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Journal articles on the topic 'QM/MM simulations'

Author: Grafiati

Published: 14 March 2023

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1

Suh, Donghyuk, Kwangho Nam, and Wonpil Im. "CHARMM-GUI QM/MM interfacer for the hybrid QM/MM molecular dynamics simulations." Biophysical Journal 122, no. 3 (February 2023): 424a. http://dx.doi.org/10.1016/j.bpj.2022.11.2299.

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2

Kulkarni, Prajakta U., Harshil Shah, and Vivek K. Vyas. "Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-Based Drug Design and Discovery." Mini-Reviews in Medicinal Chemistry 22, no. 8 (May 2022): 1096–107. http://dx.doi.org/10.2174/1389557521666211007115250.

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Abstract: Quantum Mechanics (QM) is the physics-based theory that explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, when combined, hybrid quantum mechanics and molecular mechanics (QM/MM) can act as computer-based methods that can be used to calculate the structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical processes in solutions, as well as in the proteins, and has a great scope in structure-based drug design (SBDD) and discovery. Hybrid QM/MM can also be applied to HTS to derive QSAR models. Due to the availability of many protein crystal structures, it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however, the rest is defined through the molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.

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3

Watanabe, Hiroshi C., and Qiang Cui. "Quantitative Analysis of QM/MM Boundary Artifacts and Correction in Adaptive QM/MM Simulations." Journal of Chemical Theory and Computation 15, no. 7 (May 16, 2019): 3917–28. http://dx.doi.org/10.1021/acs.jctc.9b00180.

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4

de la Lande, Aurélien, Aurelio Alvarez-Ibarra, Karim Hasnaoui, Fabien Cailliez, Xiaojing Wu, Tzonka Mineva, Jérôme Cuny, et al. "Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review." Molecules 24, no. 9 (April 26, 2019): 1653. http://dx.doi.org/10.3390/molecules24091653.

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deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born–Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.

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5

König, Gerhard, Frank Pickard, Jing Huang, Walter Thiel, Alexander MacKerell, Bernard Brooks, and Darrin York. "A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes." Molecules 23, no. 10 (October 19, 2018): 2695. http://dx.doi.org/10.3390/molecules23102695.

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Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree–Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard–Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute–solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.

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6

Liang, Dongyue, Jiewei Hong, Dong Fang, Joseph W. Bennett, Sara E. Mason, Robert J. Hamers, and Qiang Cui. "Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations." Physical Chemistry Chemical Physics 20, no. 5 (2018): 3349–62. http://dx.doi.org/10.1039/c7cp06709g.

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7

Yang, Wei, Ryan Bitetti-Putzer, and Martin Karplus. "Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials." Journal of Chemical Physics 120, no. 20 (May 22, 2004): 9450–53. http://dx.doi.org/10.1063/1.1738106.

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8

Chalmet, S., D. Rinaldi, and M. F. Ruiz-López. "A QM/MM/continuum model for computations in solution: Comparison with QM/MM molecular dynamics simulations." International Journal of Quantum Chemistry 84, no. 5 (2001): 559–64. http://dx.doi.org/10.1002/qua.1410.

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9

Shimada, J., T. Sakuma, K. Nakata, T. Wasiho, and T. Takada. "3K1015 BioMolecular Simulations : MD and QM/MM calculations." Seibutsu Butsuri 42, supplement2 (2002): S180. http://dx.doi.org/10.2142/biophys.42.s180_2.

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10

Solt, Iván, Petr Kulhánek, István Simon, Steven Winfield, Mike C. Payne, Gábor Csányi, and Monika Fuxreiter. "Evaluating Boundary Dependent Errors in QM/MM Simulations." Journal of Physical Chemistry B 113, no. 17 (April 30, 2009): 5728–35. http://dx.doi.org/10.1021/jp807277r.

