1
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Khire SS, Gadre SR. Development and testing of an algorithm for efficient MP2/CCSD(T) energy estimation of molecular clusters with the 2-body approach. J Comput Chem 2023; 44:261-267. [PMID: 35514315 DOI: 10.1002/jcc.26881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 12/31/2022]
Abstract
This work reports the development and testing of an automated algorithm for estimating the energies of weakly bound molecular clusters employing correlated theory. Firstly, the monomers and dimers of (homo/hetero) clusters are identified, and the sum of one-body and two-body contributions to correlation energy is calculated. The addition of this contribution to the Hartree-Fock full calculation (FC) energies provides a good estimate of the total energies at Møller-Plesset second-order perturbation theory (MP2)/coupled-cluster method with singles and doubles (CCSD) (T)-level theory using augmented Dunning basis sets. The estimated energies for several test clusters show an excellent agreement with their FC counterparts, with a substantial wall-clock time saving employing off-the-shelf hardware. Furthermore, the complete basis set (CBS) limit for MP2 energy computed using the two-body approach also agrees with its CBS energy with its FC counterpart.
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Affiliation(s)
- Subodh S Khire
- Department of Scientific Computing, Modelling, and Simulation, Savitribai Phule Pune University, Pune, India
| | - Shridhar R Gadre
- Department of Scientific Computing, Modelling, and Simulation, Savitribai Phule Pune University, Pune, India
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2
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Speake BT, Irons TJP, Wibowo M, Johnson AG, David G, Teale AM. An Embedded Fragment Method for Molecules in Strong Magnetic Fields. J Chem Theory Comput 2022; 18:7412-7427. [PMID: 36414537 DOI: 10.1021/acs.jctc.2c00865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An extension of the embedded fragment method for calculations on molecular clusters is presented, which includes strong external magnetic fields. The approach is flexible, allowing for calculations at the Hartree-Fock, current-density-functional theory, Møller-Plesset perturbation theory, and coupled-cluster levels using London atomic orbitals. For systems consisting of discrete molecular subunits, calculations using London atomic orbitals can be performed in a computationally tractable manner for systems beyond the reach of conventional calculations, even those accelerated by resolution-of-the-identity or Cholesky decomposition methods. To assess the applicability of the approach, applications to water clusters are presented, showing how strong magnetic fields enhance binding within the clusters. However, our calculations suggest that, contrary to previous suggestions in the literature, this enhanced binding may not be directly attributable to strengthening of hydrogen bonding. Instead, these results suggest that this arises for larger field strengths as a response of the system to the presence of the external field, which induces a charge density build up between the monomer units. The approach is embarrassingly parallel and its computational tractability is demonstrated for clusters of up to 103 water molecules in triple-ζ basis sets, which would correspond to conventional calculations with more than 12 000 basis functions.
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Affiliation(s)
- Benjamin T Speake
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United KIngdom
| | - Tom J P Irons
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United KIngdom
| | - Meilani Wibowo
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United KIngdom
| | - Andrew G Johnson
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United KIngdom
| | - Grégoire David
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United KIngdom.,Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, F-35000 Rennes, France
| | - Andrew M Teale
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United KIngdom.,Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
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3
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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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4
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Chen B, Xu X. XO-PBC: An Accurate and Efficient Method for Molecular Crystals. J Chem Theory Comput 2020; 16:4271-4285. [PMID: 32456429 DOI: 10.1021/acs.jctc.0c00232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we propose the XO-PBC method, which combines the eXtended ONIOM method (XO) with the periodic boundary condition (PBC) for the description of molecular crystals. XO-PBC tries to embed a finite cluster cut out from the solid into the periodic environment, making it feasible to employ advanced molecular quantum chemistry methods, which are usually prohibitively expensive for direct PBC calculations. In particular, XO-PBC utilizes the results from force calculations to design the scheme to fragment the molecule when crystals are made of large molecules and to select cluster model systems automatically consisting of dimer up to tetramer interactions for embedding. By applying an appropriate theory to each model, a satisfactory accuracy for the system under study is ensured, while a high efficiency is achieved with massively parallel computing by distributing model systems onto different processors. A comparison of the XO-PBC calculations with the conventional direct PBC calculations at the B3LYP level demonstrates its accuracy at substantially low cost for the description of molecular crystals. The usefulness of the XO-PBC method is further exemplified, showing that XO-PBC is able to predict the lattice energies of various types of molecular crystals within chemical accuracy (<4 kJ/mol) when the doubly hybrid density functional XYG3 is used as the target high level and the periodic PBE as the basic low level. The XO-PBC method provides a general protocol that brings the great predictive power of advanced electronic structure methods from molecular systems to the extended solids.
