1
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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2
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A computational study of TyrGly hydration. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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3
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Alamiddine Z, Selvam B, Graton J, Laurent AD, Landagaray E, Lebreton J, Mathé-Allainmat M, Thany SH, Le Questel JY. Binding of Sulfoxaflor to Aplysia californica-AChBP: Computational Insights from Multiscale Approaches. J Chem Inf Model 2019; 59:3755-3769. [PMID: 31361951 DOI: 10.1021/acs.jcim.9b00272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural features and binding properties of sulfoxaflor (SFX) with Ac-AChBP, the surrogate of the insect nAChR ligand binding domain (LBD), are reported herein using various complementary molecular modeling approaches (QM, molecular docking, molecular dynamics, and QM/QM'). The different SFX stereoisomers show distinct behaviors in terms of binding and interactions with Ac-AChBP. Molecular docking and Molecular Dynamics (MD) simulations highlight the specific intermolecular contacts involved in the binding of the different SFX isomers and the relative contribution of the SFX functional groups. QM/QM' calculations provide further insights and a significant refinement of the geometric and energetic contributions of the various residues leading to a preference for the SS and RR stereoisomers. Notable differences in terms of binding interactions are pointed out for the four stereoisomers. The results point out the induced fit of the Ac-AChBP binding site according to the SFX stereoisomer. In this process, the water molecules-mediated contacts play a key role, their energetic contribution being among the most important for the various stereoisomers. In all cases, the interaction with Trp147 is the major binding component, through CH···π and π···π interactions. This study provides a rationale for the binding of SFX to insect nAChR, in particular with respect to the new class of sulfoximine-based insect nAChR competitive modulators, and points out the requirements of various levels of theory for an accurate description of ligand-receptor interactions.
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Affiliation(s)
- Zakaria Alamiddine
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes , 2 rue de la Houssinière , BP 92208, Nantes F-44322 , France
| | - Balaji Selvam
- University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Roger Adams Laboratory , Urbana , Illinois 61801 , United States
| | - Jérôme Graton
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes , 2 rue de la Houssinière , BP 92208, Nantes F-44322 , France
| | - Adèle D Laurent
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes , 2 rue de la Houssinière , BP 92208, Nantes F-44322 , France
| | - Elodie Landagaray
- Université d'Orléans, Institut de Chimie Organique Analytique, UMR CNRS 7311 , rue de Chartres , BP 6759, Orléans 45067 Cedex 2 , France
| | - Jacques Lebreton
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes , 2 rue de la Houssinière , BP 92208, Nantes F-44322 , France
| | - Monique Mathé-Allainmat
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes , 2 rue de la Houssinière , BP 92208, Nantes F-44322 , France
| | - Steeve H Thany
- Université d'Orléans, Laboratoire Biologie des Ligneux et des Grandes Cultures, USC INRA 1328 . Rue de Chartres , BP 6759, Orléans 45067 Cedex 2 , France
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes , 2 rue de la Houssinière , BP 92208, Nantes F-44322 , France
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4
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Alamiddine Z, Thany S, Graton J, Le Questel JY. Conformations and Binding Properties of Thiametoxam and Clothianidin Neonicotinoid Insecticides to Nicotinic Acetylcholine Receptors: The Contribution of σ-Hole Interactions. Chemphyschem 2018; 19:3069-3083. [DOI: 10.1002/cphc.201800656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Zakaria Alamiddine
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2 rue de la Houssinière BP 92208 Nantes F- 44322 France
| | - Steeve Thany
- Université d'Orléans; Laboratoire Biologie des Ligneux et des Grandes Cultures; UPRES EA 1207-USC INRA 1328; Rue de Chartres BP 6759. 45067 Orléans Cedex 2 France
| | - Jérôme Graton
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2 rue de la Houssinière BP 92208 Nantes F- 44322 France
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2 rue de la Houssinière BP 92208 Nantes F- 44322 France
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5
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BenNasr F, Pérez-Mellor A, Alata I, Lepere V, Jaïdane NE, Zehnacker A. Stereochemistry-dependent hydrogen bonds stabilise stacked conformations in jet-cooled cyclic dipeptides: (LD) vs. (LL) cyclo tyrosine-tyrosine. Faraday Discuss 2018; 212:399-419. [PMID: 30229773 DOI: 10.1039/c8fd00079d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Tyrosine-containing cyclic dipeptides based on a diketopiperazine (DKP) ring are studied under jet-cooled conditions using resonance-enhanced multi-photon ionisation (REMPI), conformer-selective IR-UV double resonance vibrational spectroscopy and quantum chemical calculations. The conformational landscape of the dipeptide containing natural L tyrosine (Tyr), namely c-LTyr-LTyr strongly differs from that of its diastereomer c-LTyr-DTyr. A similar family of conformers exists in both systems, with one aromatic ring folded on the dipeptide DKP ring and the other one extended. Weak NHπ and CHπ interactions are observed, which are slightly different in c-LTyr-LTyr and c-LTyr-DTyr. These structures are identical to those of LL and LD cyclo diphenylalanine, which only differ from c-Tyr-Tyr by the absence of hydroxyl on the benzene rings. While this is the only conformation observed for c-LTyr-DTyr, c-LTyr-LTyr exhibits an additional form stabilised by the interaction of the two hydroxyls, in which the two aromatic rings are in a stacked geometry. Stereochemical effects are still visible in the radical cation, for which one structure is observed for c-LTyr-DTyr, while the spectrum of the c-LTyr-LTyr radical cation is explained in terms of two co-existing structures.
