Computations of molecular properties

B.T. Pickup. Theory and computation of molecular properties. In S. Wilson, editor, Methods in Computational Chemistry, Volume 5 Atomic and Molecular Properties, pages 157-265. Plenum Press, New York, 1992. 

Computations. Efforts to compute pair polarizabilities from first principles, using perturbation techniques or modern quantum chemical methods, have been known for many years and are reviewed by Hunt [80] in the desirable detail. Amos s review of ab initio methods applied to the computation of molecular properties considers supermolecular properties, too [2]. 

The ab initio computation of molecular properties - including those associated with time-dependent external electric and magnetic fields - has advanced significantly in the last several decades, yielding accurate models for linear, quadratic, and higher-order response functions. When electron correlation effects play a pivotal... 

Code for Distributed Computing Of Molecular Properties Using ChemStar ... 

Due to the noncrystalline, nonequilibrium nature of polymers, a statistical mechanical description is rigorously most correct. Thus, simply hnding a minimum-energy conformation and computing properties is not generally suf-hcient. It is usually necessary to compute ensemble averages, even of molecular properties. The additional work needed on the part of both the researcher to set up the simulation and the computer to run the simulation must be considered. When possible, it is advisable to use group additivity or analytic estimation methods. 

A number of molecular properties can be computed. These include ESR and NMR simulations. Hyperpolarizabilities and Raman intensities are computed using the TDDFT method. The population analysis algorithm breaks down the wave function by molecular fragments. IR intensities can be computed along with frequency calculations. 

The ab initio methods in Gaussian are also capable of handling any type of atom, including metals. Gaussian computes a variety of molecular properties in addition to the energies and structures. Gaussian can investigate molecules in their excited states and in solution. 

It is clear from the forgoing discussions that the important material properties of liquid crystals are closely related to the details of the structure and bonding of the individual molecules. However, emphasis in computer simulations has focused on refining and implementing intermolecular interactions for condensed phase simulations. It is clear that further work aimed at better understanding of molecular electronic structure of liquid crystal molecules will be a major step forward in the design and application of new materials. In the following section we outline a number of techniques for predictive calculation of molecular properties. 

The genesis of in silico oral bioavailability predictions can be traced back to Lip-inski s Rule of Five and others qualitative attempts to describe drug-like molecules [13-15]. These processes are useful primarily as a qualitative tool in the early stage library design and in the candidate selection. Despite its large number of falsepositive results, Lipinski s Rule of Five has come into wide use as a qualitative tool to help the chemist design bioavailable compounds. It was concluded that compounds are most likely to have poor absorption when the molecular weight is >500, the calculated octan-l-ol/water partition coefficient (c log P) is >5, the number of H-bond donors is >5, and the number of H-bond acceptors is >10. Computation of these properties is now available as an ADME (absorption, distribution, metabolism, excretion) screen in commercial software such as Tsar (from Accelrys). The rule-of-5 should be seen as a qualitative, rather than quantitative, predictor of absorption and permeability [16, 17]. 

The use of computational methods for the calculation of molecular properties has been a perennial goal of chemists. In recent years, the field of computational chemistry has become a firmly established discipline. Computational chemists have made impressive contributions to almost every aspect of chemistry, ranging from structural organic and inorganic chemistry to the prediction of polymer properties and the design of medicinally important therapeutic agents. While many computer-based methods are robust and widely utilized, the continued development and refinement of software and the underlying theory remains an active area of research.1,2... 

During the last decade MO-theory became by far the most well developed quantum mechanical method for numerical calculations on molecules. Small molecules, mainly diatomics, or highly symmetric structures were treated most accurately. Now applicability and limitations of the independent particle, or Hartree-Fock (H. F.), approximation in calculations of molecular properties are well understood. An impressive number of molecular calculations including electron correlation is available today. Around the equilibrium geometries of molecules, electron-pair theories were found to be the most economical for actual calculations of correlation effects ). Unfortunately, accurate calculations as mentioned above are beyond the present computational possibilities for larger molecular structures. Therefore approximations have to be introduced in the investigation of problems of chemical interest. Consequently the reliability of calculated results has to be checked carefully for every kind of application. Three types of approximations are of interest in connection with this article. 

Theoretical calculation of any atomic or molecular property through application of computational methods based on quantum mechanics or other sophisticated approach is typically practicable through approximate methods. The internuclear potential energy V(i ) independent of mass is conventionally derived from the results of computations of molecular electronic structure according to a scheme of wave mechanics,... 

Fundamental challenges in computational chemistry include the high computational cost of ab initio calculations in terms of time, memory, and disk space requirements difficulties that arise when standard advanced computational treatments are used to describe processes such as bond breaking determination of the best approach toward functional development in density functional theorgy, understanding the means for quantitative prediction of thermonuclear kinetics and computational chemistry treatment of transition metal systems for reliable prediction of molecular properties. This book addresses these important problems, featuring chapters by leading computational chemists and physicists. 

The Molecular Surface (MS) first introduced by Richards (19) was chosen as the 3D space where the MLP will be calculated. MS specifically refers to a molecular envelope accessible by a solvent molecule. Unlike the solvent accessible surface (20), which is defined by the center of a spherical probe as it is rolled over a molecule, the MS (19), or Connolly surface (21) is traced by the inwardfacing surface of the spherical probe (Fig. 2). The MS consists of three types of faces, namely contact, saddle, and concave reentrant, where the spherical probe touches molecule atoms at one, two, or three points, simultaneously. Calculation of molecular properties on the MS and integration of a function over the MS require a numerical representation of the MS as a manifold S(Mk, nk, dsk), where Mk, nk, dsk are, respectively, the coordinates, the normal vector, and the area of a small element of the MS. Among the published computational methods for a triangulated MS (22,23), the method proposed by Connolly (21,24) was used because it provides a numerical presentation of the MS as a collection of dot coordinates and outward normal vectors. In order to build the 3D-logP descriptor independent from the calculation parameters of the MS, the precision of the MS area computation was first estimated as a function of the point density and the probe radius parameters. When varying... 

Schrodinger equation. When the molecule is too large and difficult for quantum mechanical calculations, or the molecule interacts with many other molecules or an external field, we turn to the methods of molecular mechanics with empirical force fields. We compute and obtain numerical values of the partition functions, instead of precise formulas. The computation of thermodynamic properties proceeds by using a number of techniques, of which the most prominent are the molecular dynamics and the Monte Carlo methods. 

Acknowledgements. All of the original work described in this paper is a result of my very fruitful continuing collaboration with Dr. Michael Archer. The coding of molecular properties and the actual computer work was done by Mr. Andrew Edelman. 

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