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Journal articles on the topic 'Hybrid QM / MM methodologies'

Author: Grafiati

Published: 8 September 2021

Last updated: 1 February 2022

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1

Illingworth, Christopher J. R., Stuart R. Gooding, Peter J. Winn, Garth A. Jones, György G. Ferenczy, and Christopher A. Reynolds. "Classical Polarization in Hybrid QM/MM Methods." Journal of Physical Chemistry A 110, no. 20 (May 2006): 6487–97. http://dx.doi.org/10.1021/jp046944i.

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2

Pan, Xiaoliang, Edina Rosta, and Yihan Shao. "Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations." Molecules 23, no. 10 (September 29, 2018): 2500. http://dx.doi.org/10.3390/molecules23102500.

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In QM/MM calculations, it is essential to handle electrostatic interactions between the QM and MM subsystems accurately and efficiently. To achieve maximal efficiency, it is convenient to adopt a hybrid scheme, where the QM electron density is used explicitly in the evaluation of short-range QM/MM electrostatic interactions, while a multipolar representation for the QM electron density is employed to account for the long-range QM/MM electrostatic interactions. In order to avoid energy discontinuity at the cutoffs, which separate the short- and long-range QM/MM electrostatic interactions, a switching function should be utilized to ensure a smooth potential energy surface. In this study, we benchmarked the accuracy of such hybrid embedding schemes for QM/MM electrostatic interactions using different multipolar representations, switching functions and cutoff distances. For test systems (neutral and anionic oxyluciferin in MM (aqueous and enzyme) environments), the best accuracy was acquired with a combination of QM electrostatic potential (ESP) charges and dipoles and two switching functions (long-range electrostatic corrections (LREC) and Switch) in the treatment of long-range QM/MM electrostatics. It allowed us to apply a 10Å distance cutoff and still obtain QM/MM electrostatics/polarization energies within 0.1 kcal/mol and time-dependent density functional theory (TDDFT)/MM vertical excitation energies within 10−3 eV from theoretical reference values.

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3

Apostolov, Rossen, Y. Yonezawa, and H. Nakamura. "Aquaporin1 channel proteins : Hybrid-QM/MM Computer Simulation." Seibutsu Butsuri 43, supplement (2003): S185. http://dx.doi.org/10.2142/biophys.43.s185_2.

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4

Tchougréeff, Andrei L., and Andrei M. Tokmachev. "Physical Principles of Constructing Hybrid QM/MM Methods." Journal of Computational Methods in Sciences and Engineering 2, no. 3-4 (August 1, 2002): 309–14. http://dx.doi.org/10.3233/jcm-2002-23-403.

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5

Hillier, Ian H. "Chemical reactivity studied by hybrid QM/MM methods." Journal of Molecular Structure: THEOCHEM 463, no. 1-2 (April 1999): 45–52. http://dx.doi.org/10.1016/s0166-1280(98)00391-1.

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6

Wang, Yingjie, and Jiali Gao. "Projected Hybrid Orbitals: A General QM/MM Method." Journal of Physical Chemistry B 119, no. 3 (October 15, 2014): 1213–24. http://dx.doi.org/10.1021/jp507983u.

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7

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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8

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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9

Nakata, K., Y. Yonezawa, H. Nakamura, and T. Takada. "2P098 Development of the Method of Hybrid QM/MM Simulation including chemical bond on QM/MM boundary." Seibutsu Butsuri 45, supplement (2005): S144. http://dx.doi.org/10.2142/biophys.45.s144_2.

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10

Hagiwara, Yohsuke, Takehiro Ohta, and Masaru Tateno. "QM/MM hybrid calculation of biological macromolecules using a new interface program connecting QM and MM engines." Journal of Physics: Condensed Matter 21, no. 6 (January 20, 2009): 064234. http://dx.doi.org/10.1088/0953-8984/21/6/064234.

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11

Loco, Daniele, Louis Lagardère, Stefano Caprasecca, Filippo Lipparini, Benedetta Mennucci, and Jean-Philip Piquemal. "Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding." Journal of Chemical Theory and Computation 13, no. 9 (August 14, 2017): 4025–33. http://dx.doi.org/10.1021/acs.jctc.7b00572.