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Affiliation(s)
- Feriel BenNasr
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France. and Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA), Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Ivan Alata
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valeria Lepere
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Nejm-Eddine Jaïdane
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA), Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
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6
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Hameed R, Khan A, van Mourik T. Intramolecular BSSE and dispersion affect the structure of a dipeptide conformer. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1418029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rabia Hameed
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Afsar Khan
- Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Tanja van Mourik
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
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7
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Wałęsa R, Broda MA. The influence of solvent on conformational properties of peptides with Aib residue-a DFT study. J Mol Model 2017; 23:349. [PMID: 29164349 PMCID: PMC5698364 DOI: 10.1007/s00894-017-3508-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/24/2017] [Indexed: 12/30/2022]
Abstract
The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results, the available conformations of similar X-ray structures from the Cambridge Crystallographic Data Center (CCDC) were analyzed. The results of the calculations show that both derivatives with the Aib residue in the gas phase prefer structures stabilized by intramolecular N-H⋯O hydrogen bonds, i.e., C5 and C7 conformations, while polar solvent promotes helical conformation with φ, ψ values equal to +/-60°, +/-40°. In addition, in the case of molecule 2, the helical conformation is the only one available in the polar environment. This result is fully consistent with the X-ray data. Graphical abstract Effect of solvent on the Ramachandran maps of the model peptides with Aib residue.
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Affiliation(s)
- Roksana Wałęsa
- Faculty of Chemistry, University of Opole, 48, Oleska St., 45-052 Opole, Poland
| | - Małgorzata A. Broda
- Faculty of Chemistry, University of Opole, 48, Oleska St., 45-052 Opole, Poland
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8
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Zhou J, Wang YS. Rational redesign of a cation···π···π stacking at cardiovascular Fbw7–Skp1 complex interface and its application for deriving self-inhibitory peptides to disrupt the complex interaction. J Mol Model 2017; 23:296. [DOI: 10.1007/s00894-017-3456-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/05/2017] [Indexed: 12/19/2022]
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9
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Iuzzolino L, Reilly AM, McCabe P, Price SL. Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules. J Chem Theory Comput 2017; 13:5163-5171. [PMID: 28892623 DOI: 10.1021/acs.jctc.7b00623] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.
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Affiliation(s)
- Luca Iuzzolino
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, England
| | - Anthony M Reilly
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Patrick McCabe
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Sarah L Price
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, England
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10
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Baggioli A, Cavallotti CA, Famulari A. Exploring short intramolecular interactions in alkylaromatic substrates. Phys Chem Chem Phys 2016; 18:29616-29628. [PMID: 27753437 DOI: 10.1039/c6cp03323g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From proteins and peptides to semiconducting polymers, aliphatic chains on aromatic groups are recurring motifs in macromolecules from very diverse application fields. Fields in which molecular folding and packing determine the macroscopic physical properties that make such advanced materials appealing in the first place. Within each macromolecule, the intrinsic structure of each unit defines how it interacts with its neighbours, ultimately opening up or denying certain backbone conformations. This eventually also determines how macromolecules interact with each other. This account deals specifically with the conformational problem of many common alkylaromatic units, examining the features of an intramolecular interaction involving a side chain with as few as three methylene groups. A set of 23 model compounds featuring an intramolecular interaction between an aliphatic X-H (X = C, N, O, and S) bond and an aromatic ring was considered. Quantitative computational analysis was made possible, thanks to complete basis set extrapolated CCSD(T) calculations and NCI topological analysis, the latter of which revealed an elaborate network of dispersive and steric interactions leading to somewhat unintuitive and unexpected results, such as the higher energetic stability of certain twisted conformational isomers over those with extended side chains. Vicinal covalent effects from polarizing groups and various heteroatoms, along with the occurrence of non-dispersive phenomena, were also investigated. The conclusions drawn from the investigation include a comprehensive set of guidelines intended to aid in the prediction of the most stable conformation for this class of building blocks. Our findings affect a variety of different research fields, including the tailoring of functional materials for organic electronics and photovoltaics, with insights into a rational treatment of conformational disorder, and the study of protein- and peptide-folding preferences, putting an emphasis on peculiar interactions between the backbone and aromatic residues.
