1
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Sahu N, Khire SS, Gadre SR. Combining fragmentation method and high-performance computing: Geometry optimization and vibrational spectra of proteins. J Chem Phys 2023; 159:044309. [PMID: 37522406 DOI: 10.1063/5.0149572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
Exploring the structures and spectral features of proteins with advanced quantum chemical methods is an uphill task. In this work, a fragment-based molecular tailoring approach (MTA) is appraised for the CAM-B3LYP/aug-cc-pVDZ-level geometry optimization and vibrational infrared (IR) spectra calculation of ten real proteins containing up to 407 atoms and 6617 basis functions. The use of MTA and the inherently parallel nature of the fragment calculations enables a rapid and accurate calculation of the IR spectrum. The applicability of MTA to optimize the protein geometry and evaluate its IR spectrum employing a polarizable continuum model with water as a solvent is also showcased. The typical errors in the total energy and IR frequencies computed by MTA vis-à-vis their full calculation (FC) counterparts for the studied protein are 5-10 millihartrees and 5 cm-1, respectively. Moreover, due to the independent execution of the fragments, large-scale parallelization can also be achieved. With increasing size and level of theory, MTA shows an appreciable advantage in computer time as well as memory and disk space requirement over the corresponding FCs. The present study suggests that the geometry optimization and IR computations on the biomolecules containing ∼1000 atoms and/or ∼15 000 basis functions using MTA and HPC facility can be clearly envisioned in the near future.
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Affiliation(s)
- Nityananda Sahu
- Theoretische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Subodh S Khire
- RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Shridhar R Gadre
- Departments of Scientific Computing, Modelling & Simulation and Chemistry, Savitribai Phule Pune University, Pune 411007, India
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2
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Clavaguéra C, Thaunay F, Ohanessian G. Manifolds of low energy structures for a magic number of hydrated sulfate: SO 42-(H 2O) 24. Phys Chem Chem Phys 2021; 23:24428-24438. [PMID: 34693943 DOI: 10.1039/d1cp03123f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low energy structures of SO42-(H2O)24 have been obtained using a combination of classical molecular dynamics simulations and refinement of structures and energies by quantum chemical calculations. Extensive exploration of the potential energy surface led to a number of low-energy structures, confirmed by accurate calibration calculations. An overall analysis of this large set was made after devising appropriate structural descriptors such as the numbers of cycles and their combinations. Low energy structures bear common motifs, the most prominent being fused cycles involving alternatively four and six water molecules. The latter adopt specific conformations which ensure the appropriate surface curvature to form a closed cage without dangling O-H bonds and at the same time provide 12-coordination of the sulfate ion. A prominent feature to take into account is isomerism via inversion of hydrogen bond orientations along cycles. This generates large families of ca. 100 isomers for this cluster size, spanning energy windows of 10-30 kJ mol-1. This relatively ignored isomerism must be taken into account to identify reliably the lowest energy minima. The overall picture is that the magic number cluster SO42-(H2O)24 does not correspond to formation of a single, remarkable structure, but rather to a manifold of structural families with similar stabilities. Extensive calculations on isomerization mechanisms within a family indicate that large barriers are associated to direct inversion of hydrogen bond networks. Possible implications of these results for magic number clusters of other anions are discussed.
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Affiliation(s)
- Carine Clavaguéra
- Institut de Chimie Physique, Université Paris-Saclay - CNRS, UMR 8000, 91405 Orsay, France.
| | - Florian Thaunay
- Laboratoire de Chimie Moléculaire (LCM), CNRS, École Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.
| | - Gilles Ohanessian
- Laboratoire de Chimie Moléculaire (LCM), CNRS, École Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France.
