51
|
Sedghamiz E, Nagy B, Jensen F. Probing the Importance of Charge Flux in Force Field Modeling. J Chem Theory Comput 2017. [PMID: 28635293 DOI: 10.1021/acs.jctc.7b00296] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ∼900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles, and torsional angles and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields and indications for how to design improved force fields. The torsional degrees of freedom are the main contribution to conformational changes of atomic charges and molecular dipole moments, but indirect effects due to change in bond distances and angles account for ∼25% of the variation. Charge flux effects dominate for changes in bond distances and are also the main component of the variation in bond angles, while they are ∼25% compared to the geometry variations for torsional degrees of freedom. The geometry and charge flux contributions to some extent produce compensating effects.
Collapse
Affiliation(s)
- Elaheh Sedghamiz
- Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus, Denmark.,Department of Chemistry, University of Isfahan , Isfahan 81746-73441, Iran
| | - Balazs Nagy
- Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus, Denmark
| |
Collapse
|
52
|
Witzke S, List NH, Olsen JMH, Steinmann C, Petersen M, Beerepoot MTP, Kongsted J. An averaged polarizable potential for multiscale modeling in phospholipid membranes. J Comput Chem 2017; 38:601-611. [PMID: 28160294 DOI: 10.1002/jcc.24718] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 01/28/2023]
Abstract
A set of average atom-centered charges and polarizabilities has been developed for three types of phospholipids for use in polarizable embedding calculations. The lipids investigated are 1,2-dimyristoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, and 1-palmitoyl-2-oleoyl-sn-glycerol-3-phospho-L-serine given their common use both in experimental and computational studies. The charges, and to a lesser extent the polarizabilities, are found to depend strongly on the molecular conformation of the lipids. Furthermore, the importance of explicit polarization is underlined for the description of larger assemblies of lipids, that is, membranes. In conclusion, we find that specially developed polarizable parameters are needed for embedding calculations in membranes, while common non-polarizable point-charge force fields usually perform well enough for structural and dynamical studies. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Sarah Witzke
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, DK-5230, Denmark
| | - Nanna Holmgaard List
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | | | - Casper Steinmann
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Michael Petersen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, DK-5230, Denmark
| | - Maarten T P Beerepoot
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, Tromsø, N-9037, Norway
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, DK-5230, Denmark
| |
Collapse
|
53
|
Wang H, Yang W. Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory. J Chem Phys 2017; 144:224107. [PMID: 27305996 DOI: 10.1063/1.4953558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics' force fields and nontransferable molecule-specific atomic polarizabilities.
Collapse
Affiliation(s)
- Hao Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| |
Collapse
|
54
|
Huang J, Mei Y, König G, Simmonett AC, Pickard FC, Wu Q, Wang LP, MacKerell AD, Brooks BR, Shao Y. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches. J Chem Theory Comput 2017; 13:679-695. [PMID: 28081366 DOI: 10.1021/acs.jctc.6b01125] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.
Collapse
Affiliation(s)
- Jing Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States.,Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Gerhard König
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, NRW Germany, EU
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Frank C Pickard
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Qin Wu
- Center for Functional Nanomaterials, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California , 1 Shields Avenue, Davis, California 95616, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States.,Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| |
Collapse
|
55
|
Verstraelen T, Vandenbrande S, Heidar-Zadeh F, Vanduyfhuys L, Van Speybroeck V, Waroquier M, Ayers PW. Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development. J Chem Theory Comput 2016; 12:3894-912. [DOI: 10.1021/acs.jctc.6b00456] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toon Verstraelen
- Center
for Molecular Modeling (CMM), Member of the QCMM Ghent−Brussels
Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Steven Vandenbrande
- Center
for Molecular Modeling (CMM), Member of the QCMM Ghent−Brussels
Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Farnaz Heidar-Zadeh
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 West
Main Street, Hamilton, Ontario L8S 4M1, Canada
| | - Louis Vanduyfhuys
- Center
for Molecular Modeling (CMM), Member of the QCMM Ghent−Brussels
Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Veronique Van Speybroeck
- Center
for Molecular Modeling (CMM), Member of the QCMM Ghent−Brussels
Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Michel Waroquier
- Center
for Molecular Modeling (CMM), Member of the QCMM Ghent−Brussels
Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Paul W. Ayers
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 West
Main Street, Hamilton, Ontario L8S 4M1, Canada
| |
Collapse
|
56
|
Debiec KT, Cerutti DS, Baker LR, Gronenborn AM, Case DA, Chong LT. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model. J Chem Theory Comput 2016; 12:3926-47. [PMID: 27399642 PMCID: PMC4980686 DOI: 10.1021/acs.jctc.6b00567] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We present the AMBER
ff15ipq force field for proteins, the second-generation
force field developed using the Implicitly Polarized Q (IPolQ) scheme
for deriving implicitly polarized atomic charges in the presence of
explicit solvent. The ff15ipq force field is a complete rederivation
including more than 300 unique atomic charges, 900 unique torsion
terms, 60 new angle parameters, and new atomic radii for polar hydrogens.
The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of
proteins and enables direct calculation of nuclear magnetic resonance
(NMR) relaxation parameters from molecular dynamics simulations. The
atomic radii improve the accuracy of modeling salt bridge interactions
relative to contemporary fixed-charge force fields, rectifying a limitation
of ff14ipq that resulted from its use of pair-specific Lennard-Jones
radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants
exceptionally well, gives reasonable agreement with NMR relaxation
rates, and maintains the expected conformational propensities of structured
proteins/peptides, as well as disordered peptides—all on the
microsecond (μs) time scale, which is a critical regime for
drug design applications. These encouraging results demonstrate the
power and robustness of our automated methods for deriving new force
fields. All parameters described here and the mdgx program used to
fit them are included in the AmberTools16 distribution.
