Computational molecular modelling

At present, conformational searches provide for the most important application of computer molecular modeling in biology. In contrast, in statistical physics, from which MC and MD methods were originally borrowed, they are primarily used for studying... 

The pharmacophore concept has now been widely accepted and used in the medicinal chemistry community as well as the field of computational molecular modeling. Two closely related definitions of pharmacophore have been employed by both the medicinal chemist and molecular modelers, and the root of this concept can be traced back to more than hundred years ago. 

Table 2 Commercially Available Computational Molecular Modeling Software Used in the Studies Described in This Chapter... 

Computer molecular modeling indicated that the hydroxylations at C-6 occurred because, with only two binding points for the substrate (into the two cyclodextrins on opposite sides of the porphyrin), the substrate could rotate so as to point its edge toward the Mn=0 species that performs the hydroxylation. To solve this, we... 

Fig-1 Data from computational molecular modeling and instrumental analysis are used for group exploration and concept invention in POGIL classroom activities... 

Our main focus in current and future work is to base guided-inquiry activities for both lecture and laboratory portions of General Chemistry on data that can be obtained from modem chemical instmmentation or computational molecular modeling as illustrated by the shaded bold arrows in Fig. 1. This approach tries to instill an interactive view of chemical sub-disciplines in students learning. 

Xie XQ, Yang DP, Melvin LS, Makriyannis A (1994) Conformational analysis of the prototype nonclassical cannabinoid CP-47,497, using 2D NMR and computer molecular modeling. J Med Chem 37 1418-1426... 

Xie XQ, Pavlopoulos S, DiMeglio CM, Makriyannis A (1998) Conformational studies on a diastereoisomeric pair of tricyclic nonclassical cannabinoids by NMR spectroscopy and computer molecular modeling. J Med Chem 41 167-174... 

Rabinowitz, J. R., Goldsmith, M. R., Little, S. B., and Pasquinelli, M. A. (2(X)8). Computational molecular modeling for evaluating the toxicity of environmental chemicals Prioritizing bioassay requirements. Environ Health Perspect 116, 573-577. 

From the results in the last section it is clear that for particular applied radiative frequencies or frequency multiples, close to resonance with particular molecular states, each molecular tensor will be dominated by certain terms in the summation of states as a result of their diminished denominators—a principle that also applies to all other multiphoton interactions. This invites the possibility of excluding, in the sum over molecular states, certain states that much less significantly contribute. Then it is expedient to replace the infinite sum over all molecular states by a sum over a finite set—this is the technique employed by computational molecular modelers, their results often producing excellent theoretical data. In the pursuit of analytical results for near-resonance behavior, it is often defensible to further limit the sum over states and consider just the ground and one electronically excited state. Indeed, the literature is replete with calculations based on two-level approximations to simplify the optical properties of complex molecular systems. On the other hand, the coherence features that arise through adoption of the celebrated Bloch equations are limited to exact two-level systems and are rarely applicable to the optical response of complex molecular media. 

Recently, Keimowitz et al [38], aware that the cannabinoid side chain is a key pharmacophore, studied a series of 36 side-chain substituted A8-THCs with a wide range of pharmacological potency using computational molecular modelling and QSAR analysis. They showed that for optimum affinity and potency, the side chain must have conformational freedom that allows its terminus to fold back and come into proximity with the phenolic ring. In vivo THC is oxidized to the more potent ll-OH-A9-THC. Modifications of this structure yield 9-nor-9P-OH-hexahydrocannobinol (HHC) that has exhibited enhanced analgesic activity. 

Two major categories of physics-based, computational molecular models exist macroscopic and microscopic. Macroscopic models describe the coarse-grained features of a system or a process but do not describe the atomic or molecular features. Microscopic or atomistic models take full account of all atoms in the system. 

The Chemistry of Life course incorporates active learning methods, including computational molecular modeling, simulations, experiments, and student papers and presentations. As described below, activities have been designed that use commercial software packages to enable students to visualize chemical and physical processes that influence and support life. 

Because the shape of a molecule determines whether it will be recognized by a receptor and, therefore, whether it will exhibit biological activity, compounds with similar biological activity often have similar structures. Because computers can draw molecular models of compounds on a video display and move them around to assume different conformations, computer molecular modeling allows more rational dmg design. There are computer programs that allow chemists to scan existing collections of thousands of compounds to find those with appropriate structural and conformational properties. 

Computational chemistry provides an array of valuable tools for in silico drug design and virtual screening, and it continues to expand its role in modern drug discovery. Computer molecular modeling, molecular graphic representations, and easy-to-access structural... 

Refinement of the predicted model. Computational molecular modeling including energy minimization and dynamic simulation is carried to refine the model(s) obtained from the comparative structure modeling. 

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