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Lu T. A comprehensive electron wavefunction analysis toolbox for chemists, Multiwfn. J Chem Phys 2024; 161:082503. [PMID: 39189657 DOI: 10.1063/5.0216272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024] Open
Abstract
Analysis of electron wavefunction is a key component of quantum chemistry investigations and is indispensable for the practical research of many chemical problems. After more than ten years of active development, the wavefunction analysis program Multiwfn has accumulated very rich functions, and its application scope has covered numerous aspects of theoretical chemical research, including charge distribution, chemical bond, electron localization and delocalization, aromaticity, intramolecular and intermolecular interactions, electronic excitation, and response property. This article systematically introduces the features and functions of the latest version of Multiwfn and provides many representative examples. Through this article, readers will be able to fully understand the characteristics and recognize the unique value of Multiwfn. The source code and precompiled executable files of Multiwfn, as well as the manual containing a detailed introduction to theoretical backgrounds and very rich tutorials, can all be downloaded for free from the Multiwfn website (http://sobereva.com/multiwfn).
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Affiliation(s)
- Tian Lu
- Beijing Kein Research Center for Natural Sciences, Beijing 100024, People's Republic of China
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2
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Deepakvijay K, Prakasam A. Exploring the effects of mono-bromination on hole-electron transport and distribution in dibenzofuran and dibenzothiophene isomers: a first-principles study. J Mol Model 2024; 30:171. [PMID: 38761303 DOI: 10.1007/s00894-024-05966-5] [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: 03/25/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024]
Abstract
CONTEXT This study delves into hole-electron transport and distribution properties inherent in mono-brominated dibenzofuran (DBF) and dibenzothiophene (DBT) isomers. As determined by frontier molecular orbitals, all brominated structures have narrower bandgaps than their primary structures. The TD-DFT calculation showed that 2BDBT had the highest absorption wavelength of all molecules at 315.35 nm. Notably, the study unveils remarkably low electron and hole reorganization energies due to bromine substitution in DBF and DBT molecules. Specifically, the 4BDBF has the lowest hole reorganization energy of all DBF configurations, 0.229 eV. In addition, 3BDBF has 0.226 eV less electron reorganization energy than all other molecules. Compared to DBT, 3BDBT has the lowest electron reorganization energy of 0.254 eV. Overall, this research sheds significant light on the fundamental electronic and hole transport characteristics of bromine-substituted DBF and DBT isomers, highlighting their promising role in polymer design as donors/acceptors for advanced organic electronic applications. METHODS Molecular structures were optimized using Density Functional Theory (DFT) B3LYP/6-311 + + G (d, p) level of theory, and the study further elucidates these molecules' energy levels and absorption spectra through Time-Dependent Density Functional Theory TD-DFT; these calculations were performed using Gaussian 09W software package. The key parameters such as reorganization energies, Electron Localization Function map, Laplacian Bond Order, and NCI-RDG were meticulously examined for the molecules with the results of DFT calculations were analyzed and displayed by utilizing the software packages VMD 1.9.4 and Multiwfn 3.8, aiming to comprehend their charge transport and distribution properties.
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Affiliation(s)
- K Deepakvijay
- Computational & Theoretical Physics Laboratory, PG & Research Department of Physics, Thiruvalluvar Govt. Arts College, Rasipuram, 637408, Tamil Nadu, India.
| | - A Prakasam
- Computational & Theoretical Physics Laboratory, PG & Research Department of Physics, Thiruvalluvar Govt. Arts College, Rasipuram, 637408, Tamil Nadu, India.
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3
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Berger MB, Cisneros GA. Distal Mutations in the β-Clamp of DNA Polymerase III* Disrupt DNA Orientation and Affect Exonuclease Activity. J Am Chem Soc 2023; 145:3478-3490. [PMID: 36745735 PMCID: PMC10237177 DOI: 10.1021/jacs.2c11713] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA polymerases are responsible for the replication and repair of DNA found in all DNA-based organisms. DNA Polymerase III is the main replicative polymerase of E. coli and is composed of over 10 proteins. A subset of these proteins (Pol III*) includes the polymerase (α), exonuclease (ϵ), clamp (β), and accessory protein (θ). Mutations of residues in, or around the active site of the catalytic subunits (α and ϵ), can have a significant impact on catalysis. However, the effects of distal mutations in noncatalytic subunits on the activity of catalytic subunits are less well-characterized. Here, we investigate the effects of two Pol III* variants, β-L82E/L82'E and β-L82D/L82'D, on the proofreading reaction catalyzed by ϵ. MD simulations reveal major changes in the dynamics of Pol III*, which extend throughout the complex. These changes are mostly induced by a shift in the position of the DNA substrate inside the β-clamp, although no major structural changes are observed in the protein complex. Quantum mechanics/molecular mechanics (QM/MM) calculations indicate that the β-L82D/L82'D variant has reduced catalytic proficiency due to highly endoergic reaction energies resulting from structural changes in the active site and differences in the electric field at the active site arising from the protein and substrate. Conversely, the β-L82E/L82'E variant is predicted to maintain proofreading activity, exhibiting a similar reaction barrier for nucleotide excision compared with the WT system. However, significant differences in the reaction mechanism are obtained due to the changes induced by the mutations on the β-clamp.
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Affiliation(s)
- Madison B Berger
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
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4
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Intermolecular hydrogen bonds interactions in water clusters of ammonium sulfamate: FTIR, X-ray diffraction, AIM, DFT, RDG, ELF, NBO analysis. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117475] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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5
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Hix MA, Leddin EM, Cisneros GA. Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations. J Chem Theory Comput 2021; 17:4524-4537. [PMID: 34087064 PMCID: PMC8477969 DOI: 10.1021/acs.jctc.1c00313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Selection of residues and other molecular fragments for inclusion in the quantum mechanics (QM) region for QM/molecular mechanics (MM) simulations is an important step for these calculations. Here, we present an approach that combines protein sequence/structure evolution and electron localization function (ELF) analyses. The combination of these two analyses allows the determination of whether a residue needs to be included in the QM subsystem or can be represented by the MM environment. We have applied this approach on two systems previously investigated by QM/MM simulations, 4-oxalocrotonate tautomerase (4OT) and ten-eleven translocation-2 (TET2), that provide examples where fragments may or may not need to be included in the QM subsystem. Subsequently, we present the use of this approach to determine the appropriate QM subsystem to calculate the minimum energy path (MEP) for the reaction catalyzed by human DNA polymerase λ (Polλ) with a third cation in the active site. Our results suggest that the combination of protein evolutionary and ELF analyses provides insights into residue/molecular fragment selection for QM/MM simulations.