Collapse
Affiliation(s)
- Karl T Debiec
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh and Carnegie Mellon University , Pittsburgh, Pennsylvania, United States.,Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - David S Cerutti
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Lewis R Baker
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University , New Brunswick, New Jersey 08854, United States
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
57
|
S. Nørby M, Magnus Haugaard Olsen J, Kongsted J, Aagard Jensen HJ. Multipole moments for embedding potentials: Exploring different atomic allocation algorithms. J Comput Chem 2016; 37:1887-96. [DOI: 10.1002/jcc.24403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/07/2016] [Accepted: 04/13/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Morten S. Nørby
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark, DK-5230 Odense M, Denmark
- Department of Physics; Chemistry and Biology, Linköping University; Linköping SE 58183 Sweden
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; DK-5230 Odense M Denmark
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale De Lausanne (EPFL); Lausanne CH-1015 Switzerland
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Hans Jørgen Aagard Jensen
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark, DK-5230 Odense M, Denmark
| |
Collapse
|
58
|
Nørby MS, Vahtras O, Norman P, Kongsted J. Assessing frequency-dependent site polarisabilities in linear response polarisable embedding. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1177667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Morten S. Nørby
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Olav Vahtras
- KTH Royal Institute of Technology, School of Biotechnology, Division of Theoretical Chemistry and Biology, Stockholm, Sweden
| | - Patrick Norman
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
59
|
A Test of Various Partial Atomic Charge Models for Computations on Diheteroaryl Ketones and Thioketones. COMPUTATION 2016. [DOI: 10.3390/computation4010003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
60
|
|
61
|
Sims MT, Abbott LC, Cowling SJ, Goodby JW, Moore JN. Experimental and molecular dynamics studies of anthraquinone dyes in a nematic liquid-crystal host: a rationale for observed alignment trends. Phys Chem Chem Phys 2016; 18:20651-63. [DOI: 10.1039/c6cp03823a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The experimental alignment trend of a set of anthraquinone dyes in a nematic host is rationalised by calculated molecular order parameters and transition dipole moments.
Collapse
Affiliation(s)
- Mark T. Sims
- Department of Chemistry
- The University of York
- Heslington
- UK
| | | | | | - John W. Goodby
- Department of Chemistry
- The University of York
- Heslington
- UK
| | - John N. Moore
- Department of Chemistry
- The University of York
- Heslington
- UK
| |
Collapse
|
62
|
Finkelmann AR, Göller AH, Schneider G. Robust molecular representations for modelling and design derived from atomic partial charges. Chem Commun (Camb) 2016; 52:681-4. [DOI: 10.1039/c5cc07887c] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ab initio partial charge schemes are identified for molecular modelling purposes, and potential pitfalls of their application are discussed.
Collapse
Affiliation(s)
- A. R. Finkelmann
- Department of Chemistry and Applied Biosciences
- ETH Zürich
- 8093 Zürich
- Switzerland
| | - A. H. Göller
- Bayer Pharma AG
- Global Drug Discovery
- D-42096 Wuppertal
- Germany
| | - G. Schneider
- Department of Chemistry and Applied Biosciences
- ETH Zürich
- 8093 Zürich
- Switzerland
| |
Collapse
|
63
|
Gabrieli A, Sant M, Demontis P, Suffritti GB. Partial Charges in Periodic Systems: Improving Electrostatic Potential (ESP) Fitting via Total Dipole Fluctuations and Multiframe Approaches. J Chem Theory Comput 2015; 11:3829-43. [DOI: 10.1021/acs.jctc.5b00503] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Andrea Gabrieli
- Dipartimento di Chimica e
Farmacia, Università degli Studi di Sassari, Via Vienna
2, 07100 Sassari, Italy
| | - Marco Sant
- Dipartimento di Chimica e
Farmacia, Università degli Studi di Sassari, Via Vienna
2, 07100 Sassari, Italy
| | - Pierfranco Demontis
- Dipartimento di Chimica e
Farmacia, Università degli Studi di Sassari, Via Vienna
2, 07100 Sassari, Italy
| | - Giuseppe B. Suffritti
- Dipartimento di Chimica e
Farmacia, Università degli Studi di Sassari, Via Vienna
2, 07100 Sassari, Italy
| |
Collapse
|
64
|
Sims MT, Abbott LC, Cowling SJ, Goodby JW, Moore JN. Dyes in Liquid Crystals: Experimental and Computational Studies of a Guest-Host System Based on a Combined DFT and MD Approach. Chemistry 2015; 21:10123-30. [PMID: 26031244 PMCID: PMC4515093 DOI: 10.1002/chem.201406372] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Indexed: 11/28/2022]
Abstract
Practical applications of guest–host liquid crystal systems are critically dependent on the alignment of the guest species within the liquid crystal host. UV/Vis absorption spectroscopy shows that the 1,5-dihydroxy-2,6-bis-(4-propylphenyl)-9,10-anthraquinone dye aligns within the E7 nematic host, giving an experimental dichroic ratio of 9.40 and dye order parameter of 0.74. This alignment was modelled by using a combination of density functional theory (DFT) and molecular dynamics (MD) computational approaches that do not require the input of experimental data. Time-dependent DFT calculations show that the electronic transition dipole moment is highly aligned with the long molecular axis of the dye. Fully atomistic MD simulations show that the long axis of the dye is less highly aligned within the E7 host, indicating that this contribution limits the overall dye alignment and, thereby, the potential practical applications of this particular system. Importantly, this study demonstrates an experimental and combined DFT and MD computational approach that may be applied generally to guest–host systems, providing a potential route to their rational design.