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11

Morzan, Uriel N., Diego J. Alonso de Armiño, Nicolás O. Foglia, Francisco Ramírez, Mariano C. González Lebrero, Damián A. Scherlis, and Darío A. Estrin. "Spectroscopy in Complex Environments from QM–MM Simulations." Chemical Reviews 118, no. 7 (March 21, 2018): 4071–113. http://dx.doi.org/10.1021/acs.chemrev.8b00026.

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12

Martins Costa, M. T. C. "QM/MM simulations of polyols in aqueous solution." Journal of Molecular Structure: THEOCHEM 729, no. 1-2 (September 2005): 47–52. http://dx.doi.org/10.1016/j.theochem.2005.03.016.

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13

Jász, Ádám, Ádám Rák, István Ladjánszki, Gábor János Tornai, and György Cserey. "Towards chemically accurate QM/MM simulations on GPUs." Journal of Molecular Graphics and Modelling 96 (May 2020): 107536. http://dx.doi.org/10.1016/j.jmgm.2020.107536.

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14

Riahi, Saleh, and Christopher N. Rowley. "QM/MM Simulations of Mg and Zn Solvation." Biophysical Journal 106, no. 2 (January 2014): 405a. http://dx.doi.org/10.1016/j.bpj.2013.11.2281.

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15

Dohm, Sebastian, Eckhard Spohr, and Martin Korth. "Developing adaptive QM/MM computer simulations for electrochemistry." Journal of Computational Chemistry 38, no. 1 (October 28, 2016): 51–58. http://dx.doi.org/10.1002/jcc.24513.

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16

Doll, K., and T. Jacob. "QM/MM description of periodic systems." Journal of Theoretical and Computational Chemistry 14, no. 07 (November 2015): 1550054. http://dx.doi.org/10.1142/s0219633615500546.

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A quantum mechanical molecular mechanics (QM/MM) implementation for periodic systems is reported. This is done for the case of molecules and for systems with two and three-dimensional periodicity, which is suitable to model electrolytes in contact with electrodes. Tests on different water-containing systems, ranging from the water dimer up to liquid water indicate the correctness of the scheme. Furthermore, molecular dynamics simulations are performed, as a possible direction to study realistic systems.

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17

Miranda, Sebastião, Jonas Feldt, Frederico Pratas, Ricardo A. Mata, Nuno Roma, and Pedro Tomás. "Efficient parallelization of perturbative Monte Carlo QM/MM simulations in heterogeneous platforms." International Journal of High Performance Computing Applications 31, no. 6 (July 27, 2016): 499–516. http://dx.doi.org/10.1177/1094342016649420.

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A novel perturbative Monte Carlo mixed quantum mechanics (QM)/molecular mechanics (MM) approach has been recently developed to simulate molecular systems in complex environments. However, the required accuracy to efficiently simulate such complex molecular systems is usually granted at the cost of long executing times. To alleviate this problem, a new parallelization strategy of multi-level Monte Carlo molecular simulations is herein proposed for heterogeneous systems. It simultaneously exploits fine-grained (at the data level), coarse-grained (at the Markov chain level) and task-grained (pure QM, pure MM and QM/MM procedures) parallelism to ensure an efficient execution in heterogeneous systems composed of central processing units and multiple and possibly different graphical processing units. This is achieved by making use of the OpenCL library, together with appropriate dynamic load balancing schemes. From the conducted evaluation with real benchmarking data, a speed-up of 56x in the computational bottleneck part was observed, which results in a global speed-up of 38x for the whole simulation, reducing the time of a typical simulation from 80 hours to only 2 hours.

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18

Tzeliou, Christina Eleftheria, Markella Aliki Mermigki, and Demeter Tzeli. "Review on the QM/MM Methodologies and Their Application to Metalloproteins." Molecules 27, no. 9 (April 20, 2022): 2660. http://dx.doi.org/10.3390/molecules27092660.