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3
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Yan Z, Li X, Chung LW. Multiscale Quantum Refinement Approaches for Metalloproteins. J Chem Theory Comput 2021; 17:3783-3796. [PMID: 34032440 DOI: 10.1021/acs.jctc.1c00148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Biomolecules with metal ion(s) (e.g., metalloproteins) play many important biological roles. However, accurate structural determination of metalloproteins, particularly those containing transition metal ion(s), is challenging due to their complicated electronic structure, complex bonding of metal ions, and high number of conformations in biomolecules. Quantum refinement, which was proposed to combine crystallographic data with computational chemistry methods by several groups, can improve the local structures of some proteins. In this study, a quantum refinement method combining several multiscale computational schemes with experimental (X-ray diffraction) information was developed for metalloproteins. Various quantum refinement approaches using different ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) combinations of quantum mechanics (QM), semiempirical (SE), and molecular mechanics (MM) methods were conducted to assess the performance and reliability on the refined local structure in two metalloproteins. The structures for two (Cu- or Zn-containing) metalloproteins were refined by combining two-layer ONIOM2(QM1/QM2) and ONIOM2(QM/MM) and three-layer ONIOM3(QM1/QM2/MM) schemes with experimental data. The accuracy of the quantum-refined metal binding sites was also examined and compared in these multiscale quantum refinement calculations. ONIOM3(QM/SE/MM) schemes were found to give good results with lower computational costs and were proposed to be a good choice for the multiscale computational scheme for quantum refinement calculations of metal binding site(s) in metalloproteins with high efficiency. Additionally, a two-center ONIOM approach was employed to speed up the quantum refinement calculations for the Zn metalloprotein with two remote active sites/ligands. Moreover, a recent quantum-embedding wavefunction-in-density functional theory (WF-in-DFT) method was also adopted as the high-level method in unprecedented ONIOM2(CCSD-in-B3LYP/MM) and ONIOM3(CCSD-in-B3LYP/SE/MM) calculations, which can be regarded as novel pseudo-three- and pseudo-four-layer ONIOM methods, respectively, to refine the key Zn binding site at the coupled-cluster singles and doubles (CCSD) level. These refined results indicate that multiscale quantum refinement schemes can be used to improve the structural accuracy obtained for local metal binding site(s) in metalloproteins with high efficiency.
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Affiliation(s)
- Zeyin Yan
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
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4
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Tripathy V, Saha A, Raghavachari K. Electrostatically embedded molecules-in-molecules approach and its application to molecular clusters. J Comput Chem 2021; 42:719-734. [PMID: 33586802 DOI: 10.1002/jcc.26492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/25/2020] [Accepted: 01/16/2021] [Indexed: 11/06/2022]
Abstract
We report the application of our fragment-based quantum chemistry model MIM (Molecules-In-Molecules) with electrostatic embedding. The method is termed "EE-MIM (Electrostatically Embedded Molecules-In-Molecules)" and accounts for the missing electrostatic interactions in the subsystems resulting from fragmentation. Point charges placed at the atomic positions are used to represent the interaction of each subsystem with the rest of the molecule with minimal increase in the computational cost. We have carefully calibrated this model on a range of different sizes of clusters containing up to 57 water molecules. The fragmentation methods have been applied with the goal of reproducing the unfragmented total energy at the MP2/6-311G(d,p) level. Comparative analysis has been carried out between MIM and EE-MIM to gauge the impact of electrostatic embedding. Performance of several different parameters such as the type of charge and levels of fragmentation are analyzed for the prediction of absolute energies. The use of background charges in subsystem calculations improves the performance of both one- and two-layer MIM while it is noticeably important in the case of one-layer MIM. Embedded charges for two-layer MIM are obtained from a full system calculation at the low-level. For one-layer MIM, in the absence of a full system calculation, two different types of embedded charges, namely, Geometry dependent (GD) and geometry independent (GI) charges, are used. A self-consistent procedure is employed to obtain GD charges. We have further tested our method on challenging charged systems with stronger intermolecular interactions, namely, protonated ammonia clusters (containing up to 30 ammonia molecules). The observations are similar to water clusters with improved performance using embedded charges. Overall, the performance of NPA charges as embedded charges is found to be the best.
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Affiliation(s)
- Vikrant Tripathy
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Arjun Saha
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
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5
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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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6
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Yang D, Fu F, Li L, Yang Z, Wan Z, Luo Y, Hu N, Chen X, Zeng G. Unique orientations and rotational dynamics of a 1-butyl-3-methyl-imidazolium hexafluorophosphate ionic liquid at the gas–liquid interface: the effects of the hydrogen bond and hydrophobic interactions. Phys Chem Chem Phys 2018; 20:12043-12052. [DOI: 10.1039/c8cp00839f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two-stage rotational motions of the interfacial [BMIM]+ cations are essentially determined by both hydrophobic and hydrogen-bonding interactions.