Collapse
Affiliation(s)
- Mark T Sims
- Department of Chemistry, The University of York, Heslington, York YO10 5DD (UK), Fax: (+44) 1904-322516
| | - Laurence C Abbott
- Department of Chemistry, The University of York, Heslington, York YO10 5DD (UK), Fax: (+44) 1904-322516
| | - Stephen J Cowling
- Department of Chemistry, The University of York, Heslington, York YO10 5DD (UK), Fax: (+44) 1904-322516
| | - John W Goodby
- Department of Chemistry, The University of York, Heslington, York YO10 5DD (UK), Fax: (+44) 1904-322516
| | - John N Moore
- Department of Chemistry, The University of York, Heslington, York YO10 5DD (UK), Fax: (+44) 1904-322516.
| |
Collapse
|
65
|
Mei Y, Simmonett AC, Pickard FC, DiStasio RA, Brooks BR, Shao Y. Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions. J Phys Chem A 2015; 119:5865-82. [PMID: 25945749 DOI: 10.1021/acs.jpca.5b03159] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to carry out a detailed analysis of the molecular static polarizability, which is the response of the molecule to a uniform external electric field, the molecular polarizability was computed using the finite-difference method for 21 small molecules, using density functional theory. Within nine charge population schemes (Löwdin, Mulliken, Becke, Hirshfeld, CM5, Hirshfeld-I, NPA, CHELPG, MK-ESP) in common use, the charge fluctuation contribution is found to dominate the molecular polarizability, with its ratio ranging from 59.9% with the Hirshfeld or CM5 scheme to 96.2% with the Mulliken scheme. The Hirshfeld-I scheme is also used to compute the other contribution to the molecular polarizability coming from the induced atomic dipoles, and the atomic polarizabilities in eight small molecules and water pentamer are found to be highly anisotropic for most atoms. Overall, the results suggest that (a) more emphasis probably should be placed on the charge fluctuation terms in future polarizable force field development and (b) an anisotropic polarizability might be more suitable than an isotropic one in polarizable force fields based entirely or partially on the induced atomic dipoles.
Collapse
Affiliation(s)
- Ye Mei
- †State Key Laboratory of Precision Spectroscopy, Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China.,‡NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China.,⊥Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Andrew C Simmonett
- ⊥Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Frank C Pickard
- ⊥Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Robert A DiStasio
- §Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Bernard R Brooks
- ⊥Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Yihan Shao
- ∥Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States
| |
Collapse
|
66
|
Kessler J, Bouř P. Transfer of Frequency-Dependent Polarizabilities: A Tool To Simulate Absorption and Circular Dichroism Molecular Spectra. J Chem Theory Comput 2015; 11:2210-20. [DOI: 10.1021/acs.jctc.5b00136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiří Kessler
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 166
10 Prague, Czech Republic
- Department
of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 40 Prague, Czech Republic
| | - Petr Bouř
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 166
10 Prague, Czech Republic
| |
Collapse
|
67
|
Matin MA, Chitumalla RK, Lim M, Gao X, Jang J. Density Functional Theory Study on the Cross-Linking of Mussel Adhesive Proteins. J Phys Chem B 2015; 119:5496-504. [DOI: 10.1021/acs.jpcb.5b01152] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Xingfa Gao
- CAS Key Laboratory
for Biomedical Effects of Nanomaterials and Nanosafety, Institute
of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | | |
Collapse
|
68
|
Olsen JMH, List NH, Kristensen K, Kongsted J. Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials. J Chem Theory Comput 2015; 11:1832-42. [DOI: 10.1021/acs.jctc.5b00078] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jógvan Magnus Haugaard Olsen
- Laboratory
of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Nanna Holmgaard List
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Kasper Kristensen
- qLEAP
Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| |
Collapse
|
69
|
Torii H. Electronic Structural Basis for the Atomic Partial Charges of Planar Molecular Systems Derived from Out-of-Plane Dipole Derivatives. J Phys Chem A 2015; 119:3277-84. [DOI: 10.1021/jp512884g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hajime Torii
- Department
of Chemistry,
Faculty of Education, and Department of Optoelectronics and Nanostructure
Science, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan
| |
Collapse
|
70
|
Seidler T, Champagne B. Which charge definition for describing the crystal polarizing field and the χ(1) and χ(2) of organic crystals? Phys Chem Chem Phys 2015; 17:19546-56. [DOI: 10.1039/c5cp03248b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Crystal optical susceptibilities are probes to assess the performance of the charge definition employed to describe the crystal polarizing field.
Collapse
Affiliation(s)
- Tomasz Seidler
- Laboratoire de Chimie Théorique
- University of Namur
- Namur
- Belgium
- Faculty of Chemistry
| | | |
Collapse
|
71
|
|
72
|
Cui ZH, Lischka H, Beneberu HZ, Kertesz M. Double pancake bonds: pushing the limits of strong π-π stacking interactions. J Am Chem Soc 2014; 136:12958-65. [PMID: 25203200 PMCID: PMC4183611 DOI: 10.1021/ja505624y] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Indexed: 11/30/2022]
Abstract
The concept of a double-bonded pancake bonding mechanism is introduced to explain the extremely short π-π stacking contacts in dimers of dithiatriazines. While ordinary single pancake bonds occur between radicals and already display significantly shorter interatomic distances in comparison to van der Waals (vdW) contacts, the double-bonded pancake dimer is based on diradicaloid or antiaromatic molecules and exhibits even shorter and stronger intermolecular bonds that breach into the range of extremely stretched single bonds in terms of bond distances and binding energies. These properties give rise to promising possibilities in the design of new materials with high electrical conductivity and for the field of spintronics. The analysis of the double pancake bond is based on cutting edge electron correlation theory combining multireference (nondynamical) effects and dispersion (dynamical) contributions in a balanced way providing accurate interaction energies and distributions of unpaired spins. It is also shown that the present examples do not stand isolated but that similar mechanisms operate in several analogous nonradical molecular systems to form double-bonded π-stacking pancake dimers. We report on the amazing properties of a new type of stacking interaction mechanism between π conjugated molecules in the form of a "double pancake bond" which breaks the record for short intermolecular distances and provides formidable strength for some π-π stacking interactions.
