1
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Zhao D, Zhao Y, Xu E, Liu W, Ayers PW, Liu S, Chen D. Fragment-Based Deep Learning for Simultaneous Prediction of Polarizabilities and NMR Shieldings of Macromolecules and Their Aggregates. J Chem Theory Comput 2024; 20:2655-2665. [PMID: 38441881 DOI: 10.1021/acs.jctc.3c01415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Simultaneous prediction of the molecular response properties, such as polarizability and the NMR shielding constant, at a low computational cost is an unresolved issue. We propose to combine a linear-scaling generalized energy-based fragmentation (GEBF) method and deep learning (DL) with both molecular and atomic information-theoretic approach (ITA) quantities as effective descriptors. In GEBF, the total molecular polarizability can be assembled as a linear combination of the corresponding quantities calculated from a set of small embedded subsystems in GEBF. In the new GEBF-DL(ITA) protocol, one can predict subsystem polarizabilities based on the corresponding molecular wave function (thus electron density and ITA quantities) and DL model rather than calculate them from the computationally intensive coupled-perturbed Hartree-Fock or Kohn-Sham equations and finally obtain the total molecular polarizability via a linear combination equation. As a proof-of-concept application, we predict the molecular polarizabilities of large proteins and protein aggregates. GEBF-DL(ITA) is shown to be as accurate enough as GEBF, with mean absolute percentage error <1%. For the largest protein aggregate (>4000 atoms), GEBF-DL(ITA) gains a speedup ratio of 3 compared with GEBF. It is anticipated that when more advanced electronic structure methods are used, this advantage will be more appealing. Moreover, one can also predict the NMR chemical shieldings of proteins with reasonably good accuracy. Overall, the cost-efficient GEBF-DL(ITA) protocol should be a robust theoretical tool for simultaneously predicting polarizabilities and NMR shieldings of large systems.
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Affiliation(s)
- Dongbo Zhao
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan 650500, P. R. China
| | - Yilin Zhao
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton ONL8S4M1, Canada
| | - Enhua Xu
- Graduate School of System Informatics, Kobe University, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Wenqi Liu
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan 650500, P. R. China
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton ONL8S4M1, Canada
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan 650500, P. R. China
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2
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Kaya S, Putz MV. Atoms-In-Molecules' Faces of Chemical Hardness by Conceptual Density Functional Theory. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248825. [PMID: 36557957 PMCID: PMC9782142 DOI: 10.3390/molecules27248825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/09/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
The chemical hardness concept and its realization within the conceptual density functional theory is approached with innovative perspectives, such as the electronegativity and hardness equalization of atoms in molecules connected with the softness kernel, in order to examine the structure-reactivity equalization ansatz between the electronic sharing index and the charge transfer either in the additive or geometrical mean picture of bonding. On the other hand, the maximum hardness principle presents a relation with the chemical stability of the hardness concept. In light of the inverse relation between hardness and polarizability, the minimum polarizability principle has been proposed. Additionally, this review includes important applications of the chemical hardness concept to solid-state chemistry. The mentioned applications support the validity of the electronic structure principles regarding chemical hardness and polarizability in solid-state chemistry.
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Affiliation(s)
- Savas Kaya
- Department of Pharmacy, Health Services Vocational School, Sivas Cumhuriyet University, Sivas 58140, Turkey
- Correspondence: (S.K.); (M.V.P.)
| | - Mihai V. Putz
- Laboratory of Computational and Structural Physical-Chemistry for Nanosciences and QSAR, Biology-Chemistry Department, Faculty of Chemistry, Biology, Geography, West University of Timișoara, Pestalozzi Str. No. 16A, RO-300115 Timișoara, Romania
- Scientific Laboratory of Renewable Energies-Photovoltaics, R&D National Institute for Electrochemistry and Condensed Matter (INCEMC-Timisoara), Dr. Aurel Podeanu Str. No. 144, RO-300569 Timișoara, Romania
- Correspondence: (S.K.); (M.V.P.)
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3
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Fias S, Ayers PW, De Proft F, Geerlings P. Properties of the density functional response kernels and its implications on chemistry. J Chem Phys 2022; 157:114102. [PMID: 36137804 DOI: 10.1063/5.0094653] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An overview of mathematical properties of the non-local second order derivatives of the canonical, grand canonical, isomorphic, and grand isomorphic ensembles is given. The significance of their positive or negative semidefiniteness and the implications of these properties for atoms and molecules are discussed. Based on this property, many other interesting properties can be derived, such as the expansion in eigenfunctions, bounds on the diagonal and off-diagonal elements, and the eigenvalues of these kernels. We also prove Kato's theorem for the softness kernel and linear response and the dissociation limit of the linear responses as the sum of the linear responses of the individual fragments when dissociating a system into two non-interacting molecular fragments. Finally, strategies for the practical calculation of these kernels, their eigenfunctions, and their eigenvalues are discussed.