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Affiliation(s)
- Deshuai Yang
- Institute of Advanced Materials (IAM), State-Province Joint Engineering Laboratory of Zeolite Membrane Materials, College of Chemistry and Chemical Engineering, Jiangxi Normal University
- Nanchang 330022
- People's Republic of China
- Kuang Yaming Honors School, Nanjing University
- Nanjing 210023
| | - Fangjia Fu
- Institute of Advanced Materials (IAM), State-Province Joint Engineering Laboratory of Zeolite Membrane Materials, College of Chemistry and Chemical Engineering, Jiangxi Normal University
- Nanchang 330022
- People's Republic of China
| | - Li Li
- Institute of Advanced Materials (IAM), State-Province Joint Engineering Laboratory of Zeolite Membrane Materials, College of Chemistry and Chemical Engineering, Jiangxi Normal University
- Nanchang 330022
- People's Republic of China
| | - Zhen Yang
- Institute of Advanced Materials (IAM), State-Province Joint Engineering Laboratory of Zeolite Membrane Materials, College of Chemistry and Chemical Engineering, Jiangxi Normal University
- Nanchang 330022
- People's Republic of China
| | - Zheng Wan
- Institute of Advanced Materials (IAM), State-Province Joint Engineering Laboratory of Zeolite Membrane Materials, College of Chemistry and Chemical Engineering, Jiangxi Normal University
- Nanchang 330022
- People's Republic of China
| | - Yi Luo
- Institute of Advanced Materials (IAM), State-Province Joint Engineering Laboratory of Zeolite Membrane Materials, College of Chemistry and Chemical Engineering, Jiangxi Normal University
- Nanchang 330022
- People's Republic of China
| | - Na Hu
- Institute of Advanced Materials (IAM), State-Province Joint Engineering Laboratory of Zeolite Membrane Materials, College of Chemistry and Chemical Engineering, Jiangxi Normal University
- Nanchang 330022
- People's Republic of China
| | - Xiangshu Chen
- Institute of Advanced Materials (IAM), State-Province Joint Engineering Laboratory of Zeolite Membrane Materials, College of Chemistry and Chemical Engineering, Jiangxi Normal University
- Nanchang 330022
- People's Republic of China
| | - Guixiang Zeng
- Kuang Yaming Honors School, Nanjing University
- Nanjing 210023
- People's Republic of China
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7
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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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8
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Tao Y, Zou W, Jia J, Li W, Cremer D. Different Ways of Hydrogen Bonding in Water - Why Does Warm Water Freeze Faster than Cold Water? J Chem Theory Comput 2016; 13:55-76. [PMID: 27996255 DOI: 10.1021/acs.jctc.6b00735] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The properties of liquid water are intimately related to the H-bond network among the individual water molecules. Utilizing vibrational spectroscopy and modeling water with DFT-optimized water clusters (6-mers and 50-mers), 16 out of a possible 36 different types of H-bonds are identified and ordered according to their intrinsic strength. The strongest H-bonds are obtained as a result of a concerted push-pull effect of four peripheral water molecules, which polarize the electron density in a way that supports charge transfer and partial covalent character of the targeted H-bond. For water molecules with tetra- and pentacoordinated O atoms, H-bonding is often associated with a geometrically unfavorable positioning of the acceptor lone pair and donor σ*(OH) orbitals so that electrostatic rather than covalent interactions increasingly dominate H-bonding. There is a striking linear dependence between the intrinsic strength of H-bonding as measured by the local H-bond stretching force constant and the delocalization energy associated with charge transfer. Molecular dynamics simulations for 1000-mers reveal that with increasing temperature weak, preferentially electrostatic H-bonds are broken, whereas the number of strong H-bonds increases. An explanation for the question why warm water freezes faster than cold water is given on a molecular basis.