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Affiliation(s)
- Alberto Baggioli
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Carlo A Cavallotti
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Antonino Famulari
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
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11
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Assessing the performance of popular QM methods for calculation of conformational energies of trialanine. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.04.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Bhakhoa H, Rhyman L, Lee EPF, Ramasami P, Dyke JM. Can Cyclen Bind Alkali Metal Azides? A DFT Study as a Precursor to Synthesis. Chemistry 2016; 22:4469-82. [PMID: 26880648 DOI: 10.1002/chem.201504607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 11/10/2022]
Abstract
Can cyclen (1,4,7,10-tetraazacyclododecane) bind alkali metal azides? This question is addressed by studying the geometric and electronic structures of the alkali metal azide-cyclen [M(cyclen)N3] complexes using density functional theory (DFT). The effects of adding a second cyclen ring to form the sandwich alkali metal azide-cyclen [M(cyclen)2N3] complexes are also investigated. N3(-) is found to bind to a M(+) (cyclen) template to give both end-on and side-on structures. In the end-on structures, the terminal nitrogen atom of the azide group (N1) bonds to the metal as well as to a hydrogen atom of the cyclen ring through a hydrogen bond in an end-on configuration to the cyclen ring. In the side-on structures, the N3 unit is bonded (in a side-on configuration to the cyclen ring) to the metal through the terminal nitrogen atom of the azide group (N1), and through the other terminal nitrogen atom (N3) of the azide group by a hydrogen bond to a hydrogen atom of the cyclen ring. For all the alkali metals, the N3-side-on structure is lowest in energy. Addition of a second cyclen unit to [M(cyclen)N3] to form the sandwich compounds [M(cyclen)2N3] causes the bond strength between the metal and the N3 unit to decrease. It is hoped that this computational study will be a precursor to the synthesis and experimental study of these new macrocyclic compounds; structural parameters and infrared spectra were computed, which will assist future experimental work.
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Affiliation(s)
- Hanusha Bhakhoa
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit, 80837, Mauritius
| | - Lydia Rhyman
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit, 80837, Mauritius
| | - Edmond P F Lee
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.,Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit, 80837, Mauritius. .,Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia.
| | - John M Dyke
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
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13
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Palafox MA, Rastogi V. 6-Aminouracil: Geometries and spectra in the isolated state and in the solid state simulation. A comparison with 5-aminouracil. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Nazarski RB, Wałejko P, Witkowski S. Multi-conformer molecules in solutions: an NMR-based DFT/MP2 conformational study of two glucopyranosides of a vitamin E model compound. Org Biomol Chem 2016; 14:3142-58. [DOI: 10.1039/c5ob01865j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Overall geometries of both glucosyl derivatives of PMC were found on the basis of their NMR spectra in CDCl3and relatedδH,C/nJHHIEF-PCM(UFF,CHCl3)/DFT calculational results.
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Affiliation(s)
- Ryszard B. Nazarski
- University of Łódź
- Faculty of Chemistry
- Department of Theoretical and Structural Chemistry
- 90-236 Łódź
- Poland
| | - Piotr Wałejko
- University of Białystok
- Institute of Chemistry
- 15-245 Białystok
- Poland
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15
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Jensen F. An Atomic Counterpoise Method for Estimating Inter- and Intramolecular Basis Set Superposition Errors. J Chem Theory Comput 2015; 6:100-6. [PMID: 26614323 DOI: 10.1021/ct900436f] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An atomic counterpoise method is proposed to calculate estimates of inter- and intramolecular basis set superposition errors. The method estimates the basis set superposition error as a sum of atomic contributions and can be applied for both independent particle and electron correlation models. It is shown that the atomic counterpoise method provides results very similar to the molecular counterpoise method for intermolecular basis set superposition errors at both the HF and MP2 levels of theory with a sequence of increasingly larger basis sets. The advantage of the atomic counterpoise method is that it can be applied with equal ease to estimate intramolecular basis set superposition errors, for which few other methods exist. The atomic counterpoise method is computationally quite efficient, requiring typically double the amount of computer time as required for calculating the uncorrected energy.
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Affiliation(s)
- Frank Jensen
- Department of Chemistry, University of Aarhus Langelandsgade 140, DK-8000 Aarhus, Denmark
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16
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Alamiddine Z, Selvam B, Cerón-Carrasco JP, Mathé-Allainmat M, Lebreton J, Thany SH, Laurent AD, Graton J, Le Questel JY. Molecular recognition of thiaclopride by Aplysia californica AChBP: new insights from a computational investigation. J Comput Aided Mol Des 2015; 29:1151-67. [PMID: 26589615 DOI: 10.1007/s10822-015-9884-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/16/2015] [Indexed: 11/29/2022]
Abstract
The binding of thiaclopride (THI), a neonicotinoid insecticide, with Aplysia californica acetylcholine binding protein (Ac-AChBP), the surrogate of the extracellular domain of insects nicotinic acetylcholine receptors, has been studied with a QM/QM' hybrid methodology using the ONIOM approach (M06-2X/6-311G(d):PM6). The contributions of Ac-AChBP key residues for THI binding are accurately quantified from a structural and energetic point of view. The importance of water mediated hydrogen-bond (H-bond) interactions involving two water molecules and Tyr55 and Ser189 residues in the vicinity of the THI nitrile group, is specially highlighted. A larger stabilization energy is obtained with the THI-Ac-AChBP complex compared to imidacloprid (IMI), the forerunner of neonicotinoid insecticides. Pairwise interaction energy calculations rationalize this result with, in particular, a significantly more important contribution of the pivotal aromatic residues Trp147 and Tyr188 with THI through CH···π/CH···O and π-π stacking interactions, respectively. These trends are confirmed through a complementary non-covalent interaction (NCI) analysis of selected THI-Ac-AChBP amino acid pairs.
