Young D.C. 2001 Computational chemistry a practical guide for applying techniques to real-world problems

BIBLIOGRAPHY 317

A review of semiempirical calculation applied to polymers is

J. J. P. Stewart, Encycl. Comput. Chem. 3, 2130 (1998).

Reviews of the statistical mechanical aspects of the problem are

K. W. Foreman, K. F. Freed, Adv. Chem. Phys. 103, 335 (1998).

S. G. Whittington, Adv. Chem. Phys. 51, 1 (1982).

H. Yamakawa, Ann. Rev. Phys. Chem. 25, 179 (1974).

K. F. Freed, Adv. Chem. Phys. 22, 1 (1972).

41.7 RECOMMENDATIONS 319

41.3BAND STRUCTURES

As described in the chapter on band structures, these calculations reproduce the electronic structure of in®nite solids. This is important for a number of types of studies, such as modeling compounds for use in solar cells, in which it is important to know whether the band gap is a direct or indirect gap. Band structure calculations are ideal for modeling an in®nite regular crystal, but not for modeling surface chemistry or defect sites.

41.4DEFECT CALCULATIONS

The chemistry of interest is often not merely the in®nite crystal, but rather how some other species will interact with that crystal. As such, it is necessary to model a system that is an in®nite crystal except for a particular site where something is di¨erent. The same techniques for doing this can be used, regardless of whether it refers to a defect within the crystal or something binding to the surface. The most common technique is a Mott±Littleton defect calculation. This technique embeds a defect in an in®nite crystal, which can be considered a local perturbation to the band structure.

41.5MOLECULAR DYNAMICS AND MONTE CARLO METHODS

Molecular mechanics methods have been used particularly for simulating surface±liquid interactions. Molecular mechanics calculations are called e¨ective potential function calculations in the solid-state literature. Monte Carlo methods are useful for determining what orientation the solvent will take near a surface. Molecular dynamics can be used to model surface reactions and adsorption if the force ®eld is parameterized correctly.

41.6AMORPHOUS MATERIALS

The modeling of amorphous solids is a more di½cult problem. This is because there is no rigorous way to determine the structure of an amorphous compound or even de®ne when it has been found. There are algorithms for building up a structure that has various hybridizations and size rings according to some statistical distribution. Such calculations cannot be made more e½cient by the use of symmetry.

41.7RECOMMENDATIONS

Overall, solid-state modeling requires more time on the part of the researcher and often more CPU-intensive calculations. Researchers are advised to plan on

Cluster calculations are reviewed in

D. Michael, P. Mingos, Chem. Soc. Rev. 15, 31 (1986).

Electric double layer modeling is reviewed in

R. Parsons, Chem. Rev. 90, 813 (1990).

The application of molecular mechanics methods is reviewed in

A. M. Stoneham, J. H. Harding, Ann. Rev. Phys. Chem. 37, 53 (1986).

A review of methods for predicting properties of solids and surfaces is

E. Wimmer, Encycl. Comput. Chem. 3, 1559 (1998).

Reactions and dynamics at surfaces are reviewed in

D. G. Musaev, K. Morokuma, Adv. Chem. Phys. 95, 61 (1996). W. Schmickler, Chem. Rev. 96, 3177 (1996).

B. J. Garrison, P. B. Skodali, D. Srivastava, Chem. Rev. 96, 1327 (1996). B. J. Garrison, D. Srivastava, Ann. Rev. Phys. Chem. 46, 373 (1995).

B. J. Garrison, Chem. Soc. Rev. 21, 155 (1992).

J. W. Gadzuk, Ann. Rev. Phys. Chem. 39, 395 (1988). R. B. Gerber, Chem. Rev. 87, 29 (1987).

T. F. George, K.-T. Lee, W. C. Murphy, M. Hutchinson, H.-W. Lee, Theory of Chemical Reaction Dynamics Volume IV M. Baer, Ed., 139, CRC, Boca Ratan (1985).

Semiempirical modeling is reviewed in

F.Ruette, A. J. HernaÂndez, Computational Chemistry: Structure, Interactions, Reactivity Part B S. Fraga, Ed., 637, Elsevier, Amsterdam (1992).

Predicting the structure of crystalline solids is reviewed in

P. Verwer, Rev. Comput. Chem. 12, 327 (1998).

B. P. van Eijck, Encycl. Comput. Chem. 1, 636 (1998).

J. K. Burdett, Adv. Chem. Phys. 49, 47 (1982).

T. Kihara, A. Koide, Adv. Chem. Phys. 33, 51 (1975).

Solid vibrations and dynamics are reviewed in

M. J. Klein, L. J. Lewis, Chem. Rev. 90, 459 (1990).

W. J. Briels, A. P. J. Janson, A. van Der Avoird, Adv. Quantum Chem. 18, 131 (1986). O. Schnepp, N. Jacobi, Adv. Chem. Phys. 22, 205 (1972).