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Affiliation(s)
- Stijn Fias
- McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4L8, Canada
| | - Paul W Ayers
- McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4L8, Canada
| | - Frank De Proft
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Paul Geerlings
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
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4
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Geerlings P. From Density Functional Theory to Conceptual Density Functional Theory and Biosystems. Pharmaceuticals (Basel) 2022; 15:ph15091112. [PMID: 36145333 PMCID: PMC9505550 DOI: 10.3390/ph15091112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 12/03/2022] Open
Abstract
The position of conceptual density functional theory (CDFT) in the history of density functional theory (DFT) is sketched followed by a chronological report on the introduction of the various DFT descriptors such as the electronegativity, hardness, softness, Fukui function, local version of softness and hardness, dual descriptor, linear response function, and softness kernel. Through a perturbational approach they can all be characterized as response functions, reflecting the intrinsic reactivity of an atom or molecule upon perturbation by a different system, including recent extensions by external fields. Derived descriptors such as the electrophilicity or generalized philicity, derived from the nature of the energy vs. N behavior, complete this picture. These descriptors can be used as such or in the context of principles such as Sanderson’s electronegativity equalization principle, Pearson’s hard and soft acids and bases principle, the maximum hardness, and more recently, the minimum electrophilicity principle. CDFT has known an ever-growing use in various subdisciplines of chemistry: from organic to inorganic chemistry, from polymer to materials chemistry, and from catalysis to nanotechnology. The increasing size of the systems under study has been coped with thanks to methodological evolutions but also through the impressive evolution in software and hardware. In this flow, biosystems entered the application portfolio in the past twenty years with studies varying (among others) from enzymatic catalysis to biological activity and/or the toxicity of organic molecules and to computational peptidology. On the basis of this evolution, one can expect that “the best is yet to come”.
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Affiliation(s)
- Paul Geerlings
- Research Group of General Chemistry (ALGC), Faculty of Science and Bio-Engineering Science, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
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5
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Zhang C, Zhao DX, Feng Y, Wang J, Yang ZZ. Energetics and J-coupling constants for Ala, Gly, and Val peptides demonstrated using ABEEM polarizable force field in vacuo and an aqueous solution. Phys Chem Chem Phys 2022; 24:4232-4250. [DOI: 10.1039/d1cp05676j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of an atom-bond electronegativity equalisation method at the σπ-level (ABEEM) polarisable force field (PFF) for peptides is presented. ABEEM PFF utilises a fluctuating charge model to explicitly describe...
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6
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Rocha-Santos A, Chaves EJ, Grillo IB, de Freitas AS, Araújo DAM, Rocha GB. Thermochemical and Quantum Descriptor Calculations for Gaining Insight into Ricin Toxin A (RTA) Inhibitors. ACS OMEGA 2021; 6:8764-8777. [PMID: 33842748 PMCID: PMC8027999 DOI: 10.1021/acsomega.0c02588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/30/2020] [Indexed: 05/03/2023]
Abstract
In this work, we performed a study to assess the interactions between the ricin toxin A (RTA) subunit of ricin and some of its inhibitors using modern semiempirical quantum chemistry and ONIOM quantum mechanics/molecular mechanics (QM/MM) methods. Two approaches were followed (calculation of binding enthalpies, ΔH bind, and reactivity quantum chemical descriptors) and compared with the respective half-maximal inhibitory concentration (IC50) experimental data, to gain insight into RTA inhibitors and verify which quantum chemical method would better describe RTA-ligand interactions. The geometries for all RTA-ligand complexes were obtained after running classical molecular dynamics simulations in aqueous media. We found that single-point energy calculations of ΔH bind with the PM6-DH+, PM6-D3H4, and PM7 semiempirical methods and ONIOM QM/MM presented a good correlation with the IC50 data. We also observed, however, that the correlation decreased significantly when we calculated ΔH bind after full-atom geometry optimization with all semiempirical methods. Based on the results from reactivity descriptors calculations for the cases studied, we noted that both types of interactions, molecular overlap and electrostatic interactions, play significant roles in the overall affinity of these ligands for the RTA binding pocket.
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Affiliation(s)
- Acassio Rocha-Santos
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Elton José
Ferreira Chaves
- Department
of Biotechnology, Federal University of
Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Igor Barden Grillo
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Amanara Souza de Freitas
- Department
of Chemical Engineering, Federal University
of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | | | - Gerd Bruno Rocha
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
- . Phone/Fax: +55-83-3216-7437
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7
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Stuyver T, Shaik S. Unifying Conceptual Density Functional and Valence Bond Theory: The Hardness-Softness Conundrum Associated with Protonation Reactions and Uncovering Complementary Reactivity Modes. J Am Chem Soc 2020; 142:20002-20013. [PMID: 33180491 PMCID: PMC7735708 DOI: 10.1021/jacs.0c09041] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this study, we address the long-standing issue-arising prominently from conceptual density functional theory (CDFT)-of the relative importance of electrostatic, i.e., "hard-hard", versus spin-pairing, i.e., "soft-soft", interactions in determining regiochemical preferences. We do so from a valence bond (VB) perspective and demonstrate that VB theory readily enables a clear-cut resolution of both of these contributions to the bond formation/breaking process. Our calculations indicate that appropriate local reactivity descriptors can be used to gauge the magnitude of both interactions individually, e.g., Fukui functions or HOMO/LUMO orbitals for the spin-pairing/(frontier) orbital interactions and molecular electrostatic potentials (and/or partial charges) for the electrostatic interactions. In contrast to previous reports, we find that protonation reactions cannot generally be classified as either charge- or frontier orbital-controlled; instead, our results indicate that these two bonding contributions generally interplay in more subtle patterns, only giving the impression of a clear-cut dichotomy. Finally, we demonstrate that important covalent, i.e., spin pairing, reactivity modes can be missed when only a single spin-pairing/orbital interaction descriptor is considered. This study constitutes an important step in the unification of CDFT and VB theory.
