Acids, computational chemistry

Chemistry of Amino Acids Computational Chemistry in Biology Energetics of Protein Folding Protein Informatics Physical Chemistry in Biology... 

In computational chemistry it can be very useful to have a generic model that you can apply to any situation. Even if less accurate, such a computational tool is very useful for comparing results between molecules and certainly lowers the level of pain in using a model from one that almost always fails. The MM+ force field is meant to apply to general organic chemistry more than the other force fields of HyperChem, which really focus on proteins and nucleic acids. HyperChem includes a default scheme such that when MM+ fails to find a force constant (more generally, force field parameter), HyperChem substitutes a default value. This occurs universally with the periodic table so all conceivable molecules will allow computations. Whether or not the results of such a calculation are realistic can only be determined by close examination of the default parameters and the particular molecular situation. ... 

The overall scope of this book is the implementation and application of available theoretical and computational methods toward understanding the structure, dynamics, and function of biological molecules, namely proteins, nucleic acids, carbohydrates, and membranes. The large number of computational tools already available in computational chemistry preclude covering all topics, as Schleyer et al. are doing in The Encyclopedia of Computational Chemistry [23]. Instead, we have attempted to create a book that covers currently available theoretical methods applicable to biomolecular research along with the appropriate computational applications. We have designed it to focus on the area of biomolecular computations with emphasis on the special requirements associated with the treatment of macromolecules. 

Andzelm, J. W., D. T. Nguyen, R. Eggenberger, D. R. Salahub, and A. T. Hagler. 1995. Applications of the Adiabatic Connection Method to Conformational Equilibria and Reactions Involving Formic Acid. Computers and Chemistry 19, 145. 

The aim of this review is to focus on the hydrogen bonding, the acidity and basicity, complexing as well as some aspects of computational chemistry concerning the organo-element chemistry of germanium, tin and lead. This chapter is not exhaustive in scope, but rather consists of surveys of the most recent decade of work in this still developing area. This chapter emphasizes the synthesis, reactions and molecular structures of the class of... 

THE AROMATIC AMINO ACID HYDROXYLASE MECHANISM A PERSPECTIVE FROM COMPUTATIONAL CHEMISTRY... 

In textbooks of computational chemistry you will invariably find examples calculating the pH = - lg [H+]/(mol/l)> in weak acid - strong base or strong acid - weak base solutions. Indeed, these examples are important in the study of acids, bases and of complex formation, as well as for calculating titration curves. Following (ref. 24) we consider here the aquous solution that contains a weak tribasic acid H A and its sodium salts NaH, Na HA and Na A in known initial concentrations. The dissociation reactions and equilibrium relations are given as follows. 

There has been a phenomenal growth of interest in theoretical simulations over the past decade. The concomitant advances made in computing power and software development have changed the way that computational chemistry research is undertaken. No longer is it the exclusive realm of specialized theoreticians and supercomputers rather, computational chemistry is now accessible via user-friendly programs on moderately priced workstations. State-of-the-art calculations on the fastest, massively parallel machines are continually enlarging the scope of what is possible with these methods. These reasons, coupled with the continuing importance of solid acid catalysis within the world s petrochemical and petroleum industries, make it timely to review recent work on the theoretical study of zeolite catalysis. 

The aforementioned progress in NMR spectroscopy (and other experimental methods as well) in combination with computational chemistry has reached a stage in which an understanding of the most general features of organic reactions on solid acids may reasonably be expected in several years. This does not yet quite exist this report is written in a time at which the sophisticated application of NMR and computational quantum chemistry to solid acids is becoming widespread, and specialists in various areas are suddenly having to evaluate evidence from other specialties. 

Another fundamental molecular property of interest in pharmaceutical stress research as well as in the rest of chemistry is the pKa of acidic groups (or pKh of basic groups) in a compound. The pKa of a compound in hand is more easily—and reliably—determined experimentally than by computational chemistry. In cases where an experiment on a molecule of interest cannot be done for whatever reason, then a reasonable approach for obtaining an approximate pKa is to look in compilations of pKa values of known... 

R. Cammi, B. Mennucci, Structure and properties of molecular solutes in electronic excited states A polarizable continuum model approach based on the time-dependent density functional theory, in Radiation Induced Molecular Phenomena in Nucleic Acids A Comprehensive Theoretical and Experimental Analysis, ed. by M.K. Shukla, J. Leszczynski. Series Challenges and Advances in Computational Chemistry and Physics, vol 5 (Springer, Netherlands 2008)... 

Scarfe, G.B., Wilson, I.D., Wame, M.A., Holmes, E., Nicholson, J.K., and Lindon, J.C., Structure-metabolism relationships of substituted anilines prediction of N-acetylation and N-oxanilic acid formation using computational chemistry, Xenobiotica, 32, 267-277, 2002. 

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