A.1.1 Alchemy

Alchemy 2000 (we tested Version 2.05) is a graphic interface for running molecular mechanics and semiempirical calculations. Calculations can be done with the built-in Tripos force ®eld or by calling the MM3 or MOPAC programs, which are included with the package. Alchemy is designed by Tripos and sold by SciVision.

Molecules can be built using a two-dimensional sketch mode and are then converted to three-dimensional geometries by the program. It is also possible to build molecules in the three-dimensional mode. Libraries of organic functional groups are available. There is also a protein builder. The user can change the stereochemistry and conformational angles. Conformations are set by allowing the program to slowly change the conformation until the user tells it to stop. The builders can be used to create any organic structure; however, the author did not ®nd it as convenient to work with as some other graphic builders. The screen for setting up external MOPAC jobs was convenient to work with.

The program is able to do systematic or random conformation searches using the Tripos force ®eld. Conformation searches can include up to eight single bonds and two rings.

Output data can be printed or exported to a spreadsheet. The rendering quality is very good. Structures can be rendered and labeled in several di¨erent ways. Molecular structures can be saved in several di¨erent formats or as image ®les. The presentation mode allows molecular structures to be combined with text.

The program allows the user to create a database of structures. Calculations can then be run on the whole set of structures. These databases may also be used by some separately sold software packages.

There are a number of separately sold programs designed to interface to Alchemy. SciQSAR is a linear-regression-based QSAR program that interfaces to Alchemy and Chem3D. SciLogP interfaces with Alchemy and Chem3D to predict water±octanol partition coe½cients using linear regression and neural networks. SciPolymer interfaces to Alchemy and computes 44 di¨erent polymer properties, which include physical properties, electrical properties, optical properties, thermodynamic properties, magnetic properties, gas permeabilities, solubility, and microscopic properties.

324 APPENDIX A SOFTWARE PACKAGES

Price category: production Platforms: PC

Contact information: SciVision 128 Spring St.

Lexington, MA 02173 (781) 272-4949 http://www.scivision.com/ sales@scivision.com

A.1.2 Chem3D

Chem3D (we tested Version 5.0 Ultra) is a molecular modeling package for the PC and Macintosh. It can perform calculations using MM2 and extended HuÈckel as well as acting as a graphic interface for MOPAC (included) or Gaussian (sold separately). There are also browser plug-ins available for viewing structures and surfaces.

Chem3D can read a wide variety of popular chemical structure ®les, including Gaussian, MacroModel, MDL, MOPAC, PDB, and SYBYL. Two-dimensional structures imported from ChemDraw or ISIS/Draw are automatically converted to three-dimensional structures. The Chem3D native ®le format contains both the molecular structure and results of computations. Data can be exported in a variety of chemical-structure formats and graphics ®les.

Chem3D has both graphic and text-based structure-building modes. Structures can be generated graphically by sketching out the molecule. The builder creates carbon atoms, which can be edited by typing text to substitute other elements or functional groups. As the structure is built, the valence is ®lled with hydrogen atoms and typical bond lengths and angles are set. Several hundred prede®ned functional groups are available and users can de®ne additional ones. The text-based mode allows the user to input a simple text string (similar to SMILES, but not identical). This text mode can be used to build structures entirely or to add functional groups.

A number of mechanisms are available for manually de®ning aspects of the molecular geometry. These include de®ning dummy atoms as well as setting bond lengths, angles, and dihedral angles. It is also possible to set distances between nonbonded atoms. The molecular structure is maintained internally in both Cartesian coordinates and a Z-matrix. A number of functions for de®ning how the Z-matrix is constructed make this one of the best GUIs available for setting up calculations that must be done by Z-matrix.

Chem3D uses a MM2 force ®eld that has been extended to cover the full periodic table with the exception of the f block elements. Unknown parameters will be estimated by the program and a message generated to inform the user of this. MM2 can be used for both energy minimization and molecular dynamics calculations. The user can add custom atom types or alter the parameters used

for one speci®c atom in the calculation. Extended HuÈckel may be used for the calculation of charges and molecular surfaces.