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Affiliation(s)
- Zakaria Alamiddine
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France
| | - Balaji Selvam
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France.,Roger Adams Laboratory, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, 61801, USA
| | - José P Cerón-Carrasco
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France.,Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Science Department, Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos, 30107, Murcia, Spain
| | - Monique Mathé-Allainmat
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France
| | - Jacques Lebreton
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France
| | - Steeve H Thany
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d'Orléans, UPRES EA 1207. Rue de Chartres, BP 6759, 45067, Orléans Cedex 2, France
| | - Adèle D Laurent
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France
| | - Jérôme Graton
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France.
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17
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Palafox MA. Structure and conformational analysis of the anti-HIV reverse transcriptase inhibitor AZT using MP2 and DFT methods. Differences with the natural nucleoside thymidine. Simulation of the 1st phosphorylation step with ATP. Phys Chem Chem Phys 2015; 16:24763-83. [PMID: 25317835 DOI: 10.1039/c4cp03695f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A comprehensive quantum-chemical investigation of the conformational landscape of the HIV-1 reverse transcriptase inhibitor AZT (3'-azido-3'-deoxythymidine) nucleoside analogue was carried out. The whole conformational parameters (χ, γ, β, δ, ϕ, P, νmax) were analysed as well as the NBO charges. The search located at least 55 stable structures, 9 of which were by MP2 within a 1 kcal mol(-1) electronic energy range of the global minimum. Most conformers were anti or high-anti around the glycoside bond and with North sugar ring puckering angles. The distribution of all the conformers according to the ranges of stability of the characteristic torsional angles was established. The results obtained were in accordance with those found in related anti-HIV nucleoside analogues. The best conformer in the anti form corresponded to the calculated values by MP2 of χ = -126.9°, β = 176.4° and γ = 49.1°. An analysis of the lowest vibrations in conformer C1 was carried out. The first hydration shell was simulated and the structural differences with the natural nucleoside deoxythymidine (dT) were determined. The first phosphorylation step was simulated by interacting ATP with the best hydrated clusters of AZT and dT. The Na cations act as a bridge between the phosphate moieties of ATP making it easy for -P3O3 to receive the H5' proton from AZT or dT. A proton-transfer mechanism is proposed through the water molecules. When the number of the water molecules surrounding AZT is lower than 8, the first phosphorylation step of AZT can be carried out. However, the appropriate orientation of the O5'-H in dT avoids this limitation and it can be performed with large numbers of water molecules.
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Affiliation(s)
- M Alcolea Palafox
- Chemical Physics Department, Chemistry Faculty, Complutense University, Ciudad Universitaria, Madrid-28040, Spain.
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18
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Abstract
This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.
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19
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Wałęsa R, Man D, Engel G, Siodłak D, Kupka T, Ptak T, Broda MA. The Impact of Model Peptides on Structural and Dynamic Properties of Egg Yolk Lecithin Liposomes - Experimental and DFT Studies. Chem Biodivers 2015; 12:1007-24. [DOI: 10.1002/cbdv.201400179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Indexed: 12/21/2022]
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20
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Uzoh OG, Galek PTA, Price SL. Analysis of the conformational profiles of fenamates shows route towards novel, higher accuracy, force-fields for pharmaceuticals. Phys Chem Chem Phys 2015; 17:7936-48. [DOI: 10.1039/c4cp05525j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformational barriers of the fenamates which lead to conformational polymorphism can be represented by a novel, physically motivated, model intramolecular potential suitable for extension to other pharmaceuticals.