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12

French, Samuel A., Alexey A. Sokol, Stefan T. Bromley, C. Richard A. Catlow, Stephen C. Rogers, Frank King, and Paul Sherwood. "From CO2 to Methanol by Hybrid QM/MM Embedding." Angewandte Chemie 113, no. 23 (December 3, 2001): 4569–72. http://dx.doi.org/10.1002/1521-3757(20011203)113:23<4569::aid-ange4569>3.0.co;2-f.

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13

Ougaard Dohn, Asmus, Daniele Selli, Gianluca Fazio, Lorenzo Ferraro, Jens Mortensen, Bartolomeo Civalleri, and Cristiana Di Valentin. "Interfacing CRYSTAL/AMBER to Optimize QM/MM Lennard–Jones Parameters for Water and to Study Solvation of TiO2 Nanoparticles." Molecules 23, no. 11 (November 13, 2018): 2958. http://dx.doi.org/10.3390/molecules23112958.

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Metal oxide nanoparticles (NPs) are regarded as good candidates for many technological applications, where their functional environment is often an aqueous solution. The correct description of metal oxide electronic structure is still a challenge for local and semilocal density functionals, whereas hybrid functional methods provide an improved description, and local atomic function-based codes such as CRYSTAL17 outperform plane wave codes when it comes to hybrid functional calculations. However, the computational cost of hybrids are still prohibitive for systems of real sizes, in a real environment. Therefore, we here present and critically assess the accuracy of our electrostatic embedding quantum mechanical/molecular mechanical (QM/MM) coupling between CRYSTAL17 and AMBER16, and demonstrate some of its capabilities via the case study of TiO2 NPs in water. First, we produced new Lennard–Jones (LJ) parameters that improve the accuracy of water–water interactions in the B3LYP/TIP3P coupling. We found that optimizing LJ parameters based on water tri- to deca-mer clusters provides a less overstructured QM/MM liquid water description than when fitting LJ parameters only based on the water dimer. Then, we applied our QM/MM coupling methodology to describe the interaction of a 1 nm wide multilayer of water surrounding a spherical TiO2 nanoparticle (NP). Optimizing the QM/MM water–water parameters was found to have little to no effect on the local NP properties, which provide insights into the range of influence that can be attributed to the LJ term in the QM/MM coupling. The effect of adding additional water in an MM fashion on the geometry optimized nanoparticle structure is small, but more evident effects are seen in its electronic properties. We also show that there is good transferability of existing QM/MM LJ parameters for organic molecules–water interactions to our QM/MM implementation, even though these parameters were obtained with a different QM code and QM/MM implementation, but with the same functional.

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14

Hillier, Ian H. "ChemInform Abstract: Chemical Reactivity Studied by Hybrid QM/MM Methods." ChemInform 30, no. 24 (June 15, 2010): no. http://dx.doi.org/10.1002/chin.199924328.

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15

Amaral, M. S., M. Loos, and A. S. Ito. "A QM/MM hybrid simulation of 5-hydroxytryptophan in solution." International Journal of Quantum Chemistry 95, no. 3 (2003): 289–94. http://dx.doi.org/10.1002/qua.10697.

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16

Zhang, Yin-Jia, Alireza Khorshidi, Georg Kastlunger, and Andrew A. Peterson. "The potential for machine learning in hybrid QM/MM calculations." Journal of Chemical Physics 148, no. 24 (June 28, 2018): 241740. http://dx.doi.org/10.1063/1.5029879.

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17

Ruiz-Pernía, J. Javier, Estanislao Silla, Iñaki Tuñón, Sergio Martí, and Vicent Moliner. "Hybrid QM/MM Potentials of Mean Force with Interpolated Corrections." Journal of Physical Chemistry B 108, no. 24 (June 2004): 8427–33. http://dx.doi.org/10.1021/jp049633g.

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18

Gregersen, Brent A., Xabier Lopez, and Darrin M. York. "Hybrid QM/MM Study of Thio Effects in Transphosphorylation Reactions." Journal of the American Chemical Society 125, no. 24 (June 2003): 7178–79. http://dx.doi.org/10.1021/ja035167h.

