Software package

The software packages used lo solve CRE problems in the lext and on ihe DVD-ROM are Polymath. AspenTech and COM SOL. 

Currently there are numerous software packages that perform the ab initio or DFT calculations introduced in this section. Most of these programs are available commercially, but there are a few distributed to the scientific community free of charge. Some popular programs are briefly described below, and the list is by no means exhaustive. 

Atkins and R. S. Friedman, Molecular Quantum Mechanics, 3rdedn., Oxford University Press, Oxford, 1997. 

Ratner and G. C. Schatz, Introduction to Quantum Mechanics in Chemistry, Prentice-Hall, Upper Saddle River, NJ, 2001. 

Principles of Quantum Mechanics As Applied to Chemistry and Chemical Physics, Cambridge University Press, Cambridge, 1999. 

Simons and J. Nicholls, Quantum Mechanics in Chemistry, Oxford University Press, New York, 1997. 

Bias Difference between the average (strictly the expectation) of the test results and an accepted reference value (ISO 3534-1). 

Certified Reference Material (CRM) is a reference material, one or more of whose property values are certified by a technically valid procedure, accompanied by or traceable to a certificate or other documentation that is issued by a certifying body. 

Commutability Ability of a material to yield the same results of measurements by a given set of measurement procedures. 

Limit of Detection The lowest amount of analyte in a sample that can be detected but not quantified as an exact value. Also called lower limit of detection, minimum detectable concentration (or dose or value).  

Mati ix AH components of a material system, except the analyte. Measurand The quantity that is actually measured (e.g., the concentration of the analyte). For example, if the analyte is glucose, the measurand is the concentration of glucose. For an enzyme, the measurand may be the enzyme activity or the mass concentration of enzyme. 

---

Saboo, A. K., Morari, M., and Colberg, R. D., RESHEX An Interactive Software Package for the Synthesis and Analysis of Resilient Heat Exchanger Networks II. Discussion of Area Targeting and Network Synthesis Algorithms, Computers Chem. Eng., 10 591, 1986. 

This is the method used by the commercial software packages Crystal Ball and RISK . The method is ideally suited to computers as the description of the method will reveal. Suppose we are trying to combine two independent variables, say gross reservoir thickness and net-to-gross ratio (the ratio of the net sand thickness to the gross thickness of the reservoir section) which need to be multiplied to produce a net sand thickness. We have described the two variables as follows ... 

D-CT dataset of power saw cabinet in reverse engineering software package (STL format)... 

RADView workstation software package user manual... 

The CAChe software packages from Oxford Molecular webpage http //www.oxmol.com/aetinfo/eduf... 

Early implementations of the CIP rules for computer detection and specification of chirality were described for the LHASA [105], CHIRON [106], and CACTVS [107] software packages. Recently, several commercial molecular editors and visualizers (e.g., CambridgeSoft s ChemOffice, ACD s I-Lab, Accelrys WebLab, and MDL s AutoNom) have also implemented the CIP rules. 

ChemSketch is a professional software package that is available free of charge from Advanced Chemistry Development Inc. (ACD). Besides the editor, it has several modules (ACD/Dictionary, ACD/Tautomers), extensions, and add-ins concerning the calculation of physicochemical properties, input of spectra and chromatograms, naming of molecules, and a viewer. 

Similarity is often used as a general term to encompass either similarity or dissimilarity or both (see Section 6.4.3, on similarity measures, below). The terms "proximity" and distance are used in statistical software packages, but have not gained wide acceptance in the chemical literature. Similarity and dissimilarity can in principle lead to different rankings. 

A force field does not consist only of a mathematical eiqjression that describes the energy of a molecule with respect to the atomic coordinates. The second integral part is the parameter set itself. Two different force fields may share the same functional form, but use a completely different parameterization. On the other hand, different functional forms may lead to almost the same results, depending on the parameters. This comparison shows that force fields are empirical there is no "correct form. Because some functional forms give better results than others, most of the implementations within the various available software packages (academic and commercial) are very similar. 

Variations of these releases are implemented in almost every commercial or academic software package, which cannot be fisted in this context. A comprehensive comparison of several force fields focusing the calculation of conformational energies of organic molecules has been published by Pettersson and liljefors [1]. 

