Computational quantum mechanics semi-empirical methods

Provides a survey of quantum mechanics, semi-empirical computational methods, and the application of molecular orbital theory to organic chemistry. The concepts explored in this book should be easy for most readers to understand. 

The problem with most quantum mechanical methods is that they scale badly. This means that, for instance, a calculation for twice as large a molecule does not require twice as much computer time and resources (this would be linear scaling), but rather 2" times as much, where n varies between about 3 for DFT calculations to 4 for Hartree-Fock and very large numbers for ab-initio techniques with explicit treatment of electron correlation. Thus, the size of the molecules that we can treat with conventional methods is limited. Linear scaling methods have been developed for ab-initio, DFT and semi-empirical methods, but only the latter are currently able to treat complete enzymes. There are two different approaches available. 

HyperChem quantum mechanics calculations must start with the number of electrons (N) and how many of them have alpha spins (the remaining electrons have beta spins). HyperChem obtains this information from the charge and spin multiplicity that you specify in the Semi-empirical Options dialog box or Ab Initio Options dialog box. N is then computed by counting the electrons (valence electrons in semi-empirical methods and all electrons in fll) mitio method) associated with each (assumed neutral) atom and... 

The algorithms of the mixed classical-quantum model used in HyperChem are different for semi-empirical and ab mi/io methods. The semi-empirical methods in HyperChem treat boundary atoms (atoms that are used to terminate a subset quantum mechanical region inside a single molecule) as specially parameterized pseudofluorine atoms. However, HyperChem will not carry on mixed model calculations, using ab initio quantum mechanical methods, if there are any boundary atoms in the molecular system. Thus, if you would like to compute a wavefunction for only a portion of a molecular system using ab initio methods, you must select single or multiple isolated molecules as your selected quantum mechanical region, without any boundary atoms. 

The semi-empirical methods of HyperChem are quantum mechanical methods that can describe the breaking and formation of chemical bonds, as well as provide information about the distribution of electrons in the system. HyperChem s molecular mechanics techniques, on the other hand, do not explicitly treat the electrons, but instead describe the energetics only as interactions among the nuclei. Since these approximations result in substantial computational savings, the molecular mechanics methods can be applied to much larger systems than the quantum mechanical methods. There are many molecular properties, however, which are not accurately described by these methods. For instance, molecular bonds are neither formed nor broken during HyperChem s molecular mechanics computations the set of fixed bonds is provided as input to the computation. 

For small molecules, the accuracy of solutions to the Schrodinger equation competes with the accuracy of experimental results. However, these accurate ab initio calculations require enormous computation and are only suitable for the molecular systems with small or medium size. Ab initio calculations for very large molecules are beyond the realm of current computers, so HyperChem also supports semi-empirical quantum mechanics methods. Semi-empirical approximate solutions are appropriate and allow extensive chemical exploration. The inaccuracy of the approximations made in semi-empirical methods is offset to a degree by recourse to experimental data in defining the parameters of the method. Indeed, semi-empirical methods can sometimes be more accurate than some poorer ab initio methods, which require much longer computation times. 

Ab initio methods, unlike either molecular mechanics or semi-empirical methods, use no experimental parameters in their computations. Instead, their computations are based solely on the laws of quantum mechanics—the first principles referred to in the name ah initio—and on the values of a small number of physical constants ... 

Hpp describes the primary system by a quantum-chemical method. The choice is dictated by the system size and the purpose of the calculation. Two approaches of using a finite computer budget are found If an expensive ab-initio or density functional method is used the number of configurations that can be afforded is limited. Hence, the computationally intensive Hamiltonians are mostly used in geometry optimization (molecular mechanics) problems (see, e. g., [66]). The second approach is to use cheaper and less accurate semi-empirical methods. This is the only choice when many conformations are to be evaluated, i. e., when molecular dynamics or Monte Carlo calculations with meaningful statistical sampling are to be performed. The drawback of semi-empirical methods is that they may be inaccurate to the extent that they produce qualitatively incorrect results, so that their applicability to a given problem has to be established first [67]. 