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Affiliation(s)
- Thijs Stuyver
- Institute of Chemistry, Edmond J. Safara Campus at Givat Ram, The Hebrew University, Jerusalem 9190401, Israel
| | - Sason Shaik
- Institute of Chemistry, Edmond J. Safara Campus at Givat Ram, The Hebrew University, Jerusalem 9190401, Israel
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8
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Sheehy KJ, Bateman LM, Flosbach NT, Breugst M, Byrne PA. Competition between N and O: use of diazine N-oxides as a test case for the Marcus theory rationale for ambident reactivity. Chem Sci 2020; 11:9630-9647. [PMID: 34094230 PMCID: PMC8162281 DOI: 10.1039/d0sc02834g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/23/2020] [Indexed: 11/21/2022] Open
Abstract
The preferred site of alkylation of diazine N-oxides by representative hard and soft alkylating agents was established conclusively using the 1H-15N HMBC NMR technique in combination with other NMR spectroscopic methods. Alkylation of pyrazine N-oxides (1 and 2) occurs preferentially on nitrogen regardless of the alkylating agent employed, while O-methylation of pyrimidine N-oxide (3) is favoured in its reaction with MeOTf. As these outcomes cannot be explained in the context of the hard/soft acid/base (HSAB) principle, we have instead turned to Marcus theory to rationalise these results. Marcus intrinsic barriers (ΔG ‡ 0) and Δr G° values were calculated at the DLPNO-CCSD(T)/def2-TZVPPD/SMD//M06-2X-D3/6-311+G(d,p)/SMD level of theory for methylation reactions of 1 and 3 by MeI and MeOTf, and used to derive Gibbs energies of activation (ΔG ‡) for the processes of N- and O-methylation, respectively. These values, as well as those derived directly from the DFT calculations, closely reproduce the observed experimental N- vs. O-alkylation selectivities for methylation reactions of 1 and 3, indicating that Marcus theory can be used in a semi-quantitative manner to understand how the activation barriers for these reactions are constructed. It was found that N-alkylation of 1 is favoured due to the dominant contribution of Δr G° to the activation barrier in this case, while O-alkylation of 3 is favoured due to the dominant contribution of the intrinsic barrier (ΔG ‡ 0) for this process. These results are of profound significance in understanding the outcomes of reactions of ambident reactants in general.
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Affiliation(s)
- Kevin J Sheehy
- School of Chemistry, Analytical and Biological Chemistry Research Facility, University College Cork College Road Cork Ireland
| | - Lorraine M Bateman
- School of Chemistry, Analytical and Biological Chemistry Research Facility, University College Cork College Road Cork Ireland
- School of Pharmacy, University College Cork College Road Ireland
- SSPC (Synthesis and Solid State Pharmaceutical Centre) Cork Ireland
| | - Niko T Flosbach
- Department für Chemie, Universität zu Köln Greinstraße 4 50939 Köln Germany
| | - Martin Breugst
- Department für Chemie, Universität zu Köln Greinstraße 4 50939 Köln Germany
| | - Peter A Byrne
- School of Chemistry, Analytical and Biological Chemistry Research Facility, University College Cork College Road Cork Ireland
- SSPC (Synthesis and Solid State Pharmaceutical Centre) Cork Ireland
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9
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Hoffmann G, Balcilar M, Tognetti V, Héroux P, Gaüzère B, Adam S, Joubert L. Predicting experimental electrophilicities from quantum and topological descriptors: A machine learning approach. J Comput Chem 2020. [DOI: 10.1002/jcc.26376] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Guillaume Hoffmann
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS Mont St Aignan France
| | | | - Vincent Tognetti
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS Mont St Aignan France
| | - Pierre Héroux
- Normandie Univ., UNIROUEN, UNIHAVRE, INSA Rouen, LITIS Rouen France
| | - Benoît Gaüzère
- Normandie Univ., UNIROUEN, UNIHAVRE, INSA Rouen, LITIS Rouen France
| | - Sébastien Adam
- Normandie Univ., UNIROUEN, UNIHAVRE, INSA Rouen, LITIS Rouen France
| | - Laurent Joubert
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS Mont St Aignan France
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10
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Shi H, Gong LD, Liu C, Lu LN, Yang ZZ. ABEEM/MM OH - Models for OH -(H 2O) n Clusters and Aqueous OH -: Structures, Charge Distributions, and Binding Energies. J Phys Chem A 2020; 124:5963-5978. [PMID: 32520555 DOI: 10.1021/acs.jpca.0c03941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Based on the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), two fluctuating charge models of OH--water system were proposed. The difference between these two models is whether there is charge transfer between OH- and its first-shell water molecules. The structures, charge distributions, charge transfer, and binding energies of the OH-(H2O)n (n = 1-8, 10, 15, 23) clusters were studied by these two ABEEM/MM models, the OPLS/AA force field, the OPLS-SMOOTH/AA force field, and the QM methods. The results demonstrate that two ABEEM/MM models can search out all stable structures just as the QM methods, and the structures and charge distributions agree well with those from the QM calculations. The structures, the charge transfer, and the strength of hydrogen bonds in the first hydration shell are closely related to the coordination number of OH-. Molecular dynamics simulations on the aqueous OH- solution are performed at 298 and 278 K using ABEEM/MM-I model. The MD results show that the populations of three-, four-, and five-coordinated OH- are 29.6%, 67.1%, and 3.4% at 298 K, respectively, and those of two-, three-, four-, and five-coordinated OH- are 10.8%, 44.9%, 39.2%, and 4.9% at 278 K, respectively; the average hydrogen bond lengths and the hydrogen bond angle in the first shell increase with the temperature decreasing.