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Affiliation(s)
- Mark A Hix
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Emmett M Leddin
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
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6
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Klein J, Fleurat-Lessard P, Pilmé J. New insights in chemical reactivity from quantum chemical topology. J Comput Chem 2021; 42:840-854. [PMID: 33660292 DOI: 10.1002/jcc.26504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/07/2021] [Accepted: 02/12/2021] [Indexed: 01/13/2023]
Abstract
Based on the quantum chemical topology of the modified electron localization function ELFx , an efficient and robust mechanistic methodology designed to identify the favorable reaction pathway between two reactants is proposed. We first recall and reshape how the supermolecular interaction energy can be evaluated from only three distinct terms, namely the intermolecular coulomb energy, the intermolecular exchange-correlation energy and the intramolecular energies of reactants. Thereafter, we show that the reactivity between the reactants is driven by the first-order variation in the coulomb intermolecular energy defined in terms of the response to changes in the number of electrons. Illustrative examples with the formation of the dative bond B-N involved in the BH3 NH3 molecule and the typical formation of the hydrogen bond in the canonical water dimer are presented. For these selected systems, our approach unveils a noticeable mimicking of Edual onto the DFT intermolecular interaction energy surface calculated between the both reactants. An automated reaction-path algorithm aimed to determine the most favorable relative orientations when the two molecules approach each other is also outlined.
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Affiliation(s)
- Johanna Klein
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, Paris Cedex, France
| | - Paul Fleurat-Lessard
- Université de Bourgogne, UMR CNRS 6302, Université, Bourgogne Franche-Comté (UBFC), Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), 9 avenue Alain Savary, Dijon Cedex, 21078, France
| | - Julien Pilmé
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, Paris Cedex, France
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7
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Mechanistic insights into the reaction Cp2Nb(CO)H (Cp = η5-C5H5) with acetylenedicarboxylic acid (ADCA): DFT studies. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.119990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Vázquez-Montelongo EA, Vázquez-Cervantes JE, Cisneros GA. Polarizable ab initio QM/MM Study of the Reaction Mechanism of N- tert-Butyloxycarbonylation of Aniline in [EMIm][BF₄]. Molecules 2018; 23:E2830. [PMID: 30384470 PMCID: PMC6278528 DOI: 10.3390/molecules23112830] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 12/25/2022] Open
Abstract
N-t e r t-butoxycarbonylation of amines in solution (water, organic solvents, or ionic liquids) is a common reaction for the preparation of drug molecules. To understand the reaction mechanism and the role of the solvent, quantum mechanical/molecular mechanical simulations using a polarizable multipolar force field with long⁻range electrostatic corrections were used to optimize the minimum energy paths (MEPs) associated with various possible reaction mechanisms employing the nudged elastic band (NEB) and the quadratic string method (QSM). The calculated reaction energies and energy barriers were compared with the corresponding gas-phase and dichloromethane results. Complementary Electron Localization Function (ELF)/NCI analyses provide insights on the critical structures along the MEP. The calculated results suggest the most likely path involves a sequential mechanism with the rate⁻limiting step corresponding to the nucleophilic attack of the aniline, followed by proton transfer and the release of CO 2 without the direct involvement of imidazolium cations as catalysts.
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Affiliation(s)
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA.
- The Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, TX 76201, USA.
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Parise A, Alvarez-Ibarra A, Wu X, Zhao X, Pilmé J, Lande ADL. Quantum Chemical Topology of the Electron Localization Function in the Field of Attosecond Electron Dynamics. J Phys Chem Lett 2018; 9:844-850. [PMID: 29384381 DOI: 10.1021/acs.jpclett.7b03379] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report original analyses of attosecond electron dynamics of molecules subject to collisions by high energy charged particles based on Real-Time Time-Dependent-Density-Functional-Theory simulations coupled to Topological Analyses of the Electron Localization Function (TA-TD-ELF). We investigate irradiation of water and guanine. TA-TD-ELF enables qualitative and quantitative characterizations of bond breaking and formation, of charge migration within topological basins, or of electron attachment to the colliding particle. Whereas the Lewis-VSEPR structure of gas phase water is blown out within a few attoseconds after collision, that of guanine is far more robust and reconstitutes rapidly after impact even though the molecule remains electronically excited. This difference is accounted by the presence of the electron bath surrounding the impact point which enables energy relaxation within the molecule. Our approach should stimulate future studies to unravel the early steps following irradiation of various types of systems (isolated molecules, biomolecules, nanoclusters, solids, etc.) and is also readily applicable to irradiation by photons of various energies.
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Affiliation(s)
- Angela Parise
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS , Université Paris Saclay. 15 avenue Jean Perrin, F91405 Orsay, France
| | - Aurelio Alvarez-Ibarra
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS , Université Paris Saclay. 15 avenue Jean Perrin, F91405 Orsay, France
| | - Xiaojing Wu
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS , Université Paris Saclay. 15 avenue Jean Perrin, F91405 Orsay, France
| | - Xiaodong Zhao
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS , Université Paris Saclay. 15 avenue Jean Perrin, F91405 Orsay, France
| | - Julien Pilmé
- Laboratoire de Chimie Théorique, Sorbonne Universités, Université Pierre et Marie Curie, CNRS , F75005 Paris, France
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS , Université Paris Saclay. 15 avenue Jean Perrin, F91405 Orsay, France
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Amaouch M, Sergentu DC, Steinmetz D, Maurice R, Galland N, Pilmé J. The bonding picture in hypervalent XF 3 (X = Cl, Br, I, At) fluorides revisited with quantum chemical topology. J Comput Chem 2017; 38:2753-2762. [PMID: 28776714 DOI: 10.1002/jcc.24905] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 07/12/2017] [Accepted: 07/18/2017] [Indexed: 01/30/2023]
Abstract
Hypervalent XF3 (X = Cl, Br, I, At) fluorides exhibit T-shaped C2V equilibrium structures with the heavier of them, AtF3 , also revealing an almost isoenergetic planar D3h structure. Factors explaining this behavior based on simple "chemical intuition" are currently missing. In this work, we combine non-relativistic (ClF3 ), scalar-relativistic and two-component (X = Br - At) density functional theory calculations, and bonding analyses based on the electron localization function and the quantum theory of atoms in molecules. Typical signatures of charge-shift bonding have been identified at the bent T-shaped structures of ClF3 and BrF3 , while the bonds of the other structures exhibit a dominant ionic character. With the aim of explaining the D3h structure of AtF3 , we extend the multipole expansion analysis to the framework of two-component single-reference calculations. This methodological advance enables us to rationalize the relative stability of the T-shaped C2v and the planar D3h structures: the Coulomb repulsions between the two lone-pairs of the central atom and between each lone-pair and each fluorine ligand are found significantly larger at the D3h structures than at the C2v ones for X = Cl - I, but not with X = At. This comes with the increasing stabilization, along the XF3 series, of the planar D3h structure with respect to the global T-shaped C2v minima. Hence, we show that the careful use of principles that are at the heart of the valence shell electron pair repulsion model provides reasonable justifications for stable planar D3h structures in AX3 E2 systems. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Mohamed Amaouch