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The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was introduced in 1976, while the extensive acceptance of this methodology started in the 1990s. The combination of QM/MM approach with molecular dynamics (MD) simulation, otherwise known as the QM/MM/MD approach, is a powerful and promising tool for the investigation of chemical reactions’ mechanism of complex molecular systems, drug delivery, properties of molecular devices, organic electronics, etc. In the present review, the main methodologies in the multiscaling approaches, i.e., density functional theory (DFT), semiempirical methodologies (SE), MD simulations, MM, and their new advances are discussed in short. Then, a review on calculations and reactions on metalloproteins is presented, where particular attention is given to nitrogenase that catalyzes the conversion of atmospheric nitrogen molecules N₂ into NH₃ through the process known as nitrogen fixation and the FeMo-cofactor.

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19

Khrenova, Maria G., Egor S. Bulavko, Fedor D. Mulashkin, and Alexander V. Nemukhin. "Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials." Molecules 26, no. 13 (June 30, 2021): 3998. http://dx.doi.org/10.3390/molecules26133998.

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We report the results of calculations of the Gibbs energy profiles of the guanosine triphosphate (GTP) hydrolysis by the Arl3-RP2 protein complex using molecular dynamics (MD) simulations with ab initio type QM/MM potentials. The chemical reaction of GTP hydrolysis to guanosine diphosphate (GDP) and inorganic phosphate (Pi) is catalyzed by GTPases, the enzymes, which are responsible for signal transduction in live cells. A small GTPase Arl3, catalyzing the GTP → GDP reaction in complex with the activating protein RP2, constitute an essential part of the human vision cycle. To simulate the reaction mechanism, a model system is constructed by motifs of the crystal structure of the Arl3-RP2 complexed with a substrate analog. After selection of reaction coordinates, energy profiles for elementary steps along the reaction pathway GTP + H2O → GDP + Pi are computed using the umbrella sampling and umbrella integration procedures. QM/MM MD calculations are carried out, interfacing the molecular dynamics program NAMD and the quantum chemistry program TeraChem. Ab initio type QM(DFT)/MM potentials are computed with atom-centered basis sets 6-31G** and two hybrid functionals (PBE0-D3 and ωB97x-D3) of the density functional theory, describing a large QM subsystem. Results of these simulations of the reaction mechanism are compared to those obtained with QM/MM calculations on the potential energy surface using a similar description of the QM part. We find that both approaches, QM/MM and QM/MM MD, support the mechanism of GTP hydrolysis by GTPases, according to which the catalytic glutamine side chain (Gln71, in this system) actively participates in the reaction. Both approaches distinguish two parts of the reaction: the cleavage of the phosphorus-oxygen bond in GTP coupled with the formation of Pi, and the enzyme regeneration. Newly performed QM/MM MD simulations confirmed the profile predicted in the QM/MM minimum energy calculations, called here the pathway-I, and corrected its relief at the first elementary step from the enzyme–substrate complex. The QM/MM MD simulations also revealed another mechanism at the part of enzyme regeneration leading to pathway-II. Pathway-II is more consistent with the experimental kinetic data of the wild-type complex Arl3-RP2, whereas pathway-I explains the role of the mutation Glu138Gly in RP2 slowing down the hydrolysis rate.

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20

Ardevol, Albert, and Gerhard Hummer. "Retinal isomerization and water-pore formation in channelrhodopsin-2." Proceedings of the National Academy of Sciences 115, no. 14 (March 19, 2018): 3557–62. http://dx.doi.org/10.1073/pnas.1700091115.

