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Chemistry on the computer with HyperChem.

HyperChem is a molecular modeling and computational chemistry system for constructing molecular structures, computing their electronic energies, optimum geometries and electronic and vibrational spectra, and for simulating their vibrational motion including chemical reactions. The system is very easy to install and use, and is thus suitable for students as well as professional chemists. The menu system allows a new user to become proficient without the aid of manuals, and for the chemist who wants to understand all of the system's capabilities, comprehensive, well-written manuals facilitate both tutorial and reference study.

Beneath the user-friendly interface, it is a set of sophisticated computer programs designed to provide the user with the best available tools for computing molecular energies, geometries, and for displaying molecular structure and properties. It incorporates several different theoretical models and display modes, which the user can select to suit his particular application.

HyperChem is designed for chemists who are not necessarily experts in theoretical chemistry, but for users who want to understand the computational methods, there is a manual containing a detailed description of (and references to) the theory upon which HyperChem's algorithms are based. This theory manual is a reflection of Hypercube's philosophy of providing the user with an "open architecture".

As with any software product, new users must spend some time learning how to use the system. However, HyperChem's menus, tool-bar, and on-line Help, together with the excellent manuals, make the learning process easy.

Making and displaymg molecules

Molecules can readily be built and displayed on the computer's monitor [ILLUSTRATION FOR FIGURE 1 OMITTED] by making selections from the system's menus with the computer's mouse. A molecule is drawn with the mouse by "clicking" to add an atom, and by connecting the atoms by "dragging" the mouse. Different atoms can be added by selecting the appropriate element from a displayable periodic table. The bond between two atoms can be changed from single to double or triple, or to a conjugated bond (as in benzene). Deletion and changing of atoms and bonds is also very easy; i.e. the displayed molecule can easily be modified by editing. This is invaluable when making a new molecule from a copy of a previously created one. The display may contain more than one molecule; i.e. the atoms aren't necessarily bonded together.

When constructing a molecule in this way the system checks that the normal valency of each element is not exceeded, but the user may disable this checking in order to create other valence states or to build charged structures such as ionic complexes. To speed up construction of organic molecules there is an option to automatically add hydrogen atoms to saturate the valency of each atom during the "build" process. This made the construction of organic molecules very easy.

After sketching the structure of the molecule, the user selects "build" and the system adjusts the bond lengths and angles to standard values, and at the same time converts the 2-dimensional sketch into a 3-dimensional structure. The structure may be displayed in one of 5 renderings: as sticks connecting the nuclei, as intersecting spheres (with or without perspective shading), and as a scatter pattern of dots with or without sticks. Different elements are colour coded. Shaded spheres give the prettiest display, but they may obscure the inner and rear parts of other than very small molecules. The system measures bond angles and lengths, and dihedral (torsion) angles, and these may be displayed with a few clicks of the mouse. When building a 3-dimensional structure, the model builder evaluates the chirality of every atom and this may be displayed as a label (R or S); other, alternative labels include the chemical symbol of the atom, its charge, and its ordinal number in the construction of the molecule, all of which is displayed in the screen's information line when the atom is selected with the mouse.

The structure may be rotated about any of the 3 coordinate axes with the mouse, thus facilitating viewing the molecule from different angles. It may also be translated along the 3 coordinate axes, x and y being in the plane of the screen and z perpendicular to the screen. HyperChem has a feature called z-clipping which is useful for looking inside molecules such as fullerenes; only atoms within a slice along the z-axis are displayed. Since the molecule can be rotated before setting the viewable slice, any planar slice of the molecule can be displayed. The user may also select a non-planar part of the molecule for viewing, such as a few atoms, or the carbon "backbone" of a typical organic molecule. The selected part can be manipulated independently of the rest of the molecule, for example to display free rotation about a carbon-carbon bond.

The vibrational motion of the nuclei may be displayed by running a "Molecular Dynamics" simulation. This "video" mode of displaying molecular motion is a distinct advantage of computer modeling over static, plastic models. It literally brings chemistry to life.

Computational chemistry

The structure created by the model builder is based upon a library of bond lengths and angles. These initially assigned model parameters may be improved by performing a quantum mechanical calculation of the electronic energy to find the geometry that produces a minimum energy; this is known as "geometry optimization". HyperChem has several alternative algorithms for finding the optimum geometry. This minimum-energy, equilibrium geometry is of primary interest to the structure of stable molecules. For other purposes such as exploring the potential energy surface of a chemical reaction, HyperChem allows the user to do single-point electronic energy calculations, and to fix the nuclei at non-equilibrium positions (either with the mouse or by input of atomic coordinates).

The challenges for computational chemistry are to characterize and predict the structure and stability of chemical systems, to estimate energy differences between different states, and to explain reaction pathways and mechanism (nuclear motion) at the atomic level. HyperChem offers several different quantum mechanical methods because these calculations require much CPU time, and in practice the choice of method is usually a compromise between the time required for the calculation and the accuracy obtained.

