Molecular conformation conformational energies

Topol, I. A., and S. K. Burt. 1993. The calculations of small molecular conformation energy differences by density functional method. Chem. Phys. Lett 204,611. 

D. Shalloway, Application of the renormalization group to deterministic global minimization of molecular conformation energy functions. Journal of Global Optimization 2 (1992), 281. 

COMPASS numbers are discussed in text. Molecular conformer energies were computed in Spartan... 

The free energy differences obtained from our constrained simulations refer to strictly specified states, defined by single points in the 14-dimensional dihedral space. Standard concepts of a molecular conformation include some region, or volume in that space, explored by thermal fluctuations around a transient equilibrium structure. To obtain the free energy differences between conformers of the unconstrained peptide, a correction for the thermodynamic state is needed. The volume of explored conformational space may be estimated from the covariance matrix of the coordinates of interest, = ((Ci [13, lOj. For each of the four selected conform-... 

C.D. Maranas, IP. Androulakis and C.A. Floudas, A deterministic global optimization approach for the protein folding problem, pp. 133-150 in Global minimization of nonconvex energy functions molecular conformation and protein folding (P. M. Pardalos et al., eds.), Amer. Math. Soc., Providence, RI, 1996. 

G. Ramachandran and T. Schlick. Beyond optimization Simulating the dynamics of supercoiled DNA by a macroscopic model. In P. M. Pardalos, D. Shal-loway, and G. Xue, editors. Global Minimization of Nonconvex Energy Functions Molecular Conformation and Protein Folding, volume 23 of DIM ACS Series in Discrete Mathematics and Theoretical Computer Science, pages 215-231, Providence, Rhode Island, 1996. American Mathematical Society. 

I. Pettersson, T. Liljefors, Molecular mechanics calculated conformational energies of organic molecules a comparison of force fields, in Reviews in Computational Chemistry, Vbl. 9,... 

Quenched dynamics is a combination of high temperature molecular dynamics and energy minimization. This process determines the energy distribution of con formational families produced during molecular dynamics trajectories. To provide a better estimate of conformations, you should combine quenched dynamics with simulated annealing. 

Bostrom J, P-O Norrby and T Liljefors 1998, Conformational Energy Penalties of Protein-boun Ligands. Journal of Computer-A ided Molecular Design 12 383-396. 

In Chapter 2, a brief discussion of statistical mechanics was presented. Statistical mechanics provides, in theory, a means for determining physical properties that are associated with not one molecule at one geometry, but rather, a macroscopic sample of the bulk liquid, solid, and so on. This is the net result of the properties of many molecules in many conformations, energy states, and the like. In practice, the difficult part of this process is not the statistical mechanics, but obtaining all the information about possible energy levels, conformations, and so on. Molecular dynamics (MD) and Monte Carlo (MC) simulations are two methods for obtaining this information... 

Ah initio calculations of polymer properties are either simulations of oligomers or band-structure calculations. Properties often computed with ah initio methods are conformational energies, polarizability, hyperpolarizability, optical properties, dielectric properties, and charge distributions. Ah initio calculations are also used as a spot check to verify the accuracy of molecular mechanics methods for the polymer of interest. Such calculations are used to parameterize molecular mechanics force fields when existing methods are insulficient, which does not happen too often. 

Molecular mechanics strain energies have another use They can also be used to com pare the energies of models that share the same molecular formula that is models that are either stereoisomers or different conformations of a single molecule (allowed com parisons are shown here)... 

Stereochemistry. Cyclohexane can exist ia two molecular conformations the chair and boat forms. Conversion from one conformation to the other iavolves rotations about carbon—carbon single bonds. Energy barriers associated with this type of rotation are low and transition from one form to the other is rapid. The predominant stereochemistry of cyclohexane has no influence ia its use as a raw material for nylon manufacture or as a solvent. 

To extract the conformational properties of the molecule that is being studied, the conformational ensemble that was sampled and optimized must be analyzed. The analysis may focus on global properties, attempting to characterize features such as overall flexibility or to identify common trends in the conformation set. Alternatively, it may be used to identify a smaller subset of characteristic low energy conformations, which may be used to direct future drug development efforts. It should be stressed that the different conformational analysis tools can be applied to any collection of molecular conformations. These... 

Calculations on larger molecules have been carried out using molecular mechanics techniques and the Merck force field.- This method has proven to be suitable for the calculation of equilibrium geometries and conformational energy differences. 

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