1
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Ikeda T, Boero M. Role of van der Waals corrections in first principles simulations of alkali metal ions in aqueous solutions. J Chem Phys 2015; 143:194510. [DOI: 10.1063/1.4935932] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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2
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Karilainen T, Cramariuc O, Kuisma M, Tappura K, Hukka TI. van der Waals interactions are critical in Car-Parrinello molecular dynamics simulations of porphyrin-fullerene dyads. J Comput Chem 2015; 36:612-21. [DOI: 10.1002/jcc.23834] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/28/2014] [Accepted: 12/12/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Topi Karilainen
- Department of Physics; Tampere University of Technology; Tampere Finland
| | - Oana Cramariuc
- Department of Physics; Tampere University of Technology; Tampere Finland
| | - Mikael Kuisma
- Department of Physics; Tampere University of Technology; Tampere Finland
| | - Kirsi Tappura
- VTT Technical Research Centre of Finland; P.O. Box 1300 FI-33101 Tampere Finland
| | - Terttu I. Hukka
- Department of Chemistry and Bioengineering; Tampere University of Technology; P.O. Box 541 33101 Tampere Finland
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3
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Wang C, Jiang Y, Zhang R, Lin Z. Intermolecular π/π and H/π interactions in dimers researched by different computational methods. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The analysis of π/π and H /π interactions in complexes are a challenging aspect of theoretical research. Due to the different approximations of different levels of theory, results tend to be inconsistent. We compared the reliabilities of HF, SVWN, M06L, PW91, BLYP, B3LYP, BHandHLYP, B97D, MP2, and DFTB-D approaches in researching π/π and H /π interactions by calculating the binding energies of five benzene-containing dimers. The effects of 6-31+G**, 6-311++G** and 6-311++G(2df,2p) basis sets on the results were analyzed too. We found that the DFTB-D and B97D methods combined with the 6-311++G** basis set perform well for dimers that contain π/π and H /π interactions. With high efficiency and satisfactory precision, DFTB-D is helpful for the calculation of complexes containing π/π and H /π stacking. We further calculated the structures and properties of phenylalanine-containing dimers using the DFTB-D and B97D methods. The properties of low energy conformers such as rotational constants, dipole moments and molecular orbitals were also analyzed. These data should be helpful for research into systems that contain π/π and H /π stacking.
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Affiliation(s)
- Cuihong Wang
- School of Science, TianJin ChengJian University, Tianjin 300384, P. R. China
| | - Yue Jiang
- School of Science, TianJin ChengJian University, Tianjin 300384, P. R. China
| | - Ruiqin Zhang
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong, P. R. China
| | - Zijing Lin
- Department of Physics & Collaborative Innovation Center of Suzhou Nano Science and Technology, University of Science and Technology of China, Hefei 230026, P. R. China
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4
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Carter DJ, Rohl AL. van der Waals corrected density functional calculations of the adsorption of benzene on the Cu (111) surface. J Comput Chem 2014. [DOI: 10.1002/jcc.23745] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Damien J. Carter
- Department of Chemistry and Nanochemistry Research Institute; Curtin University; GPO Box U1987, Perth, Western Australia 6845 Australia
| | - Andrew L. Rohl
- Department of Chemistry and Nanochemistry Research Institute; Curtin University; GPO Box U1987, Perth, Western Australia 6845 Australia
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5
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Hatz R, Hänninen V, Halonen L. Dispersion Interactions in Small Zinc, Cadmium, and Mercury Clusters. J Phys Chem A 2014; 118:5734-40. [DOI: 10.1021/jp505023g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Richard Hatz
- Laboratory
of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55
(A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
| | - Vesa Hänninen
- Laboratory
of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55
(A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
| | - Lauri Halonen
- Laboratory
of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55
(A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
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6
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Carter DJ, Rohl AL. Benchmarking Calculated Lattice Parameters and Energies of Molecular Crystals Using van der Waals Density Functionals. J Chem Theory Comput 2014; 10:3423-37. [DOI: 10.1021/ct500335b] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Damien J. Carter
- Nanochemistry
Research Institute
and Department of Chemistry, Curtin University, GPO Box U1987, Perth, Western
Australia 6845, Australia
| | - Andrew L. Rohl
- Nanochemistry
Research Institute
and Department of Chemistry, Curtin University, GPO Box U1987, Perth, Western
Australia 6845, Australia
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7
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Downing CA, Sokol AA, Catlow CRA. The reactivity of CO2on the MgO(100) surface. Phys Chem Chem Phys 2014; 16:184-95. [DOI: 10.1039/c3cp53458h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Bankura A, Carnevale V, Klein ML. Hydration structure of salt solutions from ab initio molecular dynamics. J Chem Phys 2013; 138:014501. [PMID: 23298049 DOI: 10.1063/1.4772761] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.
