1
|
Luk HL, Feist J, Toppari JJ, Groenhof G. Multiscale Molecular Dynamics Simulations of Polaritonic Chemistry. J Chem Theory Comput 2017; 13:4324-4335. [DOI: 10.1021/acs.jctc.7b00388] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Johannes Feist
- Departamento
de Física Teórica de la Materia Condensada and Condensed
Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | | |
Collapse
|
2
|
Gurunathan PK, Acharya A, Ghosh D, Kosenkov D, Kaliman I, Shao Y, Krylov AI, Slipchenko LV. Extension of the Effective Fragment Potential Method to Macromolecules. J Phys Chem B 2016; 120:6562-74. [PMID: 27314461 DOI: 10.1021/acs.jpcb.6b04166] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the Cα-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the Cα-C and Cα-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV.
Collapse
Affiliation(s)
| | - Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Debashree Ghosh
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India
| | - Dmytro Kosenkov
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
- Department of Chemistry and Physics, Monmouth University , West Long Branch, New Jersey 07764, United States
| | - Ilya Kaliman
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Yihan Shao
- Q-Chem Inc. , 6601 Owens Drive, Suite 105 Pleasanton, California 94588, United States
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| |
Collapse
|
3
|
Porter MA, Molina PA. The Low-Barrier Double-Well Potential of the O(δ)(1)-H-O(δ)(1) Hydrogen Bond in Unbound HIV Protease: A QM/MM Characterization. J Chem Theory Comput 2015; 2:1675-84. [PMID: 26627038 DOI: 10.1021/ct600200s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The presence of a low-barrier hydrogen bond (LBHB) in aspartyl proteases and its implications in drug design have been the subject of intense study. Here, we present a combined quantum mechanical/molecular mechanical (QM/MM)-Numerov procedure and use it to characterize the O(δ)(1)-H-O(δ)(1) hydrogen bond (HB) in unbound HIV protease. The QM/MM scheme fully traces the shape of the HB's potential energy curve. The potential is used to obtain numerical solutions to the wave functions and vibrational energies of hydrogen, deuterium, and tritium. The vibrational eigenfunctions are used to compute expectation values for interatomic distances and vibrationally and thermally averaged spectroscopic properties of the O(δ)(1)-H-O(δ)(1) HB. Our work corroborates previous results by Piana and Carloni who found a LBHB via an ab initio molecular dynamics simulation (Piana, S.; Carloni, P. Proteins 2000, 39, 26-36). Our predictions of isotope effects on the chemical shift of unbound HIV protease are consistent with experimental measurements in similar HBs. These results support the predictive power of this method and its potential use in screening inhibitors of aspartyl proteases.
Collapse
Affiliation(s)
- Melissa A Porter
- Department of Chemistry, Murray State University, Murray, Kentucky 42071
| | - Pablo A Molina
- Department of Chemistry, Murray State University, Murray, Kentucky 42071
| |
Collapse
|
4
|
Steinmann C, Fedorov DG, Jensen JH. The effective fragment molecular orbital method for fragments connected by covalent bonds. PLoS One 2012; 7:e41117. [PMID: 22844433 PMCID: PMC3402534 DOI: 10.1371/journal.pone.0041117] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 06/19/2012] [Indexed: 11/18/2022] Open
Abstract
We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively.
Collapse
Affiliation(s)
- Casper Steinmann
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
| | | | | |
Collapse
|
5
|
Söderhjelm P, Ryde U. How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations. J Phys Chem A 2009; 113:617-27. [PMID: 19093829 DOI: 10.1021/jp8073514] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A new method to accurately estimate the interaction energy between a large molecule and a smaller ligand is presented. The method approximates the electrostatic and induction contributions classically by multipole and polarizability expansions, but uses explicit quantum-mechanical fragment calculations for the remaining (nonclassical) contributions, mainly dispersion and exchange repulsion. Thus, it represents a limit of how accurate a force field can ever become for interaction energies if pairwise additivity of the nonclassical term is assumed (e.g., all general-purpose force fields). The accuracy is tested by considering protein-ligand model systems for which the true MP2/6-31G* interaction energies can be computed. The method is shown to be more accurate than related fragmentation approaches. The remaining error (2-5 and approximately10 kJ/mol for neutral and charged ligands, respectively) can be decreased by including the polarizing effect from surrounding fragments in the quantum-mechanical calculations.
Collapse
Affiliation(s)
- Pär Söderhjelm
- Department of Theoretical Chemistry, Lund University, Chemical Center, POB 124, SE-22100 Lund, Sweden.
| | | |
Collapse
|
6
|
Werneck AS, Filho TMR, Dardenne LE. General Methodology to Optimize Damping Functions to Account for Charge Penetration Effects in Electrostatic Calculations Using Multicentered Multipolar Expansions. J Phys Chem A 2007; 112:268-80. [DOI: 10.1021/jp075566p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Araken S. Werneck
- Departamento de Física, Universidade Católica de Brasília, UCB, Brazil, Instituto de Física, Universidade de Brasília, UnB, Brazil, and Laboratório Nacional de Computação CientíficaLNCC/MCT, Av Getúlio Vargas 333 Quitandinha Petrópolis, RJ CEP: 25651-071, Brazil
| | - Tarcísio M. Rocha Filho
- Departamento de Física, Universidade Católica de Brasília, UCB, Brazil, Instituto de Física, Universidade de Brasília, UnB, Brazil, and Laboratório Nacional de Computação CientíficaLNCC/MCT, Av Getúlio Vargas 333 Quitandinha Petrópolis, RJ CEP: 25651-071, Brazil
| | - Laurent E. Dardenne
- Departamento de Física, Universidade Católica de Brasília, UCB, Brazil, Instituto de Física, Universidade de Brasília, UnB, Brazil, and Laboratório Nacional de Computação CientíficaLNCC/MCT, Av Getúlio Vargas 333 Quitandinha Petrópolis, RJ CEP: 25651-071, Brazil
| |
Collapse
|
7
|
Jensen JH, Li H, Robertson AD, Molina PA. Prediction and rationalization of protein pKa values using QM and QM/MM methods. J Phys Chem A 2007; 109:6634-43. [PMID: 16834015 DOI: 10.1021/jp051922x] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe the development and application of a computational method for the prediction and rationalization of pKa values of ionizable residues in proteins, based on ab initio quantum mechanics (QM) and the effective fragment potential (EFPs) method (a hybrid QM/MM method). The theoretical developments include (1) a covalent boundary method based on frozen localized orbitals, (2) divide-and-conquer methods for the ab initio computation of protein EFPs consisting of multipoles up to octupoles and dipole polarizability tensors, (3) a method for computing vibrational free energies for a localized molecular region, and (4) solutions of the polarized continuum model of bulk solvation equations for protein-sized systems. The QM-based pKa prediction method is one of the most accurate methods currently available and can be used in cases where other pKa prediction methods fail. Preliminary analysis of the computed results indicate that many pKa values (1) are primarily determined by hydrogen bonds rather than long-range charge-charge interactions and (2) are relatively insensitive to large-scale dynamical fluctuations of the protein structure.
Collapse
Affiliation(s)
- Jan H Jensen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA.
| | | | | | | |
Collapse
|