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Affiliation(s)
- Ogaga G. Uzoh
- Department of Chemistry
- University College London
- London
- UK
| | | | - Sarah L. Price
- Department of Chemistry
- University College London
- London
- UK
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21
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Loquais Y, Gloaguen E, Habka S, Vaquero-Vara V, Brenner V, Tardivel B, Mons M. Secondary Structures in Phe-Containing Isolated Dipeptide Chains: Laser Spectroscopy vs Quantum Chemistry. J Phys Chem A 2014; 119:5932-41. [DOI: 10.1021/jp509494c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yohan Loquais
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Sana Habka
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Vanesa Vaquero-Vara
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Benjamin Tardivel
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
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22
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Conformational analysis of a polyconjugated protein-binding ligand by joint quantum chemistry and polarizable molecular mechanics. Addressing the issues of anisotropy, conjugation, polarization, and multipole transferability. J Mol Model 2014; 20:2472. [PMID: 25367040 DOI: 10.1007/s00894-014-2472-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 09/21/2014] [Indexed: 01/13/2023]
Abstract
We investigate the conformational properties of a potent inhibitor of neuropilin-1, a protein involved in cancer processes and macular degeneration. This inhibitor consists of four aromatic/conjugated fragments: a benzimidazole, a methylbenzene, a carboxythiourea, and a benzene-linker dioxane, and these fragments are all linked together by conjugated bonds. The calculations use the SIBFA polarizable molecular mechanics procedure. Prior to docking simulations, it is essential to ensure that variations in the ligand conformational energy upon rotations around its six main-chain torsional bonds are correctly represented (as compared to high-level ab initio quantum chemistry, QC). This is done in two successive calibration stages and one validation stage. In the latter, the minima identified following independent stepwise variations of each of the six main-chain torsion angles are used as starting points for energy minimization of all the torsion angles simultaneously. Single-point QC calculations of the minimized structures are then done to compare their relative energies ΔE conf to the SIBFA ones. We compare three different methods of deriving the multipoles and polarizabilities of the central, most critical moiety of the inhibitor: carboxythiourea (CTU). The representation that gives the best agreement with QC is the one that includes the effects of the mutual polarization energy E pol between the amide and thioamide moieties. This again highlights the critical role of this contribution. The implications and perspectives of these findings are discussed.
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23
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Accuracy of density functionals in the description of dispersion interactions and IR spectra of phosphates and phosphorylated compounds. J Mol Model 2014; 20:2426. [DOI: 10.1007/s00894-014-2426-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
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24
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Katan C, Savel P, Wong BM, Roisnel T, Dorcet V, Fillaut JL, Jacquemin D. Absorption and fluorescence signatures of 1,2,3-triazole based regioisomers: challenging compounds for TD-DFT. Phys Chem Chem Phys 2014; 16:9064-73. [DOI: 10.1039/c4cp00478g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Photophysical signatures of 1,2,3-triazole regioisomers: a surprisingly challenging problem for TD-DFT.
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Affiliation(s)
- Claudine Katan
- CNRS
- Institut des Sciences Chimiques de Rennes
- UMR6226-CNRS-Université de Rennes 1
- 35042 Rennes Cedex, France
| | - Paul Savel
- CNRS
- Institut des Sciences Chimiques de Rennes
- UMR6226-CNRS-Université de Rennes 1
- 35042 Rennes Cedex, France
| | - Bryan M. Wong
- Department of Chemical & Environmental Engineering and Materials Science & Engineering Program
- University of California
- Riverside, USA
| | - Thierry Roisnel
- CNRS
- Institut des Sciences Chimiques de Rennes
- UMR6226-CNRS-Université de Rennes 1
- 35042 Rennes Cedex, France
| | - Vincent Dorcet
- CNRS
- Institut des Sciences Chimiques de Rennes
- UMR6226-CNRS-Université de Rennes 1
- 35042 Rennes Cedex, France
| | - Jean-Luc Fillaut
- CNRS
- Institut des Sciences Chimiques de Rennes
- UMR6226-CNRS-Université de Rennes 1
- 35042 Rennes Cedex, France
| | - Denis Jacquemin
- CEISAM
- UMR CNRS 6230
- BP 92208
- Université de Nantes
- 44322 Nantes Cedex 3, France
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25
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Buczek A, Broda MA. DFT study of N–H···O hydrogen bond between model dehydropeptides and water molecule. Mol Phys 2013. [DOI: 10.1080/00268976.2013.847979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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26
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Jaeqx S, Du W, Meijer EJ, Oomens J, Rijs AM. Conformational Study of Z-Glu-OH and Z-Arg-OH: Dispersion Interactions versus Conventional Hydrogen Bonding. J Phys Chem A 2012; 117:1216-27. [DOI: 10.1021/jp3053339] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Weina Du
- van’t
Hoff Institute
for Molecular Sciences and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Science Park 904, 1098 XH
Amsterdam, The Netherlands
| | - Evert Jan Meijer
- van’t
Hoff Institute
for Molecular Sciences and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Science Park 904, 1098 XH
Amsterdam, The Netherlands
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27
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Galland N, Kone S, Le Questel JY. Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry. J Comput Aided Mol Des 2012; 26:1111-26. [PMID: 22972560 DOI: 10.1007/s10822-012-9602-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 09/05/2012] [Indexed: 11/29/2022]
Abstract
A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strategy allows a full and accurate exploration of the galanthamine potential energy surface of interaction. Significantly different results are obtained according to the distances of approaches between the various molecular fragments and the conformation of the galanthamine N-methyl substituent. The geometry of the most relevant complexes has then been fully optimized through MPWB1K/6-31 + G(d,p) calculations, final energies being recomputed at the LMP2/aug-cc-pVTZ(-f) level of theory. Unexpectedly, galanthamine is found to interact mainly from its hydrogen-bond donor groups. Among those, CH groups in the vicinity of the ammonium group are prominent. The trends obtained provide rationales to the predilection of the equatorial orientation of the galanthamine N-methyl substituent for binding to AChE. The analysis of the interaction energies pointed out the independence between the various interaction sites and the rigid character of galanthamine. The comparison between the cluster calculations and the crystallographic observations in galanthamine-AChE co-crystals allows the validation of the theoretical methodology. In particular, the positions of several water molecules appearing as strongly conserved in galanthamine-AChE co-crystals are predicted by the calculations. Moreover, the experimental position and orientation of lateral chains of functionally important aminoacid residues are in close agreement with the ones predicted theoretically. Our study provides relevant information for a rational drug design of galanthamine based AChE inhibitors.