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Affiliation(s)
- Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Wenli Zou
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Junteng Jia
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, P. R. 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, P. R. China
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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9
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Sahu N, Singh G, Nandi A, Gadre SR. Toward an Accurate and Inexpensive Estimation of CCSD(T)/CBS Binding Energies of Large Water Clusters. J Phys Chem A 2016; 120:5706-14. [PMID: 27351269 DOI: 10.1021/acs.jpca.6b04519] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Owing to the steep scaling behavior, highly accurate CCSD(T) calculations, the contemporary gold standard of quantum chemistry, are prohibitively difficult for moderate- and large-sized water clusters even with the high-end hardware. The molecular tailoring approach (MTA), a fragmentation-based technique is found to be useful for enabling such high-level ab initio calculations. The present work reports the CCSD(T) level binding energies of many low-lying isomers of large (H2O)n (n = 16, 17, and 25) clusters employing aug-cc-pVDZ and aug-cc-pVTZ basis sets within the MTA framework. Accurate estimation of the CCSD(T) level binding energies [within 0.3 kcal/mol of the respective full calculation (FC) results] is achieved after effecting the grafting procedure, a protocol for minimizing the errors in the MTA-derived energies arising due to the approximate nature of MTA. The CCSD(T) level grafting procedure presented here hinges upon the well-known fact that the MP2 method, which scales as O(N(5)), can be a suitable starting point for approximating to the highly accurate CCSD(T) [that scale as O(N(7))] energies. On account of the requirement of only an MP2-level FC on the entire cluster, the current methodology ultimately leads to a cost-effective solution for the CCSD(T) level accurate binding energies of large-sized water clusters even at the complete basis set limit utilizing off-the-shelf hardware.
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Affiliation(s)
- Nityananda Sahu
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
| | - Gurmeet Singh
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
| | - Apurba Nandi
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
| | - Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
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10
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Yuan D, Shen X, Li W, Li S. Are fragment-based quantum chemistry methods applicable to medium-sized water clusters? Phys Chem Chem Phys 2016; 18:16491-500. [DOI: 10.1039/c6cp01931e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The GEBF method is demonstrated to be more accurate than the EE-MB method for medium-sized water clusters.
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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
| | - Xiaoling Shen
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - 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
| | - 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
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11
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Sahu N, Gadre SR, Rakshit A, Bandyopadhyay P, Miliordos E, Xantheas SS. Low energy isomers of (H2O)25 from a hierarchical method based on Monte Carlo temperature basin paving and molecular tailoring approaches benchmarked by MP2 calculations. J Chem Phys 2015; 141:164304. [PMID: 25362296 DOI: 10.1063/1.4897535] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We report new global minimum candidate structures for the (H2O)25 cluster that are lower in energy than the ones reported previously and correspond to hydrogen bonded networks with 42 hydrogen bonds and an interior, fully coordinated water molecule. These were obtained as a result of a hierarchical approach based on initial Monte Carlo Temperature Basin Paving sampling of the cluster's Potential Energy Surface with the Effective Fragment Potential, subsequent geometry optimization using the Molecular Tailoring Approach with the fragments treated at the second order Møller-Plesset (MP2) perturbation (MTA-MP2) and final refinement of the entire cluster at the MP2 level of theory. The MTA-MP2 optimized cluster geometries, constructed from the fragments, were found to be within <0.5 kcal/mol from the minimum geometries obtained from the MP2 optimization of the entire (H2O)25 cluster. In addition, the grafting of the MTA-MP2 energies yields electronic energies that are within <0.3 kcal/mol from the MP2 energies of the entire cluster while preserving their energy rank order. Finally, the MTA-MP2 approach was found to reproduce the MP2 harmonic vibrational frequencies, constructed from the fragments, quite accurately when compared to the MP2 ones of the entire cluster in both the HOH bending and the OH stretching regions of the spectra.