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Chimie Théorique CC 137 - 4, place Jussieu, F. 75252, Paris Cedex 05, FranceE-mail:
| | - Dumitru-Claudiu Sergentu
- SUBATECH, UMR CNRS 6457, IN2P3/IMT Atlantique/Université de Nantes, 4 Rue A. Kastler, BP 20722, Nantes Cedex 3, 44307, France.,Laboratoire CEISAM, UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssini'ere, BP 92208, Nantes Cedex 3, 44322, France
| | - David Steinmetz
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Chimie Théorique CC 137 - 4, place Jussieu, F. 75252, Paris Cedex 05, FranceE-mail:
| | - Rémi Maurice
- SUBATECH, UMR CNRS 6457, IN2P3/IMT Atlantique/Université de Nantes, 4 Rue A. Kastler, BP 20722, Nantes Cedex 3, 44307, France
| | - Nicolas Galland
- Laboratoire CEISAM, UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssini'ere, BP 92208, Nantes Cedex 3, 44322, France
| | - Julien Pilmé
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Chimie Théorique CC 137 - 4, place Jussieu, F. 75252, Paris Cedex 05, FranceE-mail:
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11
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Lepetit C, Fau P, Fajerwerg K, Kahn ML, Silvi B. Topological analysis of the metal-metal bond: A tutorial review. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.04.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Zhao L, Liu J, Zhou P. Effect of Methylation on the Photodynamical Behavior of Arylazoimidazoles: New Insight from Theoretical ab Initio Potential Energy Calculations and Molecular Dynamics Simulations. J Phys Chem A 2016; 121:141-150. [DOI: 10.1021/acs.jpca.6b10968] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Li Zhao
- State Key Laboratory
of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jianyong Liu
- State Key Laboratory
of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Panwang Zhou
- State Key Laboratory
of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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13
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Fourré I, Di Meo F, Podloucká P, Otyepka M, Trouillas P. Dimerization of quercetin, Diels-Alder vs. radical-coupling approach: a joint thermodynamics, kinetics, and topological study. J Mol Model 2016; 22:190. [PMID: 27449669 DOI: 10.1007/s00894-016-3051-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 06/22/2016] [Indexed: 12/16/2022]
Abstract
Quercetin is a prototypical antioxidant and prominent member of flavonoids, a large group of natural polyphenols. The oxidation of quercetin may lead to its dimerization, which is a paradigm of the more general polyphenol oligomerization. There exist two opposing mechanisms to describe the dimerization process, namely radical-coupling or Diels-Alder reactions. This work presents a comprehensive rationalization of this dimerization process, acquired from density functional theory (DFT) calculations. It is found that the two-step radical-coupling pathway is thermodynamically and kinetically preferred over the Diels-Alder reaction. This is in agreement with the experimental results showing the formation of only one isomer, whereas the Diels-Alder mechanism would yield two isomers. The evolution in bonding, occurring during these two processes, is investigated using the atoms in molecules (AIM) and electron localization function (ELF) topological approaches. It is shown that some electron density is accumulated between the fragments in the transition state of the radical-coupling reaction, but not in the transition state of the Diels-Alder process. Graphical Abstract Quantum chemistry calculations of the dimerization process of quercetin show that a radical coupling approach is preferred to a Diels-Alder type reaction, in agreement with experimental results. Analysis of the bonding evolution highlights the reaction mechanism.
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Affiliation(s)
- Isabelle Fourré
- Sorbonne Universités, UPMC Univ Paris 6, CNRS, Laboratoire de chimie théorique, 4 place Jussieu, 75005, Paris, France.
| | - Florent Di Meo
- Inserm U850, Univ Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, 87025, Limoges, France.,Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-58183, Linköping, Sweden
| | - Pavlína Podloucká
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Patrick Trouillas
- Inserm U850, Univ Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, 87025, Limoges, France.,Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
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15
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A Complete NCI Perspective: From New Bonds to Reactivity. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2016. [DOI: 10.1007/978-3-319-29022-5_18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Zhao L, Zhou PW, Zhao GJ. Non-adiabatic dynamics simulation exploration of the wavelength-dependent photoinduced relaxation mechanism of trans-N-1-methyl-2-(tolylazo) imidazole in the gas phase. RSC Adv 2016. [DOI: 10.1039/c6ra11416d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A comprehensive picture of the photoinduced non-adiabatic relaxation dynamics of trans-N-1-methyl-2-(tolylazo) imidazole (trans-MTAI) in different electronic excited states has been revealed using the on-the-fly surface hopping method at the ab initio CASSCF level.
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Affiliation(s)
- Li Zhao
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Pan-Wang Zhou
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Guang-Jiu Zhao
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
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17
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Amaouch M, Montavon G, Galland N, Pilmé J. What can tell the quantum chemical topology on carbon–astatine bonds? Mol Phys 2015. [DOI: 10.1080/00268976.2015.1120361] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Mohamed Amaouch
- Sorbonne Universités, UPMC Université Paris 06, Laboratoire de Chimie Théorique, Paris, France
- CNRS UMR 7616, Laboratoire de Chimie Théorique, Paris, France
| | - Gilles Montavon
- SUBATECH, UMR CNRS 6457, IN2P3/EMN Nantes/Université de Nantes, Nantes, France
| | | | - Julien Pilmé
- Sorbonne Universités, UPMC Université Paris 06, Laboratoire de Chimie Théorique, Paris, France
- CNRS UMR 7616, Laboratoire de Chimie Théorique, Paris, France
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18
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Pilmé J, Renault E, Bassal F, Amaouch M, Montavon G, Galland N. QTAIM Analysis in the Context of Quasirelativistic Quantum Calculations. J Chem Theory Comput 2014; 10:4830-41. [PMID: 26584370 DOI: 10.1021/ct500762n] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Computational chemistry currently lacks ad hoc tools for probing the nature of chemical bonds in heavy and superheavy-atom systems where the consideration of spin-orbit coupling (SOC) effects is mandatory. We report an implementation of the Quantum Theory of Atoms-In-Molecules in the framework of two-component relativistic calculations. Used in conjunction with the topological analysis of the Electron Localization Function, we show for astatine (At) species that SOC significantly lowers At electronegativity and boosts its propensity to make charge-shift bonds. Relativistic spin-dependent effects are furthermore able to change some bonds from mainly covalent to charge-shift type. The implication of the disclosed features regarding the rationalization of the labeling protocols used in nuclear medicine for (211)At radioisotope nicely illustrates the potential of the introduced methodology for investigating the chemistry of (super)heavy elements.
