1
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Yan S, Wang B, Lin H. Reshaping the QM Region On-the-Fly: Adaptive-Shape QM/MM Dynamic Simulations of a Hydrated Proton in Bulk Water. J Chem Theory Comput 2024; 20:3462-3472. [PMID: 38671391 DOI: 10.1021/acs.jctc.4c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Adaptive quantum mechanics/molecular mechanics (QM/MM) reclassifies on-the-fly a molecule or molecular fragment as QM or MM during dynamics simulations without abrupt changes in the energy or forces. Notably, the permuted adaptive-partitioning (PAP) algorithms have been applied to simulate a hydrated proton, with a mobile QM zone anchored at a pseudoatom called a proton indicator. The position of the proton indicator approximates the location of the delocalized excess proton, yielding a smooth trajectory of the proton diffusing via the Grotthuss mechanism in aqueous solutions. The mobile QM zone, which has been taken to be a sphere with a preset radius, follows the proton wherever it goes. Although the simulations are successful, the use of a spherical QM zone has one disadvantage: A large preset radius must be utilized to minimize the chance of missing water molecules that are important to proton translocation. A large radius leads to a large QM zone, which is computationally expensive. In this work, we report a new way to set up the QM zone, where one includes only the water molecules important to proton transfer. The importance of a given water molecule is quantified by its "weight" that depends on its relation to the reaction path of proton transfer. The weight varies smoothly, ensuring that a water molecule gradually appears in or disappears from the QM zone without abrupt changes, as required by the PAP method. Consequently, the shape of the QM zone evolves on-the-fly, keeping the QM zone as small as possible and as large as necessary. Test simulations demonstrate that the new algorithm significantly improves the computation efficiency while maintaining the proper descriptions of proton transfer in bulk water.
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Affiliation(s)
- Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Hai Lin
- Department of Chemistry, CB 194, University of Colorado Denver, Denver, P.O. Box 173364, Colorado 80217, United States
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2
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Tran AL, Guidez EB, Lin H. Adaptive-Partitioning Multilayer Dynamics Simulations: 2. Implementations of the Permuted and Interpolated Adaptive-Partitioning Gradients. J Phys Chem A 2023; 127:10320-10333. [PMID: 38058156 PMCID: PMC10712430 DOI: 10.1021/acs.jpca.3c05600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 12/08/2023]
Abstract
Recently, an adaptive-partitioning multilayer Q1/Q2/MM method was proposed, where Q1 and Q2 denote, respectively, two distinct quantum-mechanical levels of theory and MM, the molecular-mechanical force fields. Such a multilayer model resembles the ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) model by Morokuma and co-workers, but it is distinguished by on-the-fly reclassifying atoms to be Q1, Q2, or MM in dynamics simulations. To smoothly blend the levels of descriptions of the atoms, buffer zones are introduced between adjacent layers, and the energy is smoothly interpolated. In particular, the Q1/Q2 interaction energy was expressed in two different formalisms: permuted and interpolated adaptive-partitioning (PAP and IAP), respectively. While the PAP energy is based on a weighted many-body expansion, the IAP energy is derived via alchemical quantum calculations with interpolated Fock and overlap matrices. In this article, we examine in-depth the irregularities in the IAP energy near the boundary between the buffer and Q2 zones, which were found prominent in some calculations. These irregularities are due to basis-set linear dependencies, which can be effectively suppressed using a cutoff for the weighted atomic orbital coefficients. Furthermore, we derived and implemented the gradients for both PAP and IAP. Test calculations on a series of water cluster models show perfectly smooth gradients in PAP, while a minor discontinuity occurs in IAP gradients at the buffer/Q2 boundary. The energy and gradient discontinuities in IAP become smaller when moving the buffer/Q2 boundary further away from the Q1 center and when increasing the size of the basis sets used. Overall, those discontinuities are controllable, and possible ways to further diminish them are discussed.
