ChemPlus

The following text describes main features of ChemPlus, a suite of extensions to HyperChem. ChemPlus requires HyperChem Release 4 for Windows, and has the same hardware requirements as HyperChem. A slide show demo of ChemPlus can be accessed at the HyperChem Web site.

Product Overview

ChemPlus consists of several modules: distinct programs which interact with HyperChem. Communication between the ChemPlus modules and HyperChem takes place transparently via Dynamic Data Exchange. The ChemPlus Manager attaches these modules to appropriate places in HyperChem's menus, so that you can launch them straight from HyperChem. This close integration makes ChemPlus easy to incorporate into your normal use of HyperChem.

RMS Fit

RMS Fit provides a new tool for comparing structures of molecules in HyperChem, augmenting the existing overlay function and the flexible fitting provided by restrained optimizations. ChemPlus's RMS Fit module lets you carry out the following tasks:

• Overlay two molecules by minimizing the distance between corresponding atoms in the two target molecules, displaying the residual error.
• Have the corresponding atoms be all atoms, or selected atoms only.
• Designate the corresponding atoms by their numbering within a molecule, or by the order in which you select them.

Molecule Presentations

Molecule Presentations provides new renderings of molecules, 3D renderings of molecular orbitals, and printer-resolution images for presentations and publications. Molecule Presentations allows you flexibility in your images of molecules:

• Choose from space-filling spheres, or sphere and cylinder (ball and stick) renderings. Use either flat or shaded spheres and cylinders.
• Use CPK radii for space-filling spheres images, smaller radii for ball and stick images, or create your own custom set of atomic radii. You can mix different radius sets in the same image.
• Color atoms and bonds using any of the colors available in the Windows palate.
• Display 3D isosurfaces of molecular orbitals as wire mesh or shaded opaque surfaces.
• Control the isosurface value and grid density.
• Label atoms by element or other text.
• Copy and paste images into other applications as Windows metafiles (resolution independent images) or as bitmaps.
• Print images at full printer resolution for presentation quality illustrations.

Sequence Editor

Sequence Editor provides additional tools for manipulating strings of amino acids in HyperChem. Sequence Editor brings the following capabilities to HyperChem:

• Read FASTA files consisting of strings of one- letter amino acid designators.
• Specify secondary structure, including alpha helix, extended, parallel and anti-parallel beta sheets, three types of beta turns, and random coil, and put the resulting structure into HyperChem.
• Get polypeptides from HyperChem with secondary structure designators.
• Search for specific amino acid sequences in a polypeptide.
• Show the polarity of each amino acid in the sequence, and display the distribution of each type.
• Compare the similarity of two polypeptides, using a Dayhoff matrix (dot plot) approach.

Crystal Builder

With Crystal Builder you can build up crystals in HyperChem by hand, by entering fractional coordinates, or choose from a set of samples provided. Crystal Builder gives you control over the face you view, and the size of crystal you build; it also allows you to read Cambridge Crystal Database files into HyperChem. Crystal Builder includes the following features:

• Read in Cambridge Crystallographic Database files, and place them in HyperChem.
• Over 20 sample crystal structures included, particularly useful in educational contexts.
• Control crystal size and shape (number of unit cells in each direction).
• Control which crystal face you view, by specifying Miller indices.
• For manual building of crystals, you can specify unit cell angles and lengths (a, b, c) for each of the eight basic crystal types, plus face centered cubic and body-centered cubic. All distinct space groups are not included, so you may need to calculate special positions as required for the different space groups.

Sugar Builder

With Sugar Builder you can construct polysaccharides from individual saccharide components. Sugar Builder's features include the following:

• Build polysaccharides from aldoses and ketoses, as well as amino sugars and N-acyl sugars, Inositol and de-oxy sugars.
• Terminate the polysaccharides using any of the thirteen blocking groups provided.
• For each saccharide, you have control over the isomer (D or L), the form (acyclic, alpha, or beta), the angles (phi, psi), and the connection site.
• Construct polymers from other, possibly non- saccharide, components using the user-defined component dialog box.
• Link polysaccharide strands, with full specification of site and angles.
• Carry out simulations, using an extension of the AMBER force field specifically intended for saccharides [S. W. Homans, Biochemistry, 29, 9110 (1990)]. This force field allows you to carry out calculations on some, but not all, polysaccharides. (HyperChem's MM+ force field will also compute properties of polysaccharides).