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Affiliation(s)
- Julien Pilmé
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Université Paris 06, UMR 7616 , F-75005 Paris, France.,Laboratoire de Chimie Théorique, CNRS UMR 7616 , F-75005 Paris, France
| | - Eric Renault
- CEISAM, UMR CNRS 6230, Université de Nantes , 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Fadel Bassal
- CEISAM, UMR CNRS 6230, Université de Nantes , 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Mohamed Amaouch
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Université Paris 06, UMR 7616 , F-75005 Paris, France.,Laboratoire de Chimie Théorique, CNRS UMR 7616 , F-75005 Paris, France
| | - Gilles Montavon
- SUBATECH, UMR CNRS 6457, IN2P3/EMN Nantes/Université de Nantes , 4 rue A. Kastler, BP 20722, 44307 Nantes Cedex 3, France
| | - Nicolas Galland
- CEISAM, UMR CNRS 6230, Université de Nantes , 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
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Chaudret R, Contreras-Garcia J, Delcey M, Parisel O, Yang W, Piquemal JP. Revisiting H 2O Nucleation around Au + and Hg 2+: The Peculiar "Pseudo-Soft" Character of the Gold Cation. J Chem Theory Comput 2014; 10:1900-1909. [PMID: 24860276 PMCID: PMC4025583 DOI: 10.1021/ct4006135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Indexed: 01/01/2023]
Abstract
In this contribution, we propose a deeper understanding of the electronic effects affecting the nucleation of water around the Au+ and Hg2+ metal cations using quantum chemistry. To do so, and in order to go beyond usual energetical studies, we make extensive use of state of the art quantum interpretative techniques combining ELF/NCI/QTAIM/EDA computations to capture all ranges of interactions stabilizing the well characterized microhydrated structures. The Electron Localization Function (ELF) topological analysis reveals the peculiar role of the Au+ outer-shell core electrons (subvalence) that appear already spatially preorganized once the addition of the first water molecule occurs. Thus, despite the addition of other water molecules, the electronic structure of Au(H2O)+ appears frozen due to relativistic effects leading to a maximal acceptation of only two waters in gold's first hydration shell. As the values of the QTAIM (Quantum Theory of Atoms in Molecules) cations's charge is discussed, the Non Covalent Interactions (NCI) analysis showed that Au+ appears still able to interact through longer range van der Waals interaction with the third or fourth hydration shell water molecules. As these types of interaction are not characteristic of either a hard or soft metal cation, we introduced the concept of a "pseudo-soft" cation to define Au+ behavior. Then, extending the study, we performed the same computations replacing Au+ with Hg2+, an isoelectronic cation. If Hg2+ behaves like Au+ for small water clusters, a topological, geometrical, and energetical transition appears when the number of water molecules increases. Regarding the HSAB theory, this transition is characteristic of a shift of Hg2+ from a pseudosoft form to a soft ion and appears to be due to a competition between the relativistic and correlation effects. Indeed, if relativistic effects are predominant, then mercury will behave like gold and have a similar subvalence/geometry; otherwise when correlation effects are predominant, Hg2+ behaves like a soft cation.
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Affiliation(s)
- Robin Chaudret
- Sorbonne
Universités, UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS,
UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Julia Contreras-Garcia
- Sorbonne
Universités, UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS,
UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Mickaël Delcey
- Sorbonne
Universités, UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS,
UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- Department
of Chemistry − Uppsala University, Ångström Laboratory, Theoretical Chemistry, Ångströmlaboratoriet
Lägerhyddsvägen 1751 20 Uppsala, Sweden
| | - Olivier Parisel
- Sorbonne
Universités, UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS,
UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Weitao Yang
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jean-Philip Piquemal
- Sorbonne
Universités, UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS,
UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
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20
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Castro B, Chaudret R, Ricci G, Kurz M, Ochsenbein P, Kretzschmar G, Kraft V, Rossen K, Eisenstein O. Nonclassical CH−π Supramolecular Interactions in Artemisinic Acid Favor a Single Conformation, Yielding High Diastereoselectivity in the Reduction with Diazene. J Org Chem 2014; 79:5939-47. [DOI: 10.1021/jo500233z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Bertrand Castro
- Institut Charles
Gerhardt, CNRS 5253, Université Montpellier 2, cc 1501,
place E. Bataillon, F-34095 Montpellier, France
| | - Robin Chaudret
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison Cedex, France
| | - Gino Ricci
- Sanofi Chimie, 45 chemin
de Meteline 04200 Sisteron, France
| | - Michael Kurz
- Sanofi-Aventis Deutschland GmbH, Chemistry & Biotechnology Department, Industriepark Höchst, D-65926 Frankfurt am Main, Germany
| | - Philippe Ochsenbein
- Sanofi-Aventis R & D, 371 rue du Professeur Joseph Blayac, 34184 Montpellier Cedex 04, France
| | - Gerhard Kretzschmar
- Sanofi-Aventis Deutschland GmbH, Chemistry & Biotechnology Department, Industriepark Höchst, D-65926 Frankfurt am Main, Germany
| | - Volker Kraft
- Sanofi-Aventis Deutschland GmbH, Chemistry & Biotechnology Department, Industriepark Höchst, D-65926 Frankfurt am Main, Germany
| | - Kai Rossen
- Sanofi-Aventis Deutschland GmbH, Chemistry & Biotechnology Department, Industriepark Höchst, D-65926 Frankfurt am Main, Germany
| | - Odile Eisenstein
- Institut Charles
Gerhardt, CNRS 5253, Université Montpellier 2, cc 1501,
place E. Bataillon, F-34095 Montpellier, France
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21
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Fourré I, Alvarez E, Chaquin P. Organohelium compounds: structures, stabilities and chemical bonding analyses. Chemphyschem 2014; 15:467-77. [PMID: 24488791 DOI: 10.1002/cphc.201300932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Indexed: 11/11/2022]
Abstract
This paper deals with the possibility of forming short and relatively strong carbon-helium bonds in small typical organic molecules through substitution of one or several H atoms by He(+). A structural and energetics study (based on high-level calculations) of this unusual bonding, as well as a topological characterization of the resulting cations, is undertaken. Stable species generally requires substitution of about half of the hydrogen atoms for formation. Under these conditions, the number of such species appears to be potentially unlimited. "True" C-He bonds exhibit equilibrium distances ranging from 1.327 (C2H2He2(2+)) to 1.129 Å (He2CO(2+)). The energies of neutral He releasing range from approximately 5 kcal mol(-1) [He2CO(2+), (Z)-C2H2He2(2+)] to 25 kcal mol(-1) (C2HHe3(3+)), but remain most frequently around 10 kcal mol(-1). However, most of He(+)-substituted hydrocarbons are metastable with respect to C-C cleavage, except derivatives of ethene. Atoms in molecules (AIM) and electron localization function (ELF) topological descriptors classify the C-He bond as a weak charge-shift interaction [S. Shaik, D. Danovich, B. Silvi, D. L. Lauvergnat, P. C. Hiberty, Chem. Eur. J. 2005, 11, 6358-6371] in agreement with a recent publication by Rzepa [S. H. Rzepa, Nat. Chem. 2010, 2, 390-393]. He2CO(2+) is the only investigated compound that presents a C-He bonding ELF basin, which indicates a non-negligible covalent contribution to the bond. Other modifications in the electronic structure, such as the breaking of the triple bond in ethyne derivatives or the loss of aromaticity in C6H3He3(3+), are also nicely revealed by the ELF topology.