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Affiliation(s)
- Hua Shi
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.,School of Marine Science and Environment, Dalian Ocean University, Dalian 116023, People's Republic of China
| | - Li-Dong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China
| | - Li-Nan Lu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China
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11
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Study of organic reactions using chemical reactivity descriptors derived through a temperature-dependent approach. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-2557-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Bettens T, Alonso M, Geerlings P, De Proft F. The hunt for reactive alkynes in bio-orthogonal click reactions: insights from mechanochemical and conceptual DFT calculations. Chem Sci 2019; 11:1431-1439. [PMID: 34123268 PMCID: PMC8148320 DOI: 10.1039/c9sc04507d] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In our effort to implement the mechanical force used to activate single molecules in mechanochemistry in the context of conceptual density functional theory, we present a theoretical investigation of strained alkynes for rationalizing structural trends as well as the reactivity of cyclic alkynes that are of great importance in in vivo click reactions. The strain on the triple bond in cyclic alkynes is modeled by angular constraints in a 2-butyne fragment and the corresponding bending force is calculated by means of an extended COGEF (constrained geometries simulate external forces) model. In general, the force required to bend the triple bond is smaller with electron-withdrawing groups on the propargylic C-atom, which elegantly results in smaller angles around the triple bond in cyclic alkynes with such substitution pattern. By means of conceptual DFT descriptors, the electrophilic and nucleophilic character of bent triple bonds was investigated revealing moderate activation for small distortions from the linear geometry (0° to 15°) and a drastically more reactive π-space if the triple bond is bent further. This analysis of the intrinsic reactivity of the triple bond is in line with experimental observations, explaining the reactive nature of cyclooctynes and cycloheptynes, whereas larger cyclic systems do not drastically activate the triple bond.
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Affiliation(s)
- Tom Bettens
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) Pleinlaan 2 1050 Brussels Belgium
| | - Mercedes Alonso
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) Pleinlaan 2 1050 Brussels Belgium
| | - Paul Geerlings
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) Pleinlaan 2 1050 Brussels Belgium
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) Pleinlaan 2 1050 Brussels Belgium
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13
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Vidhya V, Austine A, Arivazhagan M. Quantum chemical determination of molecular geometries and spectral investigation of 4-ethoxy-2, 3-difluoro benzamide. Heliyon 2019; 5:e02365. [PMID: 31844688 PMCID: PMC6895590 DOI: 10.1016/j.heliyon.2019.e02365] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 06/14/2019] [Accepted: 08/21/2019] [Indexed: 11/27/2022] Open
Abstract
The present work reports the application of density functional theory (DFT) at B3LYP with various basis sets which provide the relationship between the structural and spectral properties of 4-ethoxy-2, 3-difluoro benzamide (4EDFB). A Complete vibrational analysis has been performed at the density functional theory (DFT) method with various basis sets in the ground state. The results of vibrational wave numbers are in good agreement with the experimental spectra (Infrared and Raman). Energy gap of the molecule is evaluated using frontier molecular orbital energies (HOMO-LUMO). The frontier energy gap value reveals the chemical reactivity and intermolecular charge transfer occur within the molecule. Global chemical descriptors provide the local and global softness and local reactivity parameters used to identify the nucleophilic and electrophilic behavior of a specific site within the compound. The dimer structure is performed to evaluate the intermolecular hydrogen bond (O-H-O). The title molecule is capable of receiving second harmonic generation (SHG) is due to high value of hyperpolarizability indicates the NLO activity of the molecule. Apart from NLO entities, aromaticity and the molecular electrostatic potential surface (MEP) explain the hydrogen bonding and provide the reactive behavior of the molecule. The Mulliken population analysis leads to redistribution of electron density in the ring.
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Affiliation(s)
- V. Vidhya
- Department of Physics, Trichy Engineering College, Trichy, 621132, India
| | - A. Austine
- PG&Research Department of Physics, A.A.Government Arts College, Musiri, 621211, India
| | - M. Arivazhagan
- PG&Research Department of Physics, Government Arts College, Trichy, 620022, India
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14
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Bhattacharjee R, Verma K, Zhang M, Li T. Locality and strength of intermolecular interactions in organic crystals: using conceptual density functional theory (CDFT) to characterize a highly polymorphic system. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2508-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Li H, Wang D, Zhao X, Lu LN, Liu C, Gong LD, Zhao DX, Yang ZZ. Reaction mechanism of NO with hydrolysates of NAMI-A: an MD simulation by combining the QM/MM(ABEEM) with the MD-FEP method. J Comput Chem 2019; 40:1141-1150. [PMID: 30375671 DOI: 10.1002/jcc.25734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 09/27/2018] [Accepted: 09/28/2018] [Indexed: 11/06/2022]
Abstract
Nitrosylation reaction mechanisms of the hydrolysates of NAMI-A and hydrolysis reactions of ruthenium nitrosyl complexes were investigated in the triplet state and the singlet state. Activation free energies were calculated by combining the QM/MM(ABEEM) method with free energy perturbation theory, and the explicit solvent environment was simulated by an ABEEMσπ polarizable force field. Our results demonstrate that nitrosylation reactions of the hydrolysates of NAMI-A occur in both the triplet and the singlet states. The Ru-N-O angle of the triplet ruthenium nitrosyl complexes is in the range of 132.0°-138.2°. However, all the ruthenium nitrosyl complexes at the singlet state show an almost linear Ru-N-O angle. The nitrosylation reaction happens prior to the hydrolysis reaction for the first-step hydrolysates. The activation free energies of the nitrosylation reactions show that the H2 O-NO exchange reaction of [RuCl4 (Im)(H2 O)] in the singlet spin sate is the most likely one. Comparing with the activation free energies of the hydrolysis reactions of the ruthenium nitrosyl complexes, the results indicate that the rate of the DMSO-H2 O exchange reaction of [RuCl3 (NO)(Im)(DMSO)] is faster than that of [RuCl3 (H2 O)(Im)(DMSO)] in both the triplet spin state and the singlet spin state. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Hui Li
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China.,Department of Chemistry, Bohai University, Jinzhou 121013, China