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19

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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20

Banáš, Pavel, Petr Jurečka, Nils G. Walter, Jiří Šponer, and Michal Otyepka. "Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM." Methods 49, no. 2 (October 2009): 202–16. http://dx.doi.org/10.1016/j.ymeth.2009.04.007.

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21

HAYASHI, Shigehiko. "Chemical Reactions in Biological Systems Studied by Hybrid QM/MM Simulations." Seibutsu Butsuri 46, no. 2 (2006): 76–81. http://dx.doi.org/10.2142/biophys.46.76.

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22

Colombo, Maria Carola, Leonardo Guidoni, Alessandro Laio, Alessandra Magistrato, Patrick Maurer, Stefano Piana, Ute Röhrig, et al. "Hybrid QM/MM Car-Parrinello Simulations of Catalytic and Enzymatic Reactions." CHIMIA International Journal for Chemistry 56, no. 1 (January 1, 2002): 13–19. http://dx.doi.org/10.2533/000942902777680865.

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23

Bessac, Fabienne, Fabienne Alary, Yannick Carissan, Jean-Louis Heully, Jean-Pierre Daudey, and Romuald Poteau. "Effective group potentials: a powerful tool for hybrid QM/MM methods?" Journal of Molecular Structure: THEOCHEM 632, no. 1-3 (August 2003): 43–59. http://dx.doi.org/10.1016/s0166-1280(03)00287-2.

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24

Sebastiani, Daniel, and Ursula Rothlisberger. "Nuclear Magnetic Resonance Chemical Shifts from Hybrid DFT QM/MM Calculations." Journal of Physical Chemistry B 108, no. 9 (March 2004): 2807–15. http://dx.doi.org/10.1021/jp0364304.

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25

Gao, Jiali, and Marek Freindorf. "Hybrid ab Initio QM/MM Simulation ofN-Methylacetamide in Aqueous Solution." Journal of Physical Chemistry A 101, no. 17 (April 1997): 3182–88. http://dx.doi.org/10.1021/jp970041q.

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26

Shigeta, Yasuteru. "Hybrid QM/MM studies on energetics of malonaldehyde in condensed phase." International Journal of Quantum Chemistry 96, no. 1 (2003): 32–41. http://dx.doi.org/10.1002/qua.10790.

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27

Yin, Jun, and Ya-Pu Zhao. "Hybrid QM/MM simulation of the hydration phenomena of dipalmitoylphosphatidylcholine headgroup." Journal of Colloid and Interface Science 329, no. 2 (January 2009): 410–15. http://dx.doi.org/10.1016/j.jcis.2008.09.070.

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28

Takahashi, H., T. Hori, H. Hashimoto, and T. Nitta. "A hybrid QM/MM method employing real space grids for QM water in the TIP4P water solvents." Journal of Computational Chemistry 22, no. 12 (2001): 1252–61. http://dx.doi.org/10.1002/jcc.1082.

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29

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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30

Khodarahmi, Ghadamali, Parvin Asadi, Hossein Farrokhpour, Farshid Hassanzadeh, and Mohammad Dinari. "Design of novel potential aromatase inhibitors via hybrid pharmacophore approach: docking improvement using the QM/MM method." RSC Advances 5, no. 71 (2015): 58055–64. http://dx.doi.org/10.1039/c5ra10097f.

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31

Torras, Juan. "Multiple active zones in hybrid QM/MM molecular dynamics simulations for large biomolecular systems." Physical Chemistry Chemical Physics 17, no. 15 (2015): 9959–72. http://dx.doi.org/10.1039/c5cp00905g.

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32

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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33

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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34

Liu, Wei, Xiangyu Jia, Meiting Wang, Pengfei Li, Xiaohui Wang, Wenxin Hu, Jun Zheng, and Ye Mei. "Calculations of the absolute binding free energies for Ralstonia solanacearum lectins bound with methyl-α-l-fucoside at molecular mechanical and quantum mechanical/molecular mechanical levels." RSC Advances 7, no. 61 (2017): 38570–80. http://dx.doi.org/10.1039/c7ra06215j.