Collapse
Affiliation(s)
- Zhong-hua Cui
- Department
of Chemistry, Georgetown University, 37th and O Streets, NW, Washington, D.C. 20057-1227, United States
| | - Hans Lischka
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79409-1061, United States
- Institute
for Theoretical Chemistry, University of
Vienna, A-1090 Vienna, Austria
| | - Habtamu Z. Beneberu
- Department
of Chemistry, Georgetown University, 37th and O Streets, NW, Washington, D.C. 20057-1227, United States
- Department
of Chemistry, University of the District
of Columbia, Washington, D.C. 20008, United
States
| | - Miklos Kertesz
- Department
of Chemistry, Georgetown University, 37th and O Streets, NW, Washington, D.C. 20057-1227, United States
| |
Collapse
|
73
|
Zhou N, Lu Z, Wu Q, Zhang Y. Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis. J Chem Phys 2014; 140:214117. [PMID: 24908000 PMCID: PMC4048451 DOI: 10.1063/1.4881255] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/21/2014] [Indexed: 11/14/2022] Open
Abstract
We examine interatomic interactions for rare gas dimers using the density-based energy decomposition analysis (DEDA) in conjunction with computational results from CCSD(T) at the complete basis set (CBS) limit. The unique DEDA capability of separating frozen density interactions from density relaxation contributions is employed to yield clean interaction components, and the results are found to be consistent with the typical physical picture that density relaxations play a very minimal role in rare gas interactions. Equipped with each interaction component as reference, we develop a new three-term molecular mechanical force field to describe rare gas dimers: a smeared charge multipole model for electrostatics with charge penetration effects, a B3LYP-D3 dispersion term for asymptotically correct long-range attractions that is screened at short-range, and a Born-Mayer exponential function for the repulsion. The resulted force field not only reproduces rare gas interaction energies calculated at the CCSD(T)/CBS level, but also yields each interaction component (electrostatic or van der Waals) which agrees very well with its corresponding reference value.
Collapse
Affiliation(s)
- Nengjie Zhou
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Zhenyu Lu
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Qin Wu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003, USA
| |
Collapse
|
74
|
Bennett T, Adnan RH, Alvino JF, Golovko V, Andersson GG, Metha GF. Identification of the vibrational modes in the far-infrared spectra of ruthenium carbonyl clusters and the effect of gold substitution. Inorg Chem 2014; 53:4340-9. [PMID: 24758282 DOI: 10.1021/ic403040u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-quality far-IR absorption spectra for a series of ligated atomically precise clusters containing Ru3, Ru4, and AuRu3 metal cores have been observed using synchrotron radiation, the latter two for the first time. The experimental spectra are compared with predicted IR spectra obtained following complete geometric optimization of the full cluster, including all ligands, using DFT. We find strong correlations between the experimental and predicted transitions for the low-frequency, low-intensity metal core vibrations as well as the higher frequency and intensity metal-ligand vibrations. The metal core vibrational bands appear at 150 cm(-1) for Ru3(CO)12, and 153 and 170 cm(-1) for H4Ru4(CO)12, while for the bimetallic Ru3(μ-AuPPh3)(μ-Cl)(CO)10 cluster these are shifted to 177 and 299 cm(-1) as a result of significant restructuring of the metal core and changes in chemical composition. The computationally predicted IR spectra also reveal the expected atomic motions giving rise to the intense peaks of metal-ligand vibrations at ca. 590 cm(-1) for Ru3, 580 cm(-1) for Ru4, and 560 cm(-1) for AuRu3. The obtained correlations allow an unambiguous identification of the key vibrational modes in the experimental far-IR spectra of these clusters for the first time.
Collapse
Affiliation(s)
- Trystan Bennett
- Department of Chemistry, University of Adelaide , North Terrace, Adelaide, South Australia 5005, Australia
| | | | | | | | | | | |
Collapse
|
75
|
Jia X, Zeng J, Zhang JZH, Mei Y. Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis. J Comput Chem 2014; 35:737-47. [PMID: 24500844 DOI: 10.1002/jcc.23547] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 11/15/2013] [Accepted: 01/05/2014] [Indexed: 12/12/2022]
Abstract
The reliability of the linear interaction energy (LIE) depends on the atomic charge model used to delineate the Coulomb interaction between the ligand and its environment. In this work, the polarized protein-specific charge (PPC) implementing a recently proposed fitting scheme has been examined in the LIE calculations of the binding affinities for avidin and β-secretase binding complexes. This charge fitting scheme, termed delta restrained electrostatic potential, bypasses the prevalent numerical difficulty of rank deficiency in electrostatic-potential-based charge fitting methods via a dual-step fitting strategy. A remarkable consistency between the predicted binding affinities and the experimental measurement has been observed. This work serves as a direct evidence of PPC's applicability in rational drug design.
Collapse
Affiliation(s)
- Xiangyu Jia
- State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China
| | | | | | | |
Collapse
|
76
|
Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chem Rev 2014; 114:779-814. [PMID: 23981057 PMCID: PMC3947274 DOI: 10.1021/cr300461d] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
77
|
Burger SK, Schofield J, Ayers PW. Quantum mechanics/molecular mechanics restrained electrostatic potential fitting. J Phys Chem B 2013; 117:14960-6. [PMID: 24176005 DOI: 10.1021/jp409568h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a quantum mechanics/molecular mechanics (QM/MM) method to evaluate the partial charges of amino acid residues for use in MM potentials based on their protein environment. For each residue of interest, the nearby residues are included in the QM system while the rest of the protein is treated at the MM level of theory. After a short structural optimization, the partial charges of the central residue are fit to the electrostatic potential using the restrained electrostatic potential (RESP) method. The resulting charges and electrostatic potential account for the individual environment of the residue, although they lack the transferable nature of library partial charges. To evaluate the quality of the QM/MM RESP charges, thermodynamic integration is used to measure the pKa shift of the aspartic acid residues in three different proteins, turkey egg lysozyme, beta-cryptogein, and Thioredoxin. Compared to the AMBER ff99SB library values, the QM/MM RESP charges show better agreement between the calculated and experimental pK(a) values for almost all of the residues considered.
