Quantum mechanics and molecular

Singh, U.C., Kollman, P.A. A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems Applications to the CH3CI 4- Cl exchange reaction and gas phase protonation of polyethers. J. Comput. Chem. 7 (1986) 718-730. 

Field, M.J., Bash, P.A., Karplus, M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comput. Chem. 11 (1990) 700-733. 

Bakowies, D., Thiel, W. Hybrid models for combined quantum mechanical and molecular mechanical approaches. J. Phys. Chem. 100 (1996) 10580-10594. 

The book is organised so that some of the techniques discussed in later chapters refer to material discussed earlier, though I have tried to make each chapter as independent of the ofhers as possible. Some readers may therefore be pleased to know that it is not essential to completely digest the chapters on quantum mechanics and molecular mechanics in order to read about methods for searching conformational space Readers with experience in one or more areas may, of course, wish to be more selective. 

We will use the term energy surface to refer not only to systems in which the bonding remains unchanged, as in these two examples, but also where bonds are broken and/or formed. Our discussion will be appropriate to both quantum mechanics and molecular mechanics, except where otherwise stated. 

In order to use a derivative minimisation method it is obviously necessary to be able to calculate the derivatives of fhe energy wifh respecf to the variables (i.e. the Cartesian or interna] coordinates, as appropriate). Derivatives may be obtained either analytically or numerically. The use of analytical derivatives is preferable as fhey are exact, and because they can be calculated more quickly if only numerical derivatives are available then it may be more effective to use a non-derivative minimisation algorithm. The problems of calculating analytical derivatives with quantum mechanics and molecular mechanics were discussed in Sections 3.4.3 and 4.16, respectively. 

Amara P and M J Field 1998. Combined Quantum Mechanical and Molecular Mechanical Potentials. In Schleyer, P v R, N L Allinger, T Clark, J Gasteiger, P A Kolhnan H F Schaefer HI and P R Schreiner (Editors). The Encyclopedia of Computational Chemistry. Chichester, John Wiley Sons. 

Gao J 1995. Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials. In Lipkowitz K B and D B Boyd (Editors) Reviews in Computational Chemistry Volume 7. New York, VCH Publishers, pp. 119-185. 

Field M J, P A Bash and M Karplus 1990. A Combined Quantum Mechanical and Molecular Mechanical Potential for Molecular Dynamics Simulations. Journal of Computational Chemistry 11 700-733. 

SPARTAN, A Quantum Mechanical and Molecular Modeling Program Suite, available from Wavefunction, Inc., Irvine, Calif. 

HYBRID QUANTUM-MECHANICAL AND MOLECULAR MECHANICAL METHODS... 

A combination of quantum mechanics and molecular mechanics, where one treats a small part of the system (e.g. the solute) by means of quantum mechanics and the remainder by MM, provides a powerful tool for studies of structure and reactivity. It all started with the classic paper due to Warshel and Levitt. 

Chapter I has been reorganized in this edition to give readers a gentler introduction to atoms and their structure. Atoms and molecules, including discussions of quantum mechanics and molecular orbitals, provide the foundation for understanding bulk properties and models of gases, liquids, and solids. 

Quantum mechanics is essential for studying enzymatic processes [1-3]. Depending on the specific problem of interest, there are different requirements on the level of theory used and the scale of treatment involved. This ranges from the simplest cluster representation of the active site, modeled by the most accurate quantum chemical methods, to a hybrid description of the biomacromolecular catalyst by quantum mechanics and molecular mechanics (QM/MM) [1], to the full treatment of the entire enzyme-solvent system by a fully quantum-mechanical force field [4-8], In addition, the time-evolution of the macromolecular system can be modeled purely by classical mechanics in molecular dynamicssimulations, whereas the explicit incorporation... 

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... 

Zhang Y, Lee TS, Yang W (1999) A pseudobond approach to combining quantum mechanical and molecular mechanical methods. J Chem Phys 110 46-54... 

Hawkins GD, Zhu T, Li J, Chambers CC, Giesen DJ, Liotard DA, Cramer CJ, Truhlar DG (1998) Combined quantum mechanical and molecular mechanical methods, 201-219, ACS Symposium Series 712, Oxford University Press, New York. 

The system studied by use of structurally coupled QM/MM is described with a Hamiltonian comprising of both the quantum mechanically and molecular mechanically treated part. The effective Hamiltonian, Heff, representing the interactions of the whole QM/MM system is ... 

Jorgensen et al. [49] developed a combined quantum mechanical and molecular mechanical approach for study of organic reactions and applied it with success to many solution reactions. Inspired by this Kollman et al. [50, 51] developed the approach further for study of enzyme reactions. This quantum mechanical/free energy (QM/... 

I. Antes, W. Thiel, On the Treatment of Link Atoms in Hybrid Methods, in Combined Quantum Mechanical and Molecular Mechanical Methods, J. Gao, M. A. Thompson (eds), American Chemical Society, Washington, DC, 1998, pp. 50-65. 

Jiali Gao, Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials. 

In order to examine the nature of the unusual geometric distortions observed in the X-ray structures of complexes 3 and 4, we have performed a series of density functional theory (DFT) and combined quantum mechanics and molecular mechanics (QM/MM) calculations [22-27], Although the computational resources to wholly treat both 3 and 4 at the DFT level are available, we have employed the combined QM/MM method to unravel the... 

In this and subsequent sections, we investigate the reaction mechanism of the palladium catalyzed hydrosilylation of styrene via ah initio molecular dynamics and combined quantum mechanics and molecular mechanics (QM/MM) techniques. Both methodologies constitute powerful approaches for the study of the catalytic activity and selectivity of transition metal... 

There are many computational chemistry software packages available that enable students to make and study the properties of molecules, by quantum mechanics and molecular mechanics methods. These include Gaussian, HyperChem, Spartan, and Biosym. The first four homework problems assume that the student has one of... 

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