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Affiliation(s)
- Anh L. Tran
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Emilie B. Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Hai Lin
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
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3
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Yan S, Wang B, Lin H. Tracking the Delocalized Proton in Concerted Proton Transfer in Bulk Water. J Chem Theory Comput 2023; 19:448-459. [PMID: 36630655 DOI: 10.1021/acs.jctc.2c01097] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A solvated proton in water is often characterized as a charge or structural defect, and it is important to track its evolution on-the-fly in certain dynamics simulations. Previously, we introduced the proton indicator, a pseudo-atom, whose position approximates the location of the excess proton modeled as a structural defect. The proton indicator generally yields a smooth trajectory of a hydrated proton diffusing in aqueous solutions, including in the events of stepwise proton transfer via the Grotthuss mechanism; however, the proton indicator did not perform well in the events of concerted proton transfer, for which it occasionally yielded large position displacements between two successive time steps. To overcome this hurdle, we develop a new algorithm of a proton indicator with greatly enhanced performance for concerted proton transfer in bulk water. A protocol is proposed to exhaustively explore the hydrogen-bonding network of the water wires over which the excess proton is delocalized and to properly account for the contributions of the water molecules in this network as the geometry evolves. The new proton indicator (called Indicator 2.0) is assessed in dynamics simulations of an excess proton in bulk water and in specially constructed model systems of more complex architectures. The results demonstrate that the new indicator yields a smooth trajectory in both stepwise and concerted proton transfers.
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Affiliation(s)
- Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen360015P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen360015P. R. China
| | - Hai Lin
- Department of Chemistry, CB 194, University of Colorado Denver, P.O. Box 173364, Denver, Colorado80217, United States
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4
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Bachmann J, Doltsinis NL. Adaptive partitioning molecular dynamics using an extended Hamiltonian approach. J Chem Phys 2021; 155:144104. [PMID: 34654314 DOI: 10.1063/5.0059206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A recently proposed extended Hamiltonian approach to switching interaction potentials is generalized to enable adaptive partitioning molecular dynamics simulations. Switching is performed along a fictitious classical degree of freedom whose value determines the mixing ratio of the two potentials on a time scale determined by its associated mass. We propose to choose this associated fictitious mass adaptively so as to ensure a constant time scale for all switching processes. For different model systems, including a harmonic oscillator and a Lennard-Jones fluid, we investigate the window of switching time scales that guarantees the conservation of the extended Hamiltonian for a large number of switching events. The methodology is first applied in the microcanonical ensemble and then generalized to the canonical ensemble using a Nosé-Hoover chain thermostat. It is shown that the method is stable for thousands of consecutive switching events during a single simulation, with constant temperature and a conserved extended Hamiltonian. A slight modification of the original Hamiltonian is introduced to avoid accumulation of small numerical errors incurred after each switching process.
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Affiliation(s)
- Jim Bachmann
- Institut für Festkörpertheorie, Westfälische Wilhelms-Universität Münster and Center for Multiscale Theory and Computation, Wilhelm-Klemm-Str. 10, 48149 Münster, Germany
| | - Nikos L Doltsinis
- Institut für Festkörpertheorie, Westfälische Wilhelms-Universität Münster and Center for Multiscale Theory and Computation, Wilhelm-Klemm-Str. 10, 48149 Münster, Germany
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5
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Mato J, Duster AW, Guidez EB, Lin H. Adaptive-Partitioning Multilayer Dynamics Simulations: 1. On-the-Fly Switch between Two Quantum Levels of Theory. J Chem Theory Comput 2021; 17:5456-5465. [PMID: 34448578 DOI: 10.1021/acs.jctc.1c00556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We propose to generalize the previously developed two-layer permuted adaptive-partitioning quantum-mechanics/molecular-mechanics (QM/MM), which reclassifies atoms as QM or MM on-the-fly in dynamics simulations, to multilayer adaptive-partitioning algorithms that enable multiple levels of theory. In this work, we formulate two new algorithms that smoothly interpolate the energy between two QM (Q1 and Q2) levels of theory. The first "permuted adaptive-partitioning" scheme is based on the weighted many-body expansion of the potential, as in the adaptive-partitioning QM/MM. Unconventional and potentially more efficient, the second "interpolated adaptive-partitioning" method employs alchemical QM calculations with Q1/Q2-mixed basis sets, Fock matrices, and overlap matrices. To our knowledge, this is the first time that such alchemical calculations are performed in QM, although they are routinely done in MM. Test calculations on water-cluster models show that both new algorithms indeed yield smooth energy curves when water molecules shift between Q1 and Q2.