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Affiliation(s)
- Nityananda Sahu
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Avijit Rakshit
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Evangelos Miliordos
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, USA
| | - Sotiris S Xantheas
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, USA
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12
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Sahu N, Khire SS, Gadre SR. Structures, energetics and vibrational spectra of (H2O)32clusters: a journey from model potentials to correlated theory. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1062150] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Raghavachari K, Saha A. Accurate Composite and Fragment-Based Quantum Chemical Models for Large Molecules. Chem Rev 2015; 115:5643-77. [PMID: 25849163 DOI: 10.1021/cr500606e] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Krishnan Raghavachari
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Arjun Saha
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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14
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Affiliation(s)
- Michael A Collins
- †Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Ryan P A Bettens
- ‡Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
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15
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Gadre SR, Yeole SD, Sahu N. Quantum chemical investigations on molecular clusters. Chem Rev 2014; 114:12132-73. [PMID: 25341561 DOI: 10.1021/cr4006632] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
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16
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Li S, Li W, Ma J. Generalized energy-based fragmentation approach and its applications to macromolecules and molecular aggregates. Acc Chem Res 2014; 47:2712-20. [PMID: 24873495 DOI: 10.1021/ar500038z] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Conspectus The generalized energy-based fragmentation (GEBF) approach provides a very simple way of approximately evaluating the ground-state energy or properties of a large system in terms of ground-state energies of various small "electrostatically embedded" subsystems, which can be calculated with any traditional ab initio quantum chemistry (X) method (X = Hartree-Fock, density functional theory, and so on). Due to its excellent parallel efficiency, the GEBF approach at the X theory level (GEBF-X) allows full quantum mechanical (QM) calculations to be accessible for systems with hundreds and even thousands of atoms on ordinary workstations. The implementation of the GEBF approach at various theoretical levels can be easily done with existing quantum chemistry programs. This Account reviews the methodology, implementation, and applications of the GEBF-X approach. This method has been successfully applied to optimize the structures of various large systems including molecular clusters, polypeptides, proteins, and foldamers. Such investigations could allow us to elucidate the origin and nature of the cooperative interaction in secondary structures of long peptides or the driving force of the self-assembly processes of aromatic oligoamides. These GEBF-based QM calculations reveal that the structures and stability of various complex systems result from a subtle balance of many types of noncovalent interactions such as hydrogen bonding and van der Waals interactions. The GEBF-based ab initio molecular dynamics (AIMD) method also allows the investigation of dynamic behaviors of large systems on the order of tens of picoseconds. It was demonstrated that the conformational dynamics of two model peptides predicted by GEBF-based AIMD are noticeably different from those predicted by the classical force field MD method. With the target of extending QM calculations to molecular aggregates in the condensed phase, we have implemented the GEBF-based multilayer hybrid models, which could provide satisfactory descriptions of the binding energies between a solute molecule and its surrounding waters and the chain-length dependence of the conformational changes of oligomers in aqueous solutions. A coarse-grained polarizable molecular mechanics model, furnished with GEBF-X dipole moments of subsystems, exhibits some advantages of treating the electrostatic polarization with reduced computational costs. We anticipate that the GEBF approach will continue to develop with the ultimate goal of studying complicated phenomena at mesoscopic scales and serve as a practical tool to elucidate the structure and dynamics of chemical and biological systems.
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Affiliation(s)
- Shuhua Li
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute
of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Wei Li
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute
of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Jing Ma
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute
of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
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17
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Wang K, Li W, Li S. Generalized Energy-Based Fragmentation CCSD(T)-F12a Method and Application to the Relative Energies of Water Clusters (H2O)20. J Chem Theory Comput 2014; 10:1546-53. [DOI: 10.1021/ct401060m] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kedong Wang
- School
of Physics and Electronical Engineering, Henan Normal University, Xinxiang, 453007, People’s Repubic of China
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18
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Marković M, Ramek M, Sabolović J. Why Does the Coordination Mode of Physiological Bis(L-histidinato)copper(II) Differ in the Gas Phase, Crystal Lattice, and Aqueous Solutions? A Quantum Chemical Study. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201300746] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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19
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Rakshit A, Bandyopadhyay P. Finding low energy minima of (H2O)25 and (H2O)30 with temperature basin paving Monte Carlo method with effective fragment potential: New ‘global minimum’ and graph theoretical characterization of low energy structures. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.07.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Sahu N, Yeole SD, Gadre SR. Appraisal of molecular tailoring approach for large clusters. J Chem Phys 2013; 138:104101. [PMID: 23514459 DOI: 10.1063/1.4793706] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
High level ab initio investigations on molecular clusters are generally restricted to those of small size essentially due to the nonlinear scaling of corresponding computational cost. Molecular tailoring approach (MTA) is a fragmentation-based method, which offers an economical and efficient route for studying larger clusters. However, due to its approximate nature, the MTA-energies carry some errors vis-à-vis their full calculation counterparts. These errors in the MTA-energies are reduced by grafting the correction at a lower basis set (e.g., 6-31+G(d)) onto a higher basis set (e.g., aug-cc-pvdz or aug-cc-pvtz) calculation at MP2 level of theory. Further, better estimates of energies are obtained by making use of many-body interaction analysis. For this purpose, R-goodness (Rg) parameters for the three- and four-body interactions in a fragmentation scheme are proposed. The procedure employing grafting and many-body analysis has been tested out on molecular clusters of water, benzene, acetylene and carbon dioxide. It is found that for the fragmentation scheme having higher three- and four-body Rg-values, the errors in MTA-grafted energies are reduced typically to ~0.2 mH at MP2 level calculation. Coupled with the advantage in terms of computational resources and CPU time, the present method opens a possibility of accurate treatment of large molecular clusters.
