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Zhu Y, Alqahtani S, Hu X. An Assessment of Dispersion-Corrected DFT Methods for Modeling Nonbonded Interactions in Protein Kinase Inhibitor Complexes. Molecules 2024; 29:304. [PMID: 38257217 PMCID: PMC11154270 DOI: 10.3390/molecules29020304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Accurate modeling of nonbonded interactions between protein kinases and their small molecule inhibitors is essential for structure-based drug design. Quantum chemical methods such as density functional theory (DFT) hold significant promise for quantifying the strengths of these key protein-ligand interactions. However, the accuracy of DFT methods can vary substantially depending on the choice of exchange-correlation functionals and associated basis sets. In this study, a comprehensive benchmarking of nine widely used DFT methods was carried out to identify an optimal approach for quantitative modeling of nonbonded interactions, balancing both accuracy and computational efficiency. From a database of 2139 kinase-inhibitor crystal structures, a diverse library of 49 nonbonded interaction motifs was extracted, encompassing CH-π, π-π stacking, cation-π, hydrogen bonding, and salt bridge interactions. The strengths of nonbonded interaction energies for all 49 motifs were calculated at the advanced CCSD(T)/CBS level of theory, which serve as references for a systematic benchmarking of BLYP, TPSS, B97, ωB97X, B3LYP, M062X, PW6B95, B2PLYP, and PWPB95 functionals with D3BJ dispersion correction alongside def2-SVP, def2-TZVP, and def2-QZVP basis sets. The RI, RIJK, and RIJCOSX approximations were used for selected functionals. It was found that the B3LYP/def2-TZVP and RIJK RI-B2PLYP/def2-QZVP methods delivered the best combination of accuracy and computational efficiency, making them well-suited for efficient modeling of nonbonded interactions responsible for molecular recognition of protein kinase inhibitors in their targets.
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Affiliation(s)
- Yan Zhu
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA; (Y.Z.); (S.A.)
| | - Saad Alqahtani
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA; (Y.Z.); (S.A.)
- Department of Chemistry, King Saud University, Riyadh 12372, Saudi Arabia
| | - Xiche Hu
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA; (Y.Z.); (S.A.)
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2
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Zhu JY, Liu Q, Jiang XN, Zheng XH, Wang L, Hao Q, Wang CS. From bonds to interactions: comprehensive molecular characterization via polarizable bond-dipole approach. Phys Chem Chem Phys 2023; 25:29867-29880. [PMID: 37888898 DOI: 10.1039/d3cp04060g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Accurately characterizing molecular interactions stands as a pivotal requirement for ensuring the reliability of molecular dynamics simulations. In line with our bond-dipole-based interaction model proposed by Gao et al. [X.-C. Gao, Q. Hao and C.-S. Wang, J. Chem. Theory Comput., 2017, 13, 2730-2741.], we have implemented an efficient and concise approach to compute electrostatic potential. This methodology capitalizes on the polarizable nature of chemical bond dipoles, resulting in a model of remarkable simplicity. In this study, we have revised the polarizable bond-dipole-based force field (PBFF) through the meticulous curation of quantum chemical data sets. These data sets encompass a comprehensive collection of 40 000 conformations, including those of water, methylamine, methanol, and N-methylacetamide. Additionally, we incorporate 520 hydrogen-bonded dimers into our data sets. In pursuit of enhanced accuracy in molecular dynamics simulations and a more faithful representation of potential energy landscapes, we undertook the re-optimization of the nonbonded parameters within the PBFF framework. Concurrently, we intricately fine-tuned the bonded parameters. The results of our comprehensive evaluation denote that this newly optimized force field method adeptly and efficiently computes structural characteristics, harmonic frequencies, and interaction energies. Overall, this study provides further validation for the applicability of PBFF in molecular dynamics simulations.
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Affiliation(s)
- Jia-Yi Zhu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| | - Qi Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| | - Xiao-Nan Jiang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| | - Xiao-Han Zheng
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| | - Lei Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| | - Qiang Hao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| | - Chang-Sheng Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
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3
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Han Y, Wei B, Guo X, Jiao T. Improved hydroxyl radical production by electric-field-induced catalysis in O3/H2O2 process: A Reactive Molecular Dynamics Perspective. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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4
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Zhou J, Jia S, Skitnevskaya AD, Wang E, Hähnel T, Grigoricheva EK, Xue X, Li JX, Kuleff AI, Dorn A, Ren X. Concerted Double Hydrogen-Bond Breaking by Intermolecular Coulombic Decay in the Formic Acid Dimer. J Phys Chem Lett 2022; 13:4272-4279. [PMID: 35522820 DOI: 10.1021/acs.jpclett.2c00957] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Hydrogen bonds are ubiquitous in nature and of fundamental importance to the chemical and physical properties of molecular systems in the condensed phase. Nevertheless, our understanding of the structural and dynamical properties of hydrogen-bonded complexes in particular in electronic excited states remains very incomplete. Here, by using formic acid (FA) dimer as a prototype of DNA base pair, we investigate the ultrafast decay process initiated by removal of an electron from the inner-valence shell of the molecule upon electron-beam irradiation. Through fragment-ion and electron coincident momentum measurements and ab initio calculations, we find that de-excitation of an outer-valence electron at the same site can initiate ultrafast energy transfer to the neighboring molecule, which is in turn ionized through the emission of low-energy electrons. Our study reveals a concerted breaking of double hydrogen-bond in the dimer initiated by the ultrafast molecular rotations of two FA+ cations following this nonlocal decay mechanism.