Collapse
Affiliation(s)
- Steven K Burger
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | | | | |
Collapse
|
78
|
Cui ZH, Lischka H, Mueller T, Plasser F, Kertesz M. Study of the Diradicaloid Character in a Prototypical Pancake-Bonded Dimer: The Stacked Tetracyanoethylene (TCNE) Anion Dimer and the Neutral K2TCNE2Complex. Chemphyschem 2013; 15:165-76. [DOI: 10.1002/cphc.201300784] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Indexed: 11/08/2022]
|
79
|
Balamurugan D, Aquino AJA, de Dios F, Flores L, Lischka H, Cheung MS. Multiscale Simulation of the Ground and Photo-Induced Charge-Separated States of a Molecular Triad in Polar Organic Solvent: Exploring the Conformations, Fluctuations, and Free Energy Landscapes. J Phys Chem B 2013; 117:12065-75. [DOI: 10.1021/jp4026927] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- D. Balamurugan
- Department
of Physics, University of Houston, Houston, Texas 77204, United States
| | - Adelia J. A. Aquino
- Department
of Chemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Francis de Dios
- Department
of Physics, University of Houston, Houston, Texas 77204, United States
| | - Lionel Flores
- Department
of Physics, University of Houston, Houston, Texas 77204, United States
| | - Hans Lischka
- Department
of Chemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Margaret S. Cheung
- Department
of Physics, University of Houston, Houston, Texas 77204, United States
| |
Collapse
|
80
|
Galimberti D, Milani A, Castiglioni C. Infrared intensities and charge mobility in hydrogen bonded complexes. J Chem Phys 2013; 139:074304. [DOI: 10.1063/1.4818416] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
81
|
Jahangiri S, Dolgonos G, Frauenheim T, Peslherbe GH. Parameterization of Halogens for the Density-Functional Tight-Binding Description of Halide Hydration. J Chem Theory Comput 2013; 9:3321-32. [DOI: 10.1021/ct300919h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Soran Jahangiri
- Centre for Research in Molecular
Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West,
Montréal, Québec, Canada H4B 1R6
| | - Grygoriy Dolgonos
- Bremen Center for Computational
Materials Science, University of Bremen, Am Fallturm 1, 28359 Bremen, Germany
| | - Thomas Frauenheim
- Bremen Center for Computational
Materials Science, University of Bremen, Am Fallturm 1, 28359 Bremen, Germany
| | - Gilles H. Peslherbe
- Centre for Research in Molecular
Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West,
Montréal, Québec, Canada H4B 1R6
| |
Collapse
|
82
|
Tognetti V, Joubert L. On the physical role of exchange in the formation of an intramolecular bond path between two electronegative atoms. J Chem Phys 2013; 138:024102. [PMID: 23320663 DOI: 10.1063/1.4770495] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this paper, we present a detailed energetic decomposition of intramolecular O···X interactions (X being O, S, or a halogen atom) based on the interacting quantum atoms approach of Pendás and co-workers. The nature of these interactions (repulsive or attractive, more or less electrostatic) is discussed in the framework of Bader's atoms in molecules theory, a particular emphasis being put on delocalization (measured by delocalization indexes and in terms of the source function) and on the exchange contributions. Notably, the concept of exchange channels introduced by Pendás and collaborators provides means of rationalizing and predicting the presence of bond critical points, enhancing the physical meaning of bond paths.
Collapse
Affiliation(s)
- Vincent Tognetti
- Normandie Université, COBRA, UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821 Mont-Saint-Aignan Cedex, France.
| | | |
Collapse
|
83
|
Galimberti D, Milani A, Castiglioni C. Charge mobility in molecules: Charge fluxes from second derivatives of the molecular dipole. J Chem Phys 2013; 138:164115. [DOI: 10.1063/1.4802009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
84
|
Hirtz M, Kumar N, Franke JH, Hao J, Lu N, Fuchs H, Chi L. Selective deposition of organic molecules onto DPPC templates – A molecular dynamics study. J Colloid Interface Sci 2013; 389:206-12. [DOI: 10.1016/j.jcis.2012.09.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 09/07/2012] [Indexed: 10/27/2022]
|
85
|
Zeng J, Duan L, Zhang JZ, Mei Y. A numerically stable restrained electrostatic potential charge fitting method. J Comput Chem 2012; 34:847-53. [DOI: 10.1002/jcc.23208] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 11/08/2012] [Accepted: 11/28/2012] [Indexed: 12/11/2022]
|
86
|
Cisneros GA. Application of Gaussian Electrostatic Model (GEM) Distributed Multipoles in the AMOEBA Force Field. J Chem Theory Comput 2012; 8:5072-80. [DOI: 10.1021/ct300630u] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- G. Andrés Cisneros
- Department
of Chemistry, Wayne State University, Detroit,
Michigan 48202, United States
| |
Collapse
|
87
|
Hu X, Jin Y, Zeng X, Hu H, Yang W. Liquid water simulations with the density fragment interaction approach. Phys Chem Chem Phys 2012; 14:7700-9. [PMID: 22466097 PMCID: PMC3856182 DOI: 10.1039/c2cp23714h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We reformulate the density fragment interaction (DFI) approach [Fujimoto and Yang, J. Chem. Phys., 2008, 129, 054102.] to achieve linear-scaling quantum mechanical calculations for large molecular systems. Two key approximations are developed to improve the efficiency of the DFI approach and thus enable the calculations for large molecules: the electrostatic interactions between fragments are computed efficiently by means of polarizable electrostatic-potential-fitted atomic charges; and frozen fragment pseudopotentials, similar to the effective fragment potentials that can be fitted from interactions between small molecules, are employed to take into account the Pauli repulsion effect among fragments. Our reformulated and parallelized DFI method demonstrates excellent parallel performance based on the benchmarks for the system of 256 water molecules. Molecular dynamics simulations for the structural properties of liquid water also show a qualitatively good agreement with experimental measurements including the heat capacity, binding energy per water molecule, and the radial distribution functions of atomic pairs of O-O, O-H, and H-H. With this approach, large-scale quantum mechanical simulations for water and other liquids become feasible.
