Display

• Rendering choices: Ball-and-stick, fused CPK spheres with optional shading and highlighting. Also vdW dots, cylinders and overlapping spheres.
• Ribbon rendering for protein backbones, with optional sidechain display.
• 3D Isosurfaces or 2D contour plots of: total charge density, molecular orbitals, spin density, electrostatic potential (ESP), ESP mapped onto 3D charge density surface
• Isosurface rendering choices: wire mesh, Jorgensen-Salem, transparent and solid surfaces, Gouraud shaded surface. User specified grid and isosurface value.
• During simulations, display and average kinetic, potential, and total energy, as well as values of user specified bond lengths, bond angles, or torsion angles.
• Animate vibrational modes.
• Display2D or 3D potential energy plots

Customize and Automate 

• Construct custom menus
• Automate routine operations with scripts
• Send selected data to files or workspace
• Add new features as menu items, or run from scripts

Interface and Extend 

• Construct a custom interface to programs written in VB, C/C++, or FORTRAN
• Send HyperChem results to MS Word or Excel
• Interface with other desktop programs

Predict

• Relative stabilities of isomers
• Heats of formation
• Activation energies
• Atomic charges
• HOMO-LUMO energy gap
• Ionization potentials
• Electron affinities
• Dipole moments
• Electronic energy levels
• MP2 electron correlation energy
• CI excited state energy
• Transition state structures and properties
• Non-bonded interaction energy
• UV-VIS absorption spectra
• IR absorption spectra
• Isotope effects on vibrations
• Collision effects on structural properties
• Stability of clusters

Save Results

• Use Import/Export option to save results of quantum mechanics calculations or to view results generated by other programs.
• Use HyperChem Data to store structures and properties in a custom molecular database.
• Create Reaction Movies in AVI format.
• Save as HTML page to store and display teh structure, orbitals, IR and UV spectra and IR spectra with normal modes.

Integrated Modules

RAYTRACE

The Raytrace module enables you to create stunning raytraced images of molecules in the workspace by bridging with the very high-level graphics visualization application known as Persistence of Vision (POV) Ray for Windows.

• Automatically generate POV-Ray input files describing the molecule.
• Run POV-Ray to generate high quality images in any of several graphic file formats supported by POV-Ray.

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.

The 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.

SEQUENCE EDITOR

Sequence Editor provides additional tools for manipulating strings of amino acids in HyperChem. The 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 the crystal you build; it also allows you to read Cambridge Crystal Database files into HyperChem. The Crystal Builder includes the following features:

• Read in Cambridge Crystallographic Database files (FDAT), 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. The Sugar Builder's features include the following:

• Build polysaccharides from aldoses and ketoses, as well as amino sugars and N-acyl sugars, Inositol and deoxy 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, a, or b), the angles (f, y and w), 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 Kolossvary 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 user specified 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.
• 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.
• 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 in the HyperChem language, 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.