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Affiliation(s)
- Arindam Bankura
- Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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9
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Jones A, Cipcigan F, Sokhan VP, Crain J, Martyna GJ. Electronically coarse-grained model for water. PHYSICAL REVIEW LETTERS 2013; 110:227801. [PMID: 23767748 DOI: 10.1103/physrevlett.110.227801] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Indexed: 06/02/2023]
Abstract
We introduce an electronically coarse-grained description of water representing all long range, many-body electronic responses via an embedded quantum oscillator. Leading-order response coefficients and gas phase electrostatic moments are exactly reproduced. Molecular dynamics, using electronic path integral sampling, shows that this framework is sufficient for a realistic liquid to emerge naturally with transferability extending further to nonambient state points and to the free water surface. The model allows the strength of many-body dispersion and polarization to be adjusted independently and these are found to have significant effects on the condensed phase.
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Affiliation(s)
- A Jones
- School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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10
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Reilly AM, Wann DA, Gutmann MJ, Jura M, Morrison CA, Rankin DWH. Predicting anisotropic displacement parameters using molecular dynamics: density functional theory plus dispersion modelling of thermal motion in benzophenone. J Appl Crystallogr 2013. [DOI: 10.1107/s0021889813006225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The benefits of combining experimental and computational methods have been demonstrated by a study of the dynamics and solid-state structure of α-benzophenone. Dispersion-corrected and -uncorrected density functional theory molecular dynamics simulations were used to obtain displacement parameters, with the dispersion-corrected simulations showing good agreement with the experimental neutron and X-ray diffraction values. At 70 K, quantum-nuclear effects resulted in poor values for the hydrogen atoms, but the heavy-atom values still show excellent agreement, suggesting that molecular dynamics simulations can be a useful tool for determining displacement parameters where experimental data are poor or limited.
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11
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Doemer M, Tavernelli I, Rothlisberger U. Intricacies of Describing Weak Interactions Involving Halogen Atoms within Density Functional Theory. J Chem Theory Comput 2012; 9:955-64. [PMID: 26588739 DOI: 10.1021/ct3007524] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work we assess the performance of different dispersion-corrected density functional theory (DFT) approaches (M06, M06-2X, DFT-D3, and DCACP) in reproducing high-level wave function based benchmark calculations on the weakly bound halogen dimers X2···X2 and X2···Ar (for X = F, Cl, Br, and I), as well as the prototype halogen bonded complexes H3CX···OCH2 (X = Cl, Br, I). In spite of the generally good performance of all tested methods for weakly bound systems, their performance for halogen-containing compounds varies largely. We find maximum errors in the energies with respect to the CCSD(T) reference values of 0.13 kcal/mol for DCACP, 0.22 kcal/mol for M06-2X, 0.47 kcal/mol for BLYP-D3, and 0.77 kcal/mol for M06. The root-mean-square deviations are 0.13 kcal/mol for DCACP and M06-2X, 0.44 kcal/mol for M06, and 0.51 kcal/mol for BLYP-D3.