The authors emphasize on their web pages that UFF is not designed to be used in conjunction with partial atomic charges, as it is the default option in several software packages. A second point is that UFF is often used to model biological... 

Modifications of the various versions of the AMBER parameter sets are implemented in numerous commercial and academic software packages. They are often referred to as AMBER. In every case, the user should read the documentation provided critically, and check the implementation by comparing the results of the implementation with original data. 

The chirality code of a molecule is based on atomic properties and on the 3D structure. Examples of atomic properties arc partial atomic charges and polarizabilities, which are easily accessible by fast empirical methods contained in the PETRA package. Other atomic properties, calculated by other methods, can in principle be used. It is convenient, however, if the chosen atomic property discriminates as much as possible between non-equivalent atoms. 3D molecular structures are easily generated by the GORINA software package (see Section 2.13), but other sources of 3D structures can be used as well. 

A number of other software packages are available to predict NMR spectra. The use of large NMR spectral databases is the most popular approach it utilizes assigned chemical structures. In an advanced approach, parameters such as solvent information can be used to refine the accuracy of the prediction. A typical application works with tables of experimental chemical shifts from experimental NMR spectra. Each shift value is assigned to a specific structural fragment. The query structure is dissected into fragments that are compared with the fragments in the database. For each coincidence, the experimental chemical shift from the database is used to compose the final set of chemical shifts for the... 

Inc, [34], is an example of a software package that can calculate 3D geometries, chemical shifts, and coupling constants using semi-empirical approaches (Figure 10.2-2). 

CIS calculations from the semiempirical wave function can be used for computing electronic excited states. Some software packages allow Cl calculations other than CIS to be performed from the semiempirical reference space. This is a good technique for modeling compounds that are not described properly by a single-determinant wave function (see Chapter 26). Semiempirical Cl... 

Most researchers do not parameterize force fields because many good force fields have already been developed. On rare occasions, a researcher will add an additional atom as described in Chapter 29. The following are some commonly used molecular mechanics force fields. Many of these have been implemented in more than one software package. There tend to be minor differences in the implementation leading to small differences in results from one software package to another. 

Molecular mechanics calculations are deceptively simple to perform. Many software packages now make molecular mechanics as easy as specifying a molecular structure and saying go, at which point the calculation will run and very soon give a result. The dilhculty is in knowing which results to trust. 

The disadvantage of molecular mechanics is that there are many chemical properties that are not even defined within the method, such as electronic excited states. Since chemical bonding tenns are explicitly included in the force field, it is not possible without some sort of mathematical manipulation to examine reactions in which bonds are formed or broken. In order to work with extremely large and complicated systems, molecular mechanics software packages often have powerful and easy-to-use graphic interfaces. Because of this, mechanics is sometimes used because it is an easy, but not necessarily a good, way to describe a system. 

An older, but still used, notation specihes how many contractions are present. For example, the acronym TZV stands for triple-zeta valence, meaning that there are three valence contractions, such as in a 6—311G basis. The acronyms SZ and DZ stand for single zeta and double zeta, respectively. A P in this notation indicates the use of polarization functions. Since this notation has been used for describing a number of basis sets, the name of the set creator is usually included in the basis set name (i.e., Ahlrichs VDZ). If the author s name is not included, either the Dunning-Hay set is implied or the set that came with the software package being used is implied. 

In spite of its deficiencies, the Mulliken population scheme is very popular. One reason is that it is very easy to implement so it is available in many software packages. Probably the most important reason for its popularity is the fact... 

There is some ambiguity about Mulliken population analysis in the literature. This is because various software packages print different portions of the analysis and may name them slightly differently. The description here follows some of the more common conventions. 

The Lowdin population analysis scheme was created to circumvent some of the unreasonable orbital populations predicted by the Mulliken scheme, which it does. It is different in that the atomic orbitals are first transformed into an orthogonal set, and the molecular orbital coefficients are transformed to give the representation of the wave function in this new basis. This is less often used since it requires more computational work to complete the orthogonalization and has been incorporated into fewer software packages. The results are still basis-set-dependent. 

This results in a population analysis scheme that is less basis set dependent than the Mulliken scheme. Flowever, basis set effects are still readily apparent. This is also a popular technique because it is available in many software packages and researchers find it convenient to use a method that classifies the type of orbital. 

---