Young D.C. - Computational chemistry (2001)(en)
.pdfA.6 SPECIAL-PURPOSE PROGRAMS 353
Price category: free
Platforms: PC (Windows and Linux), Unix, Macintosh
Contact information: http://www.ccl.net/pub/chemistry/software/UNIX/babel/
A.6.2 CHEOPS
CHEOPS (we tested Version 3.0.1) is a program for predicting polymer properties. It consists of two programs: The analysis program allows the user to draw the repeat unit structure and will then compute a whole list of properties; the synthesis program allows the user to specify a class of polymers and desired properties and will then try the various permutations of the functional groups to ®nd ones that ®t the requirements. On a Pentium Pro 200 system, the analysis computations were essentially instantaneous and the synthesis computations could take up to a few minutes. There was no automated way to transfer information between the two programs.
CHEOPS is based on the method of atomic constants, which uses atom contributions and an anharmonic oscillator model. Unlike other similar programs, this allows the prediction of polymer network and copolymer properties. A list of 39 properties could be computed. These include permeability, solubility, thermodynamic, microscopic, physical and optical properties. It also predicts the temperature dependence of some of the properties. The program supports common organic functionality as well as halides, As, B, P, Pb, S, Si, and Sn. Files can be saved with individual structures or a database of structures.
The program is very easy to use. The help screens give step-by-step directions for various operations, which are complete but somewhat di½cult to read because of poor English grammar. Additional information on the website is more readable. The synthesis program works well, although it is limited to seven classes of polymers.
Price category: departmental, institutional (initial purchase and annual license fee)
Platforms: PC
Contact information: MillionZillion Software 3306 Decatur Lane
Minneapolis, MN 55426 (612) 932-9048
http://www.millionzillion.com/cheops
ward@millionzillion.com
A.6.3 CODESSA
CODESSA (we tested Version 2.6) stands for comprehensive descriptors for structural and statistical analysis. It is a conventional QSAR/QSPR program.
354 APPENDIX A SOFTWARE PACKAGES
CODESSA reads molecular structure ®les or output ®les created by other software packages as the starting point for QSAR analysis. It can import computational results from AMPAC, MOPAC, and Gaussian as well as structures in a number of common formats.
CODESSA can compute or import over 500 molecular descriptors. These can be categorized into constitutional, topological, geometric, electrostatic, quantum chemical, and thermodynamic descriptors. There are automated procedures that will omit missing or bad descriptors. Alternatively, the user can manually de®ne any subset of structures or descriptors to be used.
The program incorporates several very automated procedures for choosing and testing possible QSAR equations. These procedures incorporate correlation and intercorrelation coe½cients to ®nd an equation with the best ®t using a minimal number of descriptors. These automated procedures performed very well when creating an equation to predict normal boiling points using a test set that was constructed by our reviewer. There are both statistical and graphic tools, which also makes this package an excellent choice for experts desiring manual control over the process. The QSAR equations obtained are multilinear.
Price category: production, departmental, institutional
Platforms: PC (Windows and Linux), SGI, RS6000, Alpha, Sun, HP-UX Contact information: Semichem
P.O. Box 1649
Shawnee Mission, KS 66222 (913) 268-3271 http://www.semichem.com/ sales@semichem.com
A.6.4 gNMR
gNMR (we tested Version 4.0.1) is a program for NMR spectral prediction and simulation. The simulation portion of the program draws the spectrum once the user has input the chemical shifts and coupling constants. gNMR can simulate spectra for any active nuclei, but can predict chemical shifts only for 1H and 13C. The computed spectrum can be compared to experimental data. Our review will only cover the prediction features pertinent to the discussion in Chapter 31.
gNMR can predict 1H and 13C chemical shifts and coupling constants for up to 23 active nuclei (increasing to 49 nuclei in Version 4.1). It uses additivity rules to predict chemical shifts. The computation time is negligible even on lowend microcomputers. The computed shifts are put in a tabular format. The user can click on atoms in the structure display in order to jump to the corresponding row of numerical data.
The program was made somewhat less convenient to use by the fact that it does not have a molecule builder. In order to predict chemical shifts, the molecular structure must be built with some other software package and then im-
A.6 SPECIAL-PURPOSE PROGRAMS 355
ported into gNMR. Structures can be imported in formats produced by a number of popular chemical drawing and modeling programs.