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Affiliation(s)
- Manuel Doemer
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Ivano Tavernelli
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Ursula Rothlisberger
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
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12
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Reddy SK, Balasubramanian S. Liquid Dimethyl Carbonate: A Quantum Chemical and Molecular Dynamics Study. J Phys Chem B 2012. [DOI: 10.1021/jp309374m] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sandeep K. Reddy
- Chemistry
and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur,
Bangalore 560 064, India
| | - Sundaram Balasubramanian
- Chemistry
and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur,
Bangalore 560 064, India
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13
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Ma Z, Zhang Y, Tuckerman ME. Ab initio molecular dynamics study of water at constant pressure using converged basis sets and empirical dispersion corrections. J Chem Phys 2012; 137:044506. [PMID: 22852630 DOI: 10.1063/1.4736712] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It is generally believed that studies of liquid water using the generalized gradient approximation to density functional theory require dispersion corrections in order to obtain reasonably accurate structural and dynamical properties. Here, we report on an ab initio molecular dynamics study of water in the isothermal-isobaric ensemble using a converged discrete variable representation basis set and an empirical dispersion correction due to Grimme [J. Comp. Chem. 27, 1787 (2006)]. At 300 K and an applied pressure of 1 bar, the density obtained without dispersion corrections is approximately 0.92 g/cm(3) while that obtained with dispersion corrections is 1.07 g/cm(3), indicating that the empirical dispersion correction overestimates the density by almost as much as it is underestimated without the correction for this converged basis. Radial distribution functions exhibit a loss of structure in the second solvation shell. Comparison of our results with other studies using the same empirical correction suggests the cause of the discrepancy: the Grimme dispersion correction is parameterized for use with a particular basis set; this parameterization is sensitive to this choice and, therefore, is not transferable to other basis sets.
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Affiliation(s)
- Zhonghua Ma
- Department of Chemistry, New York University, New York, New York 10003, USA.
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14
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Hatz R, Korpinen M, Hänninen V, Halonen L. Characterization of the Dispersion Interactions and an ab Initio Study of van der Waals Potential Energy Parameters for Coinage Metal Clusters. J Phys Chem A 2012; 116:11685-93. [DOI: 10.1021/jp307448n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Richard Hatz
- Laboratory of Physical
Chemistry, Department
of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki,
Finland
| | - Markus Korpinen
- Laboratory of Physical
Chemistry, Department
of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki,
Finland
| | - Vesa Hänninen
- Laboratory of Physical
Chemistry, Department
of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki,
Finland
| | - Lauri Halonen
- Laboratory of Physical
Chemistry, Department
of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki,
Finland
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15
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Nadler R, Sanz JF. Effect of dispersion correction on the Au(1 1 1)-H2O interface: A first-principles study. J Chem Phys 2012; 137:114709. [DOI: 10.1063/1.4752235] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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16
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Computational investigation on the new high energy density material of aluminum enriched 1, 1-diamino-2, 2-dinitroethylene. J Mol Model 2012; 19:131-8. [DOI: 10.1007/s00894-012-1533-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 07/08/2012] [Indexed: 10/28/2022]
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17
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Lin IC, Seitsonen AP, Tavernelli I, Rothlisberger U. Structure and Dynamics of Liquid Water from ab Initio Molecular Dynamics—Comparison of BLYP, PBE, and revPBE Density Functionals with and without van der Waals Corrections. J Chem Theory Comput 2012; 8:3902-10. [DOI: 10.1021/ct3001848] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- I-Chun Lin
- Department of Chemistry,
New
York University, 100 Washington Square East, New York, New York 10003,
United States
| | - Ari P. Seitsonen
- Physikalisch-Chemisches
Institut,
University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry
and Biochemistry, Ecole Polytechnique Fédérale de Lausanne,
CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry
and Biochemistry, Ecole Polytechnique Fédérale de Lausanne,
CH-1015 Lausanne, Switzerland
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18