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Affiliation(s)
- Nicolas Galland
- UMR CNRS 6230, Chimie Et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UFR Sciences & Techniques, Université de Nantes, NANTES Cedex, France
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28
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Hunter RS, van Mourik T. DNA base stacking: The stacked uracil/uracil and thymine/thymine minima. J Comput Chem 2012; 33:2161-72. [DOI: 10.1002/jcc.23052] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 06/01/2012] [Accepted: 06/04/2012] [Indexed: 01/24/2023]
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29
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Minenkov Y, Singstad Å, Occhipinti G, Jensen VR. The accuracy of DFT-optimized geometries of functional transition metal compounds: a validation study of catalysts for olefin metathesis and other reactions in the homogeneous phase. Dalton Trans 2012; 41:5526-41. [DOI: 10.1039/c2dt12232d] [Citation(s) in RCA: 358] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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30
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Cao J, Bjornsson R, Bühl M, Thiel W, van Mourik T. Modelling zwitterions in solution: 3-fluoro-γ-aminobutyric acid (3F-GABA). Chemistry 2011; 18:184-95. [PMID: 22161781 DOI: 10.1002/chem.201101674] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Indexed: 12/18/2022]
Abstract
The conformations and relative stabilities of folded and extended 3-fluoro-γ-aminobutyric acid (3F-GABA) conformers were studied using explicit solvation models. Geometry optimisations in the gas phase with one or two explicit water molecules favour folded and neutral structures containing intramolecular NH···O-C hydrogen bonds. With three or five explicit water molecules zwitterionic minima are obtained, with folded structures being preferred over extended conformers. The stability of folded versus extended zwitterionic conformers increases on going from a PCM continuum solvation model to the microsolvated complexes, though extended structures become less disfavoured with the inclusion of more water molecules. Full explicit solvation was studied with a hybrid quantum-mechanical/molecular-mechanical (QM/MM) scheme and molecular dynamics simulations, including more than 6000 TIP3P water molecules. According to free energies obtained from thermodynamic integration at the PM3/MM level and corrected for B3LYP/MM total energies, the fully extended conformer is more stable than folded ones by about -4.5 kJ mol(-1). B3LYP-computed (3)J(F,H) NMR spin-spin coupling constants, averaged over PM3/MM-MD trajectories, agree best with experiment for this fully extended form, in accordance with the original NMR analysis. The seeming discrepancy between static PCM calculations and experiment noted previously is now resolved. That the inexpensive semiempirical PM3 method performs so well for this archetypical zwitterion is encouraging for further QM/MM studies of biomolecular systems.
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Affiliation(s)
- Jie Cao
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, UK
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31
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New insights on the molecular features and electrophysiological properties of dinotefuran, imidacloprid and acetamiprid neonicotinoid insecticides. Bioorg Med Chem 2011; 19:7623-34. [PMID: 22056840 DOI: 10.1016/j.bmc.2011.10.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 11/23/2022]
Abstract
Structural features and hydrogen-bond interactions of dinotefuran (DIN), imidacoloprid (IMI) and acetamiprid (ACE) have been investigated experimentally through analyses of new crystal structures and observations in structural databases, as well as by Density Functional Theory quantum chemical calculations. Several conformations are observed experimentally in the solid state, highlighting the large flexibility of these compounds. This feature is confirmed by the theoretical calculations in the gas phase, the numerous and different energetic minima of the three neonicotinoids being located within a 10kJ/mol range. Comparisons of the observed and simulated data sheds light on the hydrogen-bond (HB) strength of the functional group at the tip of the electronegative fragment of each pharmacophore (NO(2) for DIN and IMI and CN for ACE). This effect originates in the 'push-pull' nature of these fragments and the related extensive electron delocalization. Molecular electrostatic potential calculations provide a ranking of the two fragments of the three neonicotinoid in terms of HB strength. Thus, the NO(2) group of DIN is the strongest HB acceptor of the electronegative fragment, closely followed by the cyano group of ACE. These two groups are significantly more potent than the NO(2) group of IMI. With respect to the other fragments of the three neonicotinoids, the nitrogen atom of the pyridine of IMI and ACE are stronger HB acceptors than the oxygen atom of the furanyl moiety of DIN. Finally, compared to electrophysiological studies obtained from cockroach synaptic and extrasynaptic receptors, DIN appears more effective than IMI and ACE because it strongly increases dose-dependently the ganglionic depolarisation and the currents amplitudes. These data suggest that DIN, IMI and ACE belong to two subgroups which act differently as agonists of insect nicotinic receptors.