Collapse
Affiliation(s)
- Xiangqian Hu
- Department of Chemistry, Duke University, Durham, NC 27708
| | - Yingdi Jin
- Department of Chemistry, The University of Hong Kong, Hong Kong
| | - Xiancheng Zeng
- Department of Chemistry, Duke University, Durham, NC 27708
| | - Hao Hu
- Department of Chemistry, The University of Hong Kong, Hong Kong
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, NC 27708
| |
Collapse
|
88
|
Wang B, Truhlar DG. Partial Atomic Charges and Screened Charge Models of the Electrostatic Potential. J Chem Theory Comput 2012; 8:1989-98. [PMID: 26593833 DOI: 10.1021/ct2009285] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We propose a new screened charge method for calculating partial atomic charges in molecules by electrostatic potential (ESP) fitting. The model, called full density screening (FDS), is used to approximate the screening effect of full charge densities of atoms in molecules. The results are compared to the conventional ESP fitting method based on point charges and to our previously proposed outer density screening (ODS) method, in which the parameters are reoptimized for the present purpose. In ODS, the charge density of an atom is represented by the sum of a point charge and a smeared negative charge distributed in a Slater-type orbital (STO). In FDS, the charge density of an atom is taken to be the sum of the charge density of the neutral atom and a partial atomic charge (of either sign) distributed in an STO. The ζ values of the STOs used in these two models are optimized in the present study to best reproduce the electrostatic potentials. The quality of the fit to the electrostatics is improved in the screened charge methods, especially for the regions that are within one van der Waals radius of the centers of atoms. It is also found that the charges derived by fitting electrostatic potentials with screened charges are less sensitive to the positions of the fitting points than are those derived with conventional electrostatic fitting. Moreover, we found that the electrostatic-potential-fitted (ESP) charges from the screened charge methods are similar to those from the point-charge method except for molecules containing the methyl group, where we have explored the use of restraints on nonpolar H atoms. We recommend the FDS model if the only goal is ESP fitting to obtain partial atomic charges or a fit to the ESP field. However, the ODS model is more accurate for electronic embedding in combined quantum mechanical and molecular mechanical (QM/MM) modeling and is more accurate than point-charge models for ESP fitting, and it is recommended for applications involving QM/MM methods. Since the screened charges describe the electrostatic potentials more accurately than point charges, since they asymptotically act as point charges at long distances, and since the electrostatic potential in terms of the screened charges is still a sum of functions centered at the atoms, the screened-charge representation of the electrostatic potential can be used in the same way as the conventional point-charge representation to model the electrostatic interactions, but it is more realistic. For the H atom and p block elements, the error in the fit to the electrostatic potential is reduced by about a factor of 3, and the sensitivity of the derived partial atomic charges to the choice of fitting points is reduced by about a factor of 2. For s and d block elements, there are also improvements in the inner regions but not necessarily in the outer regions.
Collapse
Affiliation(s)
- Bo Wang
- Department of Chemistry and Supercomputing Institute, University of Minnesota , 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota , 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431, United States
| |
Collapse
|
89
|
Chen Z, Wei GW. Differential geometry based solvation model. III. Quantum formulation. J Chem Phys 2012; 135:194108. [PMID: 22112067 DOI: 10.1063/1.3660212] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Solvation is of fundamental importance to biomolecular systems. Implicit solvent models, particularly those based on the Poisson-Boltzmann equation for electrostatic analysis, are established approaches for solvation analysis. However, ad hoc solvent-solute interfaces are commonly used in the implicit solvent theory. Recently, we have introduced differential geometry based solvation models which allow the solvent-solute interface to be determined by the variation of a total free energy functional. Atomic fixed partial charges (point charges) are used in our earlier models, which depends on existing molecular mechanical force field software packages for partial charge assignments. As most force field models are parameterized for a certain class of molecules or materials, the use of partial charges limits the accuracy and applicability of our earlier models. Moreover, fixed partial charges do not account for the charge rearrangement during the solvation process. The present work proposes a differential geometry based multiscale solvation model which makes use of the electron density computed directly from the quantum mechanical principle. To this end, we construct a new multiscale total energy functional which consists of not only polar and nonpolar solvation contributions, but also the electronic kinetic and potential energies. By using the Euler-Lagrange variation, we derive a system of three coupled governing equations, i.e., the generalized Poisson-Boltzmann equation for the electrostatic potential, the generalized Laplace-Beltrami equation for the solvent-solute boundary, and the Kohn-Sham equations for the electronic structure. We develop an iterative procedure to solve three coupled equations and to minimize the solvation free energy. The present multiscale model is numerically validated for its stability, consistency and accuracy, and is applied to a few sets of molecules, including a case which is difficult for existing solvation models. Comparison is made to many other classic and quantum models. By using experimental data, we show that the present quantum formulation of our differential geometry based multiscale solvation model improves the prediction of our earlier models, and outperforms some explicit solvation model.
