Computer Software for Chemistry

CambridgeSoft at http //www.cambridgesoft.com/products offers a variety of tools including the software suite, ChemOffice . The combination package consists of ChemDraw , Chem3D , and ChemFinder . Every undergraduate 

ChemDraw Ultra 7.0, Chem3D Ultra 7.0, and ChemFinder Pro 7.0 became available in 2002. E-Notebook Ultra 7.0, BioAssay Pro 7.0, MOPAC, Gaussian GAMESS interfaces, ChemSAR Server Excel, CLogP, Purchasing for Excel, CombiChem/Excel, as well as the full set of Chemlnfo databases, including ChemACX ChemACX-SC, The Merck Index and ChemMSDX have been added to ChemOffice Pro. 

Ab-initio CAChe features all of the above plus ab-initio and density functional methods. This program requires a workstation (Windows NT minimum or SGI and IBM unix-based machines) and can be used to build and visualize results from ab-initio programs (e.g., Gaussian, see description under Gaussian, Inc.). Also, CAChe directly interfaces to Dgauss , a computational chemistry package that uses density functional theory to predict molecular structures, properties, and energetics. 

CAChe 5.0, available in 2002, includes a new, more powerful, semiempirical method that uses the PM5 Hamiltonian, a MOPAC 2002 offering, modeling of molecules with up to 20,000 atoms, the inclusion of all main group elements in one semiempirical method, and using MOPAC AMl-d, supports the transition metals Pt, Fe, Cu, Ag, Mo, V, and Pd. Researchers can now import and display, in 3D, proteins from the Protein Data Bank (PDB), optimize proteins, dock ligands, and model reactions on protein molecules. 

Gaussian 98M , available in 2002, is an implementation of the Gaussian 98 electronic structure modeling program for the Mac OS X environment. It models a broad range of molecular systems under a variety of conditions, and performs its computations starting from the basic laws of quantum mechanics. 

Hypercube, Inc. at http //www.hyper.com offers molecular modeling packages under the HyperChem name. HyperChem s newest version, Hyper-Chem Release 7.5, is a full 32-bit application, developed for the Windows 95, 98, NT, ME, 2000, and XP operating systems. Density Functional Theory (DFT) has been added as a basic computational engine to complement Molecular Mechanics, Semiempirical Quantum Mechanics and ab initio Quantum Mechanics. The DFT engine includes four combination or hybrid functions, such as the popular B3-LYP or Becke-97 methods. The Bio+ force field in HyperChem represents a version of the Chemistry at HARvard using Molecular Mechanics (CHARMM) force field. Release 7.5 of HyperChem updates 

Unix workstation platform user, visualizes results that can be displayed across many computer platforms including Macintosh and Windows. 

SemiChem products are available at http //www.semichem.com. AMPAC , available as a stand-alone product with Windows-based and workstation level interfaces, is a semiempirical quantum mechanical program featuring SAMI, AMI, MNDO, MNDO/d, PM3, MNDO/C, MINDO/3 semiempirical methods. AMPAC also includes a graphical user interface (GUI) that builds molecules and offers full visualization of results. The SYBYL/Base program offered by Tripos, Inc. (products described below) provides an interface with interactive graphing and structural display tools that can be used to access AMPAC s calculation tools. 

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Most chemists want to avoid the paper-and-pencil type of work that theoretical chemistry in its truest form entails. However, keep in mind that it is precisely for this kind of painstaking and exacting research that many Nobel prizes have been awarded. This book will focus almost exclusively on the knowledge needed to effectively use existing computer software for molecular modeling. 

In a modern laboratory, automated computer software for data acquisition and processing performs most of data reduction. Raw data for organic compound and trace element analyses comprise standardized calibration and quantitation reports from various instruments, mass spectra, and chromatograms. Laboratory data reduction for these instrumental analytical methods is computerized. Contrary to instrumental analyses, most general chemistry analyses and sample preparation methods are not sufficiently automated, and their data are recorded and reduced manually in laboratory notebooks and bench sheets. The SOP for every analytical method performed by the laboratory should contain a section that details calculations used in the method s data reduction. 

V. Khavryutchenko, CLUSTER-Zl COSPECO, Personal Computer Software for Quantum Chemistry and Computation Vibration Spectroscopy, Computation Chemistry Group, Kiev, Ukraine, 1990-1998. 

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... 

Computational chemistry and quantum chemistry have enlisted the computer and software in an entirely new kind of experimental methodology. Computational chemists, for example, don t study matter directly. In the past, chemists who wanted to determine molecular properties chose their instrumentation, prepared a sample, observed the reactions of the sample, and deduced the molecule s properties. Computational chemists now choose their computer and software packages and get their information by modeling and mathematical analyses. 

Many other approaches for finding a correct structural model are possible. A short description of ab-initio, density functional, and semiempirical methods are included here. This information has been summarized from the paperback book Chemistry with Computation An Introduction to Spartan. The Spartan program is described in the Computer Software section below.65 Another description of computational chemistry including more mathematical treatments of quantum mechanical, molecular mechanical, and statistical mechanical methods is found in the Oxford Chemistry Primers volume Computational Chemistry,52... 

From the above it is obvious that a systems designer for laboratory automation must be conversant with and able to utilize a whole range of disciplines, from chemistry to electronics, and from computer software to statistics and instrument design. The users of the automation, their managers and the customer for the analytical results also have a contribution to make in deciding the spedflcation. 

The use of computational chemistry to address issues relative to process design was discussed in an article. The need for efficient software for massively parallel architectures was described. Methods to predict the electronic structure of molecules are described for the molecular orbital and density functional theory approaches. Two examples of electronic stracture calculations are given. The first shows that one can now make extremely accurate predictions of the thermochemistry of small molecules if one carefully considers all of the details such as zero-point energies, core-valence corrections, and relativistic corrections. The second example shows how more approximate computational methods, still based on high level electronic structure calculations, can be used to address a complex waste processing problem at a nuclear production facility (Dixon and Feller, 1999). 

Computational chemistry is essential in a modem physical chemistry course. One approach would be to use laboratory time to have students work through a number of exercises accompanied by elaboration of the concepts in lecture or pre-laboratory discussions. Each of die major computational chemistry software packages come with workbooks or tutorials for learning the software. For example, students can learn by completing exercises in the Spartan tutorials (57). Similar approaches can be taken when using Gaussian (38) and Hyperchem (39) tutorial or exercise collections. 

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