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Affiliation(s)
- Jiaqi Zhou
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, Heidelberg 69117, Germany
| | - Shaokui Jia
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Anna D Skitnevskaya
- Laboratory of Quantum Chemistry, Irkutsk State University, Irkutsk 664003, Russia
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
| | - Enliang Wang
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, Heidelberg 69117, Germany
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Theresa Hähnel
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
| | - Emma K Grigoricheva
- Laboratory of Quantum Chemistry, Irkutsk State University, Irkutsk 664003, Russia
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
| | - Xiaorui Xue
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jian-Xing Li
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Alexander I Kuleff
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
| | - Alexander Dorn
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, Heidelberg 69117, Germany
| | - Xueguang Ren
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, Heidelberg 69117, Germany
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Dolgonosov AM, Prudkovskii AG, Zaitseva EA, Kolotilina NK, Dolgonosov AA. Mathematical Modelling in Analytical Chromatography: Problems and Solutions. JOURNAL OF ANALYTICAL CHEMISTRY 2021. [DOI: 10.1134/s1061934821110046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Based on an analysis of the results of original research performed in the Laboratory of Sorption Methods of the Vernadsky Institute of Geochemistry and Analytical Chemistry of the Russian Academy of Sciences within the project “Mathematical Chromatograph,” the review covers the aim and strategy of the imitation modeling of high-performance chromatography; associated problems of the theory of intermolecular interactions; classifications of polar stationary phases by their selectivity; descriptions of the kinetics and dynamics of sorption processes, choice of the composition of multicomponent mobile phases in HPLC and ion chromatography using the method of the dynamic map of a chromatographic system; and the development of alternating gradient modes using a mathematical experiment.
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The interplay and the formation of σ-hole in the π···LiX and pseudo-π···LiX (X = F, Cl and CN) lithium bonds involving unsaturated and homocyclic hydrocarbons. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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7
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Dolgonosov AM, Zaitсeva EA. A MODEL OF INTERMOLECULAR INTERACTION ASSOCIATED WITH HYDROGEN BOND FORMATION AND ITS APPLICATION TO THE CHARACTERIZATION OF THE SELECTIVITY OF CHROMATOGRAPHIC PHASES ON THE EXAMPLE OF POLYETHYLENE GLYCOLS. J STRUCT CHEM+ 2020. [DOI: 10.1134/s0022476620080089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Dolgonosov AM. A MODEL OF HYDROGEN BOND FORMATION
BETWEEN THE MOLECULES IN VAPOR AND LIQUID. J STRUCT CHEM+ 2020. [DOI: 10.1134/s0022476620070069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Grinvald II, Kalagaev IY, Petukhov AN, Kapustin RV. IR Manifestation of Non-Covalent Interaction in Organic Liquids. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2020. [DOI: 10.1134/s0036024419130107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Dolgonosov AM. Understanding Hydrogen Bonding in Terms of the Theory of Generalized Charges. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619110015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Almásy L, Bende A. Intermolecular Interaction in Methylene Halide ( CH2F2, CH2Cl2, CH2Br2 and CH2I2) Dimers. Molecules 2019; 24:E1810. [PMID: 31083344 PMCID: PMC6539938 DOI: 10.3390/molecules24091810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 04/27/2019] [Accepted: 05/01/2019] [Indexed: 02/06/2023] Open
Abstract
The intermolecular interaction in difluoromethane, dichloromethane, dibromomethane, and diiodomethane dimers has been investigated using high level quantum chemical methods. The potential energy curve of intermolecular interaction along the C⋯C bond distance obtained using the coupled-cluster theory with singles, doubles, and perturbative triples excitations CCSD(T) were compared with values given by the same method, but applying the local (LCCSD(T)) and the explicitly correlated (CCSD(T)-F12) approximations. The accuracy of other theoretical methods-Hartree-Fock (HF), second order Møller-Plesset perturbation (MP2), and dispersion corrected DFT theory-were also presented. In the case of MP2 level, the canonical and the local-correlation cases combined with the density-fitting technique (DF-LMP2)theories were considered, while for the dispersion-corrected DFT, the empirically-corrected BLYP-D and the M06-2Xexchange-correlation functionals were applied. In all cases, the aug-cc-pVTZ basis set was used, and the results were corrected for the basis set superposition error (BSSE) using the counterpoise method. For each molecular system, several dimer geometries were found, and their mutual orientations were compared with the nearest neighbor orientations obtained in recent neutron scattering studies. The nature of the intermolecular interaction energy was discussed.
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MESH Headings
- Dimerization
- Hydrocarbons, Brominated/analysis
- Hydrocarbons, Brominated/chemistry
- Hydrocarbons, Chlorinated/analysis
- Hydrocarbons, Chlorinated/chemistry
- Hydrocarbons, Fluorinated/analysis
- Hydrocarbons, Fluorinated/chemistry
- Hydrocarbons, Iodinated/analysis
- Hydrocarbons, Iodinated/chemistry
- Inorganic Chemicals/analysis
- Inorganic Chemicals/chemistry
- Models, Chemical
- Models, Molecular
- Quantum Theory
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Affiliation(s)
- László Almásy
- State Key Laboratory of Environment-friendly Energy Materials, Southwest University of Science and Technology, Mianyang 621010, China.
