1
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Li XL, Li CM, Zhu JY, Zhou Z, Hao Q, Wang CS. A scheme for rapid evaluation of the intermolecular three-body polarization effect in water clusters. J Comput Chem 2023; 44:677-686. [PMID: 36408852 DOI: 10.1002/jcc.27032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/22/2022] [Accepted: 10/24/2022] [Indexed: 11/22/2022]
Abstract
The ability to accurately and rapidly evaluate the intermolecular many-body polarization effect of the water system is very important for computer simulations of biomolecule in aqueous. In this paper, a scheme is proposed based on the polarizable dipole-dipole interaction model and used to rapidly estimate the intermolecular many-body polarization effect in water clusters. We use a bond-dipole-based polarization function to evaluate the polarization energy. We regard two OH bonds of a water molecule as two bond-dipoles and set the permanent OH bond-dipole moment of a water molecule to be 1.51 Debye. We estimate the induced OH bond-dipole moment via a simple formula in which only one correction factor is needed. This scheme is then applied to tens of water clusters to calculate the three- and four-body interaction energies. The three-body interaction energies of 93 water clusters produced by our scheme are compared with those produced by the counterpoise-corrected CCSD(T)/aug-cc-pVDZ, MP2/aug-cc-pVDZ, M06-2X/jul-cc-pVTZ methods, by the AMOEBApro13, iAMOEBA, AMOEBA+, AMOEBA+(CF) methods, and by the MB-pol method. The four-body interaction energies of 47 water clusters yielded by our scheme are compared with those yielded by the counterpoise-corrected MP2/aug-cc-pVDZ and M06-2X/ jul-cc-pVTZ methods, by the AMOEBApro13, AMOEBA+, AMOEBA+(CF) methods, and by the MB-pol method. The comparison results show that the scheme proposed in this paper can reproduce the counterpoise-corrected CCSD(T)/aug-cc-pVDZ three-body interaction energies and reproduce the counterpoise-corrected MP2/aug-cc-pVDZ four-body interaction energies both accurately and efficiently. We anticipate the scheme proposed here can be useful for computer simulations of liquid water and aqueous solutions.
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Affiliation(s)
- Xiao-Lei Li
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Chao-Ming Li
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Jia-Yi Zhu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Zhan Zhou
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Qiang Hao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Chang-Sheng Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
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2
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Wang F, Lin H, Tong J, Tai J, Wu J, Yao Y, Liu Y. Effects of Morphology and Solvent/Temperature on THz Spectra: Take Nucleosides as Example. Molecules 2023; 28:molecules28041528. [PMID: 36838517 PMCID: PMC9965851 DOI: 10.3390/molecules28041528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/18/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Water molecules were easy to combine with organic molecules and embed into the lattice of solid molecules to form a hydrate. Compared with anhydrous compounds, a hydrate has completely different physical and chemical properties. In this paper, terahertz (THz) spectra of five nucleosides in the solid and liquid phases were studied experimentally by Fourier-transform infrared spectroscopy (FTIR) in the frequency of 0.5-9 THz. In addition, the lattice energy, geometric structure, and vibration spectrum of the molecular crystal of the nucleosides were analyzed theoretically by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF). Furthermore, different nucleoside molecular morphology (monomer, polymer, and crystal), solvent (implicit and explicit water), and temperature/theoretical model effect on the THz spectra were mainly investigated. It was found that in the low-frequency band, the vibrational modes were generally originated from the collective vibration of all molecules involved (more than 99% of them were vibration; only less than 1% of them were rotation and translation), which can reflect the molecular structure and spatial distribution of different substances. The Gibbs free energy of thymidine monomer, dimer, tetramer, and crystal was studied. It was found that the cell-stacking energy had the greatest influence on the spectrum, indicating that only the crystal structure constrained by the periodic boundary conditions could well describe the experimental results. In addition, hydrophobic forces dominated the formation of new chemical bonds and strong inter-molecular interactions; the free water had little contribution to the THz spectrum of nucleosides, while crystalline water had a great influence on the spectrum.