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21
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Kazachenko S, Thakkar AJ. Water nanodroplets: Predictions of five model potentials. J Chem Phys 2013; 138:194302. [DOI: 10.1063/1.4804399] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Song GL, Li ZH, Fan KN. Extended Energy Divide-and-Conquer Method Based on Charge Conservation. J Chem Theory Comput 2013; 9:1992-9. [DOI: 10.1021/ct300850q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guo-Liang Song
- Shanghai Key Laboratory of Molecular
Catalysts and
Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Zhen Hua Li
- Shanghai Key Laboratory of Molecular
Catalysts and
Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Kang-Nian Fan
- Shanghai Key Laboratory of Molecular
Catalysts and
Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
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23
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Li W. Linear scaling explicitly correlated MP2-F12 and ONIOM methods for the long-range interactions of the nanoscale clusters in methanol aqueous solutions. J Chem Phys 2013; 138:014106. [DOI: 10.1063/1.4773011] [Citation(s) in RCA: 27] [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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24
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Furtado JP, Rahalkar AP, Shanker S, Bandyopadhyay P, Gadre SR. Facilitating Minima Search for Large Water Clusters at the MP2 Level via Molecular Tailoring. J Phys Chem Lett 2012; 3:2253-2258. [PMID: 26295779 DOI: 10.1021/jz300663u] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Water clusters (H2O)20 and (H2O)25 are explored at the Møller-Plesset second-order perturbation (MP2) level of theory. Geometry optimization is carried out on favorable structures, initially generated by the temperature basin paving (TBP) method, utilizing the fragment-based molecular tailoring approach (MTA). MTA-based stabilization energies at the complete basis set limit are accurately estimated by grafting the energy correction using a smaller basis set. For prototypical cases, the minima are established via MTA-based vibrational frequency calculations at the MP2/aug-cc-pVDZ level. The potential of MTA in tackling large clusters is further demonstrated by performing geometry optimization at MP2/aug-cc-pVDZ starting with the global minimum of (H2O)30 reported by Monte Carlo (MC) and molecular dynamics (MD) investigations. The present study brings out the efficacy of MTA in performing computationally expensive ab initio calculations with minimal off-the-shelf hardware without significant loss of accuracy.