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Konkoly Thege út 29-33, 1121 Budapest, Hungary.
| | - Attila Bende
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Donat Street, No. 67-103, Ro-400293 Cluj-Napoca, Romania.
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12
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Masumian E, Nowroozi A. Comparative study of resonance-inhibited hydrogen bonded (RIHB) systems with different atoms involved: the leading role of σ-planarity. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1557350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Ehsan Masumian
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Alireza Nowroozi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
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13
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Deepa P. Does the stability of the stacking motif surpass the planar motif in 2-amino-4-nitrophenol? - a CCSD(T) analysis. J Mol Model 2018; 25:6. [PMID: 30564979 DOI: 10.1007/s00894-018-3884-4] [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: 07/06/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
Abstract
In this work we analyzed O-H...O, O-H...N, and N-H...O contacts existing in the 2-amino-4-nitrophenol structure engaged in ANP molecules through quantum chemical methods. Furthermore, the above contacts were favored to comprehensively understand the stability of noncovalent interactions, π stacking and hydrogen bonding, surviving in 2-amino-4-nitrophenol. The geometries of π stacking and hydrogen bond interactions between two 2-amino-4-nitrophenols were optimized at BLYP-D3/def2-QZVP with dispersion 3 and MP2/cc-pVTZ levels of theory, and their stability was compared using the CCSD(T) interaction energies. The analyses predicted a particularly strong π stacking interaction of 2-amino-4-nitrophenol with hydrogen bond due to the narrow equivalent configuration of NO2 interactions with the other 2-amino-4-nitrophenols. Furthermore, this work focused on analyzing the stability of the individual hydrogen bonds existing in planar and stacked arrangements. Graphical abstract Stacked and planar motif in 2-amino-4-nitrophenol.
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Affiliation(s)
- Palanisamy Deepa
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, 627012, India.
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14
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Negi I, Kathuria P, Sharma P, Wetmore SD. How do hydrophobic nucleobases differ from natural DNA nucleobases? Comparison of structural features and duplex properties from QM calculations and MD simulations. Phys Chem Chem Phys 2018; 19:16365-16374. [PMID: 28657627 DOI: 10.1039/c7cp02576a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Computational (DFT and MD simulation) methods are employed to systematically characterize the structural and energetic properties of five hydrophobic nucleobases (FEMO, MMO2, NaM, 5SICS and TPT3) that constitute four unnatural base pairs (FEMO:5SICS, MMO2:5SICS, NaM:5SICS and TPT3:NaM). These hydrophobic bases have been recently shown to be replicated when present between natural bases in DNA duplexes, with the highest replication fidelity and efficiency occuring for the TPT3:NaM pair. Our QM calculations suggest that the preferred (anti) glycosidic orientations of nucleosides containing hydrophobic bases are similar to the natural DNA nucleosides despite differences in their chemical structures. However, due to the inability to form interbase hydrogen bonds, hydrophobic base pairs intrinsically prefer nonplanar, distorted geometries, many of which are stabilized through π-π stacking interactions. Furthermore, the intrinsic stacking potential between a hydrophobic and a natural base is similar to that between two natural bases, indicating that the strength of stacking interactions in DNA duplexes containing hydrophobic bases is likely comparable to natural DNA. However, in contrast to the isolated base-pair geometries, our MD simulations suggest that the hydrophobic base pairs adopt variable geometries within DNA, which range from stacked (5SICS:FEMO) to nearly planar (5SICS:NaM and SICS:MMO2) to planar (TPT3:NaM). As a result, the duplex structural features at the site of modification depend on the identity of the hydrophobic base pair, where the TPT3:NaM pair causes the least structural changes compared to natural DNA. Overall, the structural insight obtained from our calculations on DNA containing hydrophobic base pairs explains the experimentally-observed higher fidelity and efficiency during replication of TPT3:NaM compared to other hydrophobic nucleobase pairs. By providing valuable structural information that explains the intrinsic and duplex properties of this class of unnatural nucleobases, the present work may aid the future design of improved hydrophobic analogues.
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Affiliation(s)
- Indu Negi
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India.
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15
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Faginas-Lago N, Yeni D, Huarte F, Wang Y, Alcamí M, Martin F. Adsorption of Hydrogen Molecules on Carbon Nanotubes Using Quantum Chemistry and Molecular Dynamics. J Phys Chem A 2016; 120:6451-8. [PMID: 27467122 DOI: 10.1021/acs.jpca.5b12574] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Physisorption and storage of molecular hydrogen on single-walled carbon nanotube (SWCNT) of various diameters and chiralities are studied by means of classical molecular dynamics (MD) simulations and a force field validated using DFT-D2 and CCSD(T) calculations. A nonrigid carbon nanotube model is implemented with stretching (C-C) and valence angle potentials (C-C-C) formulated as Morse and Harmonic cosine potentials, respectively. Our results evidence that the standard Lennard-Jones potential fails to describe the H2-H2 binding energies. Therefore, our simulations make use of a potential that contains two-body term with parameters obtained from fitting CCSD(T)/CBS binding energies. From our MD simulations, we have analyzed the interaction energies, radial distribution functions, gravimetric densities (% wt), and the distances of the adsorbed H2 layers to the three zigzag type of nanotubes (5,0), (10,0), and (15,0) at 100 and 300 K.