| | - Di Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Xin Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Li-Nan Lu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Li-Dong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
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16
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Franco-Pérez M, Polanco-Ramírez CA, Gázquez JL, Ayers PW. Local and nonlocal counterparts of global descriptors: the cases of chemical softness and hardness. J Mol Model 2018; 24:285. [DOI: 10.1007/s00894-018-3823-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/04/2018] [Indexed: 10/28/2022]
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17
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Zhou PP, Liu S, Ayers PW, Zhang RQ. Bonding reactivity descriptor from conceptual density functional theory and its applications to elucidate bonding formation. J Chem Phys 2017; 147:134303. [DOI: 10.1063/1.5004406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Pan-Pan Zhou
- Beijing Computational Science Research Center, Beijing 100084, People’s Republic of China
- Department of Chemistry, Lanzhou University, Lanzhou 730000, People’s Republic of China
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Paul W. Ayers
- Department of Chemistry, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Rui-Qin Zhang
- Beijing Computational Science Research Center, Beijing 100084, People’s Republic of China
- Department of Physics, City University of Hong Kong, Hong Kong SAR, People’s Republic of China
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18
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Studies on hydrolysis mechanism of anticancer ruthenium drug ImH[trans-Ru(Im)2Cl4] via ABEEMσπ polarizable force field combined with QM and MD-FEP. Chem Res Chin Univ 2017. [DOI: 10.1007/s40242-017-6401-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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19
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Mendizabal F, Mera-Adasme R, Xu WH, Sundholm D. Electronic and optical properties of metalloporphyrins of zinc on TiO2 cluster in dye-sensitized solar-cells (DSSC). A quantum chemistry study. RSC Adv 2017. [DOI: 10.1039/c7ra08648b] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Dye-sensitized solar-cell (DSSC) systems have been investigated by calculating light-absorption and electron-injection processes of zinc-porphyrin-dye based sensitizers adsorbed on a TiO2 cluster simulating the semiconductor.
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Affiliation(s)
| | - Raúl Mera-Adasme
- Departamento de Ciencias del Ambiente
- Facultad de Química y Biología
- Universidad de Santiago de
- Chile
| | - Wen-Hua Xu
- Department of Chemistry
- University of Helsinki
- FI-00014 Helsinki
- Finland
- College of Chemistry and Materials Science
| | - Dage Sundholm
- Department of Chemistry
- University of Helsinki
- FI-00014 Helsinki
- Finland
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20
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Franco-Pérez M, Ayers PW, Gázquez JL, Vela A. Local chemical potential, local hardness, and dual descriptors in temperature dependent chemical reactivity theory. Phys Chem Chem Phys 2017; 19:13687-13695. [DOI: 10.1039/c7cp00692f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From the definition of a local chemical potential, well-behaved expressions for the local hardness and the dual descriptors are derived.
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Affiliation(s)
- Marco Franco-Pérez
- Department of Chemistry
- McMaster University
- Hamilton
- Canada
- Departamento de Química
| | - Paul W. Ayers
- Department of Chemistry
- McMaster University
- Hamilton
- Canada
| | - José L. Gázquez
- Departamento de Química
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México
- Mexico
| | - Alberto Vela
- Departamento de Química
- Centro de Investigación y de Estudios Avanzados
- Ciudad de México
- Mexico
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21
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Polanco-Ramírez CA, Franco-Pérez M, Carmona-Espíndola J, Gázquez JL, Ayers PW. Revisiting the definition of local hardness and hardness kernel. Phys Chem Chem Phys 2017; 19:12355-12364. [DOI: 10.1039/c7cp00691h] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Local hardness is redefined following similar rules to those of local softness. The new concept describes chemical trends correctly.
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Affiliation(s)
| | - Marco Franco-Pérez
- Departamento de Química
- Universidad Autónoma Metropolitana-Iztapalapa
- México
- Mexico
- Department of Chemistry
| | | | - José L. Gázquez
- Departamento de Química
- Universidad Autónoma Metropolitana-Iztapalapa
- México
- Mexico
| | - Paul W. Ayers
- Department of Chemistry
- McMaster University
- Hamilton
- Canada
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22
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23
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Janesko BG, Wiberg KB, Scalmani G, Frisch MJ. Electron Delocalization Range in Atoms and on Molecular Surfaces. J Chem Theory Comput 2016; 12:3185-94. [DOI: 10.1021/acs.jctc.6b00343] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Giovanni Scalmani
- Gaussian, Inc., 340
Quinnipiac St., Bldg. 40, Wallingford, Connecticut 06492, United States
| | - Michael J. Frisch
- Gaussian, Inc., 340
Quinnipiac St., Bldg. 40, Wallingford, Connecticut 06492, United States
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24
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Fast calculation of molecular total energy with ABEEMσπ/MM method – For some series of organic molecules and peptides. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Inostroza N, Mendizabal F, Arratia-Pérez R, Orellana C, Linares-Flores C. Improvement of photovoltaic performance by substituent effect of donor and acceptor structure of TPA-based dye-sensitized solar cells. J Mol Model 2016; 22:25. [PMID: 26744295 DOI: 10.1007/s00894-015-2893-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 12/18/2015] [Indexed: 11/25/2022]
Abstract
We report a computational study of a series of organic dyes built with triphenylamine (TPA) as an electron donor group. We designed a set of six dyes called (TPA-n, where n = 0-5). In order to enhance the electron-injection process, the electron-donor effect of some specific substituent was studied. Thus, we gave insights into the rational design of organic TPA-based chromophores for use in dye-sensitized solar cells (DSSCs). In addition, we report the HOMO, LUMO, the calculated excited state oxidized potential E(dye*)(eV) and the free energy change for electron-injection ΔGinject(eV), and the UV-visible absorption bands for TPA-n dyes by a time-dependent density functional theory (TDDFT) procedure at the B3LYP and CAM-B3LYP levels with solvent effect. The results demonstrate that the introduction of the electron-acceptor groups produces an intramolecular charge transfer showing a shift of the absorption wavelengths of TPA-n under studies. Graphical Abstract Several organic dyes TPA-n with different donors and acceptors are modeled. A strong conjugation acrros the donor and anchoring groips (TPA-n) bas been studied. Candidate TPA-3 shows a promising results.