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Affiliation(s)
- Jonathan P Furtado
- †Department of Chemistry, Indian Institute of Technology, Kanpur - 208016, India
| | - Anuja P Rahalkar
- †Department of Chemistry, Indian Institute of Technology, Kanpur - 208016, India
| | - Sudhanshu Shanker
- ‡School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi - 110067, India
| | - Pradipta Bandyopadhyay
- ‡School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi - 110067, India
| | - Shridhar R Gadre
- †Department of Chemistry, Indian Institute of Technology, Kanpur - 208016, India
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25
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Richard RM, Herbert JM. A generalized many-body expansion and a unified view of fragment-based methods in electronic structure theory. J Chem Phys 2012; 137:064113. [DOI: 10.1063/1.4742816] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Buchner F, Ritze HH, Beutler M, Schultz T, Hertel IV, Lübcke A. Role of alkali cations for the excited state dynamics of liquid water near the surface. J Chem Phys 2012; 137:024503. [DOI: 10.1063/1.4732582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Li F, Liu Y, Wang L, Zhao J, Chen Z. Improved stability of water clusters (H2O)30–48: a Monte Carlo search coupled with DFT computations. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1163-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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29
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Yeole SD, Sahu N, Gadre SR. Structures, energetics and vibrational spectra of CO2 clusters through molecular tailoring and cluster building algorithm. Phys Chem Chem Phys 2012; 14:7718-23. [DOI: 10.1039/c2cp23761j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Cobar EA, Horn PR, Bergman RG, Head-Gordon M. Examination of the hydrogen-bonding networks in small water clusters (n = 2–5, 13, 17) using absolutely localized molecular orbital energy decomposition analysis. Phys Chem Chem Phys 2012; 14:15328-39. [DOI: 10.1039/c2cp42522j] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Yeole SD, Gadre SR. Topography of scalar fields: molecular clusters and π-conjugated systems. J Phys Chem A 2011; 115:12769-79. [PMID: 21932861 DOI: 10.1021/jp2038976] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pioneering works due to Bader and co-workers have generated widespread interest in the study of the topography of molecular scalar fields, the first step of which is the identification and characterization of the corresponding critical points (CPs). The topography of a molecular system becomes successively richer in going from the bare nuclear potential (BNP) to the molecular electrostatic potential (MESP) through the molecular electron density (MED). The present work clearly demonstrates, through the study of some π-conjugated test molecules as well as molecular clusters, that the CPs could be economically located by following this path within ab initio level theory. Further, the topography mapping of large molecules, especially at a higher level of theory, is known to be a demanding task. However, it is rendered possible by following the above sequential mapping assisted by a divide-and-conquer-type method termed as the molecular tailoring approach (MTA). This is demonstrated with the topography mapping of β-carotene and benzene nonamer at MP2 and a (H(2)O)(32) cluster at the HF level of theory, which are rather challenging problems with contemporary off-the-shelf computer hardware.
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Affiliation(s)
- Sachin D Yeole
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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32
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Hua S, Xu L, Li W, Li S. Cooperativity in Long α- and 310-Helical Polyalanines: Both Electrostatic and van der Waals Interactions Are Essential. J Phys Chem B 2011; 115:11462-9. [DOI: 10.1021/jp203423w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shugui Hua
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Lina Xu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
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33
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Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem Rev 2011; 112:632-72. [DOI: 10.1021/cr200093j] [Citation(s) in RCA: 836] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Spencer R. Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Lyudmila V. Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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34
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Yeole SD, Gadre SR. Molecular cluster building algorithm: electrostatic guidelines and molecular tailoring approach. J Chem Phys 2011; 134:084111. [PMID: 21361531 DOI: 10.1063/1.3556819] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nano-sized clusters of various materials are recent experimental targets, since they exhibit size-dependent physico-chemical properties. A vast amount of literature is available on the study of molecular clusters but general methods for systematic evolution of their growth are rather scarce. The present work reports a molecular cluster building algorithm based on the electrostatic guidelines, followed by ab initio investigations, enabled by the application of molecular tailoring approach. Applications of the algorithm for generating geometries and interaction energies of large molecular clusters of zinc sulfide, benzene, and water are presented.
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35
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Yang Z, Hua S, Hua W, Li S. Structures of Neutral and Protonated Water Clusters Confined in Predesigned Hosts: A Quantum Mechanical/Molecular Mechanical Study. J Phys Chem B 2011; 115:8249-56. [DOI: 10.1021/jp2030736] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhen Yang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of the Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People's Republic of China
| | - Shugui Hua
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of the Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People's Republic of China
| | - Weijie Hua
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of the Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People's Republic of China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of the Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People's Republic of China
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36
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Jiang N, Tan RX, Ma J. Simulations of Solid-State Vibrational Circular Dichroism Spectroscopy of (S)-Alternarlactam by Using Fragmentation Quantum Chemical Calculations. J Phys Chem B 2011; 115:2801-13. [DOI: 10.1021/jp110152q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nan Jiang
- School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing, Jiangsu, 210093, People’s Republic of China
| | - Ren Xiang Tan
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu 210093, People’s Republic of China
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing, Jiangsu, 210093, People’s Republic of China
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