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Channelrhodopsin-2 (ChR2) is a light-sensitive ion channel widely used in optogenetics. Photoactivation triggers a trans-to-cis isomerization of a covalently bound retinal. Ensuing conformational changes open a cation-selective channel. We explore the structural dynamics in the early photocycle leading to channel opening by classical (MM) and quantum mechanical (QM) molecular simulations. With QM/MM simulations, we generated a protein-adapted force field for the retinal chromophore, which we validated against absorption spectra. In a 4-µs MM simulation of a dark-adapted ChR2 dimer, water entered the vestibules of the closed channel. Retinal all-trans to 13-cis isomerization, simulated with metadynamics, triggered a major restructuring of the charge cluster forming the channel gate. On a microsecond time scale, water penetrated the gate to form a membrane-spanning preopen pore between helices H1, H2, H3, and H7. This influx of water into an ion-impermeable preopen pore is consistent with time-resolved infrared spectroscopy and electrophysiology experiments. In the retinal 13-cis state, D253 emerged as the proton acceptor of the Schiff base. Upon proton transfer from the Schiff base to D253, modeled by QM/MM simulations, we obtained an early-M/P2390–like intermediate. Rapid rotation of the unprotonated Schiff base toward the cytosolic side effectively prevents its reprotonation from the extracellular side. From MM and QM simulations, we gained detailed insight into the mechanism of ChR2 photoactivation and early events in pore formation. By rearranging the network of charges and hydrogen bonds forming the gate, water emerges as a key player in light-driven ChR2 channel opening.

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21

Watanabe, Hiroshi. "Improvement of Performance, Stability and Continuity by Modified Size-Consistent Multipartitioning Quantum Mechanical/Molecular Mechanical Method." Molecules 23, no. 8 (July 27, 2018): 1882. http://dx.doi.org/10.3390/molecules23081882.

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For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because of temporal and spatial discontinuity problems. To overcome these problems, in a previous study, we proposed a corrective QM/MM method, size-consistent multipartitioning (SCMP) QM/MM and successfully demonstrated that, using SCMP, it is possible to perform stable molecular dynamics simulations by effectively taking into account solvent quantum chemical effects. The SCMP method is characterized by two original features: size-consistency of a QM region among all QM/MM partitioning and partitioning update. However, in our previous study, the performance was not fully elicited compared to the theoretical upper bound and the optimal partitioning update protocol and parameters were not fully verified. To elicit the potential performance, in the present study, we simplified the theoretical framework and modified the partitioning protocol.

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22

Peguiron, Anke, Lucio Colombi Ciacchi, Alessandro De Vita, James R. Kermode, and Gianpietro Moras. "Accuracy of buffered-force QM/MM simulations of silica." Journal of Chemical Physics 142, no. 6 (February 14, 2015): 064116. http://dx.doi.org/10.1063/1.4907786.

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23

Messner, Christoph B., Günther K. Bonn, and Thomas S. Hofer. "QM/MM MD simulations of La(iii)–phosphopeptide complexes." Molecular BioSystems 11, no. 1 (2015): 232–38. http://dx.doi.org/10.1039/c4mb00424h.

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24

Wang, Meiting, Ye Mei, and Ulf Ryde. "Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations." Journal of Chemical Theory and Computation 14, no. 12 (October 26, 2018): 6613–22. http://dx.doi.org/10.1021/acs.jctc.8b00685.

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25

Bulo, Rosa E., Bernd Ensing, Jetze Sikkema, and Lucas Visscher. "Toward a Practical Method for Adaptive QM/MM Simulations." Journal of Chemical Theory and Computation 5, no. 9 (July 30, 2009): 2212–21. http://dx.doi.org/10.1021/ct900148e.

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26

Lu, Xiya, Dong Fang, Shingo Ito, Yuko Okamoto, Victor Ovchinnikov, and Qiang Cui. "QM/MM free energy simulations: recent progress and challenges." Molecular Simulation 42, no. 13 (July 5, 2016): 1056–78. http://dx.doi.org/10.1080/08927022.2015.1132317.

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27

Cooper, April M., and Johannes Kästner. "Averaging Techniques for Reaction Barriers in QM/MM Simulations." ChemPhysChem 15, no. 15 (September 5, 2014): 3264–69. http://dx.doi.org/10.1002/cphc.201402382.

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28

Sun, Zhaoxi. "BAR-based multi-dimensional nonequilibrium pulling for indirect construction of QM/MM free energy landscapes: from semi-empirical to ab initio." Physical Chemistry Chemical Physics 21, no. 39 (2019): 21942–59. http://dx.doi.org/10.1039/c9cp04113c.