Price category: individual, production Platforms: PC
Contact information: Cherwell Scienti®c Publishing The Magdalen Centre
Oxford Science Park Oxford, OX4 4GA UK
‡44 (0)1865 784800 http://gNMR.cherwell.com/ gNMR@cherwell.com
A.6.5 MedChem Explorer
WebLab9 MedChem ExplorerTM (we tested Version 1.6) is a drug re®nement package designed for researchers who do not specialize in computational chemistry. It works as a client±server system so that all functionality is available from a PC. WebLab9 ViewerProTM integrates with MedChem Explorer for molecule building and display. A Web-enabled system is then used to submit the calculations to a server.
The functionality available in MedChem Explorer is broken down into a list of available computational experiments, including activity prediction, align/ pharmacophore, overlay molecules, conformer generation, property calculation, and database access. Within each experiment, the Web system walks the user through a series of questions that must be answered sequentially. The task is then submitted to a remote server, where it is performed. The user can view the progress of the work in their Web browser at any time. Once complete, the results of the calculation are stored on the server. The user can then run subsequent experiments starting with those results. The Web interface includes links to help pages at every step of the process.
Activity prediction is based on a list of models (i.e., QSAR models, pharmacophore models, etc.) that are maintained on the server. There is a second level of access so that only authorized users may be allowed to add or delete model entries.
The align/pharmacophore experiment orients the molecules to obtain maximum similarity in chemical features. This application can then generate a pharmacophore model consistent with all the molecules.
The molecular overlay experiment orients the molecules to ®nd the best RMS or ®eld ®t. The ®eld ®t is based on electrostatic and steric interactions. The application can ®nd either the best total alignment of all molecules or the best match of all molecules to a speci®ed target molecule. Alignment can include a database search for conformers that show the best alignment based on the molecules under study.
356 APPENDIX A SOFTWARE PACKAGES
Conformer generation is used to obtain a list of likely conformers of the molecule. This list can include a set number of the lowest-energy conformers or a number of conformers that give the most diversity of possible shapes.
The property calculation experiment o¨ers a list of 34 molecular properties, including thermodynamic, electrostatic, graph theory, geometric properties, and Lipinski properties. These properties are useful for traditional QSAR activity prediction. Some are computed with MOPAC; others are displayed in the browser without units. A table of computed properties can be exported to a Microsoft Excel spreadsheet.
Database access is used to search external databases for molecules most similar to a speci®ed target molecule. MedChem Explorer o¨ers the following databases: ACD, BioByte, National Cancer Institute, Derwent Drug Index, Maybridge, MDL ISISTM, and Daylight, as well as any in-house or corporate databases that the user may have in any of the ISIS, Catalyst, or Daylight formats. The software is con®gured to link to the in-house informatics environment during installation. The user can search with queries based on shape, topology, substructure, or property information.
Overall, WebLab MedChem Explorer is very easy to use. The stepwise job setup works well, assuming that all users will be following a conventional drug re®nement process. It is not a program that can be used for complex simulations requiring the researcher to manually control many details of the simulation.
Price category: contact Client platforms: PC
Contact information: Molecular Simulations, Inc. 9685 Scranton Road
San Diego, CA 92121-3752 (888) 249-2292 http://www.msi.com/
A.6.6 POLYRATE
POLYRATE (we tested Version 8.0) is a program for computing chemical reaction rates. The MORATE, GAUSSRATE, and AMSOLRATE programs are derived from POLYRATE and designed to work with the MOPAC, GAUSSIAN, and AMSOL programs, respectively.
POLYRATE can be used for computing reaction rates from either the output of electronic structure calculations or using an analytic potential energy surface. If an analytic potential energy surface is used, the user must create subroutines to evaluate the potential energy and its derivatives then relink the program. POLYRATE can be used for unimolecular gas-phase reactions, bimolecular gas-phase reactions, or the reaction of a gas-phase molecule or adsorbed molecule on a solid surface.
The input to POLYRATE is a free-format ASCII ®le. There are a large
A.6 SPECIAL-PURPOSE PROGRAMS 357
number of input keywords, which the user must be familiar with to use all the features, but almost every keyword has a default value that is recommended by the authors. So, if the user is willing to accept the default, it is not necessary to understand all the options. The program output is a well-formatted ASCII ®le.
The reaction-rate calculations available include TST, CVT, ICVT, and mVT. A number of options to account for anharmonicity are available. Semiclassical corrections for tunneling and nonclassical re¯ection can also be included, and in fact the small-curvature and large-curvature multidimensional tunneling corrections available in this program are one of its key features. Dual-level calculations allow for additional corrections to energetics or both energetics and frequencies using levels of theory too time-consuming to apply to the entire potential energy surface.