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Lin IC, Seitsonen AP, Tavernelli I, Rothlisberger U. Structure and Dynamics of Liquid Water from ab Initio Molecular Dynamics—Comparison of BLYP, PBE, and revPBE Density Functionals with and without van der Waals Corrections. J Chem Theory Comput 2012. [DOI: 10.10.1021/ct3001848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- I-Chun Lin
- Department of Chemistry,
New
York University, 100 Washington Square East, New York, New York 10003,
United States
| | - Ari P. Seitsonen
- Physikalisch-Chemisches
Institut,
University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry
and Biochemistry, Ecole Polytechnique Fédérale de Lausanne,
CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry
and Biochemistry, Ecole Polytechnique Fédérale de Lausanne,
CH-1015 Lausanne, Switzerland
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19
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Hiratsuka M, Ohmura R, Sum AK, Yasuoka K. Molecular vibrations of methane molecules in the structure I clathrate hydrate from ab initio molecular dynamics simulation. J Chem Phys 2012; 136:044508. [PMID: 22299892 DOI: 10.1063/1.3677231] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Vibrational frequencies of guest molecules in clathrate hydrates reflect the molecular environment and dynamical behavior of molecules. A detailed understanding of the mechanism for the vibrational frequency changes of the guest molecules in the clathrate hydrate cages is still incomplete. In this study, molecular vibrations of methane molecules in a structure I clathrate hydrate are calculated from ab initio molecular dynamics simulation. The vibrational spectra of methane are computed by Fourier transform of autocorrelation functions, which reveal distinct separation of each vibrational mode. Calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules are lower in the large cages than in the small cages (8 and 16 cm(-1) for symmetric and asymmetric stretching, respectively). These changes are closely linked with the C-H bond length. The vibrational frequencies for the bending and rocking vibrational modes nearly overlap in each of the cages.
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Affiliation(s)
- Masaki Hiratsuka
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
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20
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Pan Z, Chen J, Lü G, Geng YZ, Zhang H, Ji Q. An ab initio molecular dynamics study on hydrogen bonds between water molecules. J Chem Phys 2012; 136:164313. [DOI: 10.1063/1.4705371] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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21
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Sakuma H. Potential energy surface of 4-hexyl-4′-cyanobiphenyl (6CB) on graphite surface: a DFT study with van der Waals corrections. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2011.557833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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Carter DJ, Rohl AL. Noncovalent Interactions in SIESTA Using the vdW-DF Functional: S22 Benchmark and Macrocyclic Structures. J Chem Theory Comput 2011; 8:281-9. [DOI: 10.1021/ct200679b] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Damien J. Carter
- Nanochemistry Research Institute, Department of Chemistry, Curtin University of Technology, GPO Box U1987, Perth, WA, Australia, 6845
- iVEC, 26 Dick Perry Avenue, Technology Park, Kensington, WA, Australia 6151
| | - Andrew L. Rohl
- Nanochemistry Research Institute, Department of Chemistry, Curtin University of Technology, GPO Box U1987, Perth, WA, Australia, 6845
- iVEC, 26 Dick Perry Avenue, Technology Park, Kensington, WA, Australia 6151
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23
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Fokin AA, Gerbig D, Schreiner PR. σ/σ- and π/π-Interactions Are Equally Important: Multilayered Graphanes. J Am Chem Soc 2011; 133:20036-9. [DOI: 10.1021/ja206992j] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Andrey A. Fokin
- Department of Organic Chemistry, Kiev Polytechnic Institute, 37 Pobeda Avenue, Kiev 03056, Ukraine
| | - Dennis Gerbig
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Peter R. Schreiner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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24
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Kulkarni C, Reddy SK, George SJ, Balasubramanian S. Cooperativity in the stacking of benzene-1,3,5-tricarboxamide: The role of dispersion. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.028] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Møgelhøj A, Kelkkanen AK, Wikfeldt KT, Schiøtz J, Mortensen JJ, Pettersson LGM, Lundqvist BI, Jacobsen KW, Nilsson A, Nørskov JK. Ab Initio van der Waals Interactions in Simulations of Water Alter Structure from Mainly Tetrahedral to High-Density-Like. J Phys Chem B 2011; 115:14149-60. [DOI: 10.1021/jp2040345] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Andreas Møgelhøj
- Center for Atomic-Scale Materials Design (CAMD), Department, of Physics, Building 307, Nano DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - André K. Kelkkanen
- Center for Atomic-Scale Materials Design (CAMD), Department, of Physics, Building 307, Nano DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - K. Thor Wikfeldt
- Department of Physics, AlbaNova, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jakob Schiøtz