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Affiliation(s)
- Isabelle Fourré
- UPMC Sorbonne Universités, UMR 7616, Laboratoire de Chimie Théorique, 4 place Jussieu, 75005 Paris (France); CNRS, UMR 7616, Laboratoire de Chimie Théorique, 4 place Jussieu, 75005 Paris (France).
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22
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Kozlowski D, Pilmé J, Fleurat-Lessard P. Using the unusual weak N…CO bond as a solvation probe. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.842995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- David Kozlowski
- Laboratoire de Chimie, UMR CNRS 5182, École Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon Cedex 7, France
| | - Julien Pilmé
- Laboratoire de Chimie Théorique, UPMC Univ Paris 06 and CNRS, UMR 7616, F-75005, Paris, France
| | - Paul Fleurat-Lessard
- Laboratoire de Chimie, UMR CNRS 5182, École Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon Cedex 7, France
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23
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Chaudret R, Parks JM, Yang W. Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs. J Chem Phys 2013; 138:045102. [PMID: 23387624 DOI: 10.1063/1.4772182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In biological systems involving nucleosides, nucleotides, or their respective analogs, the ribose sugar moiety is the most common reaction site, for example, during DNA replication and repair. However, nucleic bases, which comprise a sizable portion of nucleotide molecules, are usually unreactive during such processes. In quantum mechanical∕molecular simulations of nucleic acid reactivity, it may therefore be advantageous to describe specific ribosyl or ribosyl phosphate groups quantum mechanically and their respective nucleic bases with a molecular mechanics potential function. Here, we have extended the pseudobond approach to enable quantum mechanical∕molecular mechanical simulations involving nucleotides, nucleosides, and their analogs in which the interface between the two subsystems is located between the sugar and the base, namely, the C(sp(3))-N(sp(2)) bond. The pseudobond parameters were optimized on a training set of 10 molecules representing several nucleotide and nucleoside bases and analogs, and they were then tested on a larger test set of 20 diverse molecules. Particular emphasis was placed on providing accurate geometries and electrostatic properties, including electrostatic potential, natural bond orbital (NBO) and atoms in molecules (AIM) charges and AIM first moments. We also tested the optimized parameters on five nucleotide and nucleoside analogues of pharmaceutical relevance and a small polypeptide (triglycine). Accuracy was maintained for these systems, which highlights the generality and transferability of the pseudobond approach.
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Affiliation(s)
- Robin Chaudret
- Department of Chemistry, Duke University, 124 Science Drive, 5301 French Science Center, Durham, North Carolina 27708-0346, USA
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24
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Fang D, Lord RL, Cisneros GA. Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB. J Phys Chem B 2013; 117:6410-20. [PMID: 23642148 DOI: 10.1021/jp403116e] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
AlkB is a bacterial enzyme that catalyzes the dealkylation of alkylated DNA bases. The rate-limiting step is known to be the abstraction of an H atom from the alkyl group on the damaged base by a Fe(IV)-oxo species in the active site. We have used hybrid ab initio quantum mechanical/molecular mechanical methods to study this step in AlkB. Instead of forming an Fe(III)-oxyl radical from Fe(IV)-oxo near the C-H activation transition state, the reactant is found to be an Fe(III)-oxyl with an intermediate-spin Fe (S = 3/2) ferromagnetically coupled to the oxyl radical, which we explore in detail using molecular orbital and quantum topological analyses. The minimum energy pathway remains on the quintet surface, but there is a transition between (IS)Fe(III)-oxyl and the state with a high-spin Fe (S = 5/2) antiferromagnetically coupled to the oxyl radical. These findings provide clarity for the evolution of the well-known π and σ channels on the quintet surface in the enzyme environment. Additionally, an energy decomposition analysis reveals nine catalytically important residues for the C-H activation step, some of which are conserved in two human homologues. These conserved residues are proposed as targets for experimental mutagenesis studies.
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Affiliation(s)
- Dong Fang
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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25
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Fang D, Chaudret R, Piquemal JP, Cisneros GA. Toward a Deeper Understanding of Enzyme Reactions Using the Coupled ELF/NCI Analysis: Application to DNA Repair Enzymes. J Chem Theory Comput 2013; 9:2156-60. [PMID: 26583709 DOI: 10.1021/ct400130b] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The combined Electron Localization Funtion (ELF)/ Noncovalent Interaction (NCI) topological analysis (Gillet et al. J. Chem. Theory Comput.2012, 8, 3993) has been extended to enzymatic reaction paths. We applied ELF/NCI to the reactions of DNA polymerase λ and the ε subunit of DNA polymerase III. ELF/NCI is shown to provide insights on the interactions during the evolution of enzymatic reactions including predicting the location of TS from structures located earlier along the reaction coordinate, differential metal coordination, and on barrier differences with two different cations.