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Affiliation(s)
- Natalia Inostroza
- Inorganic Chemistry and Molecular Material center and Theoretical and computational chemistry center, Facultad de Ingeniería, Universidad Autonoma de Chile, El Llano Subercaseaux 2801, San Miguel, Santiago, Chile
| | - Fernando Mendizabal
- Departmento de Química, Facultad de Ciencias, Universidad de Chile, P.O. Box 653, Las Palmeras 3425, Ñuñoa, Santiago, Chile.
- Núcleo Milenio de Ingeniería Molecular para Catálisis y Biosensores, ICM, Santiago, Chile.
| | - Ramiro Arratia-Pérez
- Doctorado en Fisicoquímica Molecular, Relativistic Molecular Physics (ReMoPh) Group, Universidad Andrés Bello, República 275, Santiago, Chile
- Núcleo Milenio de Ingeniería Molecular para Catálisis y Biosensores, ICM, Santiago, Chile
| | - Carlos Orellana
- Departmento de Química, Facultad de Ciencias, Universidad de Chile, P.O. Box 653, Las Palmeras 3425, Ñuñoa, Santiago, Chile
- Departamento de Química, Facultad de Ciencias Básicas, Universidad Metropolitana de Ciencias de la Educación, Casilla 147, Santiago, Chile
| | - Cristian Linares-Flores
- Inorganic Chemistry and Molecular Material center and Theoretical and computational chemistry center, Facultad de Ingeniería, Universidad Autonoma de Chile, El Llano Subercaseaux 2801, San Miguel, Santiago, Chile
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26
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Mendizabal F, Lopéz A, Arratia-Pérez R, Zapata-Torres G. Interaction of LD14 and TiO2 in dye-sensitized solar-cells (DSSC): A density functional theory study. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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27
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28
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De Proft F, Forquet V, Ourri B, Chermette H, Geerlings P, Morell C. Investigation of electron density changes at the onset of a chemical reaction using the state-specific dual descriptor from conceptual density functional theory. Phys Chem Chem Phys 2015; 17:9359-68. [DOI: 10.1039/c4cp05454g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electron density changes from reactants towards the transition state of a chemical reaction is expressed as a linear combination of the state-specific dual descriptors (SSDD) of the corresponding reactant complexes.
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Affiliation(s)
- Frank De Proft
- Research group of General Chemistry
- Vrije Universiteit Brussel (VUB)
- B-1050 Brussels
- Belgium
| | - Valérian Forquet
- Université de Lyon
- Institut des Sciences Analytiques
- UMR 5280
- CNRS
- Université Claude Bernard Lyon 1
| | - Benjamin Ourri
- Université de Lyon
- Institut des Sciences Analytiques
- UMR 5280
- CNRS
- Université Claude Bernard Lyon 1
| | - Henry Chermette
- Université de Lyon
- Institut des Sciences Analytiques
- UMR 5280
- CNRS
- Université Claude Bernard Lyon 1
| | - Paul Geerlings
- Research group of General Chemistry
- Vrije Universiteit Brussel (VUB)
- B-1050 Brussels
- Belgium
| | - Christophe Morell
- Université de Lyon
- Institut des Sciences Analytiques
- UMR 5280
- CNRS
- Université Claude Bernard Lyon 1
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29
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Bitmez Ş, Sayin K, Avar B, Köse M, Kayraldız A, Kurtoğlu M. Preparation, spectral, X-ray powder diffraction and computational studies and genotoxic properties of new azo–azomethine metal chelates. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Bhattacharjee R, Roy RK. On the trends of Fukui potential and hardness potential derivatives in isolated atoms vs. atoms in molecules. Phys Chem Chem Phys 2014; 16:22237-54. [PMID: 25220183 DOI: 10.1039/c4cp03149k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present study, trends of electronic contribution to molecular electrostatic potential [Vel(r¯)(r=0)], Fukui potential [v(+)f|(r=0) and v(-)f|(r=0)] and hardness potential derivatives [Δ(+)h(k) and Δ(-)h(k)] for isolated atoms as well as atoms in molecules are investigated. The generated numerical values of these three reactivity descriptors in these two electronically different situations are critically analyzed through the relevant formalism. Values of Vel(r¯) (when r → 0, i.e., on the nucleus) are higher for atoms in molecules than that of isolated atoms. In contrast, higher values of v(+)|(r=0) and v(-)|(r=0) are observed for isolated atoms compared to the values for atoms in a molecule. However, no such regular trend is observed for the Δ(+)h(k) and Δ(-)h(k) values, which is attributed to the uncertainty in the Fukui function values of atoms in molecules. The sum of Fukui potential and the sum of hardness potential derivatives in molecules are also critically analyzed, which shows the efficacy of orbital relaxation effects in quantifying the values of these parameters. The chemical consequence of the observed trends of these descriptors in interpreting electron delocalization, electronic relaxation and non-negativity of atomic Fukui function indices is also touched upon. Several commonly used molecules containing carbon as well as heteroatoms are chosen to make the investigation more insightful.