HyperChem incorporates four molecular mechanics force fields: MM+, AMBER, BIO+, and OPLS, and several semi-empirical molecular orbital methods (CNDO, INDO, MINDO, AM1, PM3, MDDO, and ZINDO/x). The new version (4.5) has added ab initio capability based upon several alternative gaussian basis sets. Users may also define their own basis sets, since data files are kept in ASCII format (another reflection of Hypercube's "open architecture" philosophy).

The results of semi-empirical calculations can be displayed as orbital wave functions; it is interesting to view both the nodal properties and the relative sizes of the wave functions. In addition to total energy, HyperChem uses its computed wavefunctions to calculate several other properties such as dipole moment, total electron density, electrostatic potential, heats of formation, orbital energy levels, vibrational normal modes and frequencies, infrared spectrum intensities, and ultraviolet-visible spectrum frequencies and intensities. All of these computed results can be displayed or plotted, printed and saved in data files. This information is useful in determining reactivity and correlating calculational results with experimental data. For instance, spin densities help to predict the observed coupling constants in electron spin resonance (ESR) spectroscopy.

To investigate the reactivity of molecules and their functional groups, HyperChem uses Frontier Molecular orbital Theory. This provides estimates of the relative reactivity of different molecular substituents, regioselectivity of reactions, and site-selectivity of nucleophiles and electrophiles.

HyperChem has masses for all the elements in the periodic table and it uses these masses as a default when doing vibrational calculations or molecular dynamics. The user can input his own masses to explore isotope effects. In these nuclear motion simulations, the temperature (mean vibrational energy) may be varied; this reveals the effect of temperature on molecular motion.

Although HyperChem is primarily designed to be used in interactive mode, it also provides for batch input and output of commands, data and results. The former take the form of a "script" file, and the latter "log" and "snapshot" files. These permanent, machine readable records of computations are important to the professional user engaged in extensive computational projects.

HyperChem transforms computational chemistry from tedious extraction of numbers from reams of line-printer pages, to an interactive tool in which numerical results are instantly displayed in a picture of the molecule; one picture (and HyperChem produces many, including video pictures) is more revealing and comprehendible than thousands of numbers.


HyperChem provides databases containing residues for constructing proteins, polynucleotides, either as isolated molecules or within a water environment. From the 26 amino acid residues any polypeptide or protein can be constructed, and each amino acid can have a different secondary conformation. In this way, the polypeptide can have stretches of alpha-helical structure, beta-pleated sheet structure and other transitional conformations. It is also possible to produce half-cystine residues for disulfide cross-links by placing the half-cystine residues in the correct primary sequence, and then adjusting the length of the bisulfide bond between these residues.

The program also contains prestored structures of some proteins in a Protein Data Bank (PDB) compiled at the Brookhaven National Laboratory. HyperChem can display structures stored in all PDB files that contain atomic coordinates up to the limit of the computer memory, and can also store new molecular structures in PDB-type files. The Mutate command can replace a specified amino acid with a desired one in the protein.

Similar discussion also applies to nucleic acids. For instance, each nucleic acid that is added to a polynucleotide can have a different conformation. In this way, the polynucleotide can have stretches of A form DNA, B form, Z form, or another conformation. A and B forms of DNA are normally right-hand helixes, while Z form is a left-hand helix. The program makes it possible to change the direction of a helix after constructing it. The helix can then be connected to its mirror image. The hydrogen bonds may optionally be displayed.

In conclusion

HyperChem incorporates a rich variety of proven computational and modeling methods. This richness allows the user to explore a given chemical problem in different ways, but by the same token it challenges him to choose the most appropriate method for his purpose, especially since there are dependencies between the methods whose origin is not transparent to the novice user.

HyperChem is constantly being updated to keep it at the forefront of computational chemistry, and while its interactive interface makes learning and using it very easy for all users, its application in a professional environment will be most effective with a full-time chemist-operator.

HyperChem is to chemists what the wysiwyg word-processor is to secretaries; a sophisticated tool for the professional that others use occasionally. HyperChem will benefit both professional and student chemists; students especially should be excited by doing chemistry on the computer screen. This computational tool should become as ubiquitous in chemistry as the word-processor is in offices.

HyperChem is available customized for several Unix platforms and to run under Windows on an Intel 386/486/Pentium computer. The system reviewed here was release 4.5 installed on a 486DX computer running at 33 MHz. Installation requires at least 4 megabytes of Ram, 20 megabytes of free disk space, and a math co-processor. For highest quality pictures the VGA/SVGA monitor and video driver should display 256 colours. The molecular images may also be printed on popular colour and black and white printers.

HyperChem: Hypercube Inc., 419 Phillip Street, Waterloo, ON, N2L 3X2; Tel: 519-725-4040; Fax: 519-725-5193; e-mail:; URL:

Amir A. Ahari is a graduate student in the Department of Chemistry at York University, North York, ON. Geoffrey Hunter, FCIC, is a Professor in the same Department.
COPYRIGHT 1996 Chemical Institute of Canada
No portion of this article can be reproduced without the express written permission from the copyright holder.
Copyright 1996 Gale, Cengage Learning. All rights reserved.

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Author:Ahari, Amir A.; Hunter, Geoffrey
Publication:Canadian Chemical News
Date:May 1, 1996
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