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Affiliation(s)
- Joani Mato
- Department of Chemistry, University of Colorado, Denver, Denver, Colorado 80217, United States
| | - Adam W Duster
- Department of Chemistry, University of Colorado, Denver, Denver, Colorado 80217, United States
| | - Emilie B Guidez
- Department of Chemistry, University of Colorado, Denver, Denver, Colorado 80217, United States
| | - Hai Lin
- Department of Chemistry, University of Colorado, Denver, Denver, Colorado 80217, United States
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6
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Protonation Dynamics in the K-Channel of Cytochrome c Oxidase Estimated from Molecular Dynamics Simulations. Processes (Basel) 2021. [DOI: 10.3390/pr9020265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Proton transfer reactions are one of the most fundamental processes in biochemistry. We present a simplistic approach for estimating proton transfer probabilities in a membrane protein, cytochrome c oxidase. We combine short molecular dynamics simulations at discrete protonation states with a Monte Carlo approach to exchange between those states. Requesting for a proton transfer the existence of a hydrogen-bonded connection between the two source and target residues of the exchange, restricts the acceptance of transfers to only those in which a proton-relay is possible. Together with an analysis of the hydrogen-bonded connectivity in one of the proton-conducting channels of cytochrome c oxidase, this approach gives insight into the protonation dynamics of the hydrogen-bonded networks. The connectivity and directionality of the networks are coupled to the conformation of an important protein residue in the channel, K362, rendering proton transfer in the entire channel feasible in only one of the two major conformations. Proton transport in the channel can thus be regulated by K362 not only through its possible role as a proton carrier itself, but also by allowing or preventing proton transport via water residues.
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7
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Duster AW, Lin H. Tracking Proton Transfer through Titratable Amino Acid Side Chains in Adaptive QM/MM Simulations. J Chem Theory Comput 2019; 15:5794-5809. [DOI: 10.1021/acs.jctc.9b00649] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Adam W. Duster
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Hai Lin
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
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8
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Zhang B, Altarawy D, Barnes T, Turney JM, Schaefer HF. Janus: An Extensible Open-Source Software Package for Adaptive QM/MM Methods. J Chem Theory Comput 2019; 15:4362-4373. [DOI: 10.1021/acs.jctc.9b00182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Boyi Zhang
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Doaa Altarawy
- The Molecular Sciences Software Institute, Virginia Tech, Blacksburg, Virginia 24060, United States
- Department of Computer and Systems Engineering, Alexandria University, Alexandria 21544, Egypt
| | - Taylor Barnes
- The Molecular Sciences Software Institute, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Justin M. Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
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9
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Gupta AK, Thapa B, Raghavachari K. Exploring Reaction Energy Profiles Using the Molecules-in-Molecules Fragmentation-Based Approach. J Chem Theory Comput 2019; 15:3991-4002. [PMID: 31181886 DOI: 10.1021/acs.jctc.9b00152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Molecules-in-Molecules (MIM) fragmentation-based approach has been successfully used in previous studies to obtain the energies, optimized geometries, and spectroscopic properties of large molecular systems. The present work delineates a protocol to study the potential energy profiles for multistep chemical reactions using the MIM methodology. In a complex multistep chemical reaction, the fragmentation scheme needs to be changed as the reacting species transition into a new reaction step, resulting in a discontinuity in the potential energy curve of the reaction. In our approach, the fragmentation scheme for a particular step in a reaction is chosen on the basis of the nature of the bonding changes associated with that step. Thus, the reactant, transition state, and product are treated consistently throughout the reaction step, leading to an accurate energy barrier for that step. The discontinuity now occurs in describing the energies of reaction intermediates at the transition point between two reaction steps that are treated by two different fragmentation schemes. To address this issue, we propose a systematic procedure for obtaining continuous potential energy curves that are least shifted from their initial positions. The corrected MIM potential energy curves are continuous with activation energies preserved. Following this approach, energy profiles of complex reactions involving large molecular species can be obtained at high levels of theory with a reasonable computational cost.