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Affiliation(s)
- Bozhu Chen
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
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5
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Kulkarni AD. Molecular Hydration of Carbonic Acid: Ab Initio Quantum Chemical and Density Functional Theory Investigation. J Phys Chem A 2019; 123:5504-5516. [PMID: 31244117 DOI: 10.1021/acs.jpca.9b01122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular hydration of carbonic acid (H2CO3) is investigated in terms of bonding patterns in H2CO3···(H2O) n [ n = 1-4] hydrogen-bonded clusters within ab initio quantum chemical and density functional theory (DFT) frameworks. Successive addition of water molecules to H2CO3···H2O entails elongation of O-H (hydroxyl) bond as well as contraction of specific intermolecular hydrogen bonds signifying hydration of carbonic acid; these structural features get markedly enhanced under the continuum solvation framework. A comparison between the structurally similar clusters H2CO3···(H2O) n and HCOOH···(H2O) n [ n = 1-3] brings out the structural stability of the former. The present investigation in conjunction with the binding energy behavior of approaching water molecule(s) should serve as a precursor for pathways exploring aqueous dissociation of H2CO3 for larger clusters, as well as development of force-field potentials for acid dissociation process.
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Affiliation(s)
- Anant D Kulkarni
- Solid State and Structural Chemistry Unit , Indian Institute of Science , Bangalore 560012 , India
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6
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Khire SS, Gadre SR. Pragmatic Many-Body Approach for Economic MP2 Energy Estimation of Molecular Clusters. J Phys Chem A 2019; 123:5005-5011. [PMID: 31117601 DOI: 10.1021/acs.jpca.9b03481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a procedure, within the many-body analysis (MBA) framework, for an economic yet accurate estimation of the correlated method-based energies of large molecular clusters employing Dunning's augmented basis sets. The basis of the procedure is to segregate the Hartree-Fock ( EHF) and correlation energy ( EC) estimations. EHF is found to differ by tens of millihartrees (mH) from its full-calculation (FC) counterpart on truncating the MBA expansion at the two-body (MBA-2) level. On the contrary, EC is estimated with smaller error on modest hardware with limited computation time at the (MBA-2) level. In view of this, we adopt a pragmatic method wherein the EHF (accurate to five decimal places) is taken from the FC, whereas EC is estimated at the MBA-2 level. This method is applied to a variety of medium to large molecular clusters at the MP2 level. Preliminary results at the CCSD(T) level for (H2O)16 and (H2O)17 are also reported with tremendous savings in wall-clock time and resources. The typical errors in MP2 and CCSD(T) energies per monomer are up to 0.1 and 0.2 mH, respectively. Thus the present method, balancing accuracy and computational economy, opens a way for estimating energies of large molecular clusters using correlated theories with large basis sets.
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Affiliation(s)
- Subodh S Khire
- Interdisciplinary School of Scientific Computing , Savitribai Phule Pune University , Pune 411007 , India
| | - Shridhar R Gadre
- Interdisciplinary School of Scientific Computing , Savitribai Phule Pune University , Pune 411007 , India
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7
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Ruiz Pestana L, Mardirossian N, Head-Gordon M, Head-Gordon T. Ab initio molecular dynamics simulations of liquid water using high quality meta-GGA functionals. Chem Sci 2017; 8:3554-3565. [PMID: 30155200 PMCID: PMC6092720 DOI: 10.1039/c6sc04711d] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 02/24/2017] [Indexed: 01/23/2023] Open
Abstract
We have used ab initio molecular dynamics (AIMD) to characterize water properties using two meta-generalized gradient approximation (meta-GGA) functionals, M06-L-D3 and B97M-rV, and compared their performance against a standard GGA corrected for dispersion, revPBE-D3, at ambient conditions (298 K, and 1 g cm-3 or 1 atm). Simulations of the equilibrium density, radial distribution functions, self-diffusivity, the infrared spectrum, liquid dipole moments, and characterizations of the hydrogen bond network show that all three functionals have overcome the problem of the early AIMD simulations that erroneously found ambient water to be highly structured, but they differ substantially among themselves in agreement with experiment on this range of water properties. We show directly using water cluster data up through the pentamer that revPBE-D3 benefits from a cancellation of its intrinsic functional error by running classical trajectories, whereas the meta-GGA functionals are demonstrably more accurate and would require the simulation of nuclear quantum effects to realize better agreement with all cluster and condensed phase properties.