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In this work, both a molecular mechanical (MM) method and a hybrid quantum mechanical/molecular mechanical (QM/MM) method have been applied in the study of the binding affinities of methyl-α-l-fucoside to Ralstonia solanacearum lectins.

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35

Yonezawa, Y., T. Takada, T. Sakuma, K. Nakata, and H. Nakamura. "Development of the Method of the Calculation for Hybrid QM/MM Simulation." Seibutsu Butsuri 43, supplement (2003): S74. http://dx.doi.org/10.2142/biophys.43.s74_2.

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36

Sakurai, M., K. Sakata, S. Saito, and Y. Inoue. "1D1015 Hybrid QM/MM-CI study of the absorption Maximum of Halorhodopsin." Seibutsu Butsuri 42, supplement2 (2002): S23. http://dx.doi.org/10.2142/biophys.42.s23_3.

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37

Schwörer, Magnus, Christoph Wichmann, Erik Gawehn, and Gerald Mathias. "Simulated Solute Tempering in Fully Polarizable Hybrid QM/MM Molecular Dynamics Simulations." Journal of Chemical Theory and Computation 12, no. 3 (February 19, 2016): 992–99. http://dx.doi.org/10.1021/acs.jctc.5b00951.

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38

Pshetitsky, Yaron, Reuven Eitan, Gilit Verner, Amnon Kohen, and Dan Thomas Major. "Improved Sugar Puckering Profiles for Nicotinamide Ribonucleoside for Hybrid QM/MM Simulations." Journal of Chemical Theory and Computation 12, no. 10 (September 2, 2016): 5179–89. http://dx.doi.org/10.1021/acs.jctc.6b00401.

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39

Nitsche, Matías A., Manuel Ferreria, Esteban E. Mocskos, and Mariano C. González Lebrero. "GPU Accelerated Implementation of Density Functional Theory for Hybrid QM/MM Simulations." Journal of Chemical Theory and Computation 10, no. 3 (February 27, 2014): 959–67. http://dx.doi.org/10.1021/ct400308n.

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40

Mar�chal, Jean-Didier, Guada Barea, Feliu Maseras, Agust� Lled�s, Liliane Mouawad, and David P�rahia. "Theoretical modeling of the heme group with a hybrid QM/MM method." Journal of Computational Chemistry 21, no. 4 (March 2000): 282–94. http://dx.doi.org/10.1002/(sici)1096-987x(200003)21:4<282::aid-jcc4>3.0.co;2-l.

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41

Sironi, Maurizio, Arianna Fornili, and Sandro L. Fornili. "Water interaction with glycine betaine: A hybrid QM/MM molecular dynamics simulation." Physical Chemistry Chemical Physics 3, no. 6 (2001): 1081–85. http://dx.doi.org/10.1039/b009779i.

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42

Fornili, Arianna, Yohann Moreau, Maurizio Sironi, and Xavier Assfeld. "On the suitability of strictly localized orbitals for hybrid QM/MM calculations." Journal of Computational Chemistry 27, no. 4 (2006): 515–23. http://dx.doi.org/10.1002/jcc.20366.

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43

Hall, Richard J., Sally A. Hindle, Neil A. Burton, and Ian H. Hillier. "Aspects of hybrid QM/MM calculations: The treatment of the QM/MM interface region and geometry optimization with an application to chorismate mutase." Journal of Computational Chemistry 21, no. 16 (2000): 1433–41. http://dx.doi.org/10.1002/1096-987x(200012)21:16<1433::aid-jcc2>3.0.co;2-p.

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44

Shoji, Mitsuo, Yukihiro Abe, Mauro Boero, Yasuteru Shigeta, and Yoshiaki Nishiya. "Reaction mechanism of N-cyclopropylglycine oxidation by monomeric sarcosine oxidase." Physical Chemistry Chemical Physics 22, no. 29 (2020): 16552–61. http://dx.doi.org/10.1039/d0cp01679a.

