the H2O2 molecule can dissociate thermally on water droplets, as well as on the surface of ice, to form OH radicals. Furthermore, the dissociation of H2O2 was found to be very fast (less than 50 fs) on the ice surface compared with on the water droplets. We believe this route for the formation of OH radicals could be more critical than photo-dissociation, as it can take place both during the day and at night, but further studies with more sophisticated theoretical approaches or experiments are required to confirm this hypothesis.
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Affiliation(s)
- Amit Kumar
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur, 302017, India.
| | - Pradeep Kumar
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur, 302017, India.
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7
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Mando M, Grellepois F, Blanc A, Hénon E, Riguet E. Toward Efficient and Stereoselective Aromatic and Dearomative Cope Rearrangements: Experimental and Theoretical Investigations of α-Allyl-α'-Aromatic γ-Lactone Derivatives. Chemistry 2024; 30:e202304138. [PMID: 38284279 DOI: 10.1002/chem.202304138] [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: 12/12/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
The aromatic Cope rearrangement is an elusive transformation that has been the subject of a limited number of investigations compared to those seemingly close analogues, namely the Cope and aromatic Claisen rearrangement. Herein we report our investigations inspired by moderate success observed in the course of pioneering works. By careful experimental and theoretical investigations, we demonstrate that key substitutions on 1,5-hexadiene scaffold allow fruitful transformations. Especially, efficient functionalisation of the heteroaromatic rings results from the aromatic Cope rearrangement, while highly stereoselective interrupted aromatic Cope rearrangements highlight the formation of chiral compounds through a dearomative process.
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Affiliation(s)
- Morgane Mando
- Université de Reims Champagne Ardenne, CNRS, Institut de Chimie Moléculaire de Reims, UMR 7312, 51097, Reims, France
| | - Fabienne Grellepois
- Université de Reims Champagne Ardenne, CNRS, Institut de Chimie Moléculaire de Reims, UMR 7312, 51097, Reims, France
| | - Aurélien Blanc
- Université de Strasbourg, CNRS, Institut de Chimie, UMR 7177, 4 rue Blaise Pascal, CS90032, 67081, Strasbourg, France
| | - Eric Hénon
- Université de Reims Champagne Ardenne, CNRS, Institut de Chimie Moléculaire de Reims, UMR 7312, 51097, Reims, France
| | - Emmanuel Riguet
- Université de Reims Champagne Ardenne, CNRS, Institut de Chimie Moléculaire de Reims, UMR 7312, 51097, Reims, France
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8
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Liu H, Chen P, Huang X, Wei X. A physical organic strategy to predict and interpret stabilities of chemical bonds in energetic compounds for the discovery of thermal-resistant properties. J Mol Model 2024; 30:84. [PMID: 38407671 DOI: 10.1007/s00894-024-05877-5] [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: 12/26/2023] [Accepted: 02/09/2024] [Indexed: 02/27/2024]
Abstract
CONTEXT The in-depth understanding about the stability of chemical bonds in energetic compounds plays a central role for molecular design and safety-related evaluations. Most energetic compounds contain nitro as explosophores, and nitro cleavage is fundamental for thermal and mechanical stability. However, the quantum chemistry approach to accurately predict energy and temperature properties related to bond stability is challenging, due to the tradeoff between computational costs and deviations. Herein, the bond orders are proposed as accurate and computational-cost efficient descriptors for predicting the chemical bond stability and thermal-resistant properties. The intrinsic bond strength index (IBSI) demonstrates the best prediction for experimental homolytic bond dissociation energies (R2 > 0.996), which is on par with the results from high-precision quantum chemistry methods. The effects from bond connectivity and steric hindrance hierarchy were analyzed to reveal underlying mechanisms. Additionally, the IBSI descriptors are successfully applied to predict the thermal decomposition temperatures of 24 heat-resistant energetic compounds (R2 = 0.995), thus validating the effectiveness for the prediction and interpretation of chemical bond stability in energetic compounds via a physical organic approach. METHODS All DFT calculations were performed with Gaussian 09 software. To investigate the dependence of the method on functionals and basis sets, 9 DFT methods were considered (B3LYP/6-31G(d,p), B3LYP/6-311G(d,p), B3LYP/def2-TZVP, M062X/6-31G(d,p), M062X/6-311G(d,p), M062X/def2-TZVP, ωB97XD/6-31G(d,p), ωB97XD/6-311G(d,p), and ωB97XD/def2-TZVP). The bond order descriptors LBO and IBSI are obtained through the bond order analysis module in the Multiwfn software.
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Affiliation(s)
- Haitao Liu
- School of National Defense & Nuclear Science and Technology, Southwest University of Science and Technology, Mianyang, 621010, People's Republic of China
- Institute of Chemical Materials, China Academy of Engineering Physics (CAEP), Mianyang, 621900, People's Republic of China
| | - Peng Chen
- School of National Defense & Nuclear Science and Technology, Southwest University of Science and Technology, Mianyang, 621010, People's Republic of China
- Institute of Chemical Materials, China Academy of Engineering Physics (CAEP), Mianyang, 621900, People's Republic of China
| | - Xin Huang
- Institute of Chemical Materials, China Academy of Engineering Physics (CAEP), Mianyang, 621900, People's Republic of China
| | - Xianfeng Wei
- School of National Defense & Nuclear Science and Technology, Southwest University of Science and Technology, Mianyang, 621010, People's Republic of China.
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9
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Kozuch S. When, Where and Why Boron Prefers Boron to Nitrogen. Chemphyschem 2024; 25:e202300875. [PMID: 38146920 DOI: 10.1002/cphc.202300875] [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: 11/15/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 12/27/2023]
Abstract
Boron is the archetypal Lewis acid, and therefore it is only natural that it prefers to bind nitrogen, its usual Lewis base counterpart. To challenge this assumption, we present a computationally designed bicyclopentane molecule akin to [1.1.1]propellane, but with pyramidal B and N inner atoms bonded by an "inverted" dative bond. Unexpectedly, the dimer of this system prefers to interact via an atypical boron-boron bond over the supposedly obvious boron-nitrogen bond. A molecular orbital analysis shows that the boron in this peculiar entity acts both as an electron donor and an electron acceptor, making the dimerization an amphoteric-amphoteric interaction process.
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Affiliation(s)
- Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel, 84105
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10
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Groslambert L, Cornaton Y, Ditte M, Aubert E, Pale P, Tkatchenko A, Djukic JP, Mamane V. Affinity of Telluronium Chalcogen Bond Donors for Lewis Bases in Solution: A Critical Experimental-Theoretical Joint Study. Chemistry 2024; 30:e202302933. [PMID: 37970753 DOI: 10.1002/chem.202302933] [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: 09/09/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 11/17/2023]
Abstract
Telluronium salts [Ar2 MeTe]X were synthesized, and their Lewis acidic properties towards a number of Lewis bases were addressed in solution by physical and theoretical means. Structural X-ray diffraction analysis of 21 different salts revealed the electrophilicity of the Te centers in their interactions with anions. Telluroniums' propensity to form Lewis pairs was investigated with OPPh3 . Diffusion-ordered NMR spectroscopy suggested that telluroniums can bind up to three OPPh3 molecules. Isotherm titration calorimetry showed that the related heats of association in 1,2-dichloroethane depend on the electronic properties of the substituents of the aryl moiety and on the nature of the counterion. The enthalpies of first association of OPPh3 span -0.5 to -5 kcal mol-1 . Study of the affinity of telluroniums for OPPh3 by state-of-the-art DFT and ab-initio methods revealed the dominant Coulombic and dispersion interactions as well as an entropic effect favoring association in solution. Intermolecular orbital interactions between [Ar2 MeTe]+ cations and OPPh3 are deemed insufficient on their own to ensure the cohesion of [Ar2 MeTe ⋅ Bn ]+ complexes in solution (B=Lewis base). Comparison of Grimme's and Tkatchenko's DFT-D4/MBD-vdW thermodynamics of formation of higher [Ar2 MeTe ⋅ Bn ]+ complexes revealed significant molecular size-dependent divergence of the two methodologies, with MBD yielding better agreement with experiment.