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Affiliation(s)
- Luis Ruiz Pestana
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , USA .
| | - Narbe Mardirossian
- Kenneth S. Pitzer Center for Theoretical Chemistry , Department of Chemistry , University of California , Berkeley , USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry , Department of Chemistry , University of California , Berkeley , USA
| | - Teresa Head-Gordon
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , USA .
- Kenneth S. Pitzer Center for Theoretical Chemistry , Department of Chemistry , University of California , Berkeley , USA
- Departments of Chemistry , Bioengineering , Chemical and Biomolecular Engineering , University of California , Berkeley , USA
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8
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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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9
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Soniat M, Rogers DM, Rempe SB. Dispersion- and Exchange-Corrected Density Functional Theory for Sodium Ion Hydration. J Chem Theory Comput 2016; 11:2958-67. [PMID: 26575733 DOI: 10.1021/acs.jctc.5b00357] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A challenge in density functional theory is developing functionals that simultaneously describe intermolecular electron correlation and electron delocalization. Recent exchange-correlation functionals address those two issues by adding corrections important at long ranges: an atom-centered pairwise dispersion term to account for correlation and a modified long-range component of the electron exchange term to correct for delocalization. Here we investigate how those corrections influence the accuracy of binding free energy predictions for sodium-water clusters. We find that the dual-corrected ωB97X-D functional gives cluster binding energies closest to high-level ab initio methods (CCSD(T)). Binding energy decomposition shows that the ωB97X-D functional predicts the smallest ion-water (pairwise) interaction energy and larger multibody contributions for a four-water cluster than most other functionals - a trend consistent with CCSD(T) results. Also, ωB97X-D produces the smallest amounts of charge transfer and the least polarizable waters of the density functionals studied, which mimics the lower polarizability of CCSD. When compared with experimental binding free energies, however, the exchange-corrected CAM-B3LYP functional performs best (error <1 kcal/mol), possibly because of its parametrization to experimental formation enthalpies. For clusters containing more than four waters, "split-shell" coordination must be considered to obtain accurate free energies in comparison with experiment.
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Affiliation(s)
- Marielle Soniat
- Department of Chemistry, University of New Orleans , 2000 Lakeshore Drive, New Orleans, Louisiana 70148, United States
| | - David M Rogers
- Center for Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87123, United States.,Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - Susan B Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87123, United States
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10
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Dahlke EE, Truhlar DG. Electrostatically Embedded Many-Body Correlation Energy, with Applications to the Calculation of Accurate Second-Order Møller-Plesset Perturbation Theory Energies for Large Water Clusters. J Chem Theory Comput 2015; 3:1342-8. [PMID: 26633207 DOI: 10.1021/ct700057x] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electrostatically embedded many-body expansion (EE-MB), previously applied to the total electronic energy, is here applied only to the electronic correlation energy (CE), combined with a Hartree-Fock calculation on the entire system. The separate treatment of the Hartree-Fock and correlation energies provides an efficient way to approximate correlation energy for extended systems. We illustrate this here by calculating accurate Møller-Plesset second-order perturbation theory (MP2) energies for a series of clusters ranging in size from 5 to 20 water molecules. In this new method, called EE-MB-CE, where MB is pairwise additive (PA) or three-body (3B), the full Hartree-Fock energy of a system of N monomers is calculated (i.e., the many-body expansion is carried out to the Nth order), while the EE-MB method is used to calculate the correlation energy of the system. We find that not only does this new method lead to better energetics than the original EE-MB method but also that one is able to obtain excellent agreement with full MP2 calculations by considering only a two-body expansion of the correlation energy, leading to a considerable savings in computational time as compared to the three-body expansion. Additionally, we propose the use of a cutoff to further reduce the number of two-body terms that must be calculated, and we show that if a cutoff of 6 Å is used, then one can eliminate up to 44% of the pairs and still calculate energies to within 0.1% of the net interaction energy of the full cluster.