Density functional theory (DFT),32 also a semi-empirical method, is capable of handling medium-sized systems of biological interest, and it is not limited to the second row of the periodic table. DFT has been used in the study of some small protein and peptide surfaces. Nevertheless, it is still limited by computer speed and memory. DFT offers a quantum mechanically based approach from a fundamentally different perspective, using electron density with an accuracy equivalent to post Hartree-Fock theory. The ideas have been around for many years,33 34 but only in the last ten years have numerous studies been published. DFT, compared to ab initio... 

Before any computational study on molecular properties can be carried out, a molecular model needs to be established. It can be based on an appropriate crystal structure or derived using any other technique that can produce a valid model for a given compound, whether or not it has been prepared. Molecular mechanics is one such technique and, primarily for reasons of computational simplicity and efficiency, it is the most widely used. Quantum mechanical modeling of metal complexes with ab-initio or semi-empirical methods often remains prohibitive because these methods are so computationally intensive. The approximations that are introduced in order to reduce central processing unit (CPU) time and allow quantum mechanical calculations to be used routinely are often severe and such calculations are then less reliable. 

Ab-initio quantum mechanics calculations are, because of the computational cost, impractical for large transition metal compounds. In semi-empirical methods, some of the quantities of ab-initio calculations are neglected or replaced by para-... 

In Pre-lab 3.5 we discussed quantum chemical calculations and specifically the Hartree-Fock approximation. Quantum chemical calculations are often referred to as first principles or ab initio (Latin meaning from the beginning ) calculations in that they attempt to solve the molecular electronic structure problem from the fundamental laws of quantum mechanics. Although a Hartree-Fock calculation is not very computationally intensive relative to more accurate correlation methods, no ab initio methods are practical for larger molecules. Instead, semi-empirical methods are typically employed to treat molecules ranging in size from tens to hundreds of atoms. 

Although most computational studies of organotin systems employ ECPs, other methods can be used to describe tin. These methods include semi-empirical methods, all-electron relativistic methods, and hybrid energy methods, such as Morokuma s ONIOM method and hybrid quantum mechanical and molecular mechanics methods (QM/MM). 

This description of quantum mechanical methods for computing (hyper)polarizabilities demonstrates why, nowada, the determination of hyperpolarizabilities of systems containing hundreds of atoms can, at best, be achieved by adopting, for obvious computational reasons, semi-empirical schemes. In this study, the evaluation of the static and dynamic polarizabilities and first hyperpolaiizabilities was carried out at die Time-Dependent Hartree-Fock (TDOT) [39] level with the AMI [50] Hamiltonian. The dipole moments were also evaluated using the AMI scheme. The reliability of the semi-empirical AMI calculations was addressed in two ways. For small and medium-size push-pull polyenes, the TDHF/AMl approach was compared to Hartree-Fock and post Hartree-Fock [51] calculations of die static and dynamic longitudinal first hyperpolarizability. Except near resonance, the TDHF/AMl scheme was shown to perform appreciably better than the ab initio TDHF scheme. Then, the static electronic first hyperpolaiizabilities of the MNA molecule and dimer have been calculated [15] with various ab initio schemes and compared to the AMI results. In particular, the inclusion of electron correlation at the MP2 level leads to an increase of Paaa by about 50% with respect to the CPHF approach, similar to the effect calculated by Sim et al. [52] for the longitudinal p tensor component of p-nitroaniline. The use of AMI Hamiltonian predicts a p aa value that is smaller than the correlated MP2/6-31G result but larger than any of the CPHF ones, which results fi-om the implicit treatment of correlation effects, characteristic of die semi-empirical methods. This comparison confirms that a part of die electron... 

Energy calculation and minimization One of the fundamental properties of molecules is their energy content and energy level. Three major theoretical computational methods in their calculation include empirical (molecular mechanics), semi-empirical and ab initio (quantum mechanics) approaches. Energy minimization results in geometry optimization of the molecular structure. 

The semi-empirical method, the ah initio method, and the density functional theory [DFT] are the three classes of quantum chemical methods. The semi-empirical method uses parameter derived from experimental data to simplify the computations. Ah initio methods are solely based on the laws of quantum mechanics. DFT is similar to the ah initio method in many ways except that it includes one attractive feature of electron correlation. Electron correlation can be described as "the electrons in a molecular system reacts to one another s motion and attempts to keep out of one another s way" [Young, 2001 Foresman, 2004]. 

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