Molecular modeling and quantum mechanics

Sandeep Kumar received his M.S. in chemistry from the Indian Institute of Technology, Kanpur, India, in 2003. He received his Ph.D. from OSU in 2008, where he worked on the catalytic mechanism of DNA polymerases under the supervision of Professor Ming-Daw Tsai. He is currently a post-doctoral researcher with Professors Karin Musier-Forsyth and Christopher Hadad at OSU. His areas of interest include molecular modeling and quantum mechanical investigations of the enzyme mechanisms. 

Taking advantage of molecular modeling and quantum mechanical techniques to obtain relevant structural parameters and molecular properties such as conformational behavior, ionization potentials, and dipole moments, several researchers have proposed alternative predictive models of lipophilicity. Using parameters derived from the 3D molecular structure should in principle introduce the (missing) third dimension in log P calculations. 

The first attempts to quantify molecular diversity focused on physicochemical properties as a means of defining the diversity space. These properties can be calculated using standard molecular modeling and quantum mechanical packages, and include the dipole moment, HOMO and LUMO energies, heat of formation, total energy, ionization potential, number of filled... 

Addressing conformational questions is the strong suit of computational chemistry and molecular modeling. Both quantum mechanical and... 

With respect to the various spectroscopic methods not discussed so far there are four methodologically different concepts of molecular modeling (i) quantum-mechanical methods which result structural and electronic information (ii) MM-based structural modeling, followed by a single-point MO-based computation of the electronic properties (iii) spectra simulation with given electronic parameters in cases, where structural parameters (e.g., distances such as used in protein modeling, see above) are involved in the simulation (iv) structure property correlations. The latter approach will be discussed briefly at the end of this Section (redox potentials) and in Section 4. 

Both classical and quantum mechanical methods are employed for various levels of molecular modeling. While quantum mechanical methods can be used with small molecules to yield precise results, classical force-field methods provide faster yet approximate solutions for large molecules or molecular systems that could not be studied using quantum methods. Although these two types of methods differ... 

The agreement between theory and experiment for commonly computed properties can be judged from the data in Tables 6-8. These data were drawn from the literature. Ab initio calculations give results that are close to experiment on average. Since the semiempirical and ab initio tests were not done on identical sets of molecules, it is hard to evaluate exactly how much better ab initio is. Although an ab initio molecular orbital calculation is based on first principles, predictions from such a calculation are not necessarily better than those from some of the recent semiempirical molecular orbital or empirical force field methods. A carefully parameterized, general force field can, in fact, predict molecular geometries as well as or better than an ab initio MO calculation. Overall, however, molecular models built quantum mechanically will be quite realistic. 

HyperChem is a versatile molecular modeler and editor and a powerful computational package. It offers many types of molecular and quantum mechanics calculations. 

Quotation from Sommerfeld, Atomic Structures, 79. On p. vi, Sommerfeld notes that in the chapter on the natural system of the elements, "the former discussions of molecular models and atomic volumes have been thoroughly pared down." At Harvard in 1925, Edwin Kemble s course in quantum mechanics included the second edition of Sommerfeld s Aufbau, according to Schweber (1990 348). Similarly, Joseph Hirschfelder was reading it as an undergraduate at Yale according to Hirschfelder, "My Adventures in Theoretical Chemistry," Ann.Rev.P.Chem. 33 (1983) 129, on 4. 

The various types of successful approaches can be classified into two groups empirical model calculations based on molecular force fields and quantum mechanical approximations. In the first class of methods experimental data are used to evaluate the parameters which appear in the model. The shape of the potential surfaces in turn is described by expressions which were found to be appropriate by semiclassicala> or quantum mechanical methods. Most calculations of this type are based upon the electrostatic model. Another more general approach, the "consistent force field method, was recently applied to the forces in hydrogen-bonded crystals 48> 49>. 

In a recent upsurge of studies on electron transfer kinetics, importance was placed on the outer shell solvent continuum, and the solvent was replaced by an effective model potential or a continuum medium with an effective dielectric constant. Studies in which the electronic and molecular structure of the solvent molecules are explicitly considered are still very rare. No further modem quantum mechanical studies were made to advance the original molecular and quantum mechanical approach of Gurney on electron and proton (ion) transfer reactions at an electrode. 

In this article, a brief discussion will be given on the relevance of continuum theory in explaining the rate of electron transfer and the activation of species in solution we will concentrate in particular on molecular and quantum mechanical models of ET reactions at the electrode/electrolyte interface that are needed to replace those based on the continuum approach. ... 

Molecular modeling treatments of electron transfer kinetics for reactions involving bond breaking were developed much earlier than the continuum theories originated by Weiss in 1951. Gurney in 193l published a landmark paper (the foundation of quantum electrochemistry) on a molecular and quantum mechanical model of proton and electron transfer... 

A classical force-field is developed to represent the conformational characteristics of PC based upon recent experimental and quantum mechanical data. This force field is an improvement upon previously published molecular mechanics force fields because it allows for rotation about all the single bonds in the PC repeat unit. An RIS model of PC is obtained using the force field results. 

Semi-empirical molecular orbital, MO, theory uses a combination of experimental data and quantum mechanical MO methods to model the valence electronic structure of molecules. In the MNDO (8) method each atom is parameterized using experimental data. This calculation provides molecular orbital descriptions of the valence electrons, as well as effective charges of each atom in the molecule. 

In the realni of classical thermodynamics, equations of state arc assumed given. They can be derived from first principles only by the methods of statistical mechanics and quantum mechanics These rely on the adoption of suitable molecular models for substances, and so far no universal, generally applicable model has heen discovered even for narrow classes of subslunces such as gases. 

B. Mennucci, J. Tomasi and R. Cammi, Excitonic splitting in conjugated molecular materials A quantum mechanical model including interchain interactions and dielectric effects, Phys. Rev. B, 70 (2004) 205212. 

J. Li, P. Beroza, L. Noodleman and D.A. Case. Quantum mechanical modeling of active sites in metalloproteins. In L. Banci and P. Comba, (ed), Molecular Modeling and Dynamics of Bioinorganic Systems, Proceedings of NATO ASI Workshop, Kluwer, Dordrecht, pp. 279, 1997. 

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