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Affiliation(s)
- Erin E Dahlke
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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11
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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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12
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Ji C, Mei Y. Some practical approaches to treating electrostatic polarization of proteins. Acc Chem Res 2014; 47:2795-803. [PMID: 24883956 DOI: 10.1021/ar500094n] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Conspectus Electrostatic interaction plays a significant role in determining many properties of biomolecules, which exist and function in aqueous solution, a highly polar environment. For example, proteins are composed of amino acids with charged, polar, and nonpolar side chains and their specific electrostatic properties are fundamental to the structure and function of proteins. An important issue that arises in computational study of biomolecular interaction and dynamics based on classical force field is lack of polarization. Polarization is a phenomenon in which the charge distribution of an isolated molecule will be distorted when interacting with another molecule or presented in an external electric field. The distortion of charge distribution is intended to lower the overall energy of the molecular system, which is counter balanced by the increased internal energy of individual molecules due to the distorted charge distributions. The amount of the charge redistribution, which characterizes the polarizability of a molecule, is determined by the level of the charge distortion. Polarization is inherently quantum mechanical, and therefore classical force fields with fixed atomic charges are incapable of capturing this important effect. As a result, simulation studies based on popular force fields, AMBER, CHARMM, etc., lack the polarization effect, which is a widely known deficiency in most computational studies of biomolecules today. Many efforts have been devoted to remedy this deficiency, such as adding additional movable charge on the atom, allowing atomic charges to fluctuate, or including induced multipoles. Although various successes have been achieved and progress at various levels has been reported over the past decades, the issue of lacking polarization in force field based simulations is far from over. For example, some of these methods do not always give converged results, and other methods require huge computational cost. This Account reviews recent work on developing polarized and polarizable force fields based on fragment quantum mechanical calculations for proteins. The methods described here are based on quantum mechanical calculations of proteins in solution, but with a different level of rigor and different computational efficiency for the molecular dynamics applications. In the general approach, a fragment quantum mechanical calculation for protein with implicit solvation is carried out to derive a polarized protein-specific charge (PPC) for any given protein structure. The PPC correctly reflects the polarization state of the protein in a given conformation, and it can also be dynamically changed as the protein changes conformation in dynamics simulations. Another approach that is computationally more efficient is the effective polarizable bond method in which only polar bonds or groups can be polarized and their polarizabilities are predetermined from quantum mechanical calculations of these groups in external electric fields. Both methods can be employed for applications in various situations by taking advantage of their unique features.
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Affiliation(s)
- Changge Ji
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
- Institute for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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Wang B, Yang KR, Xu X, Isegawa M, Leverentz HR, Truhlar DG. Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates. Acc Chem Res 2014; 47:2731-8. [PMID: 24841937 DOI: 10.1021/ar500068a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine atoms for capping dangling bonds, and we have shown that they can greatly improve the accuracy. Finally we present a new approach that goes beyond QM/MM by combining the convenience of molecular mechanics with the accuracy of fitting a potential function to electronic structure calculations on a specific system. To make the latter practical for systems with a large number of degrees of freedom, we developed a method to interpolate between local internal-coordinate fits to the potential energy. A key issue for the application to large systems is that rather than assigning the atoms or monomers to fragments, we assign the internal coordinates to reaction, secondary, and tertiary sets. Thus, we make a partition in coordinate space rather than atom space. Fits to the local dependence of the potential energy on tertiary coordinates are arrayed along a preselected reaction coordinate at a sequence of geometries called anchor points; the potential energy function is called an anchor points reactive potential. Electrostatically embedded fragment methods and the anchor points reactive potential, because they are based on treating an entire system by quantum mechanical electronic structure methods but are affordable for large and complex systems, have the potential to open new areas for accurate simulations where combined QM/MM methods are inadequate.
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Affiliation(s)
- Bo Wang
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Ke R. Yang
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Xuefei Xu
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Miho Isegawa
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Hannah R. Leverentz
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
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14
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Ouyang JF, Cvitkovic MW, Bettens RPA. Trouble with the Many-Body Expansion. J Chem Theory Comput 2014; 10:3699-707. [DOI: 10.1021/ct500396b] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John F. Ouyang
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
| | - Milan W. Cvitkovic
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
| | - Ryan P. A. Bettens
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
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15
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Barnes TA, Goodpaster JD, Manby FR, Miller TF. Accurate basis set truncation for wavefunction embedding. J Chem Phys 2014; 139:024103. [PMID: 23862925 DOI: 10.1063/1.4811112] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)] to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.