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Affiliation(s)
- Loïc Groslambert
- LASYROC, UMR 7177 CNRS, University of Strasbourg, 1 Rue Blaise Pascal, F-67000, Strasbourg, France
| | - Yann Cornaton
- LCSOM, UMR 7177 CNRS, Université de Strasbourg, 4 rue Blaise Pascal, F-67000, Strasbourg, France
| | - Matej Ditte
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | | | - Patrick Pale
- LASYROC, UMR 7177 CNRS, University of Strasbourg, 1 Rue Blaise Pascal, F-67000, Strasbourg, France
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - Jean-Pierre Djukic
- LCSOM, UMR 7177 CNRS, Université de Strasbourg, 4 rue Blaise Pascal, F-67000, Strasbourg, France
| | - Victor Mamane
- LASYROC, UMR 7177 CNRS, University of Strasbourg, 1 Rue Blaise Pascal, F-67000, Strasbourg, France
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11
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Zgrabik JC, Bhuniya B, Branstad Phillips T, Barroso J, Vlaisavljevich B, Daly SR. Volatile lanthanide complexes with fluorinated heptadentate ligands. Dalton Trans 2024. [PMID: 38265072 DOI: 10.1039/d3dt04198k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Understanding factors that influence the volatility of lanthanide complexes remains an important goal for applications such as gas-phase f-metal separations and the synthesis of lanthanide-containing thin films. Lanthanide complexes often exhibit volatility differences that depend on the ability of ligands to saturate the lanthanide coordination sphere and attenuate intermolecular bonding in the solid state. This can make it difficult to assess how electronic factors associated with differing ligand substituents influence volatility. Here we describe the synthesis, structures, and thermal properties of a series of volatile lanthanide complexes (Ln = Nd, Er, and Yb) containing N4O3 ligands decorated with different alkyl and fluoroalkyl substituents (CF3, CF2CF2CF3, Me, and tBu). These ligands completely enveloped the tested lanthanides to form monomeric complexes with 7-coordinate distorted capped octahedral coordination geometries, as determined using single-crystal X-ray diffraction. Thermogravimetric analysis and bulk sublimation studies show how metal encapsulation affords complexes with the same volatility regardless of metal size, even with lanthanide ions with significantly different radii such as Nd3+ and Yb3+. Most notably, the results show that increasing ligand fluorination, a strategy often used to increase the volatility of metal complexes, is not always beneficial and can significantly attenuate the volatility of lanthanide complexes depending on location with respect to other substituents in the ligand framework. A pair-wise model based on density functional theory shows that the net intermolecular interactions in the unit cell can still be stronger when fluorination is present. In other words, even if individual interactions between neighboring molecules are weaker, the total number of interactions in the solid arising from the nature of crystal packing is equally important to consider.
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Affiliation(s)
- Joshua C Zgrabik
- Department of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, USA.
| | - Balaka Bhuniya
- Department of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, USA.
| | - Thomas Branstad Phillips
- Department of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, USA.
| | - Jorge Barroso
- Department of Chemistry, The University of South Dakota, 414 E Clark St, Vermillion, SD, 57069, USA
| | - Bess Vlaisavljevich
- Department of Chemistry, The University of South Dakota, 414 E Clark St, Vermillion, SD, 57069, USA
| | - Scott R Daly
- Department of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, USA.
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12
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Goswami S, Mandal P, Sarkar S, Mukherjee M, Pal S, Mallick D, Mukherjee D. Flexible NHC-aryloxido aluminum complex and its zwitterionic imidazolium aluminate precursor in ring-opening polymerization of ε-caprolactone. Dalton Trans 2024; 53:1346-1354. [PMID: 38164613 DOI: 10.1039/d3dt02932h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Anionic donor-functionalized NHC (N-heterocyclic carbene) complexes of Al are rare. We report one such case here, an NHC-aryloxido AlMe2 complex [Al(L)Me2] (2), following a stepwise synthesis from the proligand [HO-4,6-tBu2-C6H2-2-CH2{CH(NCHCHNAr)}]Br [LH2Br; Ar = 2,6-iPr2-C6H3 (Dipp)] and AlMe3via the zwitterionic intermediate [Al(LH)Me2Br] (1). The ligand's flexibility in 2 is evident from the conformational fluxionality revealed by VT-1H NMR spectroscopic analysis. The ∠O-Al-C (ca. 100.5°) bite angle is also wider than the ∠O-Ti-C (ca. 80.6°) as seen in our recently reported Ti complex [Ti(L)(NMe2)2Br]. DFT analysis showed that the CNHC-Al bond is significantly ionic, as is the CNHC-Ti bond. Both 1 and 2 are active in the ring-opening polymerization (ROP) of ε-caprolactone (CL). 2, similar to [Ti(L)(NMe2)2Br], exhibits bifunctional MLC-type monomer activation, but only at an elevated temperature. However, the 2/BnOH combination is catalytically active at room temperature, likely through a zwitterionic [Al(LH)Me2(OBn)]. The 1/BnOH combination follows a similar mechanism but surprisingly at a faster rate.
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Affiliation(s)
- Santu Goswami
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246, West Bengal, India.
| | - Pranay Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246, West Bengal, India.
| | - Subham Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246, West Bengal, India.
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India.
| | - Mainak Mukherjee
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwar, Rajasthan 342037, India.
| | - Samanwita Pal
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwar, Rajasthan 342037, India.
| | - Dibyendu Mallick
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India.
| | - Debabrata Mukherjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246, West Bengal, India.
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Pino-Rios R, Báez-Grez R, Foroutan-Nejad C. Anti-electrostatic cation⋯π-hole and cation⋯lp-hole interactions are stabilized via collective interactions. Chem Commun (Camb) 2024; 60:400-403. [PMID: 38079184 DOI: 10.1039/d3cc05451a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Collective interactions are a novel type of bond between metals and AX3 fragments with an electropositive central atom, A, and electronegative X substituents. Here, using electrostatic potential maps and state-of-the-art bonding analysis tools we have shown that collective interactions are anti-electrostatic cation⋯π-Hole or cation⋯lp-Hole interactions.
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Affiliation(s)
- Ricardo Pino-Rios
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat., Casilla 121, Iquique 1100000, Chile.
- Instituto de Estudios de la Salud, Universidad Arturo Prat, Iquique, 1100000, Chile
| | - Rodrigo Báez-Grez
- Departamento de Química, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 275, Santiago 8370146, Chile
| | - Cina Foroutan-Nejad
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
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14
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Weng W, Lin Z, Zhang H, Niu F, Wang C, Hu K, Guo J. Effect of ESIPT-Induced Photoisomerization of Keto-Enamine Linkages on the Photocatalytic Hydrogen Evolution Performance of Covalent Organic Frameworks. JACS AU 2023; 3:3391-3399. [PMID: 38155651 PMCID: PMC10751766 DOI: 10.1021/jacsau.3c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 12/30/2023]
Abstract
Photoexcitation of keto-enamine allows intramolecular proton transfer from C-NH to C=O, leading to tautomerization, while the photogenerated isomers are excluded from the study of photocatalytic applications. Herein, we demonstrate the photoisomerization of keto-enamine linkages on covalent organic frameworks (COFs) induced by excited-state intramolecular proton transfer (ESIPT). Partial enolization generates partially enolized photoisomers with a mixture of keto (C=O) and enol (OH) forms, conferring extended π-conjugation with an increase in electron density. The spatially separated D-A configuration is thus rebuilt with the enol-imine-linked branch as a donor and the keto-enamine-linked branch as an acceptor, and in turn, the photoinduced charges transfer between the two adjacent branches with a long lifetime. We further prove that the partially enolized photoisomer is a key transition instead of the keto-enamine form as an excited-state model to understand the photocatalytic behaviors. Therefore, ESIPT-induced photoisomerization must be considered for rationally designing keto-enamine-linked COFs with enhanced photocatalytic activity. Also, our study points toward the importance of controlling excited-state structures for long-lived separated charges, which is of particular interest for optoelectronic applications.