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29

Lev, Bogdan, Benoît Roux, and Sergei Yu Noskov. "Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations." Journal of Chemical Theory and Computation 9, no. 9 (August 26, 2013): 4165–75. http://dx.doi.org/10.1021/ct400296w.

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30

Pratihar, Subha, George L. Barnes, and William L. Hase. "Chemical dynamics simulations of energy transfer, surface-induced dissociation, soft-landing, and reactive-landing in collisions of protonated peptide ions with organic surfaces." Chemical Society Reviews 45, no. 13 (2016): 3595–608. http://dx.doi.org/10.1039/c5cs00482a.

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31

Senn, Hans Martin, Johannes Kästner, Jürgen Breidung, and Walter Thiel. "Finite-temperature effects in enzymatic reactions — Insights from QM/MM free-energy simulations." Canadian Journal of Chemistry 87, no. 10 (October 2009): 1322–37. http://dx.doi.org/10.1139/v09-092.

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We report potential-energy and free-energy data for three enzymatic reactions: carbon–halogen bond formation in fluorinase, hydrogen abstraction from camphor in cytochrome P450cam, and chorismate-to-prephenate Claisen rearrangement in chorismate mutase. The results were obtained by combined quantum mechanics/molecular mechanics (QM/MM) optimizations and two types of QM/MM free-energy simulations (free-energy perturbation and umbrella sampling) using semi-empirical or density-functional QM methods. Based on these results and our previously published free-energy data on electrophilic substitution in para-hydroxybenzoate hydroxylase, we discuss the importance of finite-temperature effects in the chemical step of enzyme reactions. We find that the entropic contribution to the activation barrier is generally rather small, usually of the order of 5 kJ mol–1 or less, consistent with the notion that enzymes bind and pre-organize the reactants in the active site. A somewhat larger entropic contribution is encountered in the case of chorismate mutase where the pericyclic transition state is intrinsically more rigid than the chorismate reactant (also in the enzyme). The present results suggest that barriers from QM/MM geometry optimization may often be close to free-energy barriers for the chemical step in enzymatic reactions.

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32

Hofer, Thomas S., Andreas B. Pribil, and Bernhard R. Randolf. "Capabilities of chemical simulation methods in the elucidation of structure and dynamics of solutions." Pure and Applied Chemistry 80, no. 6 (January 1, 2008): 1195–210. http://dx.doi.org/10.1351/pac200880061195.

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As a result of recent methodological developments in connection with enhanced computational capacity, theoretical methods have become increasingly valuable and reliable tools for the investigation of solutions. Simulation techniques utilizing a quantum mechanical (QM) approach for the treatment of the chemically most relevant region so-called hybrid quantum mechanical/molecular mechanical (QM/MM) simulations have reached a level of accuracy that often equals or may even surpass experimental methods. The latter is true in particular whenever ultrafast (i.e., picosecond) dynamics prevail, such as in labile hydrates or structure-breaking systems. The recent development of an improved QM/MM framework, the quantum mechanical charge field (QMCF) ansatz, enables a broad spectrum of solute systems to be elucidated. As this novel methodology does not require any solute solvent potential functions, the applicability of the QMCF method is straightforward and universal. This advantage is bought, however, at the price of a substantial increase of the QM subregion, and an attendant increase in computational periods to levels of months, and even a year, despite parallelizing high-performance computing (HPC) clusters. Molecular dynamics (MD) simulations of chemical systems showing increasing complexity have been performed, and demonstrate the superiority of the QMCF ansatz over conventional QM/MM schemes. The systems studied include Pd2+, Pt2+, and Hg22+, as well as composite anions such as PO43- and ClO4-.

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33

Duster, Adam, Chun-Hung Wang, and Hai Lin. "Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes." Molecules 23, no. 9 (August 28, 2018): 2170. http://dx.doi.org/10.3390/molecules23092170.

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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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34

Hofer, Thomas S. "Perspectives for hybrid ab initio/molecular mechanical simulations of solutions: from complex chemistry to proton-transfer reactions and interfaces." Pure and Applied Chemistry 86, no. 2 (February 1, 2014): 105–17. http://dx.doi.org/10.1515/pac-2014-5019.