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Affiliation(s)
- Taylor A Barnes
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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16
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Yu HZ, Li C, Chen BH, Yang CT, Wang D, Fu Y, Hu S, Dang Z. Promising density functional theory methods for predicting the structures of uranyl complexes. RSC Adv 2014. [DOI: 10.1039/c4ra08264h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
By examining the overall accuracy of different theoretical methods in predicting the U–X bond distances (of a series uranyl complexes), we found that both the global-hybrid meta-GGA functional of BB1K and the range-seperated LC-BLYP functional are fairly good (even better than the popular B3LYP method).
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Affiliation(s)
- Hai-Zhu Yu
- Department of Polymer Science and Engineering
- University of Science and Technology Beijing
- Beijing 100083, China
| | - Can Li
- Department of Polymer Science and Engineering
- University of Science and Technology Beijing
- Beijing 100083, China
| | - Bai-Hua Chen
- Institute of Nuclear Physics and Chemistry
- CAEP
- Mianyang, China
| | - Chu-Ting Yang
- Institute of Nuclear Physics and Chemistry
- CAEP
- Mianyang, China
| | - Dongrui Wang
- Department of Polymer Science and Engineering
- University of Science and Technology Beijing
- Beijing 100083, China
| | - Yao Fu
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026, China
| | - Sheng Hu
- Institute of Nuclear Physics and Chemistry
- CAEP
- Mianyang, China
| | - Zhimin Dang
- Department of Polymer Science and Engineering
- University of Science and Technology Beijing
- Beijing 100083, China
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17
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Rossi M, Tkatchenko A, Rempe SB, Varma S. Role of methyl-induced polarization in ion binding. Proc Natl Acad Sci U S A 2013; 110:12978-83. [PMID: 23878238 PMCID: PMC3740884 DOI: 10.1073/pnas.1302757110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The chemical property of methyl groups that renders them indispensable to biomolecules is their hydrophobicity. Quantum mechanical studies undertaken here to understand the effect of point substitutions on potassium (K-) channels illustrate quantitatively how methyl-induced polarization also contributes to biomolecular function. K- channels regulate transmembrane salt concentration gradients by transporting K(+) ions selectively. One of the K(+) binding sites in the channel's selectivity filter, the S4 site, also binds Ba(2+) ions, which blocks K(+) transport. This inhibitory property of Ba(2+) ions has been vital in understanding K-channel mechanism. In most K-channels, the S4 site is composed of four threonine amino acids. The K channels that carry serine instead of threonine are significantly less susceptible to Ba(2+) block and have reduced stabilities. We find that these differences can be explained by the lower polarizability of serine compared with threonine, because serine carries one less branched methyl group than threonine. A T→S substitution in the S4 site reduces its polarizability, which, in turn, reduces ion binding by several kilocalories per mole. Although the loss in binding affinity is high for Ba(2+), the loss in K(+) binding affinity is also significant thermodynamically, which reduces channel stability. These results highlight, in general, how biomolecular function can rely on the polarization induced by methyl groups, especially those that are proximal to charged moieties, including ions, titratable amino acids, sulfates, phosphates, and nucleotides.
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Affiliation(s)
- Mariana Rossi
- Theory Department, Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Alexandre Tkatchenko
- Theory Department, Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Susan B. Rempe
- Biological and Materials Sciences Center, Sandia National Laboratories, Albuquerque, NM 87185; and
| | - Sameer Varma
- Biological and Materials Sciences Center, Sandia National Laboratories, Albuquerque, NM 87185; and
- Department of Cell Biology, Microbiology, and Molecular Biology, and Department of Physics, University of South Florida, Tampa, FL 33620
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18
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Suárez E, Suárez D. Multibody local approximation: application to conformational entropy calculations on biomolecules. J Chem Phys 2013; 137:084115. [PMID: 22938226 DOI: 10.1063/1.4748104] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Multibody type expansions like mutual information expansions are widely used for computing or analyzing properties of large composite systems. The power of such expansions stems from their generality. Their weaknesses, however, are the large computational cost of including high order terms due to the combinatorial explosion and the fact that truncation errors do not decrease strictly with the expansion order. Herein, we take advantage of the redundancy of multibody expansions in order to derive an efficient reformulation that captures implicitly all-order correlation effects within a given cutoff, avoiding the combinatory explosion. This approach, which is cutoff dependent rather than order dependent, keeps the generality of the original expansions and simultaneously mitigates their limitations provided that a reasonable cutoff can be used. An application of particular interest can be the computation of the conformational entropy of flexible peptide molecules from molecular dynamics trajectories. By combining the multibody local estimations of conformational entropy with average values of the rigid-rotor and harmonic-oscillator entropic contributions, we obtain by far a tighter upper bound of the absolute entropy than the one obtained by the broadly used quasi-harmonic method.
