scholarly journals Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods

2008 ◽  
Vol 59 (1) ◽  
pp. 573-601 ◽  
Author(s):  
Hao Hu ◽  
Weitao Yang
Keyword(s):  
Quantum Mechanics ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Chemical Reactions ◽  
Free Energies

Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-based Drug Design and Discovery

2021 ◽  
Vol 21 ◽  
Author(s):  
Prajakta U. Kulkarni ◽  
Harshil Shah ◽  
Vivek K. Vyas
Keyword(s):  
Quantum Mechanics ◽  
Drug Design ◽  
Molecular Mechanics ◽  
Chemical Reactions ◽  
Classical Mechanics ◽  
Molecular Structures ◽  
Protein Crystal ◽  
Structure Based Drug Design ◽  
Structure And Property ◽  
Qsar Models

: Quantum mechanics (QM) is physics based theory which 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, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate 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 process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to 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 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.

Computational Photobiology and Beyond

2010 ◽  
Vol 63 (3) ◽  
pp. 413 ◽  
Author(s):  
Igor Schapiro ◽  
Mikhail N. Ryazantsev ◽  
Wan Jian Ding ◽  
Mark M. Huntress ◽  
Federico Melaccio ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Excited State ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Chemical Treatment ◽  
Quantum Chemical ◽  
Organic Molecules ◽  
Molecular Devices ◽  
Computational Studies ◽  
Computational Investigation

In this paper we review the results of a group of computational studies of the spectroscopy and photochemistry of light-responsive proteins. We focus on the use of quantum mechanics/molecular mechanics protocols based on a multiconfigurational quantum chemical treatment. More specifically, we discuss the use, limitations, and application of the ab initio CASPT2//CASSCF protocol that, presently, constitutes the method of choice for the investigation of excited state organic molecules, most notably, biological chromophores and fluorophores. At the end of this Review we will also see how the computational investigation of the visual photoreceptor rhodopsin is providing the basis for the design of light-driven artificial molecular devices.

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies

2008 ◽  
Vol 128 (1) ◽  
pp. 014109 ◽  
Author(s):  
Christopher J. Woods ◽  
Frederick R. Manby ◽  
Adrian J. Mulholland
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Efficient Method ◽  
Free Energies
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