- Center for Individual Nanoparticle Functionality (CINF), Department of Physics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Jens Jørgen Mortensen
- Center for Atomic-Scale Materials Design (CAMD), Department, of Physics, Building 307, Nano DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | | | - Bengt I. Lundqvist
- Center for Atomic-Scale Materials Design (CAMD), Department, of Physics, Building 307, Nano DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Department of Applied Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Karsten W. Jacobsen
- Center for Atomic-Scale Materials Design (CAMD), Department, of Physics, Building 307, Nano DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Anders Nilsson
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Jens K. Nørskov
- Center for Atomic-Scale Materials Design (CAMD), Department, of Physics, Building 307, Nano DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, California 94025, United States
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
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26
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Reddy SK, Kulkarni CH, Balasubramanian S. Theoretical investigations of candidate crystal structures for β-carbonic acid. J Chem Phys 2011; 134:124511. [DOI: 10.1063/1.3567307] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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27
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Hänninen V, Korpinen M, Ren Q, Hinde R, Halonen L. An ab Initio Study of van der Waals Potential Energy Parameters for Silver Clusters. J Phys Chem A 2011; 115:2332-9. [DOI: 10.1021/jp110234n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vesa Hänninen
- Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland
| | - Markus Korpinen
- Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland
| | - Qinghua Ren
- Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland
| | - Robert Hinde
- Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland
| | - Lauri Halonen
- Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland
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Gubbins KE, Liu YC, Moore JD, Palmer JC. The role of molecular modeling in confined systems: impact and prospects. Phys Chem Chem Phys 2011; 13:58-85. [DOI: 10.1039/c0cp01475c] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Ferullo RM, Domancich NF, Castellani NJ. On the performance of van der Waals corrected-density functional theory in describing the atomic hydrogen physisorption on graphite. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.10.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Gubbins KE, Moore JD. Molecular Modeling of Matter: Impact and Prospects in Engineering. Ind Eng Chem Res 2010. [DOI: 10.1021/ie901909c] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Keith E. Gubbins
- Institute for Computational Science & Engineering and Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Joshua D. Moore
- Institute for Computational Science & Engineering and Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
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Riley KE, Pitoňák M, Černý J, Hobza P. On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H···π): WFT and DFT Calculations. J Chem Theory Comput 2009; 6:66-80. [PMID: 26614320 DOI: 10.1021/ct900376r] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The strengths of noncovalent interactions are generally very sensitive to a number of geometric parameters. Among the most important of these parameters is the separation between the interacting moieties (in the case of an intermolecular interaction, this would be the intermolecular separation). Most works seeking to characterize the properties of intermolecular interactions are mainly concerned with binding energies obtained at the potential energy minimum (as determined at some particular level of theory). In this work, in order to extend our understanding of these types of noncovalent interactions, we investigate the distance dependence of several types of intermolecular interactions, these are hydrogen bonds, stacking interactions, dispersion interactions, and X-H···π interactions. There are several methods that have traditionally been used to treat noncovalent interactions as well as many new methods that have emerged within the past three or four years. Here we obtain reference data using estimated CCSD(T) values at the complete basis set limit (using the CBS(T) method); potential energy curves are also produced using several other methods thought to be accurate for intermolecular interactions, these are MP2/cc-pVTZ, MP2/aug-cc-pVDZ, MP2/6-31G*(0.25), SCS(MI)-MP2/cc-pVTZ, estimated MP2.5/CBS, DFT-SAPT/aug-cc-pVTZ, DFT/M06-2X/6-311+G(2df,2p), and DFT-D/TPSS/6-311++G(3df,3pd). The basis set superposition error is systematically considered throughout the study. It is found that the MP2.5 and DFT-SAPT methods, which are both quite computationally intensive, produce potential energy curves that are in very good agreement to those of the reference method. Among the MP2 techniques, which can be said to be of medium computational expense, the best results are obtained with MP2/cc-pVTZ and SCS(MI)-MP2/cc-pVTZ. DFT-D/TPSS/6-311++G(3df,3pd) is the DFT-based method that can be said to give the most well-balanced description of intermolecular interactions.
