Quantum mechanical-molecular mechanics

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/... 

Unlike quantum mechanics, molecular mechanics does not treat electrons explicitly. Molecular mechanics calculations cannot describe bond formation, bond breaking, or systems in which electron ic delocalization or m oleciilar orbital in teraction s play a m ajor role in determining geometry or properties. 

The theory and methods discussed in this book are HyperChem s two fundamental force-energy-generator modules one for molecular mechanics and one for quantum mechanics. Molecular mechanics and quantum mechanics are described in subsequent chapters as modules capable of delivering an energy, or derivatives of the energy. Other chapters describe the uses for these energies and their derivatives in more generic parts of HyperChem. 

Maseras F (1999) Hybrid Quantum Mechanics/Molecular Mechanics Methods in Transition Metal Chemistry. 4 165-191 Maseras F, see Drudis-Sole G (2005) 12 79-107 Mangeney P,see Rolands (2005) 15 191-229 Mayoral JA, see FraUe JM (2005) 15 149-190 Medaer BP, see Mehrmann SJ (2004) 6 153-180... 

Armrmanto, R., Schwenk, C.F. and Rode, B.M. (2003) Structure and Dynamics of Hydrated Ag (I) Ab Initio Quantum Mechanical-Molecular Mechanical Molecular Dynamics Simulation. The Journal of Physical Chemistry A, 107, 3132-3138. 

Numerical methods. Computer-intensive numerical methods like quantum mechanics, molecular mechanics, or distance geometry [8] do not normally fall into the scope of automatic model builders. However, some model builders have built-in fast geometry optimization procedures or make use of distance geometry in order to generate fragment conformations. 

Quantum mechanical/molecular mechanical study on the Favorskii rearrangement in aqueous media has been carried out.39 The results obtained by QM/MM methods show that, of the two accepted mechanisms for Favorskii rearrangement, the semibenzilic acid mechanism (a) is favored over the cyclopropanone mechanism (b) for the a-chlorocyclobutanone system (Scheme 6.2). However, the study of the ring-size effects reveals that the cyclopropanone mechanism is the energetically preferred reactive channel for the a-chlorocyclohexanone ring, probably due to the straining effects on bicycle cyclopropanone, an intermediate that does not appear on the semibenzilic acid pathway. These results provide new information on the key factors responsible for the behavior of reactant systems embedded in aqueous media. 

Abstract The development and applications of hybrid quantum mechanical/molecular mechanics... 

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],... 

The second approach described here for inclusion of environment effects is the use of hybrid quantum mechanics/molecular mechanics methods (QM/MM). In a QM/MM calculation [21,22], the system is partitioned in two regions A QM region, typically consisting of a relatively small number of atoms relevant for the specific process being studied, and a MM region with all the remaining atoms. 

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. 

Zhang Y, Lin H (2008) Hexible-boundary quantum-mechanical/molecular-mechanical calculations partial charge transfer between the quantum-mechanical and molecular-mechanical subsystems. J Chem Theory Comput 4(3) 414—425... 

Field MJ (1997) Hybrid quantum mechanical molecular mechanical fluemating charge models for condensed phase simulations. Mol Phys 91(5) 835-845... 

AB INITIO QUANTUM MECHANICAL/MOLECULAR MECHANICAL STUDIES OF HISTONE MODIFYING ENZYMES... 

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... 

Zhang Y (2005) Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods. J Chem Phys 122 024114... 

Zhang Y, Kua J, McCammon JA (2003) Influence of structural fluctuation on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies. J Phys Chem B 107 ... 

Wang S, Hu P, Zhang Y (2007) Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis the case of histone lysine methyltransferase set7/9. J Phys Chem B ASAP... 

Molecular mechanics calculations have become a well established tool in the area of coordination chemistry, including the coordination chemistry of nickel375-379 where they are often applied for the analysis or the prediction of structures,380 the computation of isomer or conformer ratios and metal ion selectivities,381,382 and for simulating spectroscopic properties in combination with AOM calculations or by hybrid quantum mechanics/molecular mechanics (QMMM) methods.383,384 Details of the various approaches, e.g., the incorporation of d-electron stabilization energy... 

Combined quantum mechanics/molecular mechanics studies have demonstrated that 7r-7r stacking interactions are important in determining the structural features of polyarene transition metal compounds such as the two ds Pd complexes.96... 

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. 

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