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Affiliation(s)
- Fang Wang
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Haifeng Lin
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
- Correspondence:
| | - Jiawen Tong
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Junbin Tai
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Jiaen Wu
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Yaru Yao
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
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3
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Wang F, Sun X, Zan J, Li M, Liu Y, Chen J. Terahertz spectra and weak intermolecular interactions of nucleosides or nucleoside drugs. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 265:120344. [PMID: 34481145 DOI: 10.1016/j.saa.2021.120344] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/18/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
In this paper, terahertz (THz) spectra of four DNA nucleosides (Adenosine, Thymidine, Cytidine and Guanosine) and two nucleoside derivatives (Ribavirin and Entecavir, first time reported) in the solid phase were studied experimentally by Fourier Transform Infrared Spectroscopy (FTIR) in the frequency of 1-10 THz. The lattice energy, geometric structure, vibration spectrum of them were analyzed theoretically by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF) and the density functional theory (DFT). The intra- and inter-molecular weak interactions corresponding to the vibrational modes of the crystal, polymer and monomer were obtained, with the help of the potential energy distribution (PED) and reduced density gradient (RDG) methods. It was found that the sum of electronic and thermal free energies increased from the monomer to polymer, and from the polymer to crystal. For example, the inter-molecular interaction energy from the monomer to dimer of adenosine increased 6.969 kcal/mol, and that from the dimer to crystal (the periodic boundary conditions were considered) increased 666.792 kcal/mol. Therefore, only the crystal structure constrained the periodic boundary conditions could well describe the experimental results, although the former scholars chose the monomer or polymer as the initial configuration due to the limitation of computing resources and methods. In THz band, the vibrational modes were generally originated from the collective vibration (more than 99% of them were vibration, only less than 1% of them were rotation and translation) of all molecules involved, which could reflect the molecular structure and spatial distribution of different substances. In order to accurately identify the spectra, we studied the location, type and contribution of all weak interactions, and found that the strong characteristic peaks corresponding to the strong hydrogen bonds came from inter-molecular, while the weak hydrogen bonds mainly originated from intra- and inter-molecular, the out-of-plane bending made the largest contribution, accounting for more than 90%. Furthermore, taking guanine, guanosine and two guanosine derivatives (Ribavirin and Entecavir) as examples, the differences of weak interaction among them caused by different molecular configuration, arrangement and substituent position were studied, and the fundamental reason of THz spectrum change was found. This research can lay a foundation for crystal engineering, supramolecular chemistry, molecular recognition and self-assembly, protein-ligand interaction, etc.
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Affiliation(s)
- Fang Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China; College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, People's Republic of China
| | - Xiaolin Sun
- School of Electronic and Information Engineering, Nanjing Vocational University of Industry Technology, Nanjing 210046, People's Republic of China
| | - Jianan Zan
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Mingshi Li
- College of Forestry, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
| | - Jingyi Chen
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, People's Republic of China
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4
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Hellmers J, König C. A unified and flexible formulation of molecular fragmentation schemes. J Chem Phys 2021; 155:164105. [PMID: 34717347 DOI: 10.1063/5.0059598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We present a flexible formulation for energy-based molecular fragmentation schemes. This framework does not only incorporate the majority of existing fragmentation expansions but also allows for flexible formulation of novel schemes. We further illustrate its application in multi-level approaches and for electronic interaction energies. For the examples of small water clusters, a small protein, and protein-protein interaction energies, we show how this flexible setup can be exploited to generate a well-suited multi-level fragmentation expansion for the given case. With such a setup, we reproduce the electronic protein-protein interaction energy of ten different structures of a neurotensin and an extracellular loop of its receptor with a mean absolute deviation to the respective super-system calculations below 1 kJ/mol.