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Affiliation(s)
- Ankur Kumar Gupta
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Bishnu Thapa
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Krishnan Raghavachari
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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10
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Duster AW, Garza CM, Aydintug BO, Negussie MB, Lin H. Adaptive Partitioning QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel. J Chem Theory Comput 2019; 15:892-905. [DOI: 10.1021/acs.jctc.8b01128] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adam W. Duster
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Christina M. Garza
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Baris O. Aydintug
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Mikias B. Negussie
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
| | - Hai Lin
- Chemistry Department, CB 194, University of Colorado, Denver, Colorado 80217, United States
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11
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Duster AW, Wang CH, Lin H. Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes. Molecules 2018; 23:E2170. [PMID: 30154373 PMCID: PMC6225285 DOI: 10.3390/molecules23092170] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 11/16/2022] Open
Abstract
In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction (HAMBC) proposed by Boreboom et al. [J. Chem. Theory Comput.2016, 12, 3441] to the permuted AP (PAP) scheme. The treatments lead to the HAMBC-PAP method (HPAP), which both conserves energy and produces accurate solvation structures in the test of "water-in-water" model system.
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Affiliation(s)
- Adam W Duster
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217, USA.
| | - Chun-Hung Wang
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217, USA.
| | - Hai Lin
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217, USA.
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12
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Hofer TS, Hünenberger PH. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration. J Chem Phys 2018; 148:222814. [DOI: 10.1063/1.5000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Centre for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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13
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Boereboom JM, Fleurat-Lessard P, Bulo RE. Explicit Solvation Matters: Performance of QM/MM Solvation Models in Nucleophilic Addition. J Chem Theory Comput 2018; 14:1841-1852. [PMID: 29438621 PMCID: PMC6023263 DOI: 10.1021/acs.jctc.7b01206] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Nucleophilic
addition onto a carbonyl moiety is strongly affected
by solvent, and correctly simulating this solvent effect is often
beyond the capability of single-scale quantum mechanical (QM) models.
This work explores multiscale approaches for the description of the
reversible and highly solvent-sensitive nucleophilic N|···C=O
bond formation in an Me2N–(CH2)3–CH=O molecule. In the first stage of this work, we
rigorously compare and test four recent quantum mechanical/molecular
mechanical (QM/MM) explicit solvation models, employing a QM description
of water molecules in spherical regions around both the oxygen and
the nitrogen atom of the solute. The accuracy of the models is benchmarked
against a reference QM simulation, focusing on properties of the solvated
Me2N–(CH2)3–CH=O
molecule in its ring-closed form. In the second stage, we select one
of the models (continuous adaptive QM/MM) and use it to obtain a reliable
free energy profile for the N|···C bond formation reaction.
We find that the dual-sphere approach allows the model to accurately
account for solvent reorganization along the entire reaction path.
In contrast, a simple microsolvation model cannot adapt to the changing
conditions and provides an incorrect description of the reaction process.
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Affiliation(s)
- Jelle M Boereboom
- Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands
| | - Paul Fleurat-Lessard
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB, UMR-CNRS 6302) , Université de Bourgogne Franche-Comté , 9 Avenue Alain Savary , 21078 Dijon Cedex , France
| | - Rosa E Bulo
- Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands
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14
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Okumura H, Higashi M, Yoshida Y, Sato H, Akiyama R. Theoretical approaches for dynamical ordering of biomolecular systems. Biochim Biophys Acta Gen Subj 2017; 1862:212-228. [PMID: 28988931 DOI: 10.1016/j.bbagen.2017.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/30/2017] [Accepted: 10/04/2017] [Indexed: 01/21/2023]
Abstract
BACKGROUND Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. SCOPE OF REVIEW We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. MAJOR CONCLUSIONS The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. GENERAL SIGNIFICANCE These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Hisashi Okumura
- Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan; Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan.