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Affiliation(s)
- Kevin E Riley
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Michal Pitoňák
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Jiří Černý
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Pavel Hobza
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
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Cascella M, Lin IC, Tavernelli I, Rothlisberger U. Dispersion Corrected Atom-Centered Potentials for Phosphorus. J Chem Theory Comput 2009; 5:2930-4. [DOI: 10.1021/ct9003756] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michele Cascella
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland, Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, New York 10003-6688, and Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, BCH 4109 Ecole Polytechnique Fédérale de Lausanne EPFL, CH-1015 Lausanne, Switzerland
| | - I-Chun Lin
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland, Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, New York 10003-6688, and Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, BCH 4109 Ecole Polytechnique Fédérale de Lausanne EPFL, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland, Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, New York 10003-6688, and Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, BCH 4109 Ecole Polytechnique Fédérale de Lausanne EPFL, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland, Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, New York 10003-6688, and Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, BCH 4109 Ecole Polytechnique Fédérale de Lausanne EPFL, CH-1015 Lausanne, Switzerland
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Balasubramanian S, Kohlmeyer A, Klein ML. Ab initio molecular dynamics study of supercritical carbon dioxide including dispersion corrections. J Chem Phys 2009; 131:144506. [DOI: 10.1063/1.3245962] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Molnar LF, He X, Wang B, Merz KM. Further analysis and comparative study of intermolecular interactions using dimers from the S22 database. J Chem Phys 2009; 131:065102. [PMID: 19691412 PMCID: PMC2738737 DOI: 10.1063/1.3173809] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Accepted: 06/18/2009] [Indexed: 12/25/2022] Open
Abstract
Accurate MP2 and CCSD(T) complete basis set (CBS) interaction energy curves (14 points for each curve) have been obtained for 20 of the dimers reported in the S22 set and analytical Morse curves have been fitted that can be used in developing updated density functional theory (DFT) and force field models. The magnitude and the effect of the basis set superposition error (BSSE) were carefully investigated. We found that going up to aug-cc-pVDZ and aug-cc-pVTZ basis sets is enough to obtain accurate CBS MP2 energies when BSSE corrected values are used but aug-cc-pVTZ and aug-cc-pVQZ basis sets are needed when the BSSE uncorrected total energies are used in CBS extrapolations. MP2 interaction energies with smaller basis sets such as 6-31G* are found to have very little dispersion energy and that the true source of dispersion attributed attractive interactions is almost entirely due to BSSE. MP2 and CCSD(T) CBS interaction energies are found to be very close to one another if aromatic systems are not involved. Comparative analyses have been performed with semiempirical and ab initio methods utilizing the moderate in size but affordable 6-31G* basis set both of which can be readily applied to macromolecular systems. The new M06-2X and M06-L DFT functionals were found to be more accurate than all methods tested herein. Interaction energy curves using the SG1 grid showed discontinuities for several of the dimer systems but this problem disappeared when finer DFT numerical grids were used.
