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Computational framework small molecules

An unbiased simulation may use a truncated basis set that represents the lowest complex surface harmonics of the atomic valence shell on a Born-Oppenheimer framework with the correct relative atomic masses. For small molecules, of less than about fifteen atoms, the nuclear framework could perhaps even be generated computationally without assumption. The required criterion is the optimal quenching of angular momentum vectors. The derivation of molecular structure by the angular-momentum criterion will be demonstrated qualitatively for some small molecules. [Pg.209]

By analogy to the framework for classical genetics developed by Morgan and colleagues, the development of an experimentally driven, computational framework for chemical genetics, which allows the mapping of the functional units (chemicals) that can induce variation in biological systems, holds the potential to revolutionize the discovery of small-molecule probes for basic... [Pg.326]

In both cases, a structural representation of a small molecule is the input parameter to a conceptual set of operations that give rise to numerical outputs such as molecular descriptors, physicochemical properties, or biological outcomes (Fig. 13.1-l(a)). However, to be useful in predictive ways, such as when used to support prospective decisions about the investment of synthetic chemistry resources, at least some of these numerical outputs must be computable given only a structure representation. Only this situation allows relationships between experimentally determined values and computed values to be used to predict experimental outcomes for new molecules, based on their structural similarity to molecules that have already been experimentally tested (Fig. 13.1-l(b)). Most broadly, chemical space is a colloquialism that refers to the ranges and distributions of computed or measured outputs based on chemical structure inputs, and serves as a mathematical framework for quantitative comparisons of similarities and differences between small molecules (Fig. 13.1-l(c)). [Pg.725]

The various analyses, examples and applications of the SSA which are presented in the sections that follow, show how reliable wavefunctions of unstable states can be obtained. These have a form which is transparent and usable regardless of whether they describe field-free or field-induced excited state systems of, say, 2, 15, or 30 electrons and of whether there is one or many open channels. In this way, additional properties and good understanding of the interplay between structure and dynamics can be (and indeed have been) obtained. The discussion, in conjunction with the corresponding references, explains how the SSA has formed the framework for the formal and computational treatment—nonperturbatively—of a variety of prototypical problems irwohring field-free as well as field-induced resonance states in atoms and in small molecules. [Pg.172]

Early molecular dynamics simulations focused on spherically shaped particles in zeolites. These particles were either noble gases, such as argon, krypton, and xenon, or small molecules like methane. For these simulations, the sorbates were treated as soft spheres interacting with the zeolite lattice via a Lennard-Jones potential. Usually the aluminum and silicon atoms in the framework were considered to be shielded by the surrounding oxygen atoms, and no aluminum and silicon interactions with the sorbates were included. The majority of those studies have concentrated on commercially important zeolites such as zeolites A and Y and silicalite (all-silica ZSM-5), for which there is a wealth of experimental information for comparison with computed properties. [Pg.192]

Due to the development of advanced numerical methods in the last decades, quantum approaches are now able to accurately describe the chemical bonds formed between two reactants. Nevertheless, when a surface is involved, the actual systems met in practice, for example a dense polymeric layer adsorbed on a rough surface, cannot yet be simulated, because this would require too large a memory size or too long a computation time. Quantum calculations, thus, cannot compete with empirical models in the prediction of adhesion strengths. However, they may allow one to check their validity in model cases, for example small molecules adsorbed on a substrate, or large molecules adsorbed on a cluster of a few atoms which simulates the substrate. This has been done in a number of cases but, to the author s knowledge, mostly for adsorption processes on metallic surfaces. Numerical results for the adsorption of molecules on oxide surfaces may be found in the literature (Henrich and Cox, 1994), but there exists no systematic discussion in the framework of acid-base interactions. [Pg.184]

The goal of the calculation is, therefore, to compute the strength of the induced magnetic field in space, relative to the strength of the external one. Because one of the main assumptions is that all fields are small on the typical energy scale of atoms or molecules, this calculation can be performed in the framework of perturbation theory. [Pg.29]


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