Simulation software, Chemistry

The GEMM software on the ST-100 is not a stand-alone package, and it requires a front-end simulation software package that runs on the host to provide data and to send command requests. It was designed and written with CHARMM (Chemistry at HARvard Macro-molecular Mechanics) (14) as the primary front-end, but additional software packages, such as AMBER (15), have subsequently been modified to drive GEMM. 

Chemical kinetics studies as practiced in industry are far more complex than the smattering of examples presented in typical undergraduate physical chemistry courses. The few hours we spend in typical physical chemistry courses do not include the more complex and more interesting examples in the literature because of the level of mathematics required. However, students can be introduced to more complex processes through the use of simulation software which is available via the WWW (40). Most important is that students develop an appreciation of what a mechanism is and what steps are taken to develop a mechanism for a new chemical reaction. Carefully designed simulations can help students develop these skills as reported by Houle (41). 

The dictionary defines simulation as the representation of the behavior or characteristics of one system through the use of another system (/). The use of simulations in chemistry is prevalent enough to have been the subject of educational research (2-5). In a lot of the corresponding software, the objects being represented are the chemicals and pieces of equipment of an actual laboratory or, equally common, cartoon-style abstractions of chemical concepts. Students thus get to manipulate simulated glassware, prepare solutions by dragging icons, or shuffle electrons to satisfy the rules of quantum mechanics. In software for beginners, they may on occasion even cause fake explosions. 

Profile Founded in 1984, this privately held company provides molecular modeling and simulation software for both life and materials science research. The company employs more than 280 people (approximately half of whom are Ph.D. scientists) it operates sales offices around the world and a research and development facility in Cambridge, England. MSI s Combinatorial Chemistry Consortium addresses the full scope of the combinatorial chemistry process and is focused on maximizing the productivity of library design and analysis. In February 1998, Molecular Simulations Inc. and Pharmacopeia Inc. announced a definitive agreement whereby Pharmacopeia will acquire all of the outstanding stock of MSI. The transaction is expected to be completed in the second quarter of 1998 upon completion MSI will become a wholly owned subsidiary. 

The last chapter differs from the rest of the book. Here we present a collection of case histories , in which we discuss examples from the chemistry research literature on what has been learned about chemical structures using all appropriate physical and computational methods. It draws on what has been derived and explained in Chapters 2-11, but from the point of view of the chemist who has a compound and wants to know as much as possible about it rather than that of someone with a particular instrument or simulation software... 

Optimal isocratic and/or gradient conditions are predicted by computer optimization software by retention time and peak width modeling, e.g., with DryLab (LC Resources, BASi Northwest Laboratory Services, Walnut Creek, CA, USA), LC Simulator (Advanced Chemistry Development, Toronto, Canada), or ChromSword (VWR International, Darmstadt, Germany). 

Thus, in the area of combinatorial chemistry, many compounds are produced in short time ranges, and their structures have to be confirmed by analytical methods. A high degree of automation is required, which has fueled the development of software that can predict NMR spectra starting from the chemical structure, and that calculates measures of similarity between simulated and experimental spectra. These tools are obviously also of great importance to chemists working with just a few compounds at a time, using NMR spectroscopy for structure confirmation. 

There has been a phenomenal growth of interest in theoretical simulations over the past decade. The concomitant advances made in computing power and software development have changed the way that computational chemistry research is undertaken. No longer is it the exclusive realm of specialized theoreticians and supercomputers rather, computational chemistry is now accessible via user-friendly programs on moderately priced workstations. State-of-the-art calculations on the fastest, massively parallel machines are continually enlarging the scope of what is possible with these methods. These reasons, coupled with the continuing importance of solid acid catalysis within the world s petrochemical and petroleum industries, make it timely to review recent work on the theoretical study of zeolite catalysis. 

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