Collapse
Affiliation(s)
- Zhan Chen
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, USA
| | | |
Collapse
|
90
|
Milani A, Tommasini M, Castiglioni C. Atomic charges from IR intensity parameters: theory, implementation and application. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1139-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
91
|
Elking DM, Perera L, Pedersen LG. HPAM: Hirshfeld Partitioned Atomic Multipoles. COMPUTER PHYSICS COMMUNICATIONS 2012; 183:390-397. [PMID: 22140274 PMCID: PMC3225920 DOI: 10.1016/j.cpc.2011.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank l(max) on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is demonstrated by increasing the atomic multipole rank from l(max) = 0 (atomic charges) to l(max) = 4 (atomic hexadecapoles). Both HD and HD-I atomic multipoles up to rank l(max) are shown to exactly reproduce ab initio molecular multipole moments of rank L for L ≤ l(max). In addition, molecular dipole moments calculated by HD, HD-I, and ChelpG atomic charges only (l(max) = 0) are compared with reference ab initio values. Significant errors in reproducing ab initio molecular dipole moments are found if only HD or HD-I atomic charges used.
Collapse
Affiliation(s)
- Dennis M. Elking
- University of North Carolina, Department of Chemistry, Chapel Hill, NC 27599, USA
| | - Lalith Perera
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - Lee G. Pedersen
- University of North Carolina, Department of Chemistry, Chapel Hill, NC 27599, USA
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| |
Collapse
|
92
|
Verstraelen T, Pauwels E, De Proft F, Van Speybroeck V, Geerlings P, Waroquier M. Assessment of Atomic Charge Models for Gas-Phase Computations on Polypeptides. J Chem Theory Comput 2012; 8:661-76. [PMID: 26596614 DOI: 10.1021/ct200512e] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The concept of the atomic charge is extensively used to model the electrostatic properties of proteins. Atomic charges are not only the basis for the electrostatic energy term in biomolecular force fields but are also derived from quantum mechanical computations on protein fragments to get more insight into their electronic structure. Unfortunately there are many atomic charge schemes which lead to significantly different results, and it is not trivial to determine which scheme is most suitable for biomolecular studies. Therefore, we present an extensive methodological benchmark using a selection of atomic charge schemes [Mulliken, natural, restrained electrostatic potential, Hirshfeld-I, electronegativity equalization method (EEM), and split-charge equilibration (SQE)] applied to two sets of penta-alanine conformers. Our analysis clearly shows that Hirshfeld-I charges offer the best compromise between transferability (robustness with respect to conformational changes) and the ability to reproduce electrostatic properties of the penta-alanine. The benchmark also considers two charge equilibration models (EEM and SQE), which both clearly fail to describe the locally charged moieties in the zwitterionic form of penta-alanine. This issue is analyzed in detail because charge equilibration models are computationally much more attractive than the Hirshfeld-I scheme. Based on the latter analysis, a straightforward extension of the SQE model is proposed, SQE+Q(0), that is suitable to describe biological systems bearing many locally charged functional groups.
Collapse
Affiliation(s)
- Toon Verstraelen
- Center For Molecular Modeling, Ghent University , Technologiepark 903, 9050 Zwijnaarde, Belgium (Member of the QCMM Ghent-Brussels Alliance Group)
| | - Ewald Pauwels
- Center For Molecular Modeling, Ghent University , Technologiepark 903, 9050 Zwijnaarde, Belgium (Member of the QCMM Ghent-Brussels Alliance Group)
| | - Frank De Proft
- Department of General Chemistry (ALGC), Free University of Brussels-VUB , Pleinlaan 2, 1050 Brussels, Belgium (Member of the QCMM Ghent-Brussels Alliance Group)
| | - Veronique Van Speybroeck
- Center For Molecular Modeling, Ghent University , Technologiepark 903, 9050 Zwijnaarde, Belgium (Member of the QCMM Ghent-Brussels Alliance Group)
| | - Paul Geerlings
- Department of General Chemistry (ALGC), Free University of Brussels-VUB , Pleinlaan 2, 1050 Brussels, Belgium (Member of the QCMM Ghent-Brussels Alliance Group)
| | - Michel Waroquier
- Center For Molecular Modeling, Ghent University , Technologiepark 903, 9050 Zwijnaarde, Belgium (Member of the QCMM Ghent-Brussels Alliance Group)
| |
Collapse
|
93
|
Olguin M, Baruah T, Zope RR. Calcium coated B80 fullerene: A study on various coating configurations of B80. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.07.094] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
94
|
Yamada K, Koyano Y, Okamoto T, Asada T, Koga N, Nagaoka M. Toward a new approach for determination of solute's charge distribution to analyze interatomic electrostatic interactions in quantum mechanical/molecular mechanical simulations. J Comput Chem 2011; 32:3092-104. [DOI: 10.1002/jcc.21893] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 06/17/2011] [Accepted: 06/24/2011] [Indexed: 01/15/2023]
|
95
|
Hu X, Hu H, Melvin JA, Clancy KW, McCafferty DG, Yang W. Autocatalytic intramolecular isopeptide bond formation in gram-positive bacterial pili: a QM/MM simulation. J Am Chem Soc 2011; 133:478-85. [PMID: 21142157 PMCID: PMC3081525 DOI: 10.1021/ja107513t] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many gram-positive pathogens possess external pili or fimbriae with which they adhere to host cells during the infection process. Unusual dual intramolecular isopeptide bonds between Asn and Lys side chains within the N-terminal and C-terminal domains of the pilus subunits have been observed initially in the Streptococcus pyogenes pilin subunit Spy0128 and subsequently in GBS52 from Streptococcus agalactiae, in the BcpA major pilin of Bacillus cereus and in the RrgB pilin of Streptococcus pneumoniae, among others. Within each pilin subunit, intramolecular isopeptide bonds serve to stabilize the protein. These bonds provide a means to withstand large external mechanical forces, as well as possibly assisting in supporting a conformation favored for pilin subunit polymerization via sortase transpeptidases. Genome-wide analyses of pili-containing gram-positive bacteria are known or suspected to contain isopeptide bonds in pilin subunits. For the autocatalytic formation of isopeptide cross-links, a conservation of three amino acids including Asn, Lys, and a catalytically important acidic Glu (or Asp) residue are responsible. However, the chemical mechanism of how isopeptide bonds form within pilin remains poorly understood. Although it is possible that several mechanistic paths could lead to isopeptide bond formation in pili, the requirement of a conserved glutamate and highly organized positioning of residues within the hydrophobic environment of the active site were found in numerous pilin crystal structures such as Spy0128 and RrgB. This suggests a mechanism involving direct coupling of lysine side chain amine to the asparagine carboxamide mediated by critical acid/base or hydrogen bonding interactions with the catalytic glutamate residue. From this mechanistic perspective, we used the QM/MM minimum free-energy path method to examine the reaction details of forming the isopeptide bonds with Spy0128 as a model pilin, specifically focusing on the role of the glutamate in catalysis. It was determined that the reaction mechanism likely consists of two major steps: the nucleophilic attack on Cγ by nitrogen in the unprotonated Lys ε-amino group and, then two concerted proton transfers occur during the formation of the intramolecular isopeptide bond to subsequently release ammonia. More importantly, within the dual active sites of Spy0128, Glu(117), and Glu(258) residues function as crucial catalysts for each isopeptide bond formation, respectively, by relaying two proton transfers. This work also suggests that domain-domain interactions within Spy0128 may modulate the reactivity of residues within each active site. Our results may hopefully shed light on the molecular mechanisms of pilin biogenesis in gram-positive bacteria.