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Affiliation(s)
- Dong Fang
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, Michigan 48202, United States
| | - Robin Chaudret
- UPMC Univ Paris 06, UMR 7616 Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005, Paris, France.,CNRS, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005, Paris, France
| | - Jean-Philip Piquemal
- UPMC Univ Paris 06, UMR 7616 Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005, Paris, France.,CNRS, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005, Paris, France
| | - G Andrés Cisneros
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, Michigan 48202, United States
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26
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Bergès J, Fourré I, Pilmé J, Kozelka J. Quantum Chemical Topology Study of the Water-Platinum(II) Interaction. Inorg Chem 2013; 52:1217-27. [DOI: 10.1021/ic301512c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jacqueline Bergès
- Laboratoire de Chimie Théorique,
UMR 7616 CNRS, Université Pierre et Marie Curie, Sorbonne Universités, Case Courier 137, 4 place Jussieu,
75252 Paris Cedex 05, France
- Université Paris Descartes, 75270
Paris, France
| | - Isabelle Fourré
- Laboratoire de Chimie Théorique,
UMR 7616 CNRS, Université Pierre et Marie Curie, Sorbonne Universités, Case Courier 137, 4 place Jussieu,
75252 Paris Cedex 05, France
| | - Julien Pilmé
- Laboratoire de Chimie Théorique,
UMR 7616 CNRS, Université Pierre et Marie Curie, Sorbonne Universités, Case Courier 137, 4 place Jussieu,
75252 Paris Cedex 05, France
| | - Jiri Kozelka
- Laboratoire
de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR-CNRS 8601, 75270
Paris, France
- Institute
of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, 61137
Brno, Czech Republic
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27
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Gillet N, Chaudret R, Contreras-Garcίa J, Yang W, Silvi B, Piquemal JP. Coupling quantum interpretative techniques: another look at chemical mechanisms in organic reactions. J Chem Theory Comput 2012; 8:3993-3997. [PMID: 23185140 PMCID: PMC3505119 DOI: 10.1021/ct300234g] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A cross ELF-NCI analysis is tested over prototypical organic reactions. The synergetic use of ELF and NCI enables the understanding of reaction mechanisms since each method can respectively identify regions of strong and weak electron pairing. Chemically intuitive results are recovered and enriched by the identification of new features. Non covalent interactions are found to foresee the evolution of the reaction from the initial steps. Within NCI, no topological catastrophe is observed as changes are continuous to such an extent that future reaction steps can be predicted from the evolution of the initial NCI critical points. Indeed, strong convergences through the reaction paths between ELF and NCI critical points enable to identify key interactions at the origin of the bond formation. VMD scripts enabling the automatic generation of movies depicting the cross NCI/ELF analysis along a reaction path (or following a Born-Oppenheimer molecular dynamics trajectory) are provided as S.I.
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Affiliation(s)
- Natacha Gillet
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Robin Chaudret
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Julia Contreras-Garcίa
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Bernard Silvi
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Jean-Philip Piquemal
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
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28
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Varadwaj A, Varadwaj PR. Can a Single Molecule of Water be Completely Isolated Within the Subnano-Space Inside the Fullerene C60Cage? A Quantum Chemical Prospective. Chemistry 2012; 18:15345-60. [DOI: 10.1002/chem.201200969] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Indexed: 11/11/2022]
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29
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Pilmé J, Renault E, Ayed T, Montavon G, Galland N. Introducing the ELF Topological Analysis in the Field of Quasirelativistic Quantum Calculations. J Chem Theory Comput 2012; 8:2985-90. [PMID: 26605711 DOI: 10.1021/ct300558k] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an original formulation of the electron localization function (ELF) in the field of relativistic two-component DFT calculations. Using I2 and At2 species as a test set, we show that the ELF analysis is suitable to evaluate the spin-orbit effects on the electronic structure. Beyond these examples, this approach opens up new opportunities for the bonding analysis of large molecular systems involving heavy and superheavy elements.
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Affiliation(s)
- Julien Pilmé
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Université Pierre et Marie Curie, Sorbonne Universités, Case Courier 137, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - Eric Renault
- CEISAM, UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Tahra Ayed
- CEISAM, UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Gilles Montavon
- SUBATECH, UMR CNRS 6457, IN2P3/EMN Nantes/Université de Nantes, 4 rue A. Kastler, BP 20722, 44307 Nantes Cedex 3, France
| | - Nicolas Galland
- CEISAM, UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
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30
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Polarisable multipolar electrostatics from the machine learning method Kriging: an application to alanine. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1137-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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31
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Toulouze M, Pilmé J, Pauzat F, Ellinger Y. Arsenic in prebiotic species: a theoretical approach. Phys Chem Chem Phys 2012; 14:10515-22. [DOI: 10.1039/c2cp41042g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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James WH, Buchanan EG, Müller CW, Dean JC, Kosenkov D, Slipchenko LV, Guo L, Reidenbach AG, Gellman SH, Zwier TS. Evolution of amide stacking in larger γ-peptides: triamide H-bonded cycles. J Phys Chem A 2011; 115:13783-98. [PMID: 21978283 DOI: 10.1021/jp205527e] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The single-conformation spectroscopy of two model γ-peptides has been studied under jet-cooled conditions in the gas phase. The methyl-capped triamides, Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and Ac-γ(2)-hAla-γ(2)-hPhe-NHMe, were probed by resonant two-photon ionization (R2PI) and resonant ion-dip infrared (RIDIR) spectroscopies. Four conformers of Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and three of Ac-γ(2)-hAla-γ(2)-hPhe-NHMe were observed and spectroscopically interrogated. On the basis of comparison with the predictions of density functional theory calculations employing a dispersion-corrected functional (ωB97X-D/6-311++G(d,p)), all seven conformers have been assigned to particular conformational families. The preference for formation of nine-membered rings (C9) observed in a previous study [James, W. H., III et al., J. Am. Chem. Soc. 2009, 131, 14243] of the smaller analog, Ac-γ(2)-hPhe-NHMe, carries over to these triamides, with four of the seven conformers forming C9/C9 sequential double-ring structures, and one conformer a C9/C14 bifurcated double ring. The remaining two conformers form C7/C7/C14 H-bonded cycles involving all three amide NH groups, unprecedented in other peptides and peptidomimetics. The amide groups in these structures form a H-bonded triangle with the two trimethylene bridges forming loops above and below the molecule's midsection. The structure is a natural extension of amide stacking, with the two terminal amides blocked from forming the amide tristack by formation of the C14 H-bond. Pair interaction energy decomposition analysis based on the fragment molecular orbital method (FMO-PIEDA) is used to determine the nonbonded contributions to the stabilization of these conformers. Natural bond orbital (NBO) analysis identifies amide stacking with a pair of n → π* interactions between the nitrogen lone pairs and π* orbitals on the carbonyl of the opposing amide groups.
