Hybrid quantum and molecular mechanical simulation

Gao, J., Hybrid Quantum and Molecular Mechanical Simulations An Alternative Avenue to Solvent Effects in Organic Chemistry. Accounts of Chemcal Research (1996) 29 298-305. 

Gao, J. (1996). Hybrid quantum and molecular mechanical simulations an alternative avenue to solvent effects in organic chemistry. Acc. Chem. Res. 29, 298-305... 

Acevedo O, Jorgensen WL (2010) Advances in quantum and molecular mechanical (QM/ MM) simulations for organic and enzymatic reactions. Acc Chem Res 43 142-151 Bands P, Jurecka P, Walter NG, Sponer J, Otyepka M (2009) Theoretical studies of RNA catalysis hybrid QM/MM methods and their comparison with MD and QM. Methods 49 202... 

Neese F, Wennmohs F, Hansen A, Becker U (2009) Effieient, approximate and parallel Hartree Fock and hybrid DFT calculations. A chain-of-spheres algorithm for the Hartree-Fock exchange. Chem Phys 356(1 3) 98 109. 10.1016/j.ehemphys.2008.10.036 Ferrer S, Ruiz-Pemia J, Marti S et al (2011) Hybrid schemes based on quantum meehanies/ molecular mechanics simulations goals to success, problems, and perspeetives. Adv Protein Chem StructBiol 85 81-142. doi 10.1016/B978-0-12-386485-7.00003-X... 

Tu, Y. and Laaksonen A., On the effect of Lennard-Jones parameters on the quantum mechanical and molecular mechanical coupling in a hybrid molecular dynamics simulation of liquid water. J. Chem.Phys. (1999) 111 7519-7525. 

Some papers concerned small flexible linear molecules. All studied compounds featured rotational variety, which was considered in the calculation. Buhl et have studied zwitterions of 3-fluoro-y-aminobutyric acid (Fig. 8a) in water solution, applying single-, two- and five-water molecules models. Full explicit solvation was studied with a hybrid quantum-mechanical/molecular mechanical (QM/MM) scheme and molecular dynamic simulations, including more than 6000 water molecules. Among numerous analyses, the authors have calculated and J(F,H) at... 

Ferrer S, Ruiz-Pernia J, Marti S, Moliner V, Tunon I, Bertran J, Andres J (2011) Hybrid schemes based on quantum mechanics/molecular mechanics simulations Goals to success, problems, and perspectives. In Christov C (ed) Advances in protein chemistry and stnictural biology, vol 85 computational chemistry methods in stnictural biology. Advances in protein chemistry and structural biology, vol 85. Elsevier Academic Press Inc, New York, pp 81-142... 

AMI AMBER A Program for Simulation of Biological and Organic Molecules CHARMM The Energy Function and Its Parameterization Combined Quantum Mechanics and Molecular Mechanics Approaches to Chemical and Biochemical Reactivity Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field Divide and Conquer for Semiempirical MO Methods Electrostatic Catalysis Force Fields A General Discussion Force Fields CFF GROMOS Force Field Hybrid Methods Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Methods Mixed Quantum-Classical Methods MNDO MNDO/d Molecular Dynamics Techniques and Applications to Proteins OPLS Force Fields Parameterization of Semiempirical MO Methods PM3 Protein Force Fields Quantum Mechanical/Molecular Mechanical (QM/MM) Coupled Potentials Quantum Mecha-nics/Molecular Mechanics (QM/MM) SINDOI Parameterization and Application. 

Delley B (1990) An all-electron numerical method for solving the local density functional for pol) tomic molecules. J Chem Phys 92(1) 508 Delley B (2000) From molecules to solids with the DMoP approach. J Chem Phys 113(18) 7756 Delley B (2002) Hardness conserving semilocal pseudopotentials. Phys RevB 66(15) 155125 Ferre N, Assfeld X, Rivah JL (2002) Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method. J Comput Chem 23(6) 610 Field MJ, Bash PA, Karplus M (1990) A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J Comput Chem 11(6) 700... 

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 final important area is the calculation of free energies with quantum mechanical models [72] or hybrid quanmm mechanics/molecular mechanics models (QM/MM) [9]. Such models are being used to simulate enzymatic reactions and calculate activation free energies, providing unique insights into the catalytic efficiency of enzymes. They are reviewed elsewhere in this volume (see Chapter 11). 

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... 

J. Wang, R. J. Boyd, and A. Laaksonen, J. Cbem. Pbys., 104, 7261. A Hybrid Quantum Mechanical Force Field Molecular Dynamics Simulation of Liquid Methanol Vibrational Frequency Shifts as a Probe of the Quantum Mechanical/Molecular Mechanical Coupling. 

G. Csanyi et al Learn on the Fly A hybrid classical and quantum-mechanical molecular dynamics simulation. Phys. Rev. Lett. 93, 175503 (2004)... 

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