Quantum mechanical-molecular mechanics QM/MM

A Fortran90 library for the simulation of molecular systems using molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM)/ MM) potential energy functions. http //www.ibs.fr/ext/labos/LDM/projet6/... 

A second approach is based on the methodology first explored in the seminal work by Warshel and Levitt as early as 1976 [21], and is the use of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations whereby a subsection of the system is treated by QM methods, the remainder (environment) is treated by standard molecular mechanics (MM) methods, and a coupling potential is used to connect the two regions [22], This methodology will then be exemplified with work developed in this group in recent years [23-26],... 

Hartree-Fock, DFT or CCSD levels. Because they can reproduce such quantities, APMM procedures should account for an accurate description of the interactions including polarization cooperative effects and charge transfer. They should also enable the reproduction of local electrostatic properties such as dipole moments an also facilitate hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) embeddings. 

In our simulations of histone modifying enzymes, the computational approaches centered on the pseudobond ab initio quantum mechanical/molecular mechanical (QM/MM) approach. This approach consists of three major components [20,26-29] a pseudobond method for the treatment of the QM/MM boundary across covalent bonds, an efficient iterative optimization procedure which allows for the use of the ab initio QM/MM method to determine the reaction paths with a realistic enzyme environment, and a free energy perturbation method to take account... 

Friesner RA, Guallar V (2005) Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. Annu Rev Phys Chem 56 389 127... 

Riccardi D, Schaefer P, Yang Y, Yu HB, Ghosh N, Prat-resina X, Konig P, Li GH, Xu DG, Guo H, Elstner M, Cui Q (2006) Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B 110 6458-6469... 

To better understand the catalytic mechanism of DHFR and to use this information for the design of potent DHFR-specific inhibitors, we evaluated the proton and hydride transfers using an integrated ab initio Quantum Mechanics/Molecular Mechanics (QM/MM) approach in combination with FEP technology. The combinatorial application of these methods enabled us to propose a precise path along which the proton and hydride ion are transferred and to address the key structural and energetic changes associated with catalysis. 

In this chapter we will focus on one particular, recently developed DFT-based approach, namely on first-principles (Car-Parri-nello) molecular dynamics (CP-MD) [9] and its latest advancements into a mixed quantum mechanical/molecular mechanical (QM/MM) scheme [10-12] in combination with the calculation of various response properties [13-18] within DFT perturbation theory (DFTPT) and time-dependent DFT theory (TDDFT) [19]. 

Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) Car-Parinello Simulations... 

To investigate this idea, which would confirm and summarize a large class of widely accepted mechanisms, the insertion reactions of (Z)- and (E)-butene with catalytic systems based on the C2-symmetric Me2Si(l-Ind)2 ligand and on the ((-symmetric Me2Si(Cp)(9-Flu) ligand have been recently studied. A double approach based on combined quantum mechanics/molecular mechanics (QM/MM) techniques and on selected ethene/2-butene copolymerization runs has recently been utilized.94... 

Despite the many experimental studies which have contributed to clarify even details of the polymerization mechanism, only recently has theoretical study (a combined quantum mechanics/molecular mechanics, QM/MM) of the... 

The description of pure quantum mechanics (QM) methods presented in Section 3 has shown how in most cases they provide an accurate description of the electronic subtleties involved at the transition metal center of a catalytic process, but that they are unable to introduce the whole bulk of the catalyst substituents, which can be critical for selectivity issues. The description of pure molecular mechanics (MM) methods presented in subsection 4.1 has shown how these methods can easily introduce the steric bulk of the substituents, and accurately describe their steric interactions, but that they struggle badly when trying to describe properly the transition metal center and its immediate environment. The logical solution to this complementary limitations is to divide the chemical system in two regions, and to use a different description for each of them, QM for the metal and its environment, MM for the rest of the system. This is precisely the basic idea of hybrid quantum mechanics / molecular mechanics (QM/MM) methods. 

The study of the enantioselective hydrosilylation reaction was performed with a series of combined quantum mechanics/molecular mechanics (QM/MM) calculations [26, 30] within the computational scheme of ab initio (AIMD) (Car-Parrinello) [62] molecular dynamics. The AIMD approach has been described in a number of excellent reviews [63-66], AIMD as well as hybrid QM/MM-AIMD calculations [26, 47] were performed with the ab initio molecular dynamics program CPMD [67] based on a pseudopotential framework, a plane wave basis set, and periodic boundary conditions. We have recently developed an interface to the CPMD package in which the coupling with a molecular mechanics force field has been implemented [26, 68],... 

The isotope independent potential energy surface was evaluated using a mixed quantum mechanics/molecular mechanics (QM/MM) method. The system (N atoms) was partitioned into Nqm quantum mechanical atoms and Nmm classical mechanical atoms. Nqm consisted of the 15 atom substrate (phospho-D-glycerate)... 

A detailed investigation using ITC and the quantum-mechanics/molecular mechanics (QM/MM) computational technique provided further insight into the ConA-septanoside interaction.125 A major focus of this study was to define how the presence and orientation of functional groups about the monosaccharide ring affected... 

Methods of Quantum Pharmacology for Molecular Geometry Optimization Quantum Mechanics, Molecular Mechanics, QM/MM Calculations... 

From its inception, the combined Quantum Mechanics/Molecular Mechanics (QM/MM) method [1-3] has played an important roll in the explicit modeling of solvent [4], Whereas Molecular Mechanics (MM) methods on their own are generally only able to describe the effect of solvent on classical properties, QM/MM methods allow one to examine the effect of the solvent on solute properties that require a quantum mechanical (QM) description. In most cases, the solute, sometimes together with a few solvent molecules, is treated at the QM level of theory. The solvent molecules, except for those included in the QM region, are then treated with an MM force field. The resulting potential can be explored using Monte Carlo (MC) or Molecular Dynamics (MD) simulations. Besides the modeling of solvent, QM/MM methods have been particularly successful in the study of biochemical systems [5] and catalysis [6],... 

The ASEP/MD method, acronym for Averaged Solvent Electrostatic Potential from Molecular Dynamics, is a theoretical method addressed at the study of solvent effects that is half-way between continuum and quantum mechanics/molecular mechanics (QM/MM) methods. As in continuum or Langevin dipole methods, the solvent perturbation is introduced into the molecular Hamiltonian through a continuous distribution function, i.e. the method uses the mean field approximation (MFA). However, this distribution function is obtained from simulations, i.e., as in QM/MM methods, ASEP/MD combines quantum mechanics (QM) in the description of the solute with molecular dynamics (MD) calculations in the description of the solvent. 

Aguilar, Sanchez, Martin, Fdez. Galvan review the ASEP/MD method, acronym for Averaged Solvent Electrostatic Potential from Molecular Dynamics, showing how this method combines aspects of quantum mechanics/molecular mechanics (QM/MM) methods with aspects of continuum models. 

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