Molecular mechanics biomolecules

The molecular mechanics force fields available include MM+, OPLS, BIO+, and AMBER. Parameters missing from the force field will be automatically estimated. The user has some control over cutoff distances for various terms in the energy expression. Solvent molecules can be included along with periodic boundary conditions. The molecular mechanics calculations tested ran without difficulties. Biomolecule computational abilities are aided by functions for superimposing molecules, conformation searching, and QSAR descriptor calculation. 

Focuses on force field calculations for understanding the dynamic properties of proteins and nucleic acids. Provides a useful introduction to several computational techniques, including molecular mechanics minimization and molecular dynamics. Includes discussions of research involving structural changes and short time scale dynamics of these biomolecules, and the influence of solvent in these processes. 

HyperChem uses two types of methods in calculations molecular mechanics and quantum mechanics. The quantum mechanics methods implemented in HyperChem include semi-empirical quantum mechanics method and ab initio quantum mechanics method. The molecular mechanics and semi-empirical quantum mechanics methods have several advantages over ab initio methods. Most importantly, these methods are fast. While this may not be important for small molecules, it is certainly important for biomolecules. Another advantage is that for specific and well-parameterized molecular systems, these methods can calculate values that are closer to experiment than lower level ab initio techniques. 

Absorption, metaboHsm, and biological activities of organic compounds are influenced by molecular interactions with asymmetric biomolecules. These interactions, which involve hydrophobic, electrostatic, inductive, dipole—dipole, hydrogen bonding, van der Waals forces, steric hindrance, and inclusion complex formation give rise to enantioselective differentiation (1,2). Within a series of similar stmctures, substantial differences in biological effects, molecular mechanism of action, distribution, or metaboHc events may be observed. Eor example, (R)-carvone [6485-40-1] (1) has the odor of spearrnint whereas (5)-carvone [2244-16-8] (2) has the odor of caraway (3,4). 

Empirical energy functions can fulfill the demands required by computational studies of biochemical and biophysical systems. The mathematical equations in empirical energy functions include relatively simple terms to describe the physical interactions that dictate the structure and dynamic properties of biological molecules. In addition, empirical force fields use atomistic models, in which atoms are the smallest particles in the system rather than the electrons and nuclei used in quantum mechanics. These two simplifications allow for the computational speed required to perform the required number of energy calculations on biomolecules in their environments to be attained, and, more important, via the use of properly optimized parameters in the mathematical models the required chemical accuracy can be achieved. The use of empirical energy functions was initially applied to small organic molecules, where it was referred to as molecular mechanics [4], and more recently to biological systems [2,3]. 

Our procedure depends on a new computer program, RAMM (RAndom Molecular Mechanics), which is applicable to any kind of biomolecule. It is described in detail elsewhere (KoS r, T./ Petrak, F. Galova, Z. TvaroSka, I. Carbohvdr. Res.. in Press). Only the basic characteristics of RAMM and its application to conformational analysis of disaccharides are discussed here, concentrating on the effect of the orientations of pendant groups on the energy values at the various < ) and f torsion angles. 

The development of molecular mechanics, which incorporates quanmm mechanical data into a simplified mathematical framework derived from the classical equations of motion to permit reasonable calculations on biomolecules of large size. 

Abstract You can calculate molecular geometries, rates and equilibria, spectra, and other physical properties. The tools of computational chemistry are molecular mechanics, ab initio, semiempirical and density functional methods, and molecular dynamics. Computational chemistry is widely used in the pharmaceutical industry to explore the interactions of potential drugs with biomolecules, for example by docking a candidate drug into the active site of an enzyme. It is also used to investigate the properties of solids (e.g. plastics) in materials science. It does not replace experiment, which remains the final arbiter of truth about Nature. 

Calculations on the structure of large molecules like proteins or DNA are done with molecular mechanics. The motions of these large biomolecules can be studied with... 

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