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Affiliation(s)
- Weijun Weng
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Zheng Lin
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Hualei Zhang
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Fushuang Niu
- Department
of Chemistry, Fudan University, Shanghai 200438, China
| | - Changchun Wang
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Ke Hu
- Department
of Chemistry, Fudan University, Shanghai 200438, China
| | - Jia Guo
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200438, China
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15
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Ovchinnikov MY, Kuzmina EV, Karaseva EV, Khursan SL, Kolosnitsyn VS. DFT Model of Elemental Sulfur in Sulfolane Solutions. J Phys Chem A 2023; 127:8971-8984. [PMID: 37862674 DOI: 10.1021/acs.jpca.3c04104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
The structure and the thermodynamic and optical (UV) properties of elemental sulfur solution in sulfolane (Sl) have been studied using density functional theory methods. The cyclic molecular form of sulfur (S8 "crown") was found using PBE1PBE/6-311+G(d,p) approximation in combination with a polarizable continuum model (the integral equation formalism variant) to exist in sulfolane medium as a Sl-S8-Sl solvate. It has been theoretically established that sulfur can form stable (S8)n clusters in concentrated solutions. An increase in the extent of association (n) of the sulfur cluster leads to a decrease in the extinction coefficient [TD-DFT(TPSSTPSS/6-311+G(d,p))] of the most intense absorption maximum lying at about 50,000 cm-1 while maintaining the shape of the remaining part of the spectrum. The observed pattern qualitatively expresses the spectral regularities of solutions with different concentrations of sulfur in sulfolane. It has been proposed that a model of the absorption spectrum of elemental sulfur suggests a minor contribution of the S12 molecular form (G298°((S12)2) - G298°((S8)3) ≈ -15.5 kJ mol-1). The findings of the study will provide deeper insights into the transformation of molecular forms of sulfur and more precisely analyze processes involving sulfur as an acting species using electronic spectroscopy.
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16
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Islam MS, Al-Majid AM, Haukka M, Parveen Z, Ravaiz N, Wadood A, Rehman AU, Ríos-Gutiérrez M, Domingo LR, Barakat A. A novel alpha-amylase inhibitor-based spirooxindole-pyrrolidine-clubbed thiochromene-pyrzaole pharmacophores: Unveiling the [3+2] cycloaddition reaction by molecular electron density theory. Chem Biol Drug Des 2023; 102:972-995. [PMID: 37563748 DOI: 10.1111/cbdd.14299] [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: 02/09/2023] [Revised: 06/29/2023] [Accepted: 07/14/2023] [Indexed: 08/12/2023]
Abstract
A novel spirooxindole-pyrrolidine clubbed thiochromene and pyrazole motifs were synthesized by [3+2] cycloaddition (32CA) reactions in one step process starting from the ethylene-based thiochromene and pyrazole scaffolds with the secondary amino-acids and substituted isatins in high yield. The 32CA reaction of AY 10 with ethylene derivative 6 has also been studied with Molecular Electron Density Theory. The high nucleophilic character of AY 10, N = 4.39 eV, allows explaining that the most favorable TS-on is 13.9 kcal mol-1 below the separated reagent. This 32CA, which takes place through a non-concerted one-step mechanism, presents a total ortho regio- and endo stereoselectivity, which is controlled by the formation of two intramolecular H… O hydrogen bonds. The design of spirooxindole-pyrrolidines engrafted thiochromene and pyrazole was tested for alpha-amylase inhibition and show a high efficacy in nanoscale range of reactivity. The key interaction between the most active hybrids and the receptor was studied by molecular docking. The physiochemical properties of the designed spirooxindole-pyrrolidines were carried out by in silico ADMET prediction. The newly synthesized most potent hybrid could be considered as a lead compound for drug discovery development for type 2 diabetes mellitus (T2DM).
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Affiliation(s)
| | | | - Matti Haukka
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Zahida Parveen
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Nabeela Ravaiz
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Mar Ríos-Gutiérrez
- Department of Organic Chemistry, University of Valencia, Valencia, Spain
| | - Luis R Domingo
- Department of Organic Chemistry, University of Valencia, Valencia, Spain
| | - Assem Barakat
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
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17
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Fachini LG, Baptistella GB, Postal K, Santana FS, de Souza EM, Ribeiro RR, Nunes GG, Sá EL. A new approach to study semi-coordination using two 2-methyl-5-nitroimidazole copper(ii) complexes of biological interest as a model system. RSC Adv 2023; 13:27997-28007. [PMID: 37736565 PMCID: PMC10510761 DOI: 10.1039/d3ra02130k] [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: 03/31/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023] Open
Abstract
Two novel copper(ii) complexes [Cu(2mni)2(H2O)2](NO3)2·2H2O (1) and [Cu(2mni)2(NO3)2] (2), where 2mni is 2-methyl-5-nitroimidazole, were prepared and characterized in the solid state using single-crystal and powder X-ray diffraction analyses, EPR, electronic and vibrational spectroscopies (FTIR and Raman), and thermogravimetric methods. Both products present an elongated distorted octahedral geometry with axial Cu-O bond lengths of 2.606(14) and 2.593(15) Å, indicating semi-coordination. Density functional theory (DFT) calculations at the B3LYP/LANL2DZ theory level were used to study the electronic properties of 1 and 2. The Independent Gradient Model (IGM) was employed to determine the Intrinsic Bond Strength Index (IBSI) of the semi-coordination and to plot δg isosurfaces for the electronic sharing between the metal center and ligands. A moderate to weak antibacterial activity against Escherichia coli cultures was found for 1 with a 50% growth inhibition (GI50) value of 0.25 mmol L-1. To the best of our knowledge, this is the first time that the semi-coordination analysis using IGM was carried out for a copper(ii) complex with axial elongation, finding a good correlation between the bond length and the IBSI, and the study was extended for a series of analogous complexes described in the literature.
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Affiliation(s)
- Lucas G Fachini
- Departamento de Química, UFPR Curitiba PR Brazil +55 41 3361 3300
| | | | - Kahoana Postal
- Departamento de Química, UFPR Curitiba PR Brazil +55 41 3361 3300
| | | | - Emanuel M de Souza
- Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba PR Brazil
| | - Ronny R Ribeiro
- Departamento de Química, UFPR Curitiba PR Brazil +55 41 3361 3300
| | - Giovana G Nunes
- Departamento de Química, UFPR Curitiba PR Brazil +55 41 3361 3300
| | - Eduardo L Sá
- Departamento de Química, UFPR Curitiba PR Brazil +55 41 3361 3300
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18
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Bagheri M, Berger E, Komsa HP. Identification of Material Dimensionality Based on Force Constant Analysis. J Phys Chem Lett 2023; 14:7840-7847. [PMID: 37624876 PMCID: PMC10494234 DOI: 10.1021/acs.jpclett.3c01635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Abstract
Identification of low-dimensional structural units from the bulk atomic structure is a widely used approach for discovering new low-dimensional materials with new properties and applications. Such analysis is usually based solely on bond-length heuristics, whereas an analysis based on bond strengths would be physically more justified. Here, we study dimensionality classification based on the interatomic force constants of a structure with different approaches for selecting the bonded atoms. The implemented approaches are applied to the existing database of first-principles calculated force constants with a large variety of materials, and the results are analyzed by comparing them to those of several bond-length-based classification methods. Depending on the approach, they can either reproduce results from bond-length-based methods or provide complementary information. As an example of the latter, we managed to identify new non-van der Waals two-dimensional material candidates.