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Abstract As a consequence of the ongoing development of enhanced computational resources, theoretical chemistry has become an increasingly valuable field for the investigation of a variety of chemical systems. Simulations employing a hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) technique have been shown to be a particularly promising approach, whenever ultrafast (i.e., picosecond) dynamical properties are to be studied, which are in many cases difficult to access via experimental techniques. Details of the quantum mechanical charge field (QMCF) ansatz, an advanced QM/MM protocol, are discussed and simulation results for various systems ranging from simple ionic hydrates to solvated organic molecules and coordination complexes in solution are presented. A particularly challenging application is the description of proton-transfer reactions in chemical simulations, which is a prerequisite to study acidified and basic systems. The methodical requirements for a combination of the QMCF methodology with a dissociative potential model for the description of the solvent are discussed. Furthermore, the possible extension of QM/MM approaches to solid/liquid interfaces is outlined.

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35

Riccardi, Demian, Patricia Schaefer, and Qiang Cui. "pKaCalculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations: A Quantitative Test of QM/MM Protocols." Journal of Physical Chemistry B 109, no. 37 (September 2005): 17715–33. http://dx.doi.org/10.1021/jp0517192.

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36

Wymore, Troy, David W. Deerfield, Martin J. Field, John Hempel, and Hugh B. Nicholas. "Initial catalytic events in class 3 aldehyde dehydrogenase: MM and QM/MM simulations." Chemico-Biological Interactions 143-144 (February 2003): 75–84. http://dx.doi.org/10.1016/s0009-2797(02)00175-8.

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37

Zurek, Jolanta, Anna L. Bowman, W. Andrzej Sokalski, and Adrian J. Mulholland. "MM and QM/MM Modeling of Threonyl-tRNA Synthetase: Model Testing and Simulations." Structural Chemistry 15, no. 5 (October 2004): 405–14. http://dx.doi.org/10.1023/b:stuc.0000037896.80027.2c.

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38

Schwenk, C. F., and B. M. Rode. "Ab initio QM/MM MD simulations of the hydrated Ca2+ ion." Pure and Applied Chemistry 76, no. 1 (January 1, 2004): 37–47. http://dx.doi.org/10.1351/pac200476010037.

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The comparison of two different combined quantum mechanical (QM)/molecular mechanical (MM) simulations treating the quantum mechanical region at Hartree-Fock (HF) and B3-LYP density functional theory (DFT) level allowed us to determine structural and dynamical properties of the hydrated calcium ion. The structure is discussed in terms of radial distribution functions, coordination number distributions, and various angular distributions and the dynamical properties, as librations and vibrations, reorientational times and mean residence times were evaluated by means of velocity autocorrelation functions. The QM/MM molecular dynamics (MD) simulation results prove an eightfold-coordinated complex to be the dominant species, yielding average coordination numbers of 7.9 in the HF and 8.0 in the DFT case. Structural and dynamical results show higher rigidity of the hydrate complex using DFT. The high instability of calcium ion's hydration shell allows the observation of water-exchange processes between first and second hydration shell and shows that the mean lifetimes of water molecules in this first shell (<100 ps) have been strongly overestimated by conclusions from experimental data.

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39

Saito, Toru, and Yu Takano. "QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease." Journal of Physical Chemistry B 126, no. 10 (March 3, 2022): 2087–97. http://dx.doi.org/10.1021/acs.jpcb.1c10200.

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Curchod, Basile F. E., Pabloc Campomanes, Andrey Laktionov, Marilisa Neri, Thomas J. Penfold, Stefano Vanni, Ivano Tavernelli, and Ursula Rothlisberger. "Mechanical (QM/MM) Simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena." CHIMIA International Journal for Chemistry 65, no. 5 (May 26, 2011): 330–33. http://dx.doi.org/10.2533/chimia.2011.330.