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Affiliation(s)
- Rituparna Bhattacharjee
- Department of Chemistry, Birla Institute of Technology and Science, Pilani-333031, Rajasthan, India.
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31
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Resolving the nature of the reactive sites of phenylsulfinate ( PhSO2-) with a single general-purpose reactivity indicator. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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32
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Yang ZZ, Wang JJ, Zhao DX. Valence state parameters of all transition metal atoms in metalloproteins-development of ABEEMσπ fluctuating charge force field. J Comput Chem 2014; 35:1690-706. [DOI: 10.1002/jcc.23676] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/01/2014] [Accepted: 06/18/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| | - Jian-Jiang Wang
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
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33
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Heidar Zadeh F, Fuentealba P, Cárdenas C, Ayers PW. An information-theoretic resolution of the ambiguity in the local hardness. Phys Chem Chem Phys 2014; 16:6019-26. [PMID: 24553911 DOI: 10.1039/c3cp52906a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A definition of the local hardness, suitable for application in the local hard/soft acid/base principle, is derived by applying information theory.
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Affiliation(s)
| | - Patricio Fuentealba
- Departamento de Física
- Facultad de Ciencias
- Universidad de Chile
- 653-Santiago, Chile
- Centro para el desarrollo de la Nanociencias y Nanotecnologia
| | - Carlos Cárdenas
- Departamento de Física
- Facultad de Ciencias
- Universidad de Chile
- 653-Santiago, Chile
- Centro para el desarrollo de la Nanociencias y Nanotecnologia
| | - Paul W. Ayers
- Dept. of Chemistry & Chemical Biology
- McMaster University
- Hamilton, Canada
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34
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Zhang M, Li T. Intermolecular interactions in organic crystals: gaining insight from electronic structure analysis by density functional theory. CrystEngComm 2014. [DOI: 10.1039/c4ce00411f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conceptual density functional theory is exploited to extend the HSAB (hard and soft acids and bases) principle for investigating the locality and regioselectivity of intermolecular interactions in organic crystals.
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Affiliation(s)
- Mingtao Zhang
- Industrial & Physical Pharmacy
- Purdue University
- West Lafayette, USA
| | - Tonglei Li
- Industrial & Physical Pharmacy
- Purdue University
- West Lafayette, USA
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35
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Bhattacharjee R, Roy RK. Relative Contribution of Combined Kinetic and Exchange Energy Terms vs the Electronic Component of Molecular Electrostatic Potential in Hardness Potential Derivatives. J Phys Chem A 2013; 117:11528-39. [DOI: 10.1021/jp406685p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rituparna Bhattacharjee
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
| | - Ram Kinkar Roy
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
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36
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Ayers PW, Cárdenas C. Communication: A case where the hard/soft acid/base principle holds regardless of acid/base strength. J Chem Phys 2013; 138:181106. [DOI: 10.1063/1.4805083] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Affiliation(s)
- Siamak Noorizadeh
- Chemistry Department, College of
Science, Shahid Chamran University, Ahvaz,
61357-43169, Iran
| | - Hadi Parsa
- Chemistry Department, College of
Science, Shahid Chamran University, Ahvaz,
61357-43169, Iran
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38
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Cárdenas C, Ayers PW. How reliable is the hard–soft acid–base principle? An assessment from numerical simulations of electron transfer energies. Phys Chem Chem Phys 2013; 15:13959-68. [DOI: 10.1039/c3cp51134k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Saha S, Bhattacharjee R, Roy RK. Hardness potential derivatives and their relation to Fukui indices. J Comput Chem 2012; 34:662-72. [DOI: 10.1002/jcc.23177] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 09/11/2012] [Accepted: 10/16/2012] [Indexed: 11/10/2022]
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40
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Walther M, Budimir A, Puchta R. Water exchange on beryllium complexes: part VIII – influence of neutral electron pair donors. J COORD CHEM 2012. [DOI: 10.1080/00958972.2012.739284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Markus Walther
- a Department of Chemistry and Pharmacy , University of Erlangen-Nürnberg – Egerlandstraße 1 – 91058 Erlangen , Germany
- b Department of Chemistry and Pharmacy, Computer Chemistry Center , University of Erlangen-Nürnberg , Nägelsbachstr. 25, 91052 Erlangen , Germany
| | - Ana Budimir
- c Faculty of Pharmacy and Biochemistry , University of Zagreb , A. Kovačića 1 – 10000 Zagreb , Croatia
| | - Ralph Puchta
- a Department of Chemistry and Pharmacy , University of Erlangen-Nürnberg – Egerlandstraße 1 – 91058 Erlangen , Germany
- b Department of Chemistry and Pharmacy, Computer Chemistry Center , University of Erlangen-Nürnberg , Nägelsbachstr. 25, 91052 Erlangen , Germany
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41
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42
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Mendizabal F, Donoso D, Burgos D. Theoretical study of the protonation of [Pt3(μ-L)3(L′)3] (L=CO, SO2, CNH; L′=PH3, CNH). Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.08.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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43
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Theoretical study of the local reactivity of electrophiles of the type MPR 3 + (M = Cu, Ag, Au ;R = −H, -Me, -Ph). J Mol Model 2011; 18:2021-9. [DOI: 10.1007/s00894-011-1213-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 08/05/2011] [Indexed: 11/25/2022]
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44