The documentation is very thorough, although it does assume some familiarity with transition-state theory. New users can expect to spend some time with the manual, which is nearly 500 pages long! A collection of example ®les is also included.
Price category: free
Client platforms: Unix, Linux
Contact information: Benjamin Lynch or Donald G. Truhlar Department of Chemistry
University of Minnesota
207 Pleasant Street SE
Minneapolis, MN 55455 http://comp.chem.umn.edu/polyrate/ lynch@chem.umn.edu
A.6.7 QCPE
QCPE (the Quantum Chemistry Program Exchange) is a repository for programs that have been contributed by many authors. Hundreds of programs are available with source code. There is no acceptance criteria for including a program, so programs range from those that are simplistic or di½cult to use to ones that are very well written and powerful pieces of software. The catalogue is on the Web page listed below and can be searched interactively by opening a telnet session to qcpe6.chem.indiana.edu (using the login ``anonymous'' and then typing ``./Catsrch''). For a small fee, updates listing new software submissions can be received.
Price category: student, individual
Platforms: varies from one program to the next
Contact information: QCPE
358 APPENDIX A SOFTWARE PACKAGES
Creative Arts Bldg. 181 Indiana University Bloomington, IN 47405 (812) 855-5539
http://server.ccl.net/cca/html pages/qcpe/index.shtml qcpe@indiana.edu
A.6.8 SynTree
SynTree (we tested Version 3.0) is a program for ®nding organic synthesis routes. It uses a retrosynthetic algorithm and a database of known reactions. The database of reactions includes 450 reactions typically included in an undergraduate organic curriculum. The algorithm includes the ability to recognize when protective groups are needed. There are utility programs to add additional reactions.
The program is used by ®rst building the target molecule. It then generates a list of possible precursors. The user can choose which precursor to use and then obtain a list of precursors to it. The reaction name and conditions can also be displayed. Once a satisfactory synthesis route is found, it can be printed without all the other possible precursors included. The drawing mode worked well and the documentation was well written.
This program is marketed as an exploratory tool for undergraduate organic chemistry students. As an educational tool, it is well designed. The program, as is, might also serve as a reminder of possible options for synthetic chemists. It could also be useful to the research community if more reactions are included in future versions.
Price category: student, individual Platforms: PC, Macintosh
Contact information: Trinity Software, Inc. 607 Tenney Mountain Hwy.
Suite 215
Plymouth, NH 03264 (800) 352-1282
http://www.trinitysoftware.com/
trsoft@lr.net
BIBLIOGRAPHY
Other listings of chemistry software packages are
D. B. Boyd, Rev. Comput. Chem. 11, 373 (1997).
BIBLIOGRAPHY 359
Computational Thermochemistry K. K. Irikura, D. J. Frurip, Eds., Appendix A., American Chemical Society, Washington (1998).
Encyclopedia of Computational Chemistry John Wiley & Sons, New York (1998). Some software packages are mentioned in sequence in this encyclopedia and others are collected at the end of volume 5.
http://server.ccl.net/
http://www.chamotlabs.com/cl/Freebies/Software.html
http://nhse.npac.syr.edu:8015/rib/repositories/csir/catalog/index.html J. P. Bays, J. Chem. Ed. 69, 209 (1992).
Reviews of individual packages are sometimes published in Journal of Computational Chemistry.
Software can be purchased directly from the company that makes it or through catalogues, such as the following. Some of these have paper catalogues as well as web stores.
http://genamics.com/software/
http://www.ChemStore.com/
http://www.chemsw.com/
http://www.falconsoftware.com/
http://www.biosoft.com/
http://www.trinitysoftware.com/
http://chemweb.com/
http://www.claessen.net/chemistry/soft en.html
http://www.sciquest.com/
Computational Chemistry: A Practical Guide for Applying Techniques to Real-World Problems. David C. Young Copyright ( 2001 John Wiley & Sons, Inc.
ISBNs: 0-471-33368-9 (Hardback); 0-471-22065-5 (Electronic)
Glossary
The following are de®nitions of terms relevant to computational chemistry. These de®nitions are based on common usage in this ®eld. They do not necessarily re¯ect the dictionary de®nitions or those in other branches of science.
