Novel Computational Methods

Determination of pharmacophoric geometry for collagenase inhibitors using a novel computational method and its veriflcation using molecular dynamics, NMR, and X-ray crystallography. J. Am. Chem. Soc., 117, 4671-4682. 

The theory and implementation of a novel computational method capable of looking at large transition-state shape-selective systems is outlined. It is then applied to the alkylation reaction of toluene in the gas phase as well as in zeolites MFI, MOR and BEA. Alkylating agents from the series methyl, ethyl, /50-propyl and /er/-butyl are employed to investigate the size and shape effects of the confinement. 

Kossoy, A. D., Risley, D. S., Kleyle, R. M., and Nurock, D. (1992). Novel computational method for the determination of partition coefficients by planar chromatography. Anal. Chem. 64 1345-1349. 

This handbook presents a comprehensive overview on the physics of the plasmon-emitter interaction, ranging from electromagnetism to quantum mechanics, from metal-enhanced fluorescence to surface-enhanced Raman scattering, and from optical microscopy to the synthesis of metal nanoparticles, filling the gap in the literature of this emerging field. It is useful for graduate students as well as researchers from various fields who want to enter the field of molecular plasmonics. The text allows experimentalists to have a solid theoretical reference at a different level of accuracy and theoreticians to find new stimuli for novel computational methods and emerging applications. 

Shen J, Zhu C, Reiling S, Vaz R. A novel computational method for comparing vibrational circular dichroism spectra. Spectrochim. Acta, Fart A 2010 76(3-4) 418-422. 

Before 1980, force field and semiempircal methods (such as CNDO, MNDO, AMI, etc.) [1] were used exclusively to study sulfur-containing compounds due to the lack of computer resources and due to inefficient quantum-chemical programs. Unfortunately, these computational methods are rather hmit-ed in their reliability. The majority of the theoretical studies under this review utilized ab initio MO methods [2]. Not only ab initio MO theory is more reliable, but also it has the desirable feature of not relying on experimental parameters. As a consequence, ab initio MO methods are apphcable to any systems of interest, particularly for novel species and transition states. 

As the availability of crystal structures increased in the early 1990s, a number of experimental and computational methods were developed to use the structure of the protein target as a route to discover novel hit compounds. The methods include de novo design, virtual screening, and fragment-based discovery. These developments are covered in more detail in the later chapters of this book, but their main features can be summarized as follows. 

The structure of CO2-V has been determined by x-ray diffraction [343], and the observed pattern could be reasonably fitted by using a tridymite-type structure (orthorhombic P2 2 2 lattice) shown in Fig. 21. The formation and structure of polymeric carbon dioxide has been smdied by computational methods [344—348] in order to fuUy characterize this novel material however. 

Computational methods combined with a novel approach in the application of scattering physics were recently employed by Barbi et al. in a synchrotron SAXS study of the nanostructure of Nafion as a function of mechanical load. A new method of multidimensional chord-distribution function (CDF) analysis was used to visualize the multiphase nano-... 

The principal use of Eq. (173) is in conjunction with a similar heat dispersion equation. Unfortunately, a system of coupled nonlinear partial differential equations then has to be solved, which is very difficult even with the aid of computers. In the oxidation of sulfur dioxide. Hall and Smith (HI) found relatively good agreement between theory and experiment near the center of the reactor. Their calculations were based on the heat-dispersion equation, and they did not take detailed mass dispersion into account. Baron (B2) later solved the mass and heat dispersion equations simultaneously by a novel graphical method, and found better agreement between his calculations and the data of Hall and Smith. 

The demand for the research will cover the development of the novel algorithms utilizing parallel computation methods. The development of a hierarchical multi-scale paradigm will consolidate theoretical analysis and will lead to large-scale decision-making criteria of the process level design based on the first-principle dynamics. 

This article presents the application of a novel technique, which combines the structural sensitivity of vibrational spectroscopy with the conformational sensitivity of chiroptical methods to study the solution conformation of biological molecules. Instrumental aspects, computational methods and spectral results for peptides and nucleic... 

Secondly, a quantitative interpretation of the amide I VCD region is possible. Using factor analysis methodology, reliable percentage of a-helical, B-sheet and other contributions have been obtained, using prototypical peptide VCD spectra as basis sets. The factor analytical data appear to agree well with solid phase X-ray structures, and to a somewhat lesser extent with UV-CD data. Thus, it appears that the instrumental and computational methods are available to utilize VCD as a novel spectroscopic technique for structural studies on peptides and proteins. 

Next follows a series of reports on important developments in computational methods or program packages incorporating novel computational features. 

The task assigned to a selector can be executed by several separation techniques. Specialized designers bring the expertise necessary to design the unit. From the practical viewpoint these can be identified with the standard unit operations, for which computation methods are available, but also with novel techniques that can... 

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