“…Here, we present large-scale quantum mechanics/molecular mechanics calculations of electrochromic shifts for the RC chromophores of photosystem II (PSII) using various quantum chemical methods evaluated against the domain-based local pair natural orbital (DLPNO) implementation of the similarity-transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD). …”
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“…[Image: see text] The excited-state properties and relaxation mechanisms after light irradiation of 6-selenoguanine (6SeG) in water and in DNA have been investigated using a quantum mechanics/molecular mechanics (QM/MM) approach with the multistate complete active space second-order perturbation theory (MS-CASPT2) method. …”
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“…Here, we investigate the viability of an endocyclic mechanism for PcCel45A using hybrid quantum mechanics/molecular mechanics (QM/MM) simulations, with the QM region treated with the self-consistent-charge density-functional tight-binding level of theory. …”
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“…The new ReaxFF-lg parameters were trained from massive quantum mechanics data and experimental values, especially including the bond dissociation curves, valence angle bending curves, dihedral angle torsion curves, and unimolecular decomposition paths of 3-Nitro-1,2,4-triazol-5-one (NTO), 1,3,5-Trinitro-1,3,5-triazine (RDX), and 1,1-Diamino-2,2-dinitroethylene (FOX-7). …”
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“…METHODS: The ESR measurement and quantum mechanics simulation were used to characterize the antioxidant ability of elemene nanoemulsion. …”
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“…Here, we structurally analyze biliverdin binding to miRFPs in real time using time-resolved stimulated Raman spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. …”
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“…We also solved the X-ray structure of the LSSmScarlet protein at the resolution of 1.4 Å that revealed a hydrogen bond network supporting excited-state proton transfer (ESPT). Quantum mechanics/molecular mechanics molecular dynamic simulations confirmed the ESPT mechanism of a large Stokes shift. …”
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“…Here, we report the use of an amphiphilic Pt(II) complex, K[Pt{(O(3)SCH(2)CH(2)CH(2))(2)bzimpy}Cl] (PtB), as a model to elucidate the key role of Pt···Pt interactions in directing self-assembly by combining temperature-dependent ultraviolet-visible (UV-Vis) spectroscopy, stopped-flow kinetic experiments, quantum mechanics (QM) calculations, and molecular dynamics (MD) simulations. …”
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“…The experimental results were in agreement with the findings obtained through quantum mechanics continuum solvation models. Compound 1 crystallized as a monoclinic system P2(1)/c, whereas compound 2 in a triclinic system P1̅. …”
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“…In this study, we explored the hydrolysis reaction mechanism of HARGI with antiferromagnetic and ferromagnetic coupling between two Mn(II) ions at the catalytic site by employing molecular dynamics simulations coupled with quantum mechanics and molecular mechanics (QM/MM). The spin states, high-spin ferromagnetic couple (S(Mn1) = 5/2, S(Mn2) = 5/2), low-spin ferromagnetic couple (S(Mn1) = 1/2, S(Mn2) = 1/2), high-spin antiferromagnetic couple (S(Mn1) = 5/2, S(Mn2) = −5/2), and low-spin antiferromagnetic couple (S(Mn1) = 1/2, S(Mn2) = −1/2) are considered, and the calculated energetics for the complex of the substrate and HARGI are compared. …”
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“…Quantum computing is a new and advanced topic that refers to calculations based on the principles of quantum mechanics. It makes certain kinds of problems be solved easier compared to classical computers. …”
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“…In our contemporary world of modern quantum physics, science plays the greatest part in our theories of light's origin--from scientific perspectives such as Sir Isaac Newton's "corpuscular theory of light" and Michael Faraday's "lines of force" to such revolutionary ideas as Max Planck's "discrete motion of a pendulum" (the basis of quantum mechanics), Albert Einstein's "particles of light" and "theory of relativity," and Niels Bohr's "quantum jumps." …”
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“…The Standard model is a quantum field theory incorporating both quantum mechanics and special relativity and encapsulates in its mathematical formulation the known fundamental symmetries of nature. …”
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“…We describe the use of combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations to explore the mechanism of PHF8, including dioxygen activation, 2OG binding modes, and substrate demethylation steps. …”
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“…This implementation is able to use one or more region layer(s), which is(are) characterized using linear-scaling, semi-empirical quantum mechanics, followed by a system layer which includes the balance of the model and which is described using a molecular mechanics functional. …”
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“…METHODS: Molecular conformation, polarizability and stability are examined using quantum mechanics (QM). Intermolecular synthons, hydrogen bonding, crystal morphology and surface chemistry are modelled using empirical force fields. …”
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“…To do so, we study the changes in the absorption band of the 19 possible mutants and construct, semi-automatically, the corresponding hybrid quantum mechanics/molecular mechanics models. We found that the P219X feature a red-shifted light absorption with the only exception of P219R. …”
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“…We corroborated the assignments of negative bands in the K-BR difference FT-IR spectrum by ab initio anharmonic vibrational calculations of all-trans retinal in BR using a quantum-mechanics/molecular mechanics approach, reproducing reasonably well the small experimental anharmonic and coupling mechanical constants. …”
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“…These same four functionals are furthermore found to reproduce the high-resolution X-ray structure of FeMoco well according to quantum mechanics/molecular mechanics (QM/MM) calculations. …”
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“…In agreement, the molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies showed a change in the H3(1–14)K9me2 substrate orientation and an increased HAT barrier. …”
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