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Affiliation(s)
- Mohammad Bagheri
- Microelectronics Research Unit, Faculty
of Information Technology and Electrical Engineering, University of Oulu, Oulu FIN-90014, Finland
| | - Ethan Berger
- Microelectronics Research Unit, Faculty
of Information Technology and Electrical Engineering, University of Oulu, Oulu FIN-90014, Finland
| | - Hannu-Pekka Komsa
- Microelectronics Research Unit, Faculty
of Information Technology and Electrical Engineering, University of Oulu, Oulu FIN-90014, Finland
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19
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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] [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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20
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Lin J, Li Y, Ke Z. Feature Analysis in High-Dimensional Data: Structure-Activity Relationships of Lewis Acid-Transition-Metal Complex-Catalyzed H 2 Activation. J Phys Chem A 2023; 127:4375-4387. [PMID: 37183362 DOI: 10.1021/acs.jpca.2c08987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Lewis acid-transition metal (LA-TM) catalysts have been proven to have an advantage in catalyzing hydrogen activation. Herein, a high-dimensional structure-activity relationship study is performed for LA-TM-catalyzed hydrogen activation by density functional theory calculations. The DPB-Ni complex is taken as the representative catalyst, and the explored Lewis acid sites and transition-metal centers include B, Al, Ga and Ni, Pd, Pt, respectively. Totally, four general hydrogen activation mechanisms are systematically studied among the nine catalytic systems. The Ga-Ni system undergoes the lowest free energy of activation (11.0 kcal/mol), which is considered to be the optimal combination of the Lewis acid site and transition-metal center. Furthermore, more than 100 parameters are used to analyze the structure-activity relationship, including the physical structure, the bond order, the atom charge, and many other properties. Key parameters of important structures are dug out to show a high correlation with the activity of the LA-TM systems, including the M-H2 distance, the H-H bond length, the second-order perturbation stabilization energy of M-H2, the bond order of the LA-TM, and so on. The multivariable analysis indicates that the feature related to the basic elemental properties and the global feature codetermine the activity of the catalyst. In the LA-TM system, the combination of IpLA/IpTM (Ip, the first ionization energy, the feature related to basic elemental properties) and the chemical hardness (the global feature) can better explain the activity of the catalyst. The IpLA/IpTM reflects the difficulty of breaking the LA-TM bond, affecting the reaction site of activating hydrogen. The hardness reflects the stability and reactivity of LA-TM-RC complexes. The above two features with the addition of the LA-TM bond length (the local feature) can better reflect the activity of the LA-TM system-catalyzed H2 activation. The feature combinations and the method of multidimensional data analysis should be informative guidance for the rational design of efficient LA-TM catalysts for H2 activation.
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Affiliation(s)
- Jiaxin Lin
- School of Materials Science and Engineering, PCFM Lab, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Yinwu Li
- School of Materials Science and Engineering, PCFM Lab, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Zhuofeng Ke
- School of Materials Science and Engineering, PCFM Lab, Sun Yat-sen University, Guangzhou 510006, P. R. China
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21
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Lefebvre C, Klein J, Khartabil H, Boisson JC, Hénon E. IGMPlot: A program to identify, characterize, and quantify molecular interactions. J Comput Chem 2023. [PMID: 37177853 DOI: 10.1002/jcc.27123] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023]
Abstract
We describe the development and features of a program called IGMPlot, which is based on the independent gradient model (IGM) and its local descriptor δ g $$ \delta g $$ . The IGM approach analyzes the gradient of the electron density (ED) in a molecular system to identify regions of space where chemical interactions take place. IGMPlot is intended for use by both experimental scientists and theoretical chemists. It is standalone software written in C++, with versions available for multiple platforms. Some key features are: probing and quantifying interactions between two given molecular fragments, determining bond strength (IBSI), estimating the atomic contributions to an intermolecular interaction and preparing data to build 2D and 3D representations of interaction regions. The software has been updated to include new features: critical point analysis of the ED, assessing ED asymmetry of a given bond (PDA) and a new descriptor called q g $$ qg $$ designed to enhance the IGM- δ g $$ \delta g $$ analysis. The program can be found at: http://igmplot.univ-reims.fr.
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Affiliation(s)
- C Lefebvre
- Laboratoire Lorrain de Chimie Moléculaire UMR CNRS 7053, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - J Klein
- Institut Charles Gerhardt Montpellier, UMR CNRS 5253, Université de Montpellier, Pôle Chimie Balard Recherche, Montpellier, France
| | - H Khartabil
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims, France
| | - J-C Boisson
- Laboratoire d'Informatique en Calcul Intensif et Image pour la Simulation (LICIIS), Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims, France
| | - E Hénon
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims, France
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22
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Morera-Boado C, Bernal-Uruchurtu MI. Interaction energy of Cl 2 and Br 2 with H 2 O: Exchange, dispersion and density the crucial ingredients. J Comput Chem 2023; 44:1073-1087. [PMID: 36578228 DOI: 10.1002/jcc.27066] [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: 03/23/2022] [Revised: 11/10/2022] [Accepted: 12/18/2022] [Indexed: 12/30/2022]
Abstract
Modern Density Functional Theory models are now suitable for many molecular and condensed phase studies. The study of noncovalent interactions, a well-known drawback, is no longer an insurmountable obstacle through design and empirical corrections. However, using empirical corrections as in the DFT-D methods might not be an all-in-one solution. This work uses a simple system, X2 -H2 O with X = Cl or Br, with two different interactions, halogen-bonded (XB) and hydrogen-halogen (HX), to investigate the capability of current density functional approximations (DFA) in predicting interaction energies with eight different exchange-correlation functionals. SAPT(DFT) provides, for all the studied cases, better predictions than the widely used supermolecular approach. In addition, the components of the interaction energy suggest where some of the shortcomings originate in each DFA. The analysis of the functionals used confirms that PBE0 and ω-B97X-D have a physically correct behavior. Using SAPT(DFT) and PBE0, and ω-B97X-D, we obtained the interaction energy of Cl2 and Br2 inside different clathrate cages and satisfactorily compared with wavefunction results; hence, the lower and upper limits of this value are defined: Cl2 @512 , -5.3 ± 0.3 kcal/mol; Cl2 @512 62 , -5.5 ± 0.1 kcal/mol; Br2 @512 62 , -7.6 ± 1.0 kcal/mol; Br2 @512 63 , -10.6 ± 1.0 kcal/mol; Br2 @512 64 , -10.9 ± 0.8 kcal/mol.