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Affiliation(s)
- Janine Hellmers
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Hannover, Germany
| | - Carolin König
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Hannover, Germany
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5
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Malloum A, Conradie J. Hydrogen bond networks of ammonia clusters: What we know and what we don’t know. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116199] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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6
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Paz ASP, Glover WJ. Diabatic Many-Body Expansion: Development and Application to Charge-Transfer Reactions. J Chem Theory Comput 2021; 17:1497-1511. [DOI: 10.1021/acs.jctc.0c01231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amiel S. P. Paz
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshang Road North, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - William J. Glover
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshang Road North, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
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7
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Liu J, He X. Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquids. Phys Chem Chem Phys 2020; 22:12341-12367. [PMID: 32459230 DOI: 10.1039/d0cp01095b] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To study large molecular systems beyond the system size that the current state-of-the-art ab initio electronic structure methods could handle, fragment-based quantum mechanical (QM) approaches have been developed over the past years, and proved to be efficient in dealing with large molecular systems at various ab initio levels. According to the fragmentation approach, a large molecular system can be divided into subsystems (fragments), and subsequently the property of the whole system can be approximately obtained by taking a proper combination of the corresponding terms of individual fragments. Therefore, the standard QM calculation of a large system could be circumvented by carrying out a series of calculations on small fragments, which significantly promotes computational efficiency. The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method is one of the fragment-based QM approaches which has been developed by our research group in recent years. This Perspective presents the theoretical framework of this fragmentation method and its applications in biomolecules, molecular clusters, molecular crystals and liquids, including total energy calculation, protein-ligand/protein binding affinity prediction, geometry optimization, vibrational spectrum simulation, ab initio molecular dynamics simulation, and prediction of excited-state properties.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
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8
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Zhao D, Shen X, Cheng Z, Li W, Dong H, Li S. Accurate and Efficient Prediction of NMR Parameters of Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method. J Chem Theory Comput 2020; 16:2995-3005. [DOI: 10.1021/acs.jctc.9b01298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dongbo Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Xiaoling Shen
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Zheng Cheng
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, People’s Republic of China
- Institute for Brain Sciences, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
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9
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Abstract
Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial "free lunch" in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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10
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Liu J, Rana B, Liu KY, Herbert JM. Variational Formulation of the Generalized Many-Body Expansion with Self-Consistent Charge Embedding: Simple and Correct Analytic Energy Gradient for Fragment-Based ab Initio Molecular Dynamics. J Phys Chem Lett 2019; 10:3877-3886. [PMID: 31251619 DOI: 10.1021/acs.jpclett.9b01214] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The many-body expansion (MBE) and its extension to overlapping fragments, the generalized (G)MBE, constitute the theoretical basis for most fragment-based approaches for large-scale quantum chemistry. We reformulate the GMBE for use with embedding charges determined self-consistently from the fragment wave functions, in a manner that preserves the variational nature of the underlying self-consistent field method. As a result, the analytic gradient retains the simple "sum of fragment gradients" form that is often assumed in practice, sometimes incorrectly. This obviates (without approximation) the need to solve coupled-perturbed equations, and we demonstrate stable, fragment-based ab initio molecular dynamics simulations using this technique. Energy conservation fails when charge-response contributions to the Fock matrix are neglected, even while geometry optimizations and vibrational frequency calculations may yet be accurate. Stable simulations can be recovered by means of straightforward modifications introduced here, providing a general paradigm for fragment-based ab initio molecular dynamics.
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Affiliation(s)
- Jie Liu
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Kuan-Yu Liu
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - John M Herbert
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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11
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Bakó I, Mayer I, Hamza A, Pusztai L. Two- and three-body, and relaxation energy terms in water clusters: Application of the hierarchical BSSE corrected decomposition scheme. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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12
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Malloum A, Fifen JJ, Dhaouadi Z, Nana Engo SG, Conradie J. Structures, relative stability and binding energies of neutral water clusters, (H2O)2–30. NEW J CHEM 2019. [DOI: 10.1039/c9nj01659g] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have revised the structures of neutral water clusters, (H2O)n=2–30, with the affordable M06-2X functional, presenting up to 25 isomers for each cluster size.
