Fragment quantum approaches

In more recent years, additional progress and new computational methodologies in macromolecular quantum chemistry have placed further emphasis on studies in transferability. Motivated by studies on molecular similarity [69-115] and electron density representations of molecular shapes [116-130], the transferability, adjustability, and additivity of local density fragments have been analyzed within the framework of an Additive Fuzzy Density Fragmentation (AFDF) approach [114, 131, 132], This AFDF approach, motivated by the early charge assignment approach of Mulliken [1, 2], is the basis of the first technique for the computation of ab initio quality electron densities of macromolecules such as proteins [133-141],... 

Electron density decreases exponentially with distance that suggests that an Additive Fuzzy Density Fragmentation (AFDF) approach can be used for both a fuzzy decomposition and construction of molecular electron densities. The simplest AFDF technique is the Mulliken-Mezey density matrix fragmentation [12,13], that is the basis of both the Molecular Electron Density Loge Assembler (MEDLA) [14-17] and the Adjustable Density Matrix Assembler (ADMA) [18-21] macromolecular quantum chemistry methods. 

It has been elsewhere suggested [109] that the predictive deficiencies of programs such as ACD/pKg are due to their fragment-based approach. It was further suggested that an approach based on quantum mechanical methods would be more reliable. However, impublished analysis (by the present author) of predicted values based on such quantum mechanical methods for a set of 40 carboxylic acids [109] indicated that many of them were still poorly estimated, with a mean deviation on the order of 0.3 log unit. The plot of predicted versus... 

N. G. j. Richards, P. B. William.s, and M. S. Tute, Int. J. Quantum Chem., 44, 219 (1992). Empirical Methods for Computing Molecular Piu-tition Coefficients. II. Inclusion of Conformational Flexibility Within Fragment-Based Approaches. 

Fujimoto K, Yang WT (2008) Density-fragment interaction approach for quantum-mechanical/molecular-mechanical calculations with application to the excited states of a Mg(2-i-)-sensitive dye. J Chem Phys 129 054102... 

Transferred electron density fragments obtained by AFDF method can provide excellent approximations. One such approach, formulated in terms of transferability of fragment density matrices within the AFDF framework is a tool that has been suggested as an approach to macromolecular quantum chemistry [114, 115, 130, 142-146] and to a new density fitting algorithm in the crystallographic structure refinement process [161]. 

As the SIBFA approach relies on the use of distributed multipoles and on approximation derived form localized MOs, it is possible to generalize the philosophy to a direct use of electron density. That way, the Gaussian electrostatic model (GEM) [2, 14-16] relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. It offers the possibility of a continuous electrostatic model going from distributed multipoles to densities and allows a direct inclusion of short-range quantum effects such as overlap and penetration effects in the molecular mechanics energies. 

In the investigations of molecular adsorption reported here our philosophy has been to first determine the orientation of the adsorbed molecule or molecular fragment using NEXAFS and/or photoelectron diffraction. Using photoemission selection rules we then assign the observed spectral features in the photoelectron spectrum. On the basis of Koopmans theorem a comparison with a quantum chemical cluster calculation is then possible, should this be available. All three types of measurement can be performed with the same angle-resolving photoelectron spectrometer, but on different monochromators. In the next Section we briefly discuss the techniques. The third Section is devoted to three examples of the combined application of NEXAFS and photoemission, whereby the first - C0/Ni(100) - is chosen mainly for didactic reasons. The results for the systems CN/Pd(111) and HCOO/Cu(110) show, however, the power of this approach in situations where no a priori predictions of structure are possible. 

One advantage of this response of molecular fragment approach [24] to condensed Fukui functions is that Equations 18.21 through 18.24 are easily evaluated from the population analysis data that accompanies the output of most quantum chemistry calculations. 

Our application of this approach to the benzene ion dissociation in collaboration with Klippenstein was noted in Section II. When it can be carried out, this is by far the most satisfactory way currently available for extrapolation to E. The necessary VTST calculations, whether by way of the Marcus variational RRKM approach or other approaches (e.g., statistical adiabatic channel theory ) are laborious, involving the quantum chemical construction of large potential maps for the interaction of the separating fragments and extensive statistical calculations for the dissociation process. Application of this approach to a variety of interesting systems is one of the outstanding opportunities for future work. 

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