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Muya JT, De Proft F, Geerlings P, Nguyen MT, Ceulemans A. Theoretical Study on the Regioselectivity of the B80 Buckyball in Electrophilic and Nucleophilic Reactions Using DFT-Based Reactivity Indices. J Phys Chem A 2011; 115:9069-80. [DOI: 10.1021/jp2050367] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Jules Tshishimbi Muya
- Department of Chemistry, and Mathematical Modeling and Computational Science Center (LMCC), Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Paul Geerlings
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Minh Tho Nguyen
- Department of Chemistry, and Mathematical Modeling and Computational Science Center (LMCC), Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Arnout Ceulemans
- Department of Chemistry, and Mathematical Modeling and Computational Science Center (LMCC), Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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45
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Mayr H, Breugst M, Ofial AR. Farewell to the HSAB treatment of ambident reactivity. Angew Chem Int Ed Engl 2011; 50:6470-505. [PMID: 21726020 DOI: 10.1002/anie.201007100] [Citation(s) in RCA: 208] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Indexed: 11/11/2022]
Abstract
The concept of hard and soft acids and bases (HSAB) proved to be useful for rationalizing stability constants of metal complexes. Its application to organic reactions, particularly ambident reactivity, has led to exotic blossoms. By attempting to rationalize all the observed regioselectivities by favorable soft-soft and hard-hard as well as unfavorable hard-soft interactions, older treatments of ambident reactivity, which correctly differentiated between thermodynamic and kinetic control as well as between different coordination states of ionic substrates, have been replaced. By ignoring conflicting experimental results and even referring to untraceable experimental data, the HSAB treatment of ambident reactivity has gained undeserved popularity. In this Review we demonstrate that the HSAB as well as the related Klopman-Salem model do not even correctly predict the behavior of the prototypes of ambident nucleophiles and, therefore, are rather misleading instead of useful guides. An alternative treatment of ambident reactivity based on Marcus theory will be presented.
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Affiliation(s)
- Herbert Mayr
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13 (Haus F), 81377 München, Germany.
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46
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Morell C, Ayers PW, Grand A, Chermette H. Application of the electron density force to chemical reactivity. Phys Chem Chem Phys 2011; 13:9601-8. [PMID: 21503299 DOI: 10.1039/c0cp02083d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper the concept of force experienced by the electron density is applied to chemical reactivity. The force is based upon the gradient of a local chemical potential. Closely related concepts such as force field lines and local electron flux are defined to provide insight in chemical reactivity. The time evolution of a molecular site density is also proposed. From the divergence of the force, the nucleophilic and electrophilic behaviour of atomic sites are characterized. Finally, the relations between the force and local conceptual DFT descriptors are also given.
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Affiliation(s)
- Christophe Morell
- CEA Grenoble -INAC/SCIB/LAN (UMR-E n°3 CEA-UJF), CEA-Grenoble, 17, rue des Martyrs, F-38054 Grenoble Cedex 9, France.
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47
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Gál T, Geerlings P, De Proft F, Torrent-Sucarrat M. A new approach to local hardness. Phys Chem Chem Phys 2011; 13:15003-15. [DOI: 10.1039/c1cp21213c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Cuevas-Saavedra R, Rabi N, Ayers PW. The unconstrained local hardness: an intriguing quantity, beset by problems. Phys Chem Chem Phys 2011; 13:19594-600. [DOI: 10.1039/c1cp21646e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Rogelio Cuevas-Saavedra
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada L8S 4M1
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Catak S, D'hooghe M, Verstraelen T, Hemelsoet K, Van Nieuwenhove A, Ha HJ, Waroquier M, De Kimpe N, Van Speybroeck V. Opposite regiospecific ring opening of 2-(cyanomethyl)aziridines by hydrogen bromide and benzyl bromide: experimental study and theoretical rationalization. J Org Chem 2010; 75:4530-41. [PMID: 20507166 DOI: 10.1021/jo100687q] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ring opening of 1-arylmethyl-2-(cyanomethyl)aziridines with HBr afforded 3-(arylmethyl)amino-4-bromobutyronitriles via regiospecific ring opening at the unsubstituted aziridine carbon. Previous experimental and theoretical reports show treatment of the same compounds with benzyl bromide to furnish 4-amino-3-bromobutanenitriles through ring opening at the substituted aziridine carbon. To gain insights into the regioselective preference with HBr, reaction paths have been analyzed with computational methods. The effect of solvation was taken into account by the use of explicit solvent molecules. Geometries were determined at the B3LYP/6-31++G(d,p) level of theory, and a Grimme-type correction term was included for long-range dispersion interactions; relative energies were refined with the meta-hybrid MPW1B95 functional. Activation barriers confirm preference for ring opening at the unsubstituted ring carbon for HBr. HBr versus benzyl bromide ring opening was analyzed through comparison of the electronic structure of corresponding aziridinium intermediates. Although the electrostatic picture fails to explain the opposite regiospecific nature of the reaction, frontier molecular orbital analysis of LUMOs and nucleophilic Fukui functions show a clear preference of attack for the substituted aziridine carbon in the benzyl bromide case and for the unsubstituted aziridine carbon in the HBr case, successfully rationalizing the experimentally observed regioselectivity.
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Affiliation(s)
- Saron Catak
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium
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Roy RK, Saha S. Studies of regioselectivity of large molecular systems using DFT based reactivity descriptors. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/b811052m] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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