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Affiliation(s)
- Laszlo Fusti Molnar
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA
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Silvestrelli PL. Van der Waals interactions in density functional theory using Wannier functions. J Phys Chem A 2009; 113:5224-34. [PMID: 19344144 DOI: 10.1021/jp811138n] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
van der Waals interactions between atoms and molecules are ubiquitous and very important for many molecular and condensed-matter structures. These systems are often studied from first principles using the density functional theory (DFT), because this approach often represents a good compromise between accuracy and efficiency. However, the commonly used DFT functionals are not able to describe properly van der Waals effects. Most attempts to correct for this problem have a basic semiempirical character, although computationally more expensive first principles schemes have been recently developed. Of course, the key issue is finding a way to include van der Waals interactions in DFT without dramatically increasing the computational cost. We here describe in detail the recently developed scheme, based on the use of the maximally localized Wannier functions, that combines the simplicity of the semiempirical formalism with the accuracy of the first principles approaches and appears to be promising, being simple, efficient, accurate, and transferable (for instance, charge polarization effects are naturally included). The results of successful applications to small molecules, bulk Ar, and the interaction of Ar, He, and H(2) with two different Al surfaces are presented. Directions for further improvements of the method are finally suggested.
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Affiliation(s)
- Pier Luigi Silvestrelli
- Dipartimento di Fisica G. Galilei, Universita di Padova, via Marzolo 8, I-35131 Padova, Italy, and DEMOCRITOS National Simulation Center, Trieste, Italy.
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Lin IC, Seitsonen AP, Coutinho-Neto MD, Tavernelli I, Rothlisberger U. Importance of van der Waals interactions in liquid water. J Phys Chem B 2009; 113:1127-31. [PMID: 19123911 DOI: 10.1021/jp806376e] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present ab initio molecular dynamics studies on liquid water using density functional theory in conjunction with either dispersion-corrected atom-centered potentials or empirical van der Waals corrections. Our results show that improving the description of van der Waals interactions in DFT-GGA leads to a softening of liquid water's structure with higher mobility. The results obtained with dispersion-corrected atom-centered potentials are especially encouraging. In particular, the radial distribution functions are in better agreement with experiment, and the self-diffusion coefficient increases by more than three-fold compared with the one predicted by the BLYP functional. This work demonstrates that van der Waals interactions are essential in fine-tuning both structural and dynamical properties of liquid water.
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Affiliation(s)
- I-Chun Lin
- Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland
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Varghese N, Mogera U, Govindaraj A, Das A, Maiti PK, Sood AK, Rao CNR. Binding of DNA Nucleobases and Nucleosides with Graphene. Chemphyschem 2009; 10:206-10. [DOI: 10.1002/cphc.200800459] [Citation(s) in RCA: 439] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Kong LT, Denniston C, Müser MH, Qi Y. Non-bonded force field for the interaction between metals and organic molecules: a case study of olefins on aluminum. Phys Chem Chem Phys 2009; 11:10195-203. [DOI: 10.1039/b906874k] [Citation(s) in RCA: 12] [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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40
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Sumpter BG, Drummond ML, Shelton WA, Valeev EF, Barnes MD. A combined theoretical and experimental study of the polymer inter-chain structure in poly(phenylene vinylene) derivatives. ACTA ACUST UNITED AC 2008. [DOI: 10.1088/1749-4699/1/1/015006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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41
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Peverati R, Baldridge KK. Implementation and Performance of DFT-D with Respect to Basis Set and Functional for Study of Dispersion Interactions in Nanoscale Aromatic Hydrocarbons. J Chem Theory Comput 2008; 4:2030-48. [DOI: 10.1021/ct800252z] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Kim K Baldridge
- University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich
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Pagliai M, Cavazzoni C, Cardini G, Erbacci G, Parrinello M, Schettino V. Anharmonic infrared and Raman spectra in Car–Parrinello molecular dynamics simulations. J Chem Phys 2008; 128:224514. [DOI: 10.1063/1.2936988] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Das A, Sood A, Maiti PK, Das M, Varadarajan R, Rao C. Binding of nucleobases with single-walled carbon nanotubes: Theory and experiment. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.01.057] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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44