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Affiliation(s)
- Cercis Morera-Boado
- CONACYT - Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico.,Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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23
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Latosińska JN, Latosińska M, Seliger J, Žagar V, Apih T, Grieb P. Elucidating the Role of Noncovalent Interactions in Favipiravir, a Drug Active against Various Human RNA Viruses; a 1H- 14N NQDR/Periodic DFT/QTAIM/RDS/3D Hirshfeld Surfaces Combined Study. Molecules 2023; 28:molecules28083308. [PMID: 37110542 PMCID: PMC10147075 DOI: 10.3390/molecules28083308] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/28/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023] Open
Abstract
Favipiravir (6-fluoro-3-hydroxypyrazine-2-carboxamide, FPV), an active pharmaceutical component of the drug discovered and registered in March 2014 in Japan under the name Avigan, with an indication for pandemic influenza, has been studied. The study of this compound was prompted by the idea that effective processes of recognition and binding of FPV to the nucleic acid are affected predominantly by the propensity to form intra- and intermolecular interactions. Three nuclear quadrupole resonance experimental techniques, namely 1H-14N cross-relaxation, multiple frequency sweeps, and two-frequency irradiation, followed by solid-state computational modelling (density functional theory supplemented by the quantum theory of atoms in molecules, 3D Hirshfeld Surfaces, and reduced density gradient) approaches were applied. The complete NQR spectrum consisting of nine lines indicating the presence of three chemically inequivalent nitrogen sites in the FPV molecule was detected, and the assignment of lines to particular sites was performed. The description of the nearest vicinity of all three nitrogen atoms was used to characterize the nature of the intermolecular interactions from the perspective of the local single atoms and to draw some conclusions on the nature of the interactions required for effective recognition and binding. The propensity to form the electrostatic N-H···O, N-H···N, and C-H···O intermolecular hydrogen bonds competitive with two intramolecular hydrogen bonds, strong O-H···O and very weak N-H···N, closing the 5-member ring and stiffening the structure, as well as π···π and F···F dispersive interactions, were analysed in detail. The hypothesis regarding the similarity of the interaction pattern in the solid and the RNA template was verified. It was discovered that the -NH2 group in the crystal participates in intermolecular hydrogen bonds N-H···N and N-H···O, in the precatalytic state only in N-H···O, while in the active state in N-H···N and N-H···O hydrogen bonds, which is of importance to link FVP to the RNA template. Our study elucidates the binding modes of FVP (in crystal, precatalytic, and active forms) in detail and should guide the design of more potent analogues targeting SARS-CoV-2. Strong direct binding of FVP-RTP to both the active site and cofactor discovered by us suggests a possible alternative, allosteric mechanism of FVP action, which may explain the scattering of the results of clinical trials or the synergistic effect observed in combined treatment against SARS-CoV-2.
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Affiliation(s)
| | - Magdalena Latosińska
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
| | - Janez Seliger
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
| | - Veselko Žagar
- "Jožef Stefan" Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Tomaž Apih
- "Jožef Stefan" Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Paweł Grieb
- Department of Experimental Pharmacology, Mossakowski Medical Research Institute, Polish Academy of Science, Adolfa Pawińskiego 5, 02-106 Warszawa, Poland
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24
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Wacha M, Helm DL, Smart MM, McMillen CD, Casabianca LB, Sachdeva R, Urick CR, Wilson LP, Thrasher JS. A New Motif in Halogen Bonding: Cooperative Intermolecular S-Br⋅⋅⋅O, O⋅⋅⋅F, and F⋅⋅⋅F Associations in the Crystal Packing of α,ω-Di(sulfonyl bromide) Perfluoroalkanes. Chem Asian J 2023; 18:e202300012. [PMID: 36735331 DOI: 10.1002/asia.202300012] [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: 01/05/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/04/2023]
Abstract
We recently reported the first examples of S-Cl⋅⋅⋅O halogen bonding complemented by short F⋅⋅⋅F contacts between neighboring chains that resulted in stabilized crystals of ClSO2 (CF2 )4 SO2 Cl and ClSO2 (CF2 )6 SO2 Cl. More recently, other researchers studied our crystallographic data further using an Independent Gradient Model (IGM), and they suggested if one goes beyond IUPAC's proposed 'less than the sum of the van der Waals radii' criterion that even more noncovalent interactions between fluorine atoms on neighboring chains as well as Cl⋅⋅⋅Cl, Cl⋅⋅⋅S, O⋅⋅⋅F, and O⋅⋅⋅S attractive interactions can be found. With that said, we have prepared samples of the related BrSO2 (CF2 )n SO2 Br derivatives (where n=4, 6, 8, and others), which give rise to even stronger S-Br⋅⋅⋅O halogen bonding interactions complemented minimally by O⋅⋅⋅F and F⋅⋅⋅F intermolecular interactions as shown by X-ray crystallography and computational chemistry using IGM isosurface plots. Additional spectroscopic characterization (multinuclear NMR, FT-IR, and MS) of the disulfonyl bromide derivatives BrSO2 (CF2 )4 SO2 Br, BrSO2 (CF2 )6 SO2 Br, and BrSO2 (CF2 )8 SO2 Br has also been obtained as well as some preliminary spectroscopic evidence for BrSO2 (CF2 )2 SO2 Br and BrSO2 CF2 O(CF2 )2 OCF2 SO2 Br. The implication of these results toward the preparation of the corresponding disulfonyl iodides is discussed.
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Affiliation(s)
- Max Wacha
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, GERMANY.,Department of Chemistry, Clemson University, Advanced Materials Research Laboratory, 91 Technology Drive, Anderson, South Carolina, 29625, USA
| | - David L Helm
- Department of Chemistry, Clemson University, Advanced Materials Research Laboratory, 91 Technology Drive, Anderson, South Carolina, 29625, USA.,Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - Megan M Smart
- Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - Colin D McMillen
- Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - Leah B Casabianca
- Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - Rakesh Sachdeva
- Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - Catherine R Urick
- Department of Chemistry, Clemson University, Advanced Materials Research Laboratory, 91 Technology Drive, Anderson, South Carolina, 29625, USA.,Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - London P Wilson
- Department of Chemistry, Clemson University, Advanced Materials Research Laboratory, 91 Technology Drive, Anderson, South Carolina, 29625, USA.,Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - Joseph S Thrasher
- Department of Chemistry, Clemson University, Advanced Materials Research Laboratory, 91 Technology Drive, Anderson, South Carolina, 29625, USA.,Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
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25
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An exotic 3-center/4-electron carbon–carbon pi long-bond: Is it tangible? Theor Chem Acc 2023. [DOI: 10.1007/s00214-023-02968-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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26
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Wieduwilt EK, Boto RA, Macetti G, Laplaza R, Contreras-García J, Genoni A. Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses. J Chem Theory Comput 2023; 19:1063-1079. [PMID: 36656682 DOI: 10.1021/acs.jctc.2c01092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The noncovalent interaction (NCI) index is nowadays a well-known strategy to detect NCIs in molecular systems. Even though it initially provided only qualitative descriptions, the technique has been recently extended to also extract quantitative information. To accomplish this task, integrals of powers of the electron distribution were considered, with the requirement that the overall electron density can be clearly decomposed as sum of distinct fragment contributions to enable the definition of the (noncovalent) integration region. So far, this was done by only exploiting approximate promolecular electron densities, which are given by the sum of spherically averaged atomic electron distributions and thus represent too crude approximations. Therefore, to obtain more quantum mechanically (QM) rigorous results from NCI index analyses, in this work, we propose to use electron densities obtained through the transfer of extremely localized molecular orbitals (ELMOs) or through the recently developed QM/ELMO embedding technique. Although still approximate, the electron distributions resulting from the abovementioned methods are fully QM and, above all, are again partitionable into subunit contributions, which makes them completely suitable for the NCI integral approach. Therefore, we benchmarked the integrals resulting from NCI index analyses (both those based on the promolecular densities and those based on ELMO electron distributions) against interaction energies computed at a high quantum chemical level (in particular, at the coupled cluster level). The performed test calculations have indicated that the NCI integrals based on ELMO electron densities outperform the promolecular ones. Furthermore, it was observed that the novel quantitative NCI-(QM/)ELMO approach can be also profitably exploited both to characterize and evaluate the strength of specific interactions between ligand subunits and protein residues in protein-ligand complexes and to follow the evolution of NCIs along trajectories of molecular dynamics simulations. Although further methodological improvements are still possible, the new quantitative ELMO-based technique could be already exploited in situations in which fast and reliable assessments of NCIs are crucial, such as in computational high-throughput screenings for drug discovery.