Chem3D comes with an implementation of MOPAC 97. The computation setup includes a number of screens in which to select the level of theory, type of calculation, and properties. Menu picks are available for commonly used functions, such as geometry optimization, transition structure optimization, dipole moments, population analysis, COSMO solvation, hyper®ne coupling constants, and polarizability. Molecular surfaces can be displayed for electron density, spin density, electrostatic potential, and molecular orbitals. Surfaces can be generated using the shape from one property and the colorization from another. This allows property mapping of solvent-accessible surfaces such as by charges or hydrophobicity. Users can also type in additional route card options. Although menu picks are available for the most frequently used options, one notable exception is the lack of a way to graphically display normal vibrational mode motion or displacement vectors. The interface to Gaussian 98W is similar to the MOPAC interface.

While a calculation is running, the Chem3D interface must be operational. The structure for the running calculation cannot be edited. However, other structures can be built while one is calculating. If multiple MM2 jobs are executed simultaneously, they will be automatically queued and run sequentially. The Macintosh version supports Apple Events, making it possible to write scripts to automate tasks. The PC version is an OLE automation server, making it possible to call Chem3D from other programs (i.e., Visual Basic programs).

A number of properties can be computed from various chemical descriptors. These include physical properties, such as surface area, volume, molecular weight, ovality, and moments of inertia. Chemical properties available include boiling point, melting point, critical variables, Henry's law constant, heat capacity, log P, refractivity, and solubility.

Several display modes are available. Molecules can be displayed as wire frames (lines), sticks (wider lines), ball and stick models (with line or cylindrical bonds), and as space-®lling models. Protein structures can be displayed as ribbons. Dot surfaces of van der Waals radii or extended HuÈckel charges may be added to any of these. In the PC version, a couple of the display modes rendered the molecule, with the lines depicting bonds not quite connecting to the spheres depicting atoms. When molecular surfaces from extended HuÈckel, MOPAC, or Gaussian calculations are displayed, a di¨erent set of rendering algorithms with improved three-dimensional shading is used. These surfaces can be displayed as solid, mesh, dots, or translucent surfaces. The graphics quality in this display mode is very good with the exception of the translucent surface algorithm, which came out looking dithered on our test platforms. Movies can be created from operations generating multiple structures, such as molecular dynamics simulations. These movies can be viewed within Chem3D, but cannot be saved in a common movie ®le format.

Several versions of Chem3D are available; they di¨er in price and functionality. These are denoted as Ltd, Std, Pro, and Ultra. Some points of di¨erence in

326 APPENDIX A SOFTWARE PACKAGES

functionality are molecular surface generation, molecular dynamics, MOPAC support, and Gaussian support. There are only a few di¨erences in functionality between the Macintosh and PC versions. This review was written just prior to the release of a new version of Chem3D, which is slated to have support for GAMESS and a new SAR component that includes descriptors from MM2, MOPAC, and GAMESS.

Price category: student, individual, production Platforms: PC (Windows), Macintosh Contact information: CambridgeSoft

100 Cambridge Park Drive Cambridge, MA 02140 (617) 588-9300 http://www.camsoft.com/ info@camsoft.com

A.1.3 ChemSketch and the ACD Software Suite

ChemSketch (we tested Version 4.01) is a graphic interface that can be used as the front end for a host of programs sold by Advanced Chemistry Development. Both free and commercial versions are available. It is a two-dimensional structure drawing program primarily designed for organic molecules. Although the drawing mode is essentially a two-dimensional drawing routine, it is also possible to rotate the molecule in three dimensions. The program automatically keeps track of the number of hydrogens bonded to each atom. The reviewer felt that the molecule sketch mode was convenient to use. The documentation is well written and includes many examples.

ChemSketch has some special-purpose building functions. The peptide builder creates a line structure from the protein sequence de®ned with the typical three-letter abbreviations. The carbohydrate builder creates a structure from a text string description of the molecule. The nucleic acid builder creates a structure from the typical one-letter abbreviations. There is a function to clean up the shape of the structure (i.e., make bond lengths equivalent). There is also a three-dimensional optimization routine, which uses a proprietary modi®cation of the CHARMM force ®eld. It is possible to set the molecule line drawing mode to obey the conventions of several di¨erent publishers.

ChemSketch can import and export a number of molecular structure and bit mapped graphic ®les. It can also export HTML or VRML ®les. The additional computation modules are callable from ChemSketch, so it is not necessary to copy or save data to access those functions.

There is an interpretive language called ChemBasic for automating tasks in ChemSketch. It is similar to commercial versions of BASIC. Some of the features of BASIC have been omitted. ChemBasic also incorporates additional