具有先进可极化势的量子力学/分子力学方法的开发与应用。
Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials.
作者信息
Nochebuena Jorge, Naseem-Khan Sehr, Cisneros G Andrés
机构信息
Department of Chemistry, University of North Texas, Denton, Texas, USA.
出版信息
Wiley Interdiscip Rev Comput Mol Sci. 2021 Jul-Aug;11(4). doi: 10.1002/wcms.1515. Epub 2021 Jan 12.
Abstract
Quantum mechanics/molecular mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed-phase and biological systems. The combination of QM and MM methods to represent a system gives rise to several challenges that need to be addressed. The increase in computational speed has allowed the expanded use of more complicated and accurate methods for both QM and MM simulations. Here, we review some approaches that address several common challenges encountered in QM/MM simulations with advanced polarizable potentials, from methods to account for boundary across covalent bonds and long-range effects, to polarization and advanced embedding potentials.
摘要
量子力学/分子力学（QM/MM）模拟是研究大型系统各种特性的常用方法。QM/MM计算的一个常见应用是研究凝聚相和生物系统中的反应机制。将QM和MM方法结合起来描述一个系统会带来一些需要解决的挑战。计算速度的提高使得在QM和MM模拟中能够更广泛地使用更复杂、更精确的方法。在这里，我们回顾一些方法，这些方法利用先进的极化势来应对QM/MM模拟中遇到的几个常见挑战，从处理共价键边界和长程效应的方法，到极化和先进的嵌入势。
相似文献
1
Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials.
Wiley Interdiscip Rev Comput Mol Sci. 2021 Jul-Aug;11(4). doi: 10.1002/wcms.1515. Epub 2021 Jan 12.
2
Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations.
Theor Chem Acc. 2016 Jul;135(7). doi: 10.1007/s00214-016-1923-8. Epub 2016 Jun 17.
3
Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity.
Acc Chem Res. 2021 Jul 6;54(13):2812-2822. doi: 10.1021/acs.accounts.0c00662. Epub 2021 May 7.
4
Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.
Acc Chem Res. 2013 Feb 19;46(2):596-603. doi: 10.1021/ar300278j. Epub 2012 Dec 18.
5
Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model.
J Chem Theory Comput. 2012 Nov 13;8(11):4527-38. doi: 10.1021/ct300722e. Epub 2012 Oct 24.
6
Conical Intersections in Solution with Polarizable Embedding: Integral-Exact Direct Reaction Field.
J Chem Theory Comput. 2022 Nov 8;18(11):6826-6839. doi: 10.1021/acs.jctc.2c00662. Epub 2022 Oct 17.
7
Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings.
Chem Sci. 2019 Jun 11;10(30):7200-7211. doi: 10.1039/c9sc01745c. eCollection 2019 Aug 14.
8
Recent advances toward a general purpose linear-scaling quantum force field.
Acc Chem Res. 2014 Sep 16;47(9):2812-20. doi: 10.1021/ar500103g. Epub 2014 Jun 17.
9
Accuracy of buffered-force QM/MM simulations of silica.
J Chem Phys. 2015 Feb 14;142(6):064116. doi: 10.1063/1.4907786.
10
Induction effects on the absorption maxima of photoreceptor proteins.
Biophys Physicobiol. 2023 Jan 24;20(Supplemental):e201007. doi: 10.2142/biophysico.bppb-v20.s007. eCollection 2023 Mar 21.
引用本文的文献
1
Comparison of Magnesium and Manganese Ions on the Structural and Catalytic Properties of Human DNA Polymerase Gamma.
J Chem Theory Comput. 2025 Jul 3. doi: 10.1021/acs.jctc.5c00435.
2
Analyzing aptamer structure and interactions: in silico modelling and instrumental methods.
Biophys Rev. 2024 Nov 20;16(6):685-700. doi: 10.1007/s12551-024-01252-z. eCollection 2024 Dec.