Collapse
Affiliation(s)
- Xiangqian Hu
- Department of Chemistry, Duke University, Durham, NC 27708
| | - Hao Hu
- Department of Chemistry, The University of Hong Kong
| | - Jeffrey A. Melvin
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27708
| | | | | | - Weitao Yang
- Department of Chemistry, Duke University, Durham, NC 27708
| |
Collapse
|
96
|
Chen DL, Stern AC, Space B, Johnson JK. Atomic Charges Derived from Electrostatic Potentials for Molecular and Periodic Systems. J Phys Chem A 2010; 114:10225-33. [DOI: 10.1021/jp103944q] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- De-Li Chen
- National Energy Technology Laboratory, Pittsburgh, Pennsylvania, 15236, Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, and Department of Chemistry, University of South Florida, Tampa Florida 33620
| | - Abraham C. Stern
- National Energy Technology Laboratory, Pittsburgh, Pennsylvania, 15236, Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, and Department of Chemistry, University of South Florida, Tampa Florida 33620
| | - Brian Space
- National Energy Technology Laboratory, Pittsburgh, Pennsylvania, 15236, Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, and Department of Chemistry, University of South Florida, Tampa Florida 33620
| | - J. Karl Johnson
- National Energy Technology Laboratory, Pittsburgh, Pennsylvania, 15236, Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, and Department of Chemistry, University of South Florida, Tampa Florida 33620
| |
Collapse
|
97
|
Hu H, Yang W. Elucidating solvent contributions to solution reactions with ab initio QM/MM methods. J Phys Chem B 2010; 114:2755-9. [PMID: 20121225 PMCID: PMC3747775 DOI: 10.1021/jp905886q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Computer simulations of reaction processes in solution in general rely on the definition of a reaction coordinate and the determination of the thermodynamic changes of the system along the reaction coordinate. The reaction coordinate often is constituted of characteristic geometrical properties of the reactive solute species, while the contributions of solvent molecules are implicitly included in the thermodynamics of the solute degrees of freedoms. However, solvent dynamics can provide the driving force for the reaction process, and in such cases explicit description of the solvent contribution in the free energy of the reaction process becomes necessary. We report here a method that can be used to analyze the solvent contributions to the reaction activation free energies from the combined QM/MM minimum free-energy path simulations. The method was applied to the self-exchange S(N)2 reaction of CH(3)Cl + Cl(-), showing that the importance of solvent-solute interactions to the reaction process. The results were further discussed in the context of coupling between solvent and solute molecules in reaction processes.
Collapse
Affiliation(s)
- Hao Hu
- Department of Chemistry, University of Hong Kong, Hong Kong
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| |
Collapse
|
98
|
Elking DM, Cisneros GA, Piquemal JP, Darden TA, Pedersen LG. Gaussian Multipole Model (GMM). J Chem Theory Comput 2009; 6:190-202. [PMID: 20209077 DOI: 10.1021/ct900348b] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An electrostatic model based on charge density is proposed as a model for future force fields. The model is composed of a nucleus and a single Slater-type contracted Gaussian multipole charge density on each atom. The Gaussian multipoles are fit to the electrostatic potential (ESP) calculated at the B3LYP/6-31G* and HF/aug-cc-pVTZ levels of theory and tested by comparing electrostatic dimer energies, inter-molecular density overlap integrals, and permanent molecular multipole moments with their respective ab initio values. For the case of water, the atomic Gaussian multipole moments Q(lm) are shown to be a smooth function of internal geometry (bond length and bond angle), which can be approximated by a truncated linear Taylor series. In addition, results are given when the Gaussian multipole charge density is applied to a model for exchange-repulsion energy based on the inter-molecular density overlap.
Collapse
Affiliation(s)
- Dennis M Elking
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | | | | | | | | |
Collapse
|
99
|
Zeng X, Hu H, Hu X, Yang W. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method. J Chem Phys 2009; 130:164111. [PMID: 19405565 DOI: 10.1063/1.3120605] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids "on-the-fly" QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.
Collapse
Affiliation(s)
- Xiancheng Zeng
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | | | | | | |
Collapse
|
100
|
Hu H, Yang W. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes. ACTA ACUST UNITED AC 2009; 898:17-30. [PMID: 24146439 DOI: 10.1016/j.theochem.2008.12.025] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes.
Collapse
Affiliation(s)
- Hao Hu
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | | |
Collapse
|