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Affiliation(s)
- William H James
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
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33
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Kozlowski D, Pilmé J. New insights in quantum chemical topology studies using numerical grid-based analyses. J Comput Chem 2011; 32:3207-17. [PMID: 21953556 DOI: 10.1002/jcc.21903] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 07/05/2011] [Accepted: 07/05/2011] [Indexed: 11/07/2022]
Abstract
New insights in Quantum Chemical Topology of one-electron density functions have been proposed here by using a recent grid-based algorithm (Tang et al., J Phys Condens Matter 2009, 21, 084204), initially designed for the decomposition of the electron density. Beyond the charge analysis, we show that this algorithm is suitable for different scalar functions showing a more complex topology, that is, the Laplacian of the electron density, the electron localization function (ELF), and the molecular electrostatic potential (MEP). This algorithm makes use of a robust methodology enabling to numerically assign the data points of three-dimensional grids to basin volumes, and it has the advantage of requiring only the values of the scalar function without details on the wave function used to build the grid. Our implementation is briefly outlined (program named TopChem), its capabilities are examined, and technical aspects in terms of CPU requirement and accuracy of the results are discussed. Illustrative examples for individual molecules and crystalline solids obtained with gaussian and plane-wave-based density functional theory calculations are presented. Special attention was given to the MEP because its topological analysis is complex and scarce.
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Affiliation(s)
- David Kozlowski
- Laboratoire de Chimie, UMR CNRS 5182, Ecole Normale Supérieure de Lyon, Lyon, France
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34
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van Severen MC, Piquemal JP, Parisel O. Enforcing hemidirectionality in Pb(II) complexes: The importance of anionic ligands. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.04.096] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Chaudret R, Piquemal JP, Cisneros GA. Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations. Phys Chem Chem Phys 2011; 13:11239-47. [PMID: 21566841 DOI: 10.1039/c0cp02550j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA polymerases require two divalent metal ions in the active site for catalysis. Mg(2+) has been confirmed to be the most probable cation utilized by most polymerases in vivo. Other metal ions are either potent mutagens or inhibitors. We used structural and topological analyses based on ab initio QM/MM calculations to study human DNA polymerase λ (Polλ) with different metals in the active site. Our results indicate a slightly longer O3'-Pα distance (∼3.6 Å) for most inhibitor cations compared to the natural and mutagenic metals (∼3.3-3.4 Å). Optimization with a larger basis set for the previously reported transition state (TS) structures (Cisneros et al., DNA Repair, 2008, 7, 1824.) gives barriers of 17.4 kcal mol(-1) and 15.1 kcal mol(-1) for the Mg(2+) and Mn(2+) catalyzed reactions respectively. Relying on the key relation between the topological signature of a metal cation and its selectivity within biological systems (de Courcy et al., J. Chem. Theor. Comput., 2010, 6, 1048.) we have performed electron localization function (ELF) topological analyses. These analyses show that all inhibitor and mutagenic metals considered, except Na(+), present a "split" of the outer-shell density of the metal. This "splitting" is not observed for the non-mutagenic Mg(2+) metal. Population and multipole analyses on the ELF basins reveal that the electronic dipolar and quadrupolar polarization is significantly different with Mg(2+) compared to all other cations. Our results shed light at the atomic level on the subtle differences between Mg(2+), mutagenic, and inhibitor metals in DNA polymerases. These results provide a correlation between the electronic distribution of the cations in the active site and the possible consequences on DNA synthesis.
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Affiliation(s)
- Robin Chaudret
- UPMC Université Paris 06, UMR 7616 Laboratoire de Chimie Théorique, Paris, France
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Chaudret R, Cisneros GA, Parisel O, Piquemal JP. Unraveling low-barrier hydrogen bonds in complex systems with a simple quantum topological criterion. Chemistry 2011; 17:2833-7. [PMID: 21308813 DOI: 10.1002/chem.201002978] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Indexed: 11/12/2022]
Affiliation(s)
- Robin Chaudret
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique case courrier 137, 4 place Jussieu, 75005, Paris, France
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Devereux M, van Severen MC, Parisel O, Piquemal JP, Gresh N. Role of Cation Polarization in holo- and hemi-Directed [Pb(H2O)n]2+ Complexes and Development of a Pb2+ Polarizable Force Field. J Chem Theory Comput 2010; 7:138-47. [DOI: 10.1021/ct1004005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mike Devereux
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Marie-Céline van Severen
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Olivier Parisel
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
| | - Nohad Gresh
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex06, France; UPMC, Université Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France; and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005 Paris, France
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de la Lande A, Maddaluno J, Parisel O, Darden TA, Piquemal JP. Study of the docking of competitive inhibitors at a model of tyrosinase active site: insights from joint broken-symmetry/Spin-Flip DFT computations and ELF topological analysis. Interdiscip Sci 2010; 2:3-11. [PMID: 20396590 DOI: 10.1007/s12539-010-0096-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Following our previous study (Piquemal et al., New J. Chem., 2003, 27, 909), we present here a DFT study of the inhibition of the Tyrosinase enzyme. Broken-symmetry DFT computations are supplemented with Spin-Flip TD-DFT calculations, which, for the first time, are applied to such a dicopper enzyme. The chosen biomimetic model encompasses a dioxygen molecule, two Cu(II) cations, and six imidazole rings. The docking energy of a natural substrate, namely phenolate, together with those of several inhibitor and non-inhibitor compounds, are reported and show the ability of the model to rank the most potent inhibitors in agreement with experimental data. With respect to broken-symmetry calculations, the Spin-Flip TD-DFT approach reinforces the possibility for theory to point out potent inhibitors: the need for the deprotonation of the substrates, natural or inhibitors, is now clearly established. Moreover, Electron Localization Function (ELF) topological analysis computations are used to deeply track the particular electronic distribution of the Cu-O-Cu three-center bonds involved in the enzymatic Cu(2)O(2) metallic core (Piquemal and Pilmé, J. Mol. Struct.: Theochem, 2006, 77, 764). It is shown that such bonds exhibit very resilient out-of-plane density expansions that play a key role in docking interactions: their 3D-orientation could be the topological electronic signature of oxygen activation within such systems.