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32
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Ryu S, Lee HW, Han YK. Performance of Density Functionals for the Calculation of Gold Clusters. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.8.2802] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Neves AR, Fernandes PA, Ramos MJ. The Accuracy of Density Functional Theory in the Description of Cation-π and π-Hydrogen Bond Interactions. J Chem Theory Comput 2011; 7:2059-67. [PMID: 26606477 DOI: 10.1021/ct2001667] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cation-π and π-hydrogen bond interactions are ubiquitous in protein folding, molecular recognition, and ligand-receptor associations. As such systems are routinely studied at the DFT level, it becomes essential to understand the underlying accuracy of the plethora of density functionals currently available for the description of these interactions. For that purpose, we carried out theoretical calculations on two small model systems (benzene-Na(+) and benzene-H2O) that represent a paradigm for those intermolecular interactions and systematically tested 46 density functionals against the results of high-level post-HF methods, ranging from MP2 to extrapolated CCSD(T)/CBS. A total of 13 basis sets were also tested to examine the convergence of the interaction energy with basis set size. The convergence was surprisingly fast, with deviations below 0.2 kcal/mol for double-ζ polarized basis sets with diffuse functions. Concerning functional benchmarking, the Truhlar group functionals were particularly well suited for the description of the π-hydrogen bond interactions. In the case of cation-π interactions, there was not a clear correlation between accuracy and functional sophistication. Despite the large number of functionals predicting interaction energies within chemical accuracy (five for π-hydrogen bond and 20 for cation-π interactions), not a single functional has shown chemical accuracy in both cases. Moreover, if we calculate the average error for these two interactions, only two density functionals resulted in an average error below 1.0 kcal/mol (M06 and HCTH, with average errors of 0.6 and 0.8 kcal/mol). The obtained results serve as a guide for future computer simulations on this kind of system.
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Affiliation(s)
- Ana Rute Neves
- REQUIMTE, Faculdade de Ciências do Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | | | - Maria João Ramos
- REQUIMTE, Faculdade de Ciências do Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
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34
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Systematic investigation on the binding of GW420867X as HIV-1 reverse transcriptase inhibitor. MONATSHEFTE FUR CHEMIE 2011. [DOI: 10.1007/s00706-011-0497-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Chakraborty A, Guchhait N, Le Barbu-Debus K, Mahjoub A, Lepère V, Zehnacker-Rentien A. Role of Conformational Isomerism in Solvent-Mediated Charge Transfer in Chiral (S) 1,2,3,4-Tetrahydro-3-isoquinoline Methanol (THIQM): Condensed-Phase to Jet-Cooled Spectroscopic Studies. J Phys Chem A 2011; 115:9354-64. [DOI: 10.1021/jp1095536] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amrita Chakraborty
- Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Kolakta 700 009, India
- CNRS, Institut des Sciences Moléculaires d’Orsay, UMR8214, Orsay, F-91405 and University Paris-Sud, Orsay, F-91405, France
| | - Nikhil Guchhait
- Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Kolakta 700 009, India
| | - Katia Le Barbu-Debus
- CNRS, Institut des Sciences Moléculaires d’Orsay, UMR8214, Orsay, F-91405 and University Paris-Sud, Orsay, F-91405, France
| | - Ahmed Mahjoub
- CNRS, Institut des Sciences Moléculaires d’Orsay, UMR8214, Orsay, F-91405 and University Paris-Sud, Orsay, F-91405, France
| | - Valeria Lepère
- CNRS, Institut des Sciences Moléculaires d’Orsay, UMR8214, Orsay, F-91405 and University Paris-Sud, Orsay, F-91405, France
| | - Anne Zehnacker-Rentien
- CNRS, Institut des Sciences Moléculaires d’Orsay, UMR8214, Orsay, F-91405 and University Paris-Sud, Orsay, F-91405, France
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36
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Riley KE, Hobza P. Noncovalent interactions in biochemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.8] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kevin E. Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic
- Department of Physical Chemistry, Palacky University, Olomouc, Czech Republic
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37
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Revilla-López G, Laurent AD, Perpète EA, Jacquemin D, Torras J, Assfeld X, Alemán C. Key Building Block of Photoresponsive Biomimetic Systems. J Phys Chem B 2011; 115:1232-42. [DOI: 10.1021/jp108341a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal 647, 08028 Barcelona, Spain
| | - Adele D. Laurent
- Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France
| | - Eric A. Perpète
- Unité de Chimie Physique Théorique et Structurale (2742), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Denis Jacquemin
- Unité de Chimie Physique Théorique et Structurale (2742), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Juan Torras
- Departament d’Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - Xavier Assfeld
- Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal 647, 08028 Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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38
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Cocinero EJ, Basterretxea FJ, Écija P, Lesarri A, Fernández JA, Castaño F. Conformational behaviour, hydrogen bond competition and intramolecular dynamics in vanillin derivatives: acetovanillone and 6-hydroxy-3-methoxyacetophenone. Phys Chem Chem Phys 2011; 13:13310-8. [DOI: 10.1039/c0cp02418j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Riley KE, Pitonák M, Jurecka P, Hobza P. Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. Chem Rev 2010; 110:5023-63. [PMID: 20486691 DOI: 10.1021/cr1000173] [Citation(s) in RCA: 562] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kevin E Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