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Santiso EE, Buongiorno Nardelli M, Gubbins KE. A remarkable shape-catalytic effect of confinement on the rotational isomerization of small hydrocarbons. J Chem Phys 2008; 128:034704. [DOI: 10.1063/1.2819238] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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45
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Inelastic neutron scattering, Raman, vibrational analysis with anharmonic corrections, and scaled quantum mechanical force field for polycrystalline l-alanine. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.09.063] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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46
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Jalkanen JP, Halonen M, Fernández-Torre D, Laasonen K, Halonen L. A Computational Study of the Adsorption of Small Ag and Au Nanoclusters on Graphite. J Phys Chem A 2007; 111:12317-26. [DOI: 10.1021/jp074969m] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jukka-Pekka Jalkanen
- Laboratory of Physical Chemistry, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland, and Department of Chemistry, P.O. Box 3000, FIN-90014 University of Oulu, Finland
| | - Marjo Halonen
- Laboratory of Physical Chemistry, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland, and Department of Chemistry, P.O. Box 3000, FIN-90014 University of Oulu, Finland
| | - Delia Fernández-Torre
- Laboratory of Physical Chemistry, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland, and Department of Chemistry, P.O. Box 3000, FIN-90014 University of Oulu, Finland
| | - Kari Laasonen
- Laboratory of Physical Chemistry, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland, and Department of Chemistry, P.O. Box 3000, FIN-90014 University of Oulu, Finland
| | - Lauri Halonen
- Laboratory of Physical Chemistry, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland, and Department of Chemistry, P.O. Box 3000, FIN-90014 University of Oulu, Finland
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Riley KE, Vondrásek J, Hobza P. Performance of the DFT-D method, paired with the PCM implicit solvation model, for the computation of interaction energies of solvated complexes of biological interest. Phys Chem Chem Phys 2007; 9:5555-60. [PMID: 17957311 DOI: 10.1039/b708089a] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we investigate the performance of the DFT method, augmented with an empirical dispersion function (DFT-D), paired with the PCM implicit solvation model, for the computation of noncovalent interaction energies of biologically-relevant, solvated model complexes. It is found that this method describes intermolecular interactions within water and ether (protein-like) environments with roughly the same accuracy as in the gas phase. Another important finding is that, when environmental effects are taken into account, the empirical dispersion term associated with the DFT-D method need be modified very little (or not at all), in order to obtain the optimum, most well balanced, performance.
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Affiliation(s)
- Kevin E Riley
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic
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Tapavicza E, Lin IC, von Lilienfeld OA, Tavernelli I, Coutinho-Neto MD, Rothlisberger U. Weakly Bonded Complexes of Aliphatic and Aromatic Carbon Compounds Described with Dispersion Corrected Density Functional Theory. J Chem Theory Comput 2007; 3:1673-9. [DOI: 10.1021/ct700049s] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Enrico Tapavicza
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - I-Chun Lin
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - O. Anatole von Lilienfeld
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Maurício D. Coutinho-Neto
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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Riley KE, Hobza P. Assessment of the MP2 method, along with several basis sets, for the computation of interaction energies of biologically relevant hydrogen bonded and dispersion bound complexes. J Phys Chem A 2007; 111:8257-63. [PMID: 17649987 DOI: 10.1021/jp073358r] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the past several years the MP2 method has been used extensively in studies of noncovalent interactions within biological systems such as proteins, DNA/RNA, and protein-ligand complexes. In this work we assess the performance that can be expected of this method, when paired with several different medium and extended basis sets, for the accurate computation of binding energies of hydrogen bonded and dispersion bound biologically derived complexes. It is found that, overall, the MP2/cc-pVTZ method produces the best, most well balanced, description of noncovalent interactions. Another interesting observation made in this study is that generally the MP2 technique, when paired with any basis set, does not yield reliable results for cyclic hydrogen bonds such as those found in nucleic acid base pairs.
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Affiliation(s)
- Kevin E Riley
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, FlemingovonAm. 2, 166 10 Prague 6, Czech Republic
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50
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Zhu YA, Dai YC, Chen D, Yuan WK. First-principles calculations of CH4 dissociation on Ni(100) surface along different reaction pathways. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.molcata.2006.09.043] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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