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Affiliation(s)
- Ernesto Suárez
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
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19
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Beran GJO, Wen S, Nanda K, Huang Y, Heit Y. Accurate and Robust Molecular Crystal Modeling Using Fragment-Based Electronic Structure Methods. Top Curr Chem (Cham) 2013; 345:59-93. [DOI: 10.1007/128_2013_502] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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20
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Manby FR, Stella M, Goodpaster JD, Miller TF. A Simple, Exact Density-Functional-Theory Embedding Scheme. J Chem Theory Comput 2012; 8:2564-2568. [PMID: 22904692 PMCID: PMC3419460 DOI: 10.1021/ct300544e] [Citation(s) in RCA: 254] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Indexed: 12/17/2022]
Abstract
Density functional theory (DFT) provides a formally exact framework for quantum embedding. The appearance of nonadditive kinetic energy contributions in this context poses significant challenges, but using optimized effective potential (OEP) methods, various groups have devised DFT-in-DFT methods that are equivalent to Kohn-Sham (KS) theory on the whole system. This being the case, we note that a very considerable simplification arises from doing KS theory instead. We then describe embedding schemes that enforce Pauli exclusion via a projection technique, completely avoiding numerically demanding OEP calculations. Illustrative applications are presented using DFT-in-DFT, wave-function-in-DFT, and wave-function-in-Hartree-Fock embedding, and using an embedded many-body expansion.
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21
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Wen S, Nanda K, Huang Y, Beran GJO. Practical quantum mechanics-based fragment methods for predicting molecular crystal properties. Phys Chem Chem Phys 2012; 14:7578-90. [DOI: 10.1039/c2cp23949c] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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22
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Wen S, Beran GJO. Accurate Molecular Crystal Lattice Energies from a Fragment QM/MM Approach with On-the-Fly Ab Initio Force Field Parametrization. J Chem Theory Comput 2011; 7:3733-42. [DOI: 10.1021/ct200541h] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shuhao Wen
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, California 92521, United States
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23
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Shields RM, Temelso B, Archer KA, Morrell TE, Shields GC. Accurate predictions of water cluster formation, (H₂O)(n=2-10). J Phys Chem A 2011; 114:11725-37. [PMID: 20882961 DOI: 10.1021/jp104865w] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An efficient mixed molecular dynamics/quantum mechanics model has been applied to the water cluster system. The use of the MP2 method and correlation consistent basis sets, with appropriate correction for BSSE, allows for the accurate calculation of electronic and free energies for the formation of clusters of 2-10 water molecules. This approach reveals new low energy conformers for (H(2)O)(n=7,9,10). The water heptamer conformers comprise five different structural motifs ranging from a three-dimensional prism to a quasi-planar book structure. A prism-like structure is favored energetically at low temperatures, but a chair-like structure is the global Gibbs free energy minimum past 200 K. The water nonamers exhibit less complexity with all the low energy structures shaped like a prism. The decamer has 30 conformers that are within 2 kcal/mol of the Gibbs free energy minimum structure at 298 K. These structures are categorized into four conformer classes, and a pentagonal prism is the most stable structure from 0 to 320 K. Results can be used as benchmark values for empirical water models and density functionals, and the method can be applied to larger water clusters.
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Affiliation(s)
- Robert M Shields
- Dean's Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, USA
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24
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Multibody effects in ion binding and selectivity. Biophys J 2011; 99:3394-401. [PMID: 21081088 DOI: 10.1016/j.bpj.2010.09.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 08/26/2010] [Accepted: 09/02/2010] [Indexed: 11/23/2022] Open
Abstract
Selective binding of ions to biomolecules plays a vital role in numerous biological processes. To understand the specific role of induced effects in selective ion binding, we use quantum chemical and pairwise-additive force-field simulations to study Na(+) and K(+) binding to various small molecules representative of ion binding functional groups in biomolecules. These studies indicate that electronic polarization significantly contributes to both absolute and relative ion-binding affinities. Furthermore, this contribution depends on both the number and the specific chemistries of the coordinating molecules, thus highlighting the complexity of ion-ligand interactions. Specifically, multibody interactions reduce as well as enhance the dipole moments of the ion-coordinating molecules, thereby affecting observables like coordination number distributions of ions. The differential polarization induced in molecules coordinating these two equivalently charged, but different-sized, ions also depends upon the number of coordinating molecules, showing the importance of multibody effects in distinguishing these ions thermodynamically. Because even small differences in ionic radii (0.4 Å for Na(+) and K(+)) produce differential polarization trends critical to distinguishing ions thermodynamically, it is likely that polarization plays an important role in thermodynamically distinguishing other ions and charged chemical and biological functional groups.