Conformational Search

The Conformational Search module is a tool for finding and saving stable structures of molecules, using stochastic approaches based on modification of torsion angles.

Conformational Search has a wide range of options to tune the search for your particular needs. The general approach is to twist selected torsion angles of the system to distort a structure and, if certain tests are met, optimize to obtain a new candidate structure. The new structure can be accepted or rejected as a structure of interest according to a variety of criteria. Here is a list of some of the more important facilities of Conformational Search:

• Select the torsion angles you wish to vary using HyperChem's selection methods.
• Study ring flexibility using our implementation of the torsional flexing method of Kolossváry and Guida [J. Comput. Chem., 14, 691, (1993)].
• Choose between random walk and a usage-directed approach [G. Chang, W. C. Guida and W. C. Still, J. Am. Chem. Soc., 111, 4379 (1989)] to generate a sequence of conformations.
• Save all acceptable structures as the run progresses, and restart previous searches.
• Filter structures prior to optimization by checking for close contacts and torsion angles that are similar to previously optimized structures, and after optimization for inversion of chiral centers.
• Following optimization, eliminate duplicate structures by comparing energies, torsion angles, and RMS fit residual errors, automatically taking account of equivalent atoms.
• Save full details of the search to a file.
• Structures can be read back in and put into HyperChem by simply selecting the structure of interest and executing a single command.
• Display results in tables that can be copied into spreadsheets for further analysis.

QSAR Properties

QSAR Properties allows calculation and estimation of a variety of molecular descriptors commonly used in Quantitative Structure-Activity Relationship (QSAR) studies. Most of the methods were developed for and are primarily applicable to organic molecules. Here are some of the properties you can estimate using QSAR Properties:

• Atomic charges, using the Gasteiger-Marsili method [Tetrahedron, 36, 3219 (1980)].
• Van der Waals and solvent-accessible surface areas, using a rapid, approximate method due to W. C. Still and coworkers [W. Hasel, T. F. Hendrickson, W. C. Still, Tet. Comput. Meth., 1, 103 (1988)], or using a slower grid-based method.
• Molecular volumes, bounded by Van der Waals or solvent-accessible surfaces, using a grid method.
• Hydration energy (for peptides and similar systems), using our implementation of a method parametrized by Scheraga et al. [T. Ooi, M. Oobatake, G. Nemethy and H. Scheraga, Proc. Natl. Acad. Sci. USA, 84, 3086 (1987)], based on the approximate surface area calculation.
• Log P (the log of the octanol-water partition coefficient), a hydrophobicity indicator, using our implementation of an atom fragment method developed by Ghose, Pritchett and Crippen [J. Comput. Chem., 9, 80 (1988)]. For a sample of organic molecules, the method yields a correlation coefficient (r) with experimental values of 0.92 and a standard error of 0.36.
• Refractivity, also using an atom-based fragment method due to Ghose and Crippen [J. Chem. Inf. Comput. Sci., 27, 21 (1987)]. For a sample of organic molecules, the method yields a correlation coefficient (r) with experimental values of 0.995 and a standard error of 1.1 ų.
• Polarizability, using an atom-based method due to K. J. Miller [J. Am. Chem. Soc., 112, 8533 (1990)]. For a sample of organic molecules, the method yields a correlation coefficient (r) with experimental values of 0.991 and a standard error of 9.3 ų.
• Mass, using a straightforward method.
• QSAR Properties can compute the property for the current system in HyperChem, or operate in standalone mode with HyperChem Input (HIN) files.
• Carry out batch calculations directly from spreadsheets supporting Windows Dynamic data Exchange, using the spreadsheet macro language.
• Send results to a results window, and save to a log file.

Script Editor

HyperChem's scripting capability is one of its most versatile features, allowing it to be controlled from outside using scripts or external programs. The Script Editor is a tool to assist you in developing scripts, and to send script messages directly to HyperChem as a command line. Script Editor's features include the following:

• Send script messages directly to HyperChem using a command line.
• Paste script messages from a dialog box, which lists all available script messages.
• Read in your existing script files, and save lists of messages for later use.
• Execute any number of script messages.
• Retrieve information from HyperChem, display it in a window, and save it to a file. Results of calculations, or details of the current molecular system, can be saved in this manner.

Final Comments

ChemPlus brings significant new functionality to the premier desktop molecular modeling system, and is integrated closely with HyperChem for ease of use. ChemPlus is a product of Hypercube, Inc., specialists in scientific software for Windows and the developers of HyperChem.

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