| | - Masahiro Higashi
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Yuichiro Yoshida
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka 819-0395, Japan
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15
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Duster AW, Lin H. Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube. J Phys Chem B 2017; 121:8585-8592. [PMID: 28820594 DOI: 10.1021/acs.jpcb.7b06657] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, a collective variable "proton indicator" was purposed for tracking an excess proton solvated in bulk water in molecular dynamics simulations. In this work, we demonstrate the feasibility of utilizing the position of this proton indicator as a reaction coordinate to model an excess proton migrating through a hydrophobic carbon nanotube in combined quantum-mechanics/molecular-mechanics simulations. Our results indicate that applying a harmonic restraint to the proton indicator in the bulk solvent near the nanotube pore entrance leads to the recruitment of water molecules into the pore. This is consistent with an earlier study that employed a multistate empirical valence bond potential and a different representation (center of excess charge) of the proton. We attribute this water recruitment to the delocalized nature of the solvated proton, which prefers to be in high-dielectric bulk solvent. While water recruitment into the pore is considered an artifact in the present simulations (because of the artificially imposed restraint on the proton), if the proton were naturally restrained, it could assist in building water wires prior to proton transfer through the pore. The potential of mean force for a proton translocation through the water-filled pore was computed by umbrella sampling, where the bias potentials were applied to the proton indicator. The free energy curve and barrier heights agree reasonably with those in the literature. The results suggest that the proton indicator can be used as a reaction coordinate in simulations of proton transport in confined environments.
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Affiliation(s)
- Adam W Duster
- Chemistry Department, CB 194, University of Colorado Denver , Denver, Colorado 80217, United States
| | - Hai Lin
- Chemistry Department, CB 194, University of Colorado Denver , Denver, Colorado 80217, United States
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16
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Frenzel J, Meyer B, Marx D. Bicanonical ab Initio Molecular Dynamics for Open Systems. J Chem Theory Comput 2017. [DOI: 10.1021/acs.jctc.7b00263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Johannes Frenzel
- Lehrstuhl für
Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Bernd Meyer
- Interdisziplinäres
Zentrum für Molekulare Materialien (ICMM) and Computer-Chemie-Centrum
(CCC), Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Dominik Marx
- Lehrstuhl für
Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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17
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Duster AW, Wang C, Garza CM, Miller DE, Lin H. Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here? WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1310] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Adam W. Duster
- Chemistry Department University of Colorado Denver Denver CO USA
| | - Chun‐Hung Wang
- Chemistry Department University of Colorado Denver Denver CO USA
| | | | | | - Hai Lin
- Chemistry Department University of Colorado Denver Denver CO USA
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18
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Krajniak J, Pandiyan S, Nies E, Samaey G. Generic Adaptive Resolution Method for Reverse Mapping of Polymers from Coarse-Grained to Atomistic Descriptions. J Chem Theory Comput 2016; 12:5549-5562. [DOI: 10.1021/acs.jctc.6b00595] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jakub Krajniak
- Department
of Computer Science, KU Leuven, Celestijnenlaan 200A, 3001 Leuven, Belgium
| | - Sudharsan Pandiyan
- Division
of Polymer Chemistry and Materials, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Eric Nies
- Division
of Polymer Chemistry and Materials, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Giovanni Samaey
- Department
of Computer Science, KU Leuven, Celestijnenlaan 200A, 3001 Leuven, Belgium
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Boereboom JM, Potestio R, Donadio D, Bulo RE. Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials. J Chem Theory Comput 2016; 12:3441-8. [PMID: 27332140 DOI: 10.1021/acs.jctc.6b00205] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system.
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Affiliation(s)
- Jelle M Boereboom
- Inorganic Chemistry and Catalysis group, Debye Institute for Nanomaterials Science, Utrecht University , Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Raffaello Potestio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Davide Donadio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.,Department of Chemistry, University of California Davis , One Shields Avenue, Davis, California 95616, United States.,Donostia International Physics Center, Paseo Manuel de Lardizabal, 4, E-20018 Donostia-San Sebastian, Spain.,IKERBASQUE, Basque Foundation for Science, E-48011 Bilbao, Spain
| | - Rosa E Bulo
- Inorganic Chemistry and Catalysis group, Debye Institute for Nanomaterials Science, Utrecht University , Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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Zheng M, Waller MP. Adaptive quantum mechanics/molecular mechanics methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1255] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Min Zheng
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation; Westfälische Wilhelms-Universität Münster; 48149 Münster, Germany
| | - Mark P. Waller
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation; Westfälische Wilhelms-Universität Münster; 48149 Münster, Germany
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