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Affiliation(s)
- N Faginas-Lago
- Dipartimento di di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia , Via Elce di Sotto 8, 06123 Perugia, Italy
| | - D Yeni
- Dipartimento di di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia , Via Elce di Sotto 8, 06123 Perugia, Italy
| | - F Huarte
- Chemical Physics Department and Institute for Theoretical and Computational Chemistry (IQTUB), Universitat de Barcelona , Martí i Franqués 1, 08028 Barcelona, Spain
| | - Y Wang
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia) , Cantoblanco, 28049 Madrid, Spain
| | - M Alcamí
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia) , Cantoblanco, 28049 Madrid, Spain
| | - F Martin
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia) , Cantoblanco, 28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , 28049 Madrid, Spain
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Chandra Sekhar M, Gowri Sankar M, Venkatesulu A. Thermodynamic and theoretical study on hydrogen bonded binary mixtures of isomeric butanols with o-toluidine at T=(303.15 to 318.15) K. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.04.034] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Theoretical in-Solution Conformational/Tautomeric Analyses for Chain Systems with Conjugated Double Bonds Involving Nitrogen(s). Int J Mol Sci 2015; 16:10767-96. [PMID: 25984602 PMCID: PMC4463675 DOI: 10.3390/ijms160510767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/02/2015] [Accepted: 05/05/2015] [Indexed: 11/16/2022] Open
Abstract
Conformational/tautomeric transformations for X=CH–CH=Y structures (X = CH2, O, NH and Y = NH) have been studied in the gas phase, in dichloromethane and in aqueous solutions. The paper is a continuation of a former study where s-cis/s-trans conformational equilibria were predicted for analogues. The s-trans conformation is preferred for the present molecules in the gas phase on the basis of its lowest internal free energy as calculated at the B97D/aug-cc-pvqz and CCSD(T)CBS (coupled-cluster singles and doubles with non-iterative triples extrapolated to the complete basis set) levels. Transition state barriers are of 29–36 kJ/mol for rotations about the central C–C bonds. In solution, an s-trans form is still favored on the basis of its considerably lower internal free energy compared with the s-cis forms as calculated by IEF-PCM (integral-equation formalism of the polarizable continuum dielectric solvent model) at the theoretical levels indicated. A tetrahydrate model in the supermolecule/continuum approach helped explore the 2solute-solvent hydrogen bond pattern. The calculated transition state barrier for rotation about the C–C bond decreased to 27 kJ/mol for the tetrahydrate. Considering explicit solvent models, relative solvation free energies were calculated by means of the free energy perturbation method through Monte Carlo simulations. These calculated values differ remarkably from those by the PCM approach in aqueous solution, nonetheless the same prevalent conformation was predicted by the two methods. Aqueous solution structure-characteristics were determined by Monte Carlo. Equilibration of conformers/tautomers through water-assisted double proton-relay is discussed. This mechanism is not viable, however, in non-protic solvents where the calculated potential of mean force curve does not predict remarkable solute dimerization and subsequent favorable orientation.
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Nagy PI. Competing intramolecular vs. intermolecular hydrogen bonds in solution. Int J Mol Sci 2014; 15:19562-633. [PMID: 25353178 PMCID: PMC4264129 DOI: 10.3390/ijms151119562] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/17/2014] [Accepted: 10/13/2014] [Indexed: 11/17/2022] Open
Abstract
A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed.
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Affiliation(s)
- Peter I Nagy
- Center for Drug Design and Development, the University of Toledo, Toledo, OH 43606-3390, USA.
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19
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Lanza G, Chiacchio MA. Ab Initio MP2 and Density Functional Theory Computational Study of AcAlaNH2Peptide Hydration: A Bottom-Up Approach. Chemphyschem 2014; 15:2785-93. [DOI: 10.1002/cphc.201402222] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Indexed: 01/15/2023]
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20
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Theoretical conformational analysis for chain systems with two conjugated double bonds in the gas phase and in solution. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.01.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Nagy PI. The syn–anti equilibrium for the COOH group reinvestigated. Theoretical conformation analysis for acetic acid in the gas phase and in solution. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.08.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Caffeine as base analogue of adenine or guanine: A theoretical study. J Mol Graph Model 2013; 42:81-91. [DOI: 10.1016/j.jmgm.2013.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 02/27/2013] [Accepted: 02/28/2013] [Indexed: 11/23/2022]
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Nagy PI. Are the intramolecular O-H···F and O-H···Cl hydrogen bonds maintained in solution? A theoretical study. J Phys Chem A 2013; 117:2812-26. [PMID: 23480798 DOI: 10.1021/jp310596c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The present case study aims at calculating the equilibrium conformer compositions for 2X-ethanol and 2X-phenol (X = F, Cl) in solution, and exploring the effect of the applied theoretical method and basis set on the obtained results, as well as considering the usefulness of the continuum solvent approach in comparison with the explicit solvent Monte Carlo model utilizing the free energy perturbation method. Gas-phase optimizations at the DFT/B97D/aug-cc-pvtz and ab initio MP2/aug-cc-pvtz levels predicted structures in good agreement with the available experimental data for three test molecules. Because in-solution geometries change only slightly according to the IEF-PCM continuum solvent calculations in carbon tetrachloride and water, the two theoretical levels were applied further on, and complete basis set (CBS) relative internal free energies were estimated for the conformers under study. The predicted OCCF gauche/trans ratio for 2F-ethanol was well reproduced in comparison with available experimental compositions. The predominant gauche structure maintains an intramolecular hydrogen bond in carbon tetrachloride (HB structure), whereas HB and NoHB gauche conformers appear in nearly the same fraction in aqueous solution. The internally hydrogen-bonded conformer is predominant also for 2X-phenol species, as calculated on the basis of relative CBS internal free energies and IEF-PCM and FEP/MC solvation free energies. Use of a trihydrate supermolecule model for 2F-ethanol conformers leads to the prediction of the aqueous-solution composition in contrast to the experiment. Solution structure modeling predicts weak hydrogen-bond formation capacity for both the covalently bound F and Cl atoms, even in conformations where they are fully exposed to hydration.