mVT (microcanonical variational theory) a variational transition state theory technique
ab initio a calculation that may use mathematical approximations, but does not utilize any experimental chemical data either in the calculation or the original creation of the method
accuracy how close a computed value is to the experimental value
adiabatic process a chemical process in which the system does not make a transition from one electronic state to another
Ahhrenius equation mathematical equation for predicting reaction rate constants
AI (arti®cial intelligence) computer algorithms that mimic some aspects of how people think
AIM (atoms in molecules) a population analysis technique AM1 (Austin model 1) a semiempirical method
AMBER (assisted model building with energy re®nement) a molecular mechanics force ®eld
amu (atomic mass unit) atomic unit of mass
ANO (atomic natural orbital) a way of deriving basis functions antisymmetric function a function that only changes sign when the identities of
two electrons are switched
approximation a numerical estimation of a solution to a mathematical problem
APW (augmented plane wave) a band structure computation method atomic mass unit (amu) atomic unit of mass
atomic units a system of units convenient for formulating theoretical derivations with a minimum number of constants in the equations
B3LYP (Becke 3 term, Lee Yang, Parr) a hybrid DFT method basis set a set of functions used to describe a wave function B96 (Becke 1996) a gradient corrected DFT method
360
GLOSSARY 361
band structure the electronic structure of a crystalline solid beads individual units in a mesoscale simulation
BLYP (Becke, Lee, Yang, Parr) a gradient corrected DFT method Bohr atomic unit of length
Boltzmann distribution statistical distribution of how many systems will be in various energy states when the system is at a given temperature
Born±Oppenheimer approximation assumption that the motion of electrons is independent of the motion of nuclei
boson a fundamental particle with an integer spin
BSSE (basis set superposition error) an error introduced when using an incomplete basis set
CAOS (computer aided organic synthesis) a program for predicting a synthesis route
Cartesian coordinates system for locating points in space based on three coordinates, which are usually given the symbols x, y, z or i, j, k
CBS (complete basis set) an ab initio method
CC (coupled cluster) a correlated ab initio method
CFF (consistent force ®eld) a class of molecular mechanics force ®elds CFMM (continuous fast multipole method) a method for fast DFT calcula-
tions on large molecules
CHAIN a relaxation method for obtaining reaction paths from semiempirical calculations
charge density (electron density, number density) number of electrons per unit volume at a point in space
CHARMM (chemistry at Harvard macromolecular mechanics) a molecular mechanics force ®eld
CHEAT (carbohydrate hydroxyls represented by external atoms) a molecular mechanics force ®eld
CHelp an electrostatic charge calculation method CHelpG an electrostatic charge calculation method
CI (con®guration interaction) a correlated ab initio method
CNDO (complete neglect of di¨erential overlap) a semiempirical method computational chemistry computer-automated means for predicting chemistry con®guration interaction (CI) a correlated ab initio method
conventional integral evaluation algorithm that stores integrals in a ®le convergence criteria for completion of a self-consistent ®eld calculation convex hull a molecular surface that is determined by running a planar probe
over a molecule
COOP (crystal orbital overlap population) a plot analogous to population analysis for band-structure calculations
362 GLOSSARY
correlation name for the statement that there is a higher probability of ®nding electrons far apart than close to one another, which is re¯ected by some but not all ab initio calculations
COSMO (conductor-like screening model) a method for including solvation e¨ects in orbital-based calculations
Coulomb's law the statement that like charges repel and unlike charges attract along with the equations for predicting the magnitude of those interactions
coupled cluster (CC) a correlated ab initio method
CPHF (coupled perturbed Hartree±Fock) ab initio method used for computing nonlinear optical properties
CPU (central processing unit) the part of a computer that does mathematical and logical operations.
CVT (canonical variational theory) a variational transition state theory technique
Davidson±Fletcher±Powell (DFP) a geometry optimization algorithm
De Novo algorithms algorithms that apply arti®cial intelligence or rational techniques to solving chemical problems
density functional theory (DFT) a computational method based on the total electron density
determinant a mathematical procedure for converting a matrix into a function or number
DFP (Davidson±Fletcher±Powell) a geometry optimization algorithm
DFT (density functional theory) a computational method based on the total electron density
DHF (Dirac±Hartree±Fock) relativistic ab initio method
DHF (derivative Hartree±Fock) a means for calculating nonlinear optical properties
diabatic process (nonadiabatic) a process in which the lowest-energy path is followed, even if it is necessary to change from one electronic state to another
di¨use functions basis functions that describe the wave function far from the nucleus
DIIS (direct inversion of the iterative subspace) algorithm used to improve SCF convergence
DIM (diatomics-in-molecules) a semiempirical method used for representing potential energy surfaces
Dirac equation one-electron relativistic quantum mechanics formulation direct integral evaluation algorithm that recomputes integrals when needed distance geometry an optimization algorithm in which some distances are held
®xed
DM (direct minimization) an algorithm for forcing SCF calculations to converge