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Affiliation(s)
- Alhadji Malloum
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Tunis
- Tunisia
| | - Serge Guy Nana Engo
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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13
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14
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Zhao D, Song R, Li W, Ma J, Dong H, Li S. Accurate Prediction of NMR Chemical Shifts in Macromolecular and Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method. J Chem Theory Comput 2017; 13:5231-5239. [DOI: 10.1021/acs.jctc.7b00380] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dongbo Zhao
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
- Kuang
Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Ruiheng Song
- Kuang
Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Wei Li
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Jing Ma
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Hao Dong
- Kuang
Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
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15
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Zhang L, Li W, Fang T, Li S. Accurate Relative Energies and Binding Energies of Large Ice–Liquid Water Clusters and Periodic Structures. J Phys Chem A 2017; 121:4030-4038. [DOI: 10.1021/acs.jpca.7b03376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lei Zhang
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei Li
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tao Fang
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuhua Li
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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16
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Yuan D, Li Y, Ni Z, Pulay P, Li W, Li S. Benchmark Relative Energies for Large Water Clusters with the Generalized Energy-Based Fragmentation Method. J Chem Theory Comput 2017; 13:2696-2704. [DOI: 10.1021/acs.jctc.7b00284] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Dandan Yuan
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Yunzhi Li
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Zhigang Ni
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Peter Pulay
- Department
of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Wei Li
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Shuhua Li
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
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17
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Chen GD, Weng J, Song G, Li ZH. Generalized Switch Functions in the Multilevel Many-Body Expansion Method and Its Application to Water Clusters. J Chem Theory Comput 2017; 13:2010-2020. [DOI: 10.1021/acs.jctc.7b00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Guo Dong Chen
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jingwei Weng
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Guoliang Song
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Zhen Hua Li
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China
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18
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Gao Z, Ding Y, Yang W, Han W. DFT study of water adsorption on lignite molecule surface. J Mol Model 2017; 23:27. [PMID: 28064378 DOI: 10.1007/s00894-016-3194-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/15/2016] [Indexed: 11/30/2022]
Abstract
High moisture content is a main characteristic of low-rank coal, such as lignite. Numerous oxygen containing functional groups in lignite make it represent some special properties, and these functional groups affect the adsorption mechanisms of water molecules on lignite surface. This study reports some typical water · · · lignite conformations, along with a detailed analysis of the geometry, electrostatic potential distribution, reduced density gradient of interaction, and interaction energy decomposition. The results show that water molecules tend to aggregate around functional groups, and hydrogen bonds play a dominant role in the interaction. The adsorption energy of water cluster on lignite surface is larger than that of isolated water molecule, a good linear relationship between the interaction distance and adsorption energy of layers has been found. Since water is a polar molecule, the local minima and maxima of electrostatic potential in conformations increase along with more water adsorbing on lignite surface. Reduced density gradient analysis shows that H-bonds, van der Waals interaction, and a little steric make up the interaction between water cluster and lignite molecule. In these studied conformations which mainly are H-bond complexes, electrostatic and exchange repulsion play a dominant role, whereas polarization and dispersion make relatively small contribution to the interaction. Attractive and repulsive interaction both affect the stability of water · · · lignite conformations.
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Affiliation(s)
- Zhengyang Gao
- The Department of Power Engineering, North China Electric Power University, Baoding, 071003, China
| | - Yi Ding
- The Department of Power Engineering, North China Electric Power University, Baoding, 071003, China
| | - Weijie Yang
- The Department of Power Engineering, North China Electric Power University, Baoding, 071003, China.
| | - Wentao Han
- The Department of Power Engineering, North China Electric Power University, Baoding, 071003, China
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19
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König C, Christiansen O. Linear-scaling generation of potential energy surfaces using a double incremental expansion. J Chem Phys 2016. [DOI: 10.1063/1.4960189] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Carolin König
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Ove Christiansen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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