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Affiliation(s)
- Peter I Nagy
- Center for Drug Design and Development, The University of Toledo, Toledo, Ohio 43606-3390, USA.
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Oliveira BGD. Structure, energy, vibrational spectrum, and Bader's analysis of π⋯H hydrogen bonds and H−δ⋯H+δdihydrogen bonds. Phys Chem Chem Phys 2013; 15:37-79. [DOI: 10.1039/c2cp41749a] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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25
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WANG CUIHONG, ZHANG RUIQIN, LIN ZIJING. A COMPARATIVE STUDY ON INTERMOLECULAR HYDROGEN BOND INTERACTIONS IN MOLECULAR DIMERS USING DIFFERENT LEVELS OF COMPUTATIONAL METHODS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633612500836] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Hydrogen bond interactions in biological systems are important scientific issues but are challenging for their theoretical determinations at quantum-mechanical level of theory. Due to the different approximations, the available theoretical approaches often predict diverse hydrogen bond lengths and strengths. In this work, we evaluated the reliabilities of a number of widely used theoretical approaches including HF, SVWN, BLYP, PW91, B3LYP, BH and HLYP, B97D, M06L, MP2, and DFTB-D in studying hydrogen bonding, by calculating the hydrogen bond lengths and binding energies of 23 dimers formed by HCOOH , NH3 and Glycine. We also compared the effects of STO-3G, 6-31+G**, 6-311++G** and 6-311++G(2df,2p) basis sets on the results. Our result shows that, M06L, B3LYP and BHandHLYP methods can predict accurate dimer structures with a moderate basis set. Moreover, DFTB-D also gives reasonably reliable results with high efficiency and satisfactory precision, being a good choice for studying complex structures which contain hydrogen bonds.
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Affiliation(s)
- CUIHONG WANG
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
- Department of Physics and Materials Sciences, City University of Hong Kong, Hong Kong S.A.R., China
- USTC-CityU Joint Advanced Research Centre, Suzhou 215123, China
| | - RUIQIN ZHANG
- Department of Physics and Materials Sciences, City University of Hong Kong, Hong Kong S.A.R., China
| | - ZIJING LIN
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
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26
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Can the substituent in the para position of anilide ion influence the N−···H–F → N–H···F− switching: a quantum chemical study. Struct Chem 2012. [DOI: 10.1007/s11224-012-0163-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
The unusual interactions in organic liquids such as methane derivatives, arenes, and alkanes by the infrared (IR) method were revealed. The transformations of molecular shapes, arising from nonclassical hydrogen and dihydrogen bonds, as well as water factor provide the existence of supramolecular structures in organic fluids. The interpretation of the obtained results in terms of the quantum-chemical calculations has been suggested.
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Nagy PI. Theoretical studies of the solvent effect on the conformation of the HO-C-C-X (X = F, NH2, NO2) moiety with competing intra- and intermolecular hydrogen bonds. J Phys Chem A 2012; 116:7726-41. [PMID: 22731938 DOI: 10.1021/jp304164g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Theoretical calculations up to the ab initio IEF-PCM/CCSD(T)/CBS//IEF-PCM/B3LYP/6-311++G** and IEF-PCM/B97D/aug-cc-pvtz levels have been performed for 2X-ethanol and 2X-phenol systems with X = F, NH(2), NO(2) in chloroform and aqueous solution. The calculated relative free energies by means of the IEF-PCM continuum dielectric method do not differ very much at the DFT and ab initio levels. Application of explicit solvent models and the FEP/MC method for determining relative solvation free energies causes, however, large deviations in the predicted equilibrium compositions, although the predominant conformation for the solute is generally in agreement with that from the corresponding IEF-PCM calculations. Existence of an intramolecular hydrogen bond (HB structure) for species with the HO-C-C-X moiety is preferred compared with a conformation when the hydrogen bond is disrupted (NoHB) for the considered F- and NO(2)-substituted molecules both in chloroform and aqueous solution. For 2NH(2)-ethanol, the HB structure is predominant in chloroform, whereas the 93:7 ratio for the OCCN trans/gauche species was obtained in aqueous solution. 2NH(2)-phenol exhibits a subtle equilibrium of the HB and NoHB conformations in both solvents. Potential of mean force calculations predict about a 10% solute association for the trans 2NH(2)-ethanol solute even in the fairly dilute 0.22 molar solution, whereas direct MC simulations do not support the maintenance of a doubly hydrogen-bonded dimer. Aqueous solution characteristics, as coordination numbers and numbers of strongly bound water molecules to the solute at T = 298 K and p = 1 atm, correspond reasonably to the derived molecular structures.
