Computational chemistry activation

It was reahzed quite some decades ago that the amount of information accumulated by chemists can, in the long run, be made accessible to the scientific community only in electronic form in other words, it has to be stored in databases. This new field, which deals with the storage, the manipulation, and the processing of chemical information, was emerging without a proper name. In most cases, the scientists active in the field said they were working in "Chemical Information . However, as this term did not make a distinction between librarianship and the development of computer methods, some scientists said they were working in "Computer Chemistry to stress the importance they attributed to the use of the computer for processing chemical information. However, the latter term could easily be confused with Computational Chemistry, which is perceived by others to be more limited to theoretical quantum mechanical calculations. 

K and G M Crippen 1986. Atomic Physicochemical Parameters for Three-dimensional Struc-directed Quantitative Structure-Activity Relationships. I. Partition Coefficients as a Measure ydrophobicity. Journal of Computational Chemistry 7 565-577. 

The successful chairmanship and the apparent qualities of personnel management landed several offers of deanships in Yngve s lap. He decided, to my delight, to remain a dedicated scientist. Administrative obligations remained, he assumed the role of Director of the Quantum Theory Project in 1983 and led this rather informal association of faculty members from Chemistry and Physics to be established, in 1987, as the "Institute for Theory and Computation in Molecular and Materials Sciences" with a well defined position in the University system. This was another demonstration of the ability to create coherence and commitment amongst a body of strong minded people with diverse interests. It is a consequence that Florida remains a world renowned hub of quantum chemistry activities. 

Boyd DB, Marsh MM. Computational chemistry in the design of biologically active molecules at Lilly. Abstracts of 183rd National Meeting of the American Chemical Society, Las Vegas, Nevada, March 28-April 2,1982. 

In this brief review we illustrated on selected examples how combinatorial computational chemistry based on first principles quantum theory has made tremendous impact on the development of a variety of new materials including catalysts, semiconductors, ceramics, polymers, functional materials, etc. Since the advent of modem computing resources, first principles calculations were employed to clarify the properties of homogeneous catalysts, bulk solids and surfaces, molecular, cluster or periodic models of active sites. Via dynamic mutual interplay between theory and advanced applications both areas profit and develop towards industrial innovations. Thus combinatorial chemistry and modem technology are inevitably intercoimected in the new era opened by entering 21 century and new millennium. 

Computational chemistry has reached a level in which adsorption, dissociation and formation of new bonds can be described with reasonable accuracy. Consequently trends in reactivity patterns can be very well predicted nowadays. Such theoretical studies have had a strong impact in the field of heterogeneous catalysis, particularly because many experimental data are available for comparison from surface science studies (e.g. heats of adsorption, adsorption geometries, vibrational frequencies, activation energies of elementary reaction steps) to validate theoretical predictions. 

The use of computational methods for the calculation of molecular properties has been a perennial goal of chemists. In recent years, the field of computational chemistry has become a firmly established discipline. Computational chemists have made impressive contributions to almost every aspect of chemistry, ranging from structural organic and inorganic chemistry to the prediction of polymer properties and the design of medicinally important therapeutic agents. While many computer-based methods are robust and widely utilized, the continued development and refinement of software and the underlying theory remains an active area of research.1,2... 

When addressing problems in computational chemistry, the choice of computational scheme depends on the applicability of the method (i.e. the types of atoms and/or molecules, and the type of property, that can be treated satisfactorily) and the size of the system to be investigated. In biochemical applications the method of choice - if we are interested in the dynamics and effects of temperature on an entire protein with, say, 10,000 atoms - will be to run a classical molecular dynamics (MD) simulation. The key problem then becomes that of choosing a relevant force field in which the different atomic interactions are described. If, on the other hand, we are interested in electronic and/or spectroscopic properties or explicit bond breaking and bond formation in an enzymatic active site, we must resort to a quantum chemical methodology in which electrons are treated explicitly. These phenomena are usually highly localized, and thus only involve a small number of chemical groups compared with the complete macromolecule. 

In order to fully exploit the information contained in the X-ray structures, interdisciplinary research is required, involving such disciplines as computational chemistry, medicinal chemistry, and molecular pharmacology in partnership with X-ray crystallography. In this context, the X-ray structures provide an excellent springboard for studying structure-activity/selectivity relationships, as well as the structure-based design of new ligands. 

Finally, one has to concede that gas-phase calculations are not the ideal way to model a reaction taking place on a catalyst surface. Computational chemistry developments in this area have been continuing but they are a long way from providing completely realistic models. For example, the overall kinetics for dehydrocyclizations are likely to be rate-limited by the binding of the alkane substrate to catalytically active sites. 

Kurt Varmuza was bom in 1942 in Vienna, Austria. He studied chemistry at the Vienna University of Technology, Austria, where he wrote his doctoral thesis on mass spectrometry and his habilitation, which was devoted to the field of chemometrics. His research activities include applications of chemometric methods for spectra-structure relationships in mass spectrometry and infrared spectroscopy, for structure-property relationships, and in computer chemistry, archaeometry (especially with the Tyrolean Iceman), chemical engineering, botany, and cosmo chemistry (mission to a comet). Since 1992, he has been working as a professor at the Vienna University of Technology, currently at the Institute of Chemical Engineering. 

Structure-activity relationships X-ray crystallography, nuclear magnetic resonance, computational chemistry... 

Levita J, Nawawi A, Mutalib A, Ibrahim S. (2010) Andrographolide A review of its anti-inflammatory activity via inhibition of NF-kB activation from computational chemistry aspects. Int J Pharmacol 6 569-576. 

Kubinyi, H. (1998) Quantitative structure-activity relationships in drug design. Encyclopedia of computational chemistry, P. von Rague Schleyer (ed.), John Wiley Sons, Chichester, Vol. 3, pp. 2309-2320. 

The complexity and importance of combustion reactions have resulted in active research in computational chemistry. It is now possible to determine reaction rate coefficients from quantum mechanics and statistical mechanics using the ideas of reaction mechanisms as discussed in Chapter 4. These rate coefficient data are then used in large computer programs that calculate reactor performance in complex chain reaction systems. These computations can sometimes be done more economically than to carry out the relevant experiments. This is especially important for reactions that may be dangerous to carry out experimentally, because no one is hurt if a computer program blows up. On the other hand, errors in calculations can lead to inaccurate predictions, which can also be dangerous. 

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