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Affiliation(s)
- A de la Lande
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, Paris, France
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Pauzat F, Pilmé J, Toulouse J, Ellinger Y. About the collapse of the 3.3 μm CH stretching band with ionization in polycyclic aromatic hydrocarbons: Configuration interaction and quantum Monte Carlo studies of the CH fragment. J Chem Phys 2010; 133:054301. [DOI: 10.1063/1.3465552] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Wu JC, Piquemal JP, Chaudret R, Reinhardt P, Ren P. Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field. J Chem Theory Comput 2010; 6:2059-2070. [PMID: 21116445 DOI: 10.1021/ct100091j] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The hydration free energy, structure, and dynamics of the zinc divalent cation are studied using a polarizable force field in molecular dynamics simulations. Parameters for the Zn(2+) are derived from gas-phase ab initio calculation of Zn(2+)-water dimer. The Thole-based dipole polarization is adjusted based on the Constrained Space Orbital Variations (CSOV) calculation while the Symmetry Adapted Perturbation Theory (SAPT) approach is also discussed. The vdW parameters of Zn(2+) have been obtained by comparing the AMOEBA Zn(2+)-water dimerization energy with results from several theory levels and basis sets over a range of distances. Molecular dynamics simulations of Zn(2+) solvation in bulk water are subsequently performed with the polarizable force field. The calculated first-shell water coordination number, water residence time and free energy of hydration are consistent with experimental and previous theoretical values. The study is supplemented with extensive Reduced Variational Space (RVS) and Electron Localization Function (ELF) computations in order to unravel the nature of the bonding in Zn(2+)(H(2)O)(n) (n=1,6) complexes and to analyze the charge transfer contribution to the complexes. Results show that the importance of charge transfer decreases as the size of Zn-water cluster grows due to anticooperativity and to changes in the nature of the metal-ligand bonds. Induction could be dominated by polarization when the system approaches condensed-phase and the covelant effects are eliminated from the Zn(II)-water interaction. To construct an "effective" classical polarizable potential for Zn(2+) in bulk water, one should therefore avoid over-fitting to the ab initio charge transfer energy of Zn(2+)-water dimer. Indeed, in order to avoid overestimation of condensed-phase many-body effects, which is crucial to the transferability of polarizable molecular dynamics, charge transfer should not be included within the classical polarization contribution and should preferably be either incorporated in to the pairwise van der Waals contribution or treated explicitly.
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Affiliation(s)
- Johnny C Wu
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712-1062, USA
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Gillespie R, Robinson E, Pilmé J. Ligand Close Packing, Molecular Compactness, the Methyl Tilt, Molecular Conformations, and a New Model for the Anomeric Effect. Chemistry 2010; 16:3663-75. [DOI: 10.1002/chem.200902599] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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de Courcy B, Pedersen LG, Parisel O, Gresh N, Silvi B, Pilmé J, Piquemal JP. Understanding selectivity of hard and soft metal cations within biological systems using the subvalence concept. I. Application to blood coagulation: direct cation-protein electronic effects vs. indirect interactions through water networks. J Chem Theory Comput 2010; 6:1048-1063. [PMID: 20419068 PMCID: PMC2856951 DOI: 10.1021/ct100089s] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Following a previous study by de Courcy et al. ((2009) Interdiscip. Sci. Comput. Life Sci. 1, 55-60), we demonstrate in this contribution, using quantum chemistry, that metal cations exhibit a specific topological signature in the electron localization of their density interacting with ligands according to its "soft" or "hard" character. Introducing the concept of metal cation subvalence, we show that a metal cation can split its outer-shell density (the so-called subvalent domains or basins) according to it capability to form a partly covalent bond involving charge transfer. Such behaviour is investigated by means of several quantum chemical interpretative methods encompasing the topological analysis of the Electron Localization Function (ELF) and Bader's Quantum Theory of Atoms in Molecules (QTAIM) and two energy decomposition analyses (EDA), namely the Restricted Variational Space (RVS) and Constrained Space Orbital Variations (CSOV) approaches. Further rationalization is performed by computing ELF and QTAIM local properties such as electrostatic distributed moments and local chemical descriptors such as condensed Fukui Functions and dual descriptors. These reactivity indexes are computed within the ELF topological analysis in addition to QTAIM offering access to non atomic reactivity local index, for example on lone pairs. We apply this "subvalence" concept to study the cation selectivity in enzymes involved in blood coagulation (GLA domains of three coagulation factors). We show that the calcium ions are clearly able to form partially covalent charge transfer networks between the subdomain of the metal ion and the carboxylate oxygen lone pairs whereas magnesium does not have such ability. Our analysis also explains the different role of two groups (high affinity and low affinity cation binding sites) present in GLA domains. If the presence of Ca(II) is mandatory in the central "high affinity" region to conserve a proper folding and a charge transfer network, external sites are better stabilised by Mg(II), rather than Ca(II), in agreement with experiment. The central role of discrete water molecules is also discussed in order to understand the stabilities of the observed X-rays structures of the Gla domain. Indeed, the presence of explicit water molecules generating indirect cation-protein interactions through water networks is shown to be able to reverse the observed electronic selectivity occuring when cations directly interact with the Gla domain without the need of water.
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Affiliation(s)
- B. de Courcy
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - L. G. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709 (USA)
| | - O. Parisel
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - N. Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45, rue des Saints-Pères, 75006 Paris
| | - B. Silvi
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - J. Pilmé
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- Université de Lyon, Université Lyon 1, Faculté de pharmacie, F-69373Lyon, Cedex 08, France
| | - J.-P. Piquemal
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
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Severen MCV, Piquemal JP, Parisel O. Beyond holo/hemidirectionality in Pb(II) complexes: Can the valence lone pair be bisdirected? Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.07.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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De Courcy B, Gresh N, Piquemal JP. Importance of lone pair interactions/redistribution in hard and soft ligands within the active site of alcohol dehydrogenase Zn-metalloenzyme: Insights from electron localization function. Interdiscip Sci 2009; 1:55-60. [DOI: 10.1007/s12539-008-0027-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 11/18/2008] [Accepted: 12/03/2008] [Indexed: 11/29/2022]
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Regioselective N-alkylation of imidazo[4,5-b]pyridine-4-oxide derivatives: an experimental and DFT study. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Cisneros G, Darden T, Gresh N, Pilmé J, Reinhardt P, Parisel O, Piquemal JP. Design Of Next Generation Force Fields From AB Initio Computations: Beyond Point Charges Electrostatics. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2009. [DOI: 10.1007/978-1-4020-9956-4_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Darley MG, Handley CM, Popelier PLA. Beyond Point Charges: Dynamic Polarization from Neural Net Predicted Multipole Moments. J Chem Theory Comput 2008; 4:1435-48. [DOI: 10.1021/ct800166r] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Michael G. Darley
- Manchester Interdisciplinary Biocentre (MIB), 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Chris M. Handley
- Manchester Interdisciplinary Biocentre (MIB), 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Paul L. A. Popelier
- Manchester Interdisciplinary Biocentre (MIB), 131 Princess Street, Manchester M1 7DN, United Kingdom
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