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Affiliation(s)
- Peter I Nagy
- Center for Drug Design and Development, The University of Toledo, Toledo, Ohio 43606-3390, USA.
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Nagy PI, Erhardt PW. On the interaction of aliphatic amines and ammonium ions with carboxylic acids in solution and in receptor pockets. J Phys Chem B 2012; 116:5425-36. [PMID: 22510106 DOI: 10.1021/jp300588q] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Association energies of the acetate ion with cationic amines bearing one to three methyl groups were calculated in the range of -14 to -17 kcal/mol in aqueous solution by means of the IEF-PCM method at the CCSD(T)/CBS//MP2/aug-cc-pvdz and DFT/B97D/CBS//B97D/aug-cc-pvtz levels. The main stabilization factor for the association is the possibility for the formation of an ionic intermolecular hydrogen bond between the elements of the complex. For a quaternary ammonium ion, the favorable electrostatic interaction energy is the only driving force, and the stabilization energy for the complex is reduced to -4 kcal/mol. The internal free energies of the ion-pair tautomers of the studied species are higher by 10-15 kcal/mol in water than those for the neutral, hydrogen-bonded forms. Monte Carlo free energy perturbation calculations at T = 298 K and p = 1 atm predict -11 to -16 kcal/mol relative solvation free energy in favor of the corresponding ionic form. As a result, the ion-pair tautomer is the prevailing form in aqueous solution and on the extracellular surface of a receptor. Modeling the complex of a protonated ligand interacting with an Asp/Glu carboxylate side-chain in the binding cavity of a receptor, two strongly bound water molecules were considered so as to form hydrogen-bonded water bridges between the elements of the ion-pair. Nonetheless, the low polarity environment mimicked by a chloroform solvent cannot stabilize the ionic tautomer. A proton jump was predicted, which suggests that acetylcholine, an inherent cation by structure, might have evolved as the natural agonist for muscarinic receptors because a quaternary ammonium system assures the maintenance of the ion-pair form with a carboxylate side-chain in a protein cavity, the latter perhaps then being needed for receptor activation.
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Affiliation(s)
- Peter I Nagy
- Center for Drug Design and Development, The University of Toledo, Toledo, Ohio 43606, USA.
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30
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Petković M. O–H Stretch in Phenol and Its Hydrogen-Bonded Complexes: Band Position and Relaxation Pathways. J Phys Chem A 2011; 116:364-71. [DOI: 10.1021/jp209897y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12, 11 158 Belgrade, Serbia
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31
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Bates DM, Smith JR, Tschumper GS. Efficient and Accurate Methods for the Geometry Optimization of Water Clusters: Application of Analytic Gradients for the Two-Body:Many-Body QM:QM Fragmentation Method to (H2O)n, n = 3–10. J Chem Theory Comput 2011; 7:2753-60. [DOI: 10.1021/ct200176t] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Desiree M. Bates
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Joshua R. Smith
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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32
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Rivera-Rivera LA, Wang Z, McElmurry BA, Willaert FF, Lucchese RR, Bevan JW, Suenram RD, Lovas FJ. A ground state morphed intermolecular potential for the hydrogen bonded and van der Waals isomers in OC:HI and a prediction of an anomalous deuterium isotope effect. J Chem Phys 2011; 133:184305. [PMID: 21073221 DOI: 10.1063/1.3505145] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An extended analysis of the noncovalent interaction OC:HI is reported using microwave and infrared supersonic jet spectroscopic techniques. All available spectroscopic data then provide the basis for generating an accurately determined vibrationally complete semiempirical intermolecular potential function using a four-dimensional potential coordinate morphing methodology. These results are consistent with the existence of four bound isomers: OC-HI, OC-IH, CO-HI, and CO-IH. Analysis also leads to unequivocal characterization of the common isotopic ground state as having the OC-HI structure and with the first excited state having the OC-IH structure with an energy of 3.4683(80) cm(-1) above the ground state. The potential is consistent with the following barriers between the pairs of isomers: 382(4) cm(-1) (OC-IH/OC-HI), 294(5) cm(-1) (CO-IH/CO-HI), 324(3) cm(-1) (OC-IH/CO-IH), and 301(2) cm(-1) (OC-HI/CO-HI) defined with respect to each lower minimum. The potential is also determined to have a linear OC-IH van der Waals global equilibrium minimum structure having R(e)=4.180(11) Å, θ(1)=0.00(1)°, and θ(2)=0.00(1)°. This is differentiated from its OC-HI ground state hydrogen bound structure having R(0)=4.895(1) Å, θ(1)=20.48(1)°, and θ(2)=155.213(1)° where the distances are defined between the centers of mass of the monomers and θ(1) and θ(2) as cos(-1)[<cos(2) θ(i)>(1/2)] for i=1 and 2. A fundamentally new molecular phenomenon - ground state isotopic isomerization is proposed based on the generated semiempirical potential. The protonated ground state hydrogen-bonded OC-HI structure is predicted to be converted on deuteration to the corresponding ground state van der Waals OC-ID isomeric structure. This results in a large anomalous isotope effect in which the R(0) center of mass distance between monomeric components changes from 4.895(1) to 4.286(1) Å. Such a proposed isotopic effect is demonstrated to be a consequence of differential zero point energy factors resulting from the shallower nature of hydrogen bonding at a local potential minimum (greater quartic character of the potential) relative to the corresponding van der Waals global minimum. Further consequences of this anomalous deuterium isotope effect are also discussed.