3
Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4, and Tinker-HP.
J Chem Phys. 2024 May 7;160(17). doi: 10.1063/5.0200722.
4
Reprogramming the Transition States to Enhance C-N Cleavage Efficiency of l-Amino Acid Oxidase.
JACS Au. 2024 Jan 16;4(2):557-569. doi: 10.1021/jacsau.3c00672. eCollection 2024 Feb 26.
5
Uncovering water effects in protein-ligand recognition: importance in the second hydration shell and binding kinetics.
Phys Chem Chem Phys. 2023 Jan 18;25(3):2098-2109. doi: 10.1039/d2cp04584b.
6
Trajectory Surface Hopping for a Polarizable Embedding QM/MM Formulation.
J Phys Chem A. 2022 Sep 29;126(38):6780-6789. doi: 10.1021/acs.jpca.2c04756. Epub 2022 Sep 15.
7
Improvement of the Gaussian Electrostatic Model by separate fitting of Coulomb and exchange-repulsion densities and implementation of a new dispersion term.
J Chem Phys. 2021 Nov 21;155(19):194103. doi: 10.1063/5.0072380.
8
Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families.
Phys Chem Chem Phys. 2021 Oct 13;23(39):22227-22240. doi: 10.1039/d1cp03800a.
9
Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations.
J Chem Theory Comput. 2021 Jul 13;17(7):4524-4537. doi: 10.1021/acs.jctc.1c00313. Epub 2021 Jun 4.
10
"Dividing and Conquering" and "Caching" in Molecular Modeling.
Int J Mol Sci. 2021 May 10;22(9):5053. doi: 10.3390/ijms22095053.
本文引用的文献
1
MMFF VI. MMFF94s option for energy minimization studies.
J Comput Chem. 1999 May;20(7):720-729. doi: 10.1002/(SICI)1096-987X(199905)20:7<720::AID-JCC7>3.0.CO;2-X.
2
A Many-Body, Fully Polarizable Approach to QM/MM Simulations.
J Chem Theory Comput. 2020 Dec 8;16(12):7462-7472. doi: 10.1021/acs.jctc.0c00932. Epub 2020 Nov 19.
3
Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation.
Sci Rep. 2020 Oct 12;10(1):16986. doi: 10.1038/s41598-020-74099-5.
4
Exchange Repulsion in Quantum Mechanical/Effective Fragment Potential Excitation Energies: Beyond Polarizable Embedding.
J Chem Theory Comput. 2020 Oct 13;16(10):6408-6417. doi: 10.1021/acs.jctc.9b01156. Epub 2020 Aug 28.
5
Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?
Phys Chem Chem Phys. 2020 Jul 8;22(26):14433-14448. doi: 10.1039/d0cp02119a.
6
ABEEM/MM OH Models for OH(HO) Clusters and Aqueous OH: Structures, Charge Distributions, and Binding Energies.
J Phys Chem A. 2020 Jul 16;124(28):5963-5978. doi: 10.1021/acs.jpca.0c03941. Epub 2020 Jul 2.
7
A self-consistent coulomb bath model using density fitting.
J Comput Chem. 2020 Jul 5;41(18):1698-1708. doi: 10.1002/jcc.26211. Epub 2020 May 5.
8
Fragment Exchange Potential for Realizing Pauli Deformation of Interfragment Interactions.
J Phys Chem Lett. 2020 May 21;11(10):4008-4016. doi: 10.1021/acs.jpclett.0c00933. Epub 2020 May 6.
9
Modified Drude model for small gold nanoparticles surface plasmon resonance based on the role of classical confinement.
Sci Rep. 2020 Apr 16;10(1):6517. doi: 10.1038/s41598-020-63066-9.
10
Structure of M from SARS-CoV-2 and discovery of its inhibitors.
Nature. 2020 Jun;582(7811):289-293. doi: 10.1038/s41586-020-2223-y. Epub 2020 Apr 9.
Zotero 插件