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25
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26
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Jing YQ, Han KL. Quantum mechanical effect in protein–ligand interaction. Expert Opin Drug Discov 2009; 5:33-49. [DOI: 10.1517/17460440903440127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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27
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Santra B, Michaelides A, Scheffler M. Coupled cluster benchmarks of water monomers and dimers extracted from density-functional theory liquid water: The importance of monomer deformations. J Chem Phys 2009; 131:124509. [DOI: 10.1063/1.3236840] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Bryantsev VS, Diallo MS, van Duin ACT, Goddard WA. Evaluation of B3LYP, X3LYP, and M06-Class Density Functionals for Predicting the Binding Energies of Neutral, Protonated, and Deprotonated Water Clusters. J Chem Theory Comput 2009; 5:1016-26. [PMID: 26609610 DOI: 10.1021/ct800549f] [Citation(s) in RCA: 272] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vyacheslav S. Bryantsev
- Materials and Process Simulation Center, Beckman Institute, MC 139-74, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16801
| | - Mamadou S. Diallo
- Materials and Process Simulation Center, Beckman Institute, MC 139-74, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16801
| | - Adri C. T. van Duin
- Materials and Process Simulation Center, Beckman Institute, MC 139-74, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16801
| | - William A. Goddard
- Materials and Process Simulation Center, Beckman Institute, MC 139-74, California Institute of Technology, Pasadena, California 91125, and Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16801
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29
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Nordlund D, Odelius M, Bluhm H, Ogasawara H, Pettersson L, Nilsson A. Electronic structure effects in liquid water studied by photoelectron spectroscopy and density functional theory. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.04.096] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Li W, Qi C, Wu X, Rong H, Gong L. Theoretical investigation of interactions between glycine cation based ionic liquids and water molecules. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.01.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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31
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Shields GC, Kirschner KN. The Limitations of Certain Density Functionals in Modeling Neutral Water Clusters. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/15533170701853918] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- George C. Shields
- a Department of Chemistry , Center for Molecular Design, Hamilton College , Clinton, New York, USA
| | - Karl N. Kirschner
- a Department of Chemistry , Center for Molecular Design, Hamilton College , Clinton, New York, USA
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32
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Du S, Francisco JS, Schenter GK, Garrett BC. Many-body decomposition of the binding energies for OH⋅(H2O)2 and OH⋅(H2O)3 complexes. J Chem Phys 2008; 128:084307. [DOI: 10.1063/1.2828522] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Kamiya M, Hirata S, Valiev M. Fast electron correlation methods for molecular clusters without basis set superposition errors. J Chem Phys 2008; 128:074103. [DOI: 10.1063/1.2828517] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Dahlke EE, Orthmeyer MA, Truhlar DG. Assessment of Multicoefficient Correlation Methods, Second-Order Møller−Plesset Perturbation Theory, and Density Functional Theory for H3O+(H2O)n (n = 1−5) and OH-(H2O)n (n = 1−4). J Phys Chem B 2008; 112:2372-81. [DOI: 10.1021/jp075823q] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Erin E. Dahlke
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Michelle A. Orthmeyer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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35
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Lee HS, Tuckerman ME. Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit. J Chem Phys 2007; 126:164501. [PMID: 17477608 DOI: 10.1063/1.2718521] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30 ps) preceded a 60 ps long production run. The temperature drift during the entire 60 ps trajectory was found to be minimal. The diffusion coefficient [0.055 A2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.