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Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Roberto A Boto
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Rubén Laplaza
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Julia Contreras-García
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
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27
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Reactivity of a model of B 3P 3-doped nanographene with up to three CO 2 molecules. Sci Rep 2023; 13:2407. [PMID: 36765069 PMCID: PMC9918725 DOI: 10.1038/s41598-023-29336-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
The reactivity of a B3P3-doped hexa-cata-hexabenzocoronene, as a model of nanographene (B3P3-NG), towards carbon dioxide was studied at the DFT M06-2X/6-311++G(3df,3pd)//M06-2X/6-31+G* level of theory. This compound can be classified as a poly-cyclic poly-Frustrated Lewis Pair (FLP) system, as it presents more than one Lewis Acid/Lewis Base pair on its surface, making the capture of several carbon dioxide molecules possible. Two scenarios were considered to fully characterize the capture of CO2 by this multi-FLP system: (i) fixation of three CO2 molecules sequentially one by one; and (ii) simultaneous contact of three CO2 molecules with the B3P3-NG surface. The resulting adducts were analyzed as function of activation barriers and the relative stability of the CO2 capture. A cooperativity effect due to the π-delocalization of the hexa-cata-hexabenzocoronene is observed. The fixation of a CO2 molecule modifies the electronic properties. It enhances the capture of additional CO2 molecules by changing the acidy and basicity of the rest of the boron and phosphorus atoms in the B3P3-NG system.
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28
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Impact of silica nanoparticles architectures on the photosensitization of O2 by immobilized Rose Bengal. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2023.114648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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29
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Muğlu H, Çavuş MS, Bakır TK, Yakan H. Synthesis of new bis(thiosemicarbazone) derivatives and DFT analysis of antioxidant characteristics in relation to HAT and SET reactions. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Experimental and theoretical study on the extraction of keratin from human hair using protic ionic liquids. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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31
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Qin C, Lu YX, Borch T, Yang LL, Li YW, Zhao HM, Hu X, Gao Y, Xiang L, Mo CH, Li QX. Interactions between Extracellular DNA and Perfluoroalkyl Acids (PFAAs) Decrease the Bioavailability of PFAAs in Pakchoi ( Brassica chinensis L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14622-14632. [PMID: 36375011 DOI: 10.1021/acs.jafc.2c04597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Perfluoroalkyl acids (PFAAs) are emerging ionic organic pollutants worldwide. Great amounts of extracellular DNA (∼mg/kg) coexist with PFAAs in the environment. However, PFAA-DNA interactions and effects of such interactions have not been well studied. Herein, we used isothermal titration calorimetry (ITC), spectroscopy, and computational simulations to investigate the PFAA-DNA interactions. ITC assays showed that specific binding affinities of PFHxA-DNA, PFOA-DNA, PFNA-DNA, and PFOS-DNA were 5.14 × 105, 3.29 × 105, 1.99 × 105, and 2.18 × 104 L/mol, respectively, which were about 1-2 orders of magnitude stronger than those of PFAAs with human serum albumin. Spectral analysis suggested interactions of PFAAs with adenine (A), cytosine (C), guanine (G), and thymine (T), among which grooves associated with thymine were the major binding sites. Molecular dynamics simulations and quantum chemical calculations suggested that hydrogen bonds and van der Waals forces were the main interaction forces. Such a PFAA-DNA binding decreased the bioavailability of PFAAs in plant seedlings. The findings will help to improve the current understanding of the interaction between PFAAs and biomacromolecules, as well as how such interactions affect the bioavailability of PFAAs.
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Affiliation(s)
- Chao Qin
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing210095, China
| | - Ying-Xin Lu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Thomas Borch
- Department of Chemistry, Colorado State University, 1872 Campus Delivery, Fort Collins, Colorado80523, United States
- Department of Soil and Crop Sciences, Colorado State University, 1170 Campus Delivery, Fort Collins, Colorado80523, United States
| | - Ling-Ling Yang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing210095, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii96822, United States
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32
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Rowland C, Healy EF. Topological Analysis of the Electron Density of Molecules with Bridging Hydrogens To Tackle the Chemical Structure Monolith. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Eamonn F. Healy
- Department of Chemistry St. Edward's University Austin TX 78704 USA
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33
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Apebende CG, idante PS, Magu TO, Asogwa FC, Onyebuenyi IB, Unimuke TO, Gber TE. Density Functional Theory Study of the Influence of Activating and Deactivating Groups on Naphthalene. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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34
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Two Cd(II)-based metal-organic frameworks as difunctional fluorescence sensors to detect enrofloxacin and Fe3+. J SOLID STATE CHEM 2022. [DOI: 10.1016/j.jssc.2022.123483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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35
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A Molecular Electron Density Theory Study of the [3+2] Cycloaddition Reaction of an Azomethine Ylide with an Electrophilic Ethylene Linked to Triazole and Ferrocene Units. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196532. [PMID: 36235069 PMCID: PMC9571756 DOI: 10.3390/molecules27196532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022]
Abstract
The [3+2] cycloaddition (32CA) reaction of an azomethine ylide (AY) with an electrophilic ethylene linked to triazole and ferrocene units has been studied within the Molecular Electron Density Theory (MEDT) at the ωB97X-D/6-311G(d,p) level. The topology of the electron localization function (ELF) of this AY allows classifying it as a pseudo(mono)radical species characterized by the presence of two monosynaptic basins, integrating a total of 0.76 e, at the C1 carbon. While the ferrocene ethylene has a strong electrophilic character, the AY is a supernucleophile, suggesting that the corresponding 32CA reaction has a high polar character and a low activation energy. The most favorable ortho/endo reaction path presents an activation enthalpy of 8.7 kcal·mol-1, with the 32CA reaction being exergonic by -42.1 kcal·mol-1. This reaction presents a total endo stereoselectivity and a total ortho regioselectivity. Analysis of the global electron density transfer (GEDT) at the most favorable TS-on (0.23 e) accounts for the high polar character of this 32CA reaction, classified as forward electron density flux (FEDF). The formation of two intermolecular hydrogen bonds between the two interacting frameworks at the most favorable TS-on accounts for the unexpected ortho regioselectivity experimentally observed.
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36
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Hamdaoui M, Liu F, Cornaton Y, Lu X, Shi X, Zhang H, Liu J, Spingler B, Djukic JP, Duttwyler S. An Iridium-Stabilized Borenium Intermediate. J Am Chem Soc 2022; 144:18359-18374. [PMID: 36173688 DOI: 10.1021/jacs.2c06298] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exploration of new organometallic systems based on polyhedral boron clusters has the potential to solve challenging chemical problems such as the stabilization of reactive intermediates and transition-state-like species postulated for E-H (E = H, B, C, Si) bond activation reactions. We report on facile and clean B-H activation of a hydroborane by a new iridium boron cluster complex. The product of this reaction is an unprecedented and fully characterized transition metal-stabilized boron cation or borenium. Moreover, this intermediate bears an unusual intramolecular B···H interaction between the hydrogen originating from the activated hydroborane and the cyclometallated metal-bonded boron atom of the boron cluster. This B···H interaction is proposed to be an arrested insertion of hydrogen into the Bcage-metal bond and the initiation step for iridium "cage-walking" around the upper surface of the boron cluster. The "cage-walking" process is supported by the hydrogen-deuterium exchange observed at the boron cluster, and a mechanism is proposed on the basis of theoretical methods with a special focus on the role of noncovalent interactions. All new compounds were isolated and fully characterized by NMR spectroscopy and elemental analysis. Key compounds were studied by single crystal X-ray diffraction and X-ray photoelectron spectroscopy.