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41

Acevedo, Orlando, and William L. Jorgensen. "Cope Elimination: Elucidation of Solvent Effects from QM/MM Simulations." Journal of the American Chemical Society 128, no. 18 (May 2006): 6141–46. http://dx.doi.org/10.1021/ja057523x.

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Riccardi, Demian, Guohui Li, and Qiang Cui. "Importance of van der Waals Interactions in QM/MM Simulations." Journal of Physical Chemistry B 108, no. 20 (May 2004): 6467–78. http://dx.doi.org/10.1021/jp037992q.

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Hudson, Phillip S., H. Lee Woodcock, and Stefan Boresch. "Use of Interaction Energies in QM/MM Free Energy Simulations." Journal of Chemical Theory and Computation 15, no. 8 (May 29, 2019): 4632–45. http://dx.doi.org/10.1021/acs.jctc.9b00084.

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Govender, Krishna K., and Kevin J. Naidoo. "Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations." Journal of Chemical Theory and Computation 10, no. 10 (September 18, 2014): 4708–17. http://dx.doi.org/10.1021/ct500373p.

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45

Lambros, Eleftherios, Filippo Lipparini, Gerardo Andrés Cisneros, and Francesco Paesani. "A Many-Body, Fully Polarizable Approach to QM/MM Simulations." Journal of Chemical Theory and Computation 16, no. 12 (November 19, 2020): 7462–72. http://dx.doi.org/10.1021/acs.jctc.0c00932.

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46

Difley, Seth, Lee-Ping Wang, Sina Yeganeh, Shane R. Yost, and Troy Van Voorhis. "Electronic Properties of Disordered Organic Semiconductors via QM/MM Simulations." Accounts of Chemical Research 43, no. 7 (July 20, 2010): 995–1004. http://dx.doi.org/10.1021/ar900246s.

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HORI, TAKUMI, HIDEAKI TAKAHASHI, and TOMOSHIGE NITTA. "HYBRID QUANTUM MECHANICAL/MOLECULAR MECHANICAL APPROACH TO ENZYMATIC REACTIONS BY UTILIZING THE REAL-SPACE GRID TECHNIQUE." Journal of Theoretical and Computational Chemistry 04, no. 03 (September 2005): 867–82. http://dx.doi.org/10.1142/s0219633605001799.

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We have developed a novel quantum mechanical/molecular mechanical (QM/MM) code based on the real-space grids in order to realize high parallel efficiency. The details of the methodology and its parallel implementation have been presented. We have computed the electronic state of the QM subsystem using the Kohn–Sham density functional theory, where the one-electron wave functions have been expressed by the real-space grids distributed over a cubic cell. We have performed QM/MM simulations for the peptide hydrolysis in human immunodeficiency virus type-1 aspartyl protease in order to examine the reliability of the present QM/MM approach. The activation energy obtained by the present calculations shows a good agreement with the experimental results and that of the other QM/MM method. Finally, we have parallelized the whole code and found that the grid approach can afford high parallel efficiency (~80%) in such a large scale electronic structure calculation. We conclude that the QM/MM approach utilizing real-space grids is adequate and efficient for the study of the enzymatic reactions.

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Kulik, Heather J. "Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer." Physical Chemistry Chemical Physics 20, no. 31 (2018): 20650–60. http://dx.doi.org/10.1039/c8cp03871f.

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Hui, Chenggong, Warispreet Singh, Derek Quinn, Chun Li, Thomas S. Moody, and Meilan Huang. "Regio- and stereoselectivity in the CYP450BM3-catalyzed hydroxylation of complex terpenoids: a QM/MM study." Physical Chemistry Chemical Physics 22, no. 38 (2020): 21696–706. http://dx.doi.org/10.1039/d0cp03083j.

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Szabla, Rafał, Holger Kruse, Petr Stadlbauer, Jiří Šponer, and Andrzej L. Sobolewski. "Sequential electron transfer governs the UV-induced self-repair of DNA photolesions." Chemical Science 9, no. 12 (2018): 3131–40. http://dx.doi.org/10.1039/c8sc00024g.

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