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Affiliation(s)
- Luis A Rivera-Rivera
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, USA
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33
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Bende A, Grosu I, Turcu I. Molecular Modeling of Phenothiazine Derivatives: Self-Assembling Properties. J Phys Chem A 2010; 114:12479-89. [DOI: 10.1021/jp105012g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Attila Bende
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Donath Street, Number 65-103, Ro-400293 Cluj-Napoca, Romania and Chair of Organic Chemistry, Faculty of Chemistry and Chemical Engineering, “Babeş-Bolyai” University, Arany Janos Street, Number 11, Ro-400028, Cluj-Napoca, Romania
| | - Ion Grosu
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Donath Street, Number 65-103, Ro-400293 Cluj-Napoca, Romania and Chair of Organic Chemistry, Faculty of Chemistry and Chemical Engineering, “Babeş-Bolyai” University, Arany Janos Street, Number 11, Ro-400028, Cluj-Napoca, Romania
| | - Ioan Turcu
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Donath Street, Number 65-103, Ro-400293 Cluj-Napoca, Romania and Chair of Organic Chemistry, Faculty of Chemistry and Chemical Engineering, “Babeş-Bolyai” University, Arany Janos Street, Number 11, Ro-400028, Cluj-Napoca, Romania
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34
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Vasilescu D, Adrian-Scotto M, Fadiel A, Hamza A. Ab Initio Study of Alkylation of Guanine-Cytosine Base Pair by Sulfur and Nitrogen Mustards. J Biomol Struct Dyn 2010; 27:465-76. [DOI: 10.1080/07391102.2010.10507331] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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35
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Nagy PI, Maheshwari A, Kim YW, Messer WS. Theoretical and experimental studies of the isomeric protonation in solution for a prototype aliphatic ring containing two nitrogens. J Phys Chem B 2010; 114:349-60. [PMID: 19994881 PMCID: PMC2827250 DOI: 10.1021/jp9082085] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Theoretical calculations were carried out for studying the tautomeric protonation of N-methylpiperazine as a prototype six-member aliphatic ring containing a secondary and a tertiary nitrogen atom. The protonation was investigated in three solvents, water, acetonitrile, and dichloromethane. Calculations were performed up to the B3LYP/aug-cc-pvtz and QCISD(T)/CBS levels by applying the IEF-PCM polarizable continuum dielectric solvent model. Relative solvation free energies also were calculated upon explicit solvent models by utilizing the free-energy perturbation theory as implemented in Monte Carlo simulations. The relative free energy for the N-methylpiperazine tautomer protonated at the secondary (NMps) rather than at the tertiary (NMpt) nitrogen was calculated at a ratio of 47/53 in infinitely dilute aqueous solution. The ratio further decreased in lower-polarity solvents. In contrast, NMR experiments suggested that the protonation takes place primarily at the secondary nitrogen in 0.37 molar aqueous solution with NMps/NMpt = 80/20. The NMps tautomer was exclusive in dichloromethane at the same concentration. The discrepancy between theory and experiment was resolved by considering association equilibria in parallel with the protonation for the solute. As a result, the theoretically predicted tautomer ratios were obtained in close agreement with the experimental values. The NMps tautomer could form a preferable dimeric structure, where one or two chloride anion(s) was/were in hydrogen bonds with protons of the associating monomers. The calculations suggest that the proton relocation may take place by solvent assistance in water or along an intramolecular proton jump in the twist-boat conformation. The predicted activation free energy was about 10 kcal/mol on the basis of variable-temperature NMR experiments in DCM.
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Affiliation(s)
- Peter I. Nagy
- Center for Drug Design and Development, The University of Toledo, Toledo, OH, 43606-3390,
- Department of Medicinal and Biological Chemistry, The University of Toledo, OH 43606
| | - Aditya Maheshwari
- Department of Medicinal and Biological Chemistry, The University of Toledo, OH 43606
| | - Yong-Wah Kim
- Department of Chemistry, The University of Toledo, Toledo, OH 43606
| | - William S. Messer
- Department of Medicinal and Biological Chemistry, The University of Toledo, OH 43606
- Department of Pharmacology, The University of Toledo, Toledo, OH, 43606-3390,
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36
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Alagona G, Ghio C, Nagy PI. The catalytic effect of water on the keto–enol tautomerism. Pyruvate and acetylacetone: a computational challenge. Phys Chem Chem Phys 2010; 12:10173-88. [DOI: 10.1039/c003999c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Canchaya JGS, Wang Y, Alcamí M, Martín F, Busnengo HF. Study of the interaction between short alkanethiols from ab initio calculations. Phys Chem Chem Phys 2010; 12:7555-65. [DOI: 10.1039/b923428d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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38
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Rutledge LR, Durst HF, Wetmore SD. Evidence for Stabilization of DNA/RNA−Protein Complexes Arising from Nucleobase−Amino Acid Stacking and T-Shaped Interactions. J Chem Theory Comput 2009; 5:1400-10. [DOI: 10.1021/ct800567q] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Holly F. Durst
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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39
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Tschumper GS. Reliable Electronic Structure Computations for Weak Noncovalent Interactions in Clusters. REVIEWS IN COMPUTATIONAL CHEMISTRY 2009. [DOI: 10.1002/9780470399545.ch2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
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40
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Iwata S. Absolutely local excited orbitals in the higher order perturbation expansion for the molecular interaction. J Phys Chem B 2008; 112:16104-9. [PMID: 19367996 DOI: 10.1021/jp805883c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Based on the locally projected molecular orbitals, the third and fourth order perturbation corrections for the molecular interaction within the single excitations are evaluated, and the calculated interaction energies are compared with the counterpoise (CP) corrected interaction energy of the Hartree-Fock level of theory. It is demonstrated that the third order calculation is a practical and powerful method to obtain the binding energy almost equal to the CP corrected energy. It requires only one more two-electron integral handling after the LP MO calculation, which is faster than a usual supermolecule HF calculation. For the perturbation expansion, the absolutely local excited orbitals are determined. For small basis sets, it is shown that the partial delocalization of the absolutely local excited orbitals is a compromizing technique to take into account the charge-transfer contribution without reintroducing a large basis set superposition error.