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Affiliation(s)
- Mustapha Hamdaoui
- Department of Chemistry, Zheijang University, Hangzhou 310027, China
| | - Fan Liu
- Department of Chemistry, Zheijang University, Hangzhou 310027, China
| | - Yann Cornaton
- Laboratoire de Chimie et Systémique Organométalliques, Institut de Chimie de Strasbourg UMR 7177 CNRS, Université de Strasbourg, Strasbourg 67000, France
| | - Xingyu Lu
- Instrumentation Service Center for Molecular Sciences, Westlake University, Hangzhou 310024, China
| | - Xiaohuo Shi
- Instrumentation Service Center for Molecular Sciences, Westlake University, Hangzhou 310024, China
| | - Huan Zhang
- Instrumentation Service Center for Molecular Sciences, Westlake University, Hangzhou 310024, China
| | - Jiyong Liu
- Department of Chemistry, Zheijang University, Hangzhou 310027, China
| | - Bernhard Spingler
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Jean-Pierre Djukic
- Laboratoire de Chimie et Systémique Organométalliques, Institut de Chimie de Strasbourg UMR 7177 CNRS, Université de Strasbourg, Strasbourg 67000, France
| | - Simon Duttwyler
- Department of Chemistry, Zheijang University, Hangzhou 310027, China
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37
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Al-Jabiri MH, Hazrah AS, Jäger W. Conformers of Vanillic Acid and Its Monohydrate: A Rotational Spectroscopic and Theoretical Study. J Phys Chem A 2022; 126:6686-6694. [DOI: 10.1021/acs.jpca.2c05120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mohamad H. Al-Jabiri
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Arsh S. Hazrah
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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38
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Two Zn(II)-based coordination polymers as dual-responsive luminescent sensors for the detection of Cr2O72− ions, levofloxacin/sulfamethoxazole. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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39
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Baykov SV, Tarasenko MV, Semenov AV, Katlenok EA, Shetnev AA, Boyarskiy VP. Dualism of 1,2,4-oxadiazole ring in noncovalent interactions with carboxylic group. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Zhang NN, Li J, Xiao H. The Key Role of Competition between Orbital and Electrostatic Interactions in the Adsorption on Transition Metal Single‐Atom Catalysts Anchored by N‐doped Graphene. ChemCatChem 2022. [DOI: 10.1002/cctc.202200275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Nan-Nan Zhang
- Tsinghua University Department of Chemistry 100084 Beijing CHINA
| | - Jun Li
- Tsinghua University Department of Chemistry 100084 Beijing CHINA
| | - Hai Xiao
- Tsinghua University Department of Chemistry Department of ChemistryTsinghua University 100084 Beijing CHINA
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41
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Takagi R, Tanimoto T. Enantioselective [2 + 2] photocycloaddition of quinolone using a C1-symmetric chiral phosphoric acid as a visible-light photocatalyst. Org Biomol Chem 2022; 20:3940-3947. [PMID: 35506886 DOI: 10.1039/d2ob00607c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The enantioselective intra- and intermolecular [2 + 2] photocycloaddition of quinolone using a C1-symmetric chiral phosphoric acid as a visible-light photocatalyst is developed. The thioxanthone chromophore on phosphoric acid plays an important role in both phototransformation and enantioselectivity.
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Affiliation(s)
- Ryukichi Takagi
- Department of Chemistry, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Takaaki Tanimoto
- Department of Chemistry, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
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42
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Ding WL, Zhang T, Wang Y, Xin J, Yuan X, Ji L, He H. Machine Learning Screening of Efficient Ionic Liquids for Targeted Cleavage of the β–O–4 Bond of Lignin. J Phys Chem B 2022; 126:3693-3704. [DOI: 10.1021/acs.jpcb.1c10684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wei-Lu Ding
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Innovation Academy for Green Manufacture Chinese Academy of Sciences, Beijing 100190, China
| | - Tao Zhang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Yanlei Wang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Innovation Academy for Green Manufacture Chinese Academy of Sciences, Beijing 100190, China
| | - Jiayu Xin
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Innovation Academy for Green Manufacture Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoqing Yuan
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Ji
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Hongyan He
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Innovation Academy for Green Manufacture Chinese Academy of Sciences, Beijing 100190, China
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43
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Fereydooni Naghani F, Emamian S, Zare K. A comprehensive theoretical analysis on the intermolecular hydrogen bond interactions with the Lewis bases having multiple hydrogen bonding ability. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Saeedreza Emamian
- Chemistry Department, Shahrood Branch Islamic Azad University Shahrood Iran
| | - Karim Zare
- Department of Chemistry, Science and Research Branch Islamic Azad University Tehran Iran
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44
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Unimuke T, Louis H, Eno EA, Agwamba EC, Adeyinka AS. Meta-Hybrid Density Functional Theory Prediction of the Reactivity, Stability, and IGM of Azepane, Oxepane, Thiepane, and Halogenated Cycloheptane. ACS OMEGA 2022; 7:13704-13720. [PMID: 35559178 PMCID: PMC9088921 DOI: 10.1021/acsomega.1c07361] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/31/2022] [Indexed: 05/09/2023]
Abstract
The application of plain cycloalkanes and heterocyclic derivatives in the synthesis of valuable natural products and pharmacologically active intermediates has increased tremendously in recent times with much attention being paid to the lower cycloalkane members. The structural and molecular properties of higher seven-membered and nonaromatic heterocyclic derivatives are less known despite their stable nature and vast application; thus, an insight into their structural and electronic properties is still needed. Appropriate quantum chemical calculations utilizing the ab initio (MP2) method, meta-hybrid (M06-2X) functional, and long-range-separated functionals (ωB97XD) have been utilized in this work to investigate the structural reactivity, stability, and behavior of substituents on cycloheptane (CHP) and its derivatives: azepane, oxepane, thiepane, fluorocycloheptane (FCHP), bromocycloheptane (BrCHP), and chlorocycloheptane (ClCHP). Molecular global reactivity descriptors such as Fukui function, frontier molecular orbitals (FMOs), and molecular electrostatic potential were computed and compared with lower members. The results of two population methods CHELPG and Atomic Dipole Corrected Hirshfeld Charges (ADCH) were equally compared to scrutinize the charge distribution in the molecules. The susceptibility of intramolecular interactions between the substituents and cycloalkane ring is revealed by natural bond orbital analysis and intramolecular weak interactions by the independent gradient model (IGM). Other properties such as atomic density of states, intrinsic bond strength index (IBSI), and dipole moments are considered. It is acclaimed that the strain effect is a major determinant effect in the energy balance of cyclic molecules; thus, the ring strain energies and validation of spectroscopic specificities with reference to the X-ray crystallographic data are also considered.
