Quantum density functional methods

Chapter 2 we worked through the two most commonly used quantum mechanical models r performing calculations on ground-state organic -like molecules, the ab initio and semi-ipirical approaches. We also considered some of the properties that can be calculated ing these techniques. In this chapter we will consider various advanced features of the ab Itio approach and also examine the use of density functional methods. Finally, we will amine the important topic of how quantum mechanics can be used to study the solid state. 

To overcome these limitations, the hybrid QM-MM potential can employ ad initio or density function methods in the quantum region. Both of these methods can ensure a higher quantitative accuracy, and the density function methods offer a computaitonally less expensive procedure for including electron correlation [5]. Several groups have reported the development of QM-MM programs that employ ab initio [8,10,13,16] or density functional methods [10,41-43]. 

To date the majority of QM-MM applications have employed density functional methods ab initio or semiempirical methods in the quantum region. The energy tenns evaluated in these methods are generally similar, but there are specific differences. The relevant equations for the density functional based methods are described first, and this is followed by a description of the specific differences associated with the other methods. 

The use of QM-MD as opposed to QM-MM minimization techniques is computationally intensive and thus precluded the use of an ab initio or density functional method for the quantum region. This study was performed with an AMi Hamiltonian, and the first step of the dephosphorylation reaction was studied (see Fig. 4). Because of the important role that phosphorus has in biological systems [62], phosphatase reactions have been studied extensively [63]. From experimental data it is believed that Cys-i2 and Asp-i29 residues are involved in the first step of the dephosphorylation reaction of BPTP [64,65]. Alaliambra et al. [30] included the side chains of the phosphorylated tyrosine, Cys-i2, and Asp-i 29 in the quantum region, with link atoms used at the quantum/classical boundaries. In this study the protein was not truncated and was surrounded with a 24 A radius sphere of water molecules. Stochastic boundary methods were applied [66]. 

In addition most of the more tractable approaches in density functional theory also involve a return to the use of atomic orbitals in carrying out quantum mechanical calculations since there is no known means of directly obtaining the functional that captures electron density exactly. The work almost invariably falls back on using basis sets of atomic orbitals which means that conceptually we are back to square one and that the promise of density functional methods to work with observable electron density, has not materialized. 

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]. 

The computational prediction of vibrational spectra is among the important areas of application for modem quantum chemical methods because it allows the interpretation of experimental spectra and can be very instrumental for the identification of unknown species. A vibrational spectrum consists of two characteristics, the frequency of the incident light at which the absorption occurs and how much of the radiation is absorbed. The first quantity can be obtained computationally by calculating the harmonic vibrational frequencies of a molecule. As outlined in Chapter 8 density functional methods do a rather good job in that area. To complete the picture, one must also consider the second quantity, i. e., accurate computational predictions of the corresponding intensities have to be provided. 

Sola, M., J. Mestres, R. Carbo, and M. Duran. 1996. A Comparative Analysis by Means of Quantum Molecular Similarity Measures of Density Distributions Derived from Conventional ab initio and Density Functional Methods. J. Chem. Phys. 104, 636. 

Chapter 1 gives a short description of ab initio methods, Hartree-Fock and post-Hartree-Fock, focusing on the Gaussian computer programs. Chapter 2 describes semi-empirical calculations and their applications to biological systems. Chapter 3 addresses itself to electrostatic properties of molecules, as determined by quantum-chemical methods. The density functional method is discussed in chapter 4. Chapter 5 compares theoretically obtained parameters to experimental data. 

The scheme analyzed so far is, in a way, a simplification of the Hartree-Fock scheme. As such, it is only a model approximation. The most serious drawback is the replacement of a fundamentally quantum mechanical term, whose very nature is to be non local, by a local approximation. Of course, when the system is in an electronic degenerate state, or when the BO approximation is no longer valid, the density functional method cannot be applied. For a discussion of this and other limitations the reader is referred to the paper by Bersuker [117],... 

A theoretical account from the point of view of DFT could be found in [1, 42,43]. For a good review of chemical applications of the above principles as described by quantum chemical methods in general and density functional methods in particular see the papers of Geerlings and De Proft [4,44,45]. 

Another hmitation is inherent to the harmonic approximation on which standard quantum mechanical force-field calculations are invariably based. Due to a fortui-tious (but surpisingly systematic) cancellation of errors, the harmonic frequencies calculated by modem density functional methods often match very well with the experimental ones, in spite of the fact that the latter involve necessarily more or less anharmonic potentials. Thus one is tempted to forget that the harmonic approx-imaton can become perilous when strong anharmonicity prevails along one or another molecular deformation coordinate. 

Sim, F., Salahub, D.R., and Chin, S. (1992) The accurate calculation of dipole moments and dipole polarizabilities using Gaussian-based density functional methods. Int. J. Quantum Chem., 43 (4), 463-479. 

Extensive tests have been carried out to establish the reliability of quantum-chemical schemes for metal oxide investigations. This includes schemes at a variety of levels of sophistication suitable for calculations of very large systems. In particular density functional methods offer good possibilities to treat sufficiently large systems to be applicable to many central problems in the field of photoelectrochemistry with reasonable accuracy and at very competitive computational costs. Semiempirical methods still offer a last possibility to perform reasonably accurate calculations on nanostructured systems containing several hundred atoms where first principles methods still cannot be applied routinely. 

Theoretical chemistry at UBC was further strengthened with the arrival of Delano Chong and Keith Mitchell in 1965 and 1966, respectively. Chong s interests in quantum chemistry have spanned the full range from semiempirical to ab initio molecular orbital methods. His long-standing interests in perturbation methods and constrained variations have figured prominently in his publications. He is probably best known for his attempts to calculate the X-ray and UV photoelectron spectra of molecules, often by means of perturbation corrections to Koopmans theorem.40 More recently he has shifted his focus to coupled pair functional methods and density functional methods, with a special interest in polarizabilities and hyperpolarizabilities.41... 

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