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Affiliation(s)
- Suehiro Iwata
- Center of Quantum Life Sciences and Graduate School of Science, Hiroshima University, Higashi-hiroshima 739-8526, Japan.
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41
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Lait LA, Rutledge LR, Millen AL, Wetmore SD. yDNA versus xDNA Pyrimidine Nucleobases: Computational Evidence for Dependence of Duplex Stability on Spacer Location. J Phys Chem B 2008; 112:12526-36. [DOI: 10.1021/jp805547p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Linda A. Lait
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Andrea L. Millen
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
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42
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Rutledge LR, Wetmore SD. Remarkably Strong T-Shaped Interactions between Aromatic Amino Acids and Adenine: Their Increase upon Nucleobase Methylation and a Comparison to Stacking. J Chem Theory Comput 2008; 4:1768-80. [DOI: 10.1021/ct8002332] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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43
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Rutledge LR, Durst HF, Wetmore SD. Computational comparison of the stacking interactions between the aromatic amino acids and the natural or (cationic) methylated nucleobases. Phys Chem Chem Phys 2008; 10:2801-12. [DOI: 10.1039/b718621e] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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44
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Xie J, Ma MT, Abrahams BF, Wedd AG. A Pillared Discrete Bilayer Formed from Guanidinium and Ferrocenedisulfonate Ions: Synthesis, Crystal Structure, and Initial Electrochemical Properties. Inorg Chem 2007; 46:9027-9. [PMID: 17902650 DOI: 10.1021/ic7011974] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solid salt [C(NH2)3]2[Fe(eta5-C5H4SO3)2] forms a two-dimensional network based upon pillared discrete bilayers formed via charge-assisted hydrogen bonds and is electrochemically active when adhered to a glassy carbon electrode.
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Affiliation(s)
- Jingli Xie
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3052, Australia.
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45
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Dreyer J. Unraveling the structure of hydrogen bond stretching mode infrared absorption bands: An anharmonic density functional theory study on 7-azaindole dimers. J Chem Phys 2007; 127:054309. [PMID: 17688342 DOI: 10.1063/1.2759213] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The structure of the linear infrared absorption spectrum of the N-H stretching mode in 7-azaindole dimers is analyzed by quartic anharmonic vibrational force field calculations based on density functional theory. It is demonstrated that a multiple Fermi resonance model including contributions from 12 fingerprint vibrational modes, most of them containing considerable contributions of N-H bending motions, combined with a single low-frequency mode satisfactorily explains the complex line shape of N-H stretching mode absorption band.
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Affiliation(s)
- Jens Dreyer
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2A, D-12489 Berlin, Germany.
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46
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Rutledge LR, Campbell-Verduyn LS, Wetmore SD. Characterization of the stacking interactions between DNA or RNA nucleobases and the aromatic amino acids. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.06.090] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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47
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Rutledge LR, Wheaton CA, Wetmore SD. A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine. Phys Chem Chem Phys 2007; 9:497-509. [PMID: 17216066 DOI: 10.1039/b606388h] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrogen-bonding and stacking interactions of hypoxanthine, a potential universal nucleobase, were calculated using a variety of methodologies (CCSD(T), MP2, B3LYP, PWB6K, AMBER). All methods predict that the hydrogen-bonding interaction in the hypoxanthine-cytosine pair is approximately 25 kJ mol(-1) stronger than that in the other dimers. Although the calculations support suggestions from experiments that hypoxanthine preferentially binds with cytosine, the trend in the calculated hydrogen-bond strengths for the remaining natural nucleobases do not show a strong correlation with the experimentally predicted binding preferences. However, our calculations suggest that the stacking interactions of hypoxanthine are similar in magnitude to the hydrogen-bonding interactions at all levels of theory (with the exception of B3LYP, which incorrectly predicts stacked dimers to be unstable). Therefore, stacking interactions should also be considered when analyzing the stability of DNA helices containing hypoxanthine and the use of larger models that account for both hydrogen-bonding and stacking within DNA duplexes will likely result in better agreement with experimental observations. For the majority of the dimers, PWB6K and AMBER provide reasonable binding strengths at reduced computational costs, and therefore will be useful techniques for considering larger models.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, Canada E4L 1G8
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