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Affiliation(s)
- Tomsmith
O. Unimuke
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540004, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540004, Nigeria
| | - Hitler Louis
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540004, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540004, Nigeria
| | - Ededet A. Eno
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540004, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540004, Nigeria
| | - Ernest C. Agwamba
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540004, Nigeria
- Department
of Chemical Sciences, Clifford University
Owerrinta, Abia State 440001, Nigeria
| | - Adedapo S. Adeyinka
- Research
Centre for Synthesis and Catalysis, Department of Chemical Sciences, University of Johannesburg, Johannesburg 2006, South Africa
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45
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Insausti A, Ma J, Yang Q, Xie F, Xu Y. Rotational Spectroscopy of 2-Furoic Acid and Its Dimer: Conformational Distribution and Double Proton Tunneling. Chemphyschem 2022; 23:e202200176. [PMID: 35390214 DOI: 10.1002/cphc.202200176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/06/2022] [Indexed: 01/18/2023]
Abstract
Structural and tunneling properties of the 2-furoic acid (FA) monomer and dimer were investigated using rotational spectroscopy and DFT calculations. CREST, a conformational ensemble space exploration tool, was used to identify all possible low energy conformations of the FA monomer and dimer, followed by the DFT geometry optimization and harmonic frequency calculations. Broadband rotational spectra in the 2-6 GHz and in the 8-12 GHz regions were recorded in a supersonic jet expansion. The monomeric FA was found to exist dominantly as three different conformers: I , II , and III in a jet, with I and II taking on the trans -COOH configuration while III having the cis -COOH configuration. For the FA dimer, only the I - II conformer was observed experimentally, whereas the symmetric I - I and II - II conformers were not observed because of their zero dipole moments. The analysis of the splittings in the rotational transitions of I - II allowed one to extract the tunneling splitting to be 1056.0(12) MHz. The barrier height was determined to be ~442 cm -1 using the scaled potential energy scans at several different levels of theory.
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Affiliation(s)
- Aran Insausti
- UPV/EHU: Universidad del Pais Vasco, Departamento de Química Física, SPAIN
| | - Jiarui Ma
- University of Alberta Department of Renewable Resources, Chemistry, CANADA
| | - Qian Yang
- University of Alberta, Chemistry, CANADA
| | - Fan Xie
- DESY Accelerator Centre: Deutsches Elektronen-Synchrotron, Spectroscopy of molecular processes, GERMANY
| | - Yunjie Xu
- University of Alberta Faculty of Science, Chemistry Department, 11227 Saskatchewan Drive, T6G 2G2, Edmonton, CANADA
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Mendoza I, Luis Paz J, González-Paz LA, Márquez EA, Vera-Villalobos J, Mora JR, Alvarado YJ, Cordova-Sintjago T, Loroño G. MA. Reaction mechanism of the gas-phase pyrolysis of N – acetylthiourea and N, N’–diacetylthiourea: a theoretical study based in density functional theory. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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47
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Du J, Jiang G. The strong interaction of actinyl ions with fullerenol driven by multiple hydrogen bonds. Dalton Trans 2022; 51:5118-5126. [PMID: 35266470 DOI: 10.1039/d1dt03996b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The removal of actinides from radioactive wastewater is an important subject with the continuous application of nuclear energy. All-electron density functional theory (DFT) calculations were carried out to understand the adsorption behaviors of actinyl ions on C60(OH)24 fullerenol in this work. The outer-sphere (OS) bonding mode is more stable than the inner-sphere one because of the formation of multiple hydrogen bonds in the OS mode. The actinyl(VI) ions can be more efficiently absorbed by fullerenol than actinyl(V) ones. The bonding nature of actinyl ions with C60(OH)24 was revealed by various electron density topological analyses. Multiple hydrogen bonds formed in the OS complexes show moderate bond strength with partial covalent nature and are responsible for their high stability. IR spectra were fingerprinted to distinguish the interaction modes of actinyl ions with C60(OH)24.
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Affiliation(s)
- Jiguang Du
- College of Physics, Sichuan University, Chengdu 610065, China.
| | - Gang Jiang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
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48
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Oliveros R. DA, Machado RA, Mora JR. Quantitative structure–property relationship analysis of the spectrochemical series by employing electronic descriptors from DFT calculations. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2040629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Deivi A. Oliveros R.
- Facultad de Ciencias, Universidad Central de Venezuela, Escuela de Química, Caracas, Venezuela
| | - Rubén A. Machado
- Centro de Química, Laboratorio de Química de Metales de Transición, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - José R. Mora
- Grupo de Química Computacional y Teórica, Departamento de Ingeniería Química, Universidad San Francisco de Quito, Instituto de Simulación Computacional, Quito, Ecuador
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Hazrah AS, Nanayakkara S, Seifert NA, Kraka E, Jäger W. Structural study of 1- and 2-naphthol: new insights into the non-covalent H-H interaction in cis-1-naphthol. Phys Chem Chem Phys 2022; 24:3722-3732. [PMID: 35080568 DOI: 10.1039/d1cp05632h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Previous microwave studies of naphthol monomers were supplemented by measuring spectra of all 13C mono-substituted isotopologues of the cis- and trans-conformers of 1-naphthol and 2-naphthol in their natural abundances. The resulting data were utilized to determine substitution structures and so-called semi-experimental effective structures. Results from electronic structure calculations show that the OH group of cis-1-naphthol points ≈6° out of plane, which is consistent with the inertial defect data of cis- and trans-1-naphthol. The non-planarity of cis-1-naphthol is a result of a close-contact H-atom-H-atom interaction. This type of H-H interaction has been the subject of much controversy in the past and we provide here an in-depth theoretical analysis of it. The naphthol system is particularly well-suited for such analysis as it provides internal standards with its four different isomers. The methods used include quantum theory of atoms in molecules, non-covalent interactions, independent gradient model, local vibrational mode, charge model 5, and natural bond orbital analyses. We demonstrate that the close-contact H-H interaction is neither a purely attractive nor repulsive interaction, but rather a mixture of the two.
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Affiliation(s)
- Arsh S Hazrah
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
| | - Sadisha Nanayakkara
- Department of Chemistry, Southern Methodist University, Dallas, TX, 75275-0314, USA.
| | - Nathan A Seifert
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, Dallas, TX, 75275-0314, USA.
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
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50
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Chalcogen Bonding in the Molecular Dimers of WCh 2 (Ch = S, Se, Te): On the Basic Understanding of the Local Interfacial and Interlayer Bonding Environment in 2D Layered Tungsten Dichalcogenides. Int J Mol Sci 2022; 23:ijms23031263. [PMID: 35163185 PMCID: PMC8835845 DOI: 10.3390/ijms23031263] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 01/28/2023] Open
Abstract
Layered two-dimensional transition metal dichalcogenides and their heterostructures are of current interest, owing to the diversity of their applications in many areas of materials nanoscience and technologies. With this in mind, we have examined the three molecular dimers of the tungsten dichalcogenide series, (WCh2)2 (Ch = S, Se, Te), using density functional theory to provide insight into which interactions, and their specific characteristics, are responsible for the interfacial/interlayer region in the room temperature 2H phase of WCh2 crystals. Our calculations at various levels of theory suggested that the Te···Te chalcogen bonding in (WTe2)2 is weak, whereas the Se···Se and S···S bonding interactions in (WSe2)2 and (WS2)2, respectively, are of the van der Waals type. The presence and character of Ch···Ch chalcogen bonding interactions in the dimers of (WCh2)2 are examined with a number of theoretical approaches and discussed, including charge-density-based approaches, such as the quantum theory of atoms in molecules, interaction region indicator, independent gradient model, and reduced density gradient non-covalent index approaches. The charge-density-based topological features are shown to be concordant with the results that originate from the extrema of potential on the electrostatic surfaces of WCh2 monomers. A natural bond orbital analysis has enabled us to suggest a number of weak hyperconjugative charge transfer interactions between the interacting monomers that are responsible for the geometry of the (WCh2)2 dimers at equilibrium. In addition to other features, we demonstrate that there is no so-called van der Waals gap between the monolayers in two-dimensional layered transition metal tungsten dichalcogenides, which are gapless, and that the (WCh2)2 dimers may be prototypes for a basic understanding of the physical chemistry of the chemical bonding environments associated with the local interfacial/interlayer regions in layered 2H-WCh2 nanoscale systems.
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