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Gloaguen E, de Courcy B, Piquemal JP, Pilmé J, Parisel O, Pollet R, Biswal HS, Piuzzi F, Tardivel B, Broquier M, Mons M. Gas-phase folding of a two-residue model peptide chain: on the importance of an interplay between experiment and theory. J Am Chem Soc 2010; 132:11860-3. [PMID: 20687601 DOI: 10.1021/ja103996q] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In order to assess the ability of theory to describe properly the dispersive interactions that are ubiquitous in peptide and protein systems, an isolated short peptide chain has been studied using both gas-phase laser spectroscopy and quantum chemistry. The experimentally observed coexistence of an extended form and a folded form in the supersonic expansion was found to result from comparable Gibbs free energies for the two species under the high-temperature conditions (< or = 320 K) resulting from the laser desorption technique used to vaporize the molecules. These data have been compared to results obtained using a series of quantum chemistry methods, including DFT, DFT-D, and post-Hartree-Fock methods, which give rise to a wide range of relative stabilities predicted for these two forms. The experimental observation was best reproduced by an empirically dispersion-corrected functional (B97-D) and a hybrid functional with a significant Hartree-Fock exchange term (M06-2X). In contrast, the popular post-Hartree-Fock method MP2, which is often used for benchmarking these systems, had to be discarded because of a very large basis-set superposition error. The applicability of the atomic counterpoise correction (ACP) is also discussed. This work also introduces the mandatory theoretical examination of experimental abundances. DeltaH(0 K) predictions are clearly not sufficient for discussion of folding, as the conformation inversion temperature is crucial to the conformation determination and requires taking into account thermodynamical corrections (DeltaG) in order to computationally isolate the most stable conformation.
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Affiliation(s)
- E Gloaguen
- CEA, IRAMIS, Service des Photons, Atomes et Molécules, and CNRS, Laboratoire Francis Perrin, URA 2453, 91191 Gif-sur-Yvette, France
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42
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Bretherick NH, van Mourik T. π Interactions Studied with Electronic Structure Methods: The Ethyne Methyl Isocyanide Complex and Thioanisole. J Chem Theory Comput 2010; 6:2687-700. [DOI: 10.1021/ct100295f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Natalie H. Bretherick
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, United Kingdom
| | - Tanja van Mourik
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, United Kingdom
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Taylor CJ, Nix MGD, Dessent CEH. Noncovalent Interactions in the Gas-Phase Conformers of Anionic Iduronate (methyl 2-O-sulfo-α-L-iduronate): Variation of Subconformer versus Ring Conformer Energetics for a Prototypical Anionic Monosaccharide Studied Using Computational Methods. J Phys Chem A 2010; 114:11153-60. [DOI: 10.1021/jp102657t] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
| | - Michael G. D. Nix
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
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Wallevik SÓ, Bjornsson R, Kvaran Á, Jonsdottir S, Girichev GV, Giricheva NI, Hassler K, Arnason I. Conformational properties of 1-fluoro-1-methyl-silacyclohexane and 1-methyl-1-trifluoromethyl-1-silacyclohexane: Gas electron diffraction, low-temperature NMR, temperature-dependent Raman spectroscopy, and quantum chemical calculations. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.02.059] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kang YK, Byun BJ. Assessment of density functionals with long-range and/or empirical dispersion corrections for conformational energy calculations of peptides. J Comput Chem 2010; 31:2915-23. [DOI: 10.1002/jcc.21587] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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46
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Biswal HS, Shirhatti PR, Wategaonkar S. O−H···O versus O−H···S Hydrogen Bonding. 2. Alcohols and Thiols as Hydrogen Bond Acceptors. J Phys Chem A 2010; 114:6944-55. [DOI: 10.1021/jp102346n] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Himansu S. Biswal
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India 400 005
| | - Pranav R. Shirhatti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India 400 005
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India 400 005
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Jacquemin D, Perpète EA, Ciofini I, Adamo C, Valero R, Zhao Y, Truhlar DG. On the Performances of the M06 Family of Density Functionals for Electronic Excitation Energies. J Chem Theory Comput 2010; 6:2071-85. [DOI: 10.1021/ct100119e] [Citation(s) in RCA: 339] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Denis Jacquemin
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Eric A. Perpète
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Ilaria Ciofini
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Carlo Adamo
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Rosendo Valero
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Yan Zhao
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Donald G. Truhlar
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
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Foster ME, Sohlberg K. Empirically corrected DFT and semi-empirical methods for non-bonding interactions. Phys Chem Chem Phys 2010; 12:307-22. [DOI: 10.1039/b912859j] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Toroz D, van Mourik T. Structure of the gas-phase glycine tripeptide. Phys Chem Chem Phys 2010; 12:3463-73. [DOI: 10.1039/b921897a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Cao J, van Mourik T. Performance of the M06-L density functional for a folded Tyr–Gly conformer. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2009.12.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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