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Affiliation(s)
- Hee-Seung Lee
- Department of Chemistry, New York University, New York 10003, USA
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36
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Auer B, Kumar R, Schmidt JR, Skinner JL. Hydrogen bonding and Raman, IR, and 2D-IR spectroscopy of dilute HOD in liquid D2O. Proc Natl Acad Sci U S A 2007; 104:14215-20. [PMID: 17576923 PMCID: PMC1964876 DOI: 10.1073/pnas.0701482104] [Citation(s) in RCA: 292] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present improvements on our previous approaches for calculating vibrational spectroscopy observables for the OH stretch region of dilute HOD in liquid D2O. These revised approaches are implemented to calculate IR and isotropic Raman spectra, using the SPC/E simulation model, and the results are in good agreement with experiment. We also calculate observables associated with three-pulse IR echoes: the peak shift and 2D-IR spectrum. The agreement with experiment for the former is improved over our previous calculations, but discrepancies between theory and experiment still exist. Using our proposed definition for hydrogen bonding in liquid water, we decompose the distribution of frequencies in the OH stretch region in terms of subensembles of HOD molecules with different local hydrogen-bonding environments. Such a decomposition allows us to make the connection with experiments and calculations on water clusters and more generally to understand the extent of the relationship between transition frequency and local structure in the liquid.
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Affiliation(s)
- B. Auer
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706
| | - R. Kumar
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706
| | - J. R. Schmidt
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706
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37
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Znamenskiy VS, Green ME. Quantum Calculations On Hydrogen Bonds In Certain Water Clusters Show Cooperative Effects. J Chem Theory Comput 2006; 3:103-114. [PMID: 19169381 DOI: 10.1021/ct600139d] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water molecules in clefts and small clusters are in a significantly different environment than in bulk water. We have carried out ab initio calculations that demonstrate this in a series of clusters, showing that cooperative effects must be taken into account in the treatment of hydrogen bonds and water clusters in such bounded systems. Hydrogen bonds between water molecules in simulations are treated most frequently by using point charge water potentials, such as TIP3P or SPC, sometimes with a polarizable extension. These produce excellent results in bulk water, for which they are calibrated. Clefts are different from bulk; it is necessary to look at smaller systems, and investigate the effect of limited numbers of neighbors. We start with a study of isolated clusters of water with varying numbers of neighbors of a hydrogen bonded pair of water molecules. The cluster as a whole is in vacuum. The clusters are defined so as to provide the possible arrangements of nearest neighbors of a central hydrogen bonded pair of water molecules. We then scan the length and angles of the central hydrogen bond of the clusters, using density functional theory, for each possible arrangement of donor and acceptor hydrogen bonds on the central hydrogen bonding pair; the potential of interaction of two water molecules varies with the number of donor and of acceptor neighbors. This also involves changes in charge on the water molecules as a function of bond length, and changes in energy and length as a function of number of neighboring donor and acceptor molecules. Energy varies by approximately 6 k(B)T near room temperature from the highest to the lowest energy when bond length alone is varied, enough to seriously affect simulations.
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Affiliation(s)
- Vasiliy S Znamenskiy
- Department of Chemistry, City College of the City University of New York, 138 St and Convent Ave, New York NY 10031
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38
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McGrath MJ, Siepmann JI, Kuo IFW, Mundy CJ. Vapor–liquid equilibria of water from first principles: comparison of density functionals and basis sets. Mol Phys 2006. [DOI: 10.1080/00268970601014781] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Lee HS, Tuckerman ME. Structure of liquid water at ambient temperature fromab initiomolecular dynamics performed in the complete basis set limit. J Chem Phys 2006; 125:154507. [PMID: 17059272 DOI: 10.1063/1.2354158] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Structural properties of liquid water at ambient temperature were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (CPAIMD) simulations combined with the Kohn-Sham (KS) density functional theory and the BLYP exchange-correlation functional for the electronic structure. Unlike other recent work on the same subject, where plane-wave (PW) or hybrid Gaussian/plane-wave basis sets were employed, in the present paper, a discrete variable representation (DVR) basis set is used to expand the KS orbitals, so that with the real-space grid adapted in the present work, the properties of liquid water could be obtained very near the complete basis set limit. Structural properties of liquid water were extracted from a 30 ps CPAIMD-BLYP/DVR trajectory at 300 K. The radial distribution functions (RDFs), spatial distribution functions, and hydrogen bond geometry obtained from the CPAIMD-BLYP/DVR simulation are generally in good agreement with the most up to date experimental measurements. Compared to recent ab initio MD simulations based on PW basis sets, less significant overstructuring was found in the RDFs and the distributions of hydrogen bond angles, suggesting that previous plane-wave and Gaussian basis set calculations have exaggerated the tendency toward overstructuring.
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Affiliation(s)
- Hee-Seung Lee
- Department of Chemistry, New York University, New York, New York 10003, USA
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