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45

Jiang, Hao, and Wenzhen Lai. "Monophenolase and catecholase activity of Aspergillus oryzae catechol oxidase: insights from hybrid QM/MM calculations." Organic & Biomolecular Chemistry 18, no. 27 (2020): 5192–202. http://dx.doi.org/10.1039/d0ob00969e.

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46

Tirler, Andreas O., and Thomas S. Hofer. "The structural influence of Ca2+ counter-ions on uranyl(vi) tricarbonate in aqueous solution." Dalton Transactions 45, no. 12 (2016): 4983–88. http://dx.doi.org/10.1039/c5dt04718h.

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The presented study elucidates the influence of calcium(ii) counter-ions on the structure of the environmentally relevant uranyl tricarbonates using hybrid quantum mechanical/molecular mechanical (QM/MM) MD simulations.

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47

Guallar, Victor, and Frank Wallrapp. "Mapping protein electron transfer pathways with QM/MM methods." Journal of The Royal Society Interface 5, suppl_3 (April 29, 2008): 233–39. http://dx.doi.org/10.1098/rsif.2008.0061.focus.

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Mixed quantum mechanics/molecular mechanics (QM/MM) methods offer a valuable computational tool for understanding the electron transfer pathway in protein–substrate interactions and protein–protein complexes. These hybrid methods are capable of solving the Schrödinger equation on a small subset of the protein, the quantum region, describing its electronic structure under the polarization effects of the remainder of the protein. By selectively turning on and off different residues in the quantum region, we are able to obtain the electron pathway for short- and large-range interactions. Here, we summarize recent studies involving the protein–substrate interaction in cytochrome P450 camphor, ascorbate peroxidase and cytochrome c peroxidase, and propose a novel approach for the long-range protein–protein electron transfer. The results on ascorbate peroxidase and cytochrome c peroxidase reveal the importance of the propionate groups in the electron transfer pathway. The long-range protein–protein electron transfer has been studied on the cytochrome c peroxidase–cytochrome c complex. The results indicate the importance of Phe82 and Cys81 on cytochrome c , and of Asn196, Ala194, Ala176 and His175 on cytochrome c peroxidase.

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48

De Vetta, Martina, Omar Baig, Dorika Steen, Juan Nogueira, and Leticia González. "Assessing Configurational Sampling in the Quantum Mechanics/Molecular Mechanics Calculation of Temoporfin Absorption Spectrum and Triplet Density of States." Molecules 23, no. 11 (November 9, 2018): 2932. http://dx.doi.org/10.3390/molecules23112932.

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The absorption properties of Temoporfin, a second-generation photosensitizer employed in photodynamic therapy, are calculated with an electrostatic-embedding quantum mechanics/molecular mechanics (QM/MM) scheme in methanol. The suitability of several ensembles of geometries generated by different sampling techniques, namely classical-molecular-dynamics (MD) and QM/MM-MD thermal sampling, Wigner quantum sampling and a hybrid protocol, which combines the thermal and quantum approaches, is assessed. It is found that a QM description of the chromophore during the sampling is needed in order to achieve a good agreement with respect to the experimental spectrum. Such a good agreement is obtained with both QM/MM-MD and Wigner samplings, demonstrating that a proper description of the anharmonic motions of the chromophore is not relevant in the computation of the absorption properties. In addition, it is also found that solvent organization is a rather fast process and a long sampling is not required. Finally, it is also demonstrated that the same exchange-correlation functional should be employed in the sampling and in the computation of the excited states properties to avoid unphysical triplet states with relative energies close or below 0 eV.

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Yagi, Kiyoshi, Kenta Yamada, Chigusa Kobayashi, and Yuji Sugita. "Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations." Journal of Chemical Theory and Computation 15, no. 3 (February 7, 2019): 1924–38. http://dx.doi.org/10.1021/acs.jctc.8b01193.

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50

Benighaus, Tobias, and Walter Thiel. "A General Boundary Potential for Hybrid QM/MM Simulations of Solvated Biomolecular Systems." Journal of Chemical Theory and Computation 5, no. 11 (October 14, 2009): 3114–28. http://dx.doi.org/10.1021/ct900437b.

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