||What is HyperChem?
HyperChem is a sophisticated molecular modeling environment
that is known for its quality, flexibility, and ease of use. Uniting 3D
visualization and animation with quantum chemical calculations, molecular
mechanics, and dynamics, HyperChem puts more molecular modeling tools at
your fingertips than any other Windows program.
What is new in HyperChem 6?
HyperChem 6 is a full 32-bit application, developed for
the more powerful Windows 95, 98, NT and Windows 2000 operating systems.
HyperChem 6 represents a major advance over earlier releases, with new
visualization capabilities and important new customization tools. HyperChem
6 provides a more powerful and flexible molecular workspace than ever before.
The new features of HyperChem 6 can be grouped into 5
Features Migrated from ChemPlus
The ChemPlus product has been integrated into HyperChem
Professional. The Molecular Presentations module has been dropped and in
its place a new module, Polymer Builder, has been added. The modules integrated
into HyperChem 6 still have a degree of separation form the core code and
should be thought of as an integral part of HyperChem even though they
integrate via Hypercube's module concept. The integrated modules are:
New Scientific Methods
Protein Sequence Editor
Polymer Builder (New)
New scientific methods are often associated with HyperChem's
back ends. Changes to the capability of these back ends involve new molecular
mechanics methods, new quantum mechanics methods and new calculated properties
form either of these technologies.
New Force Fields
HyperChem Release 6 adds significant new capability to
the AMBER method of molecular mechanics by including up-to-date modifications
of this force field. AMBER code now supports 5 parameter sets with their
associated functional forms:
Amber for saccharides
Default Parameter Scheme for AMBER and OPLS
HyperChem Release 6 extends Hypercube's default parameter
scheme, as previously implemented for MM+ to AMBER and OPLS. Thus any
AMBER or OPLS computation can now continue computing with default parameters,
when explicit parameters are missing from the relevant parameter file.
The normal AMBER and OPLS parameter scheme fails when explicit parameters
associated with "atom types" are not available. with default parameters,
no calculation fails for lack of parameters.
Release 6 now makes available, for open shell systems,
calculated values of Hyperfine Coupling constants characterizing the ESR
spectra of the system.
Polarizability tensors can now be computed in release
Major New Utilities
Some of the major new utilities in release 6 are:
Save as HTML
This feature allow you to calculate properties such as
vibrational spectra or the orbitals of a molecule and save the results
as an HTML file, which can be published on your web site using a free Active-X
control distributed with HyperChem 6. This enables easy sharing of scientific
data with colleagues across the world via your web site, where, for example,
once can view an animation of the normal modes you computed or rotate computed
molecular orbitals around for views from different angles.
Plots of Potential Energy
Release 6 allows you to select one or two structural features
(bond length, torsion angle etc.) and request a plot of the potential energy
as a function of either a single structural feature (2D plot) or two structural
features (3D plot).
Previous versions of HyperChem only allowed protein modifications
that were point mutations. These mutation operations replaced a single
amino acid with an alternative amino acid. In Release 6, it is possible
to cut and paste any amino acid sequence. That is a piece can be
cut out, a piece inserted, or a sequence of one length replaced by a new
sequence of a different length. Annealing operations are, of course, required
for the rest of the protein to adapt to these modifications.
It is now possible to superimpose an applied electric
field on any calculation. For example, a charged system will now drift
in the workspace during a molecular dynamics run if an external electric
field has been applied. Studying molecular behavior in an electric field
is now possible.
The major new module in Release 6 is that associated with
Annotations. HyperChem 6 defines a new plane for the workspace that is
distinct from the molecular plane that has always been used to draw molecules,
build 3D structures, and rotate and visualize molecules. This new plane
is the Annotation plane containing text annotations that can be used to
describe the contents of the molecular plane.
While it has always been possible to copy the rendering
of molecules in HyperChem into a file or onto the clipboard and then transfer
the rendering into a drawing or painting program to prepare overhead transparencies
or other presentation material, directly creating such material without
leaving HyperChem is now possible.
An annotation in HyperChem is a length of text that can
be placed anywhere in the workspace. Because the text can have attributes
such as a font, a color, and a size, it is possible to create annotations
such as arrows, lines, circles, rectangles and any number of other drawing
primitives. Annotating the molecules that are being modeled in HyperChem
allows you to print the workspace and more easily describe to others the
results of your modeling.
Release 6 contains a number of features associated with
creating and manipulating these annotations. Because they exist in a plane
or layer that is independent of the molecular or modeling plane, they augment
rather than collide with the modeling of earlier versions of HyperChem.
At the same time by being able to show or print both planes at the same
time, a rich set of annotation options is possible.
While that is not the primary intent, HyperChem could
now be used to prepare illustrations independent of chemistry and molecular
A number of other improvements have been implemented in
HyperChem 6 that do not fall under the above topics:
Charge and Multiplicity are Saved
The total charge and spin multiplicity are now stored
in the HIN file and are restored when a molecular HIN file is read. Earlier,
these had to be set interactively for any new molecule in the workspace.
It is now possible to constrain your drawing of 2D molecules
so that the the resultant drawn molecule has uniform bond lengths and angles
and resembles a standard 2D molecular representation as might be seen in
textbooks. These constraints have no effect on the subsequent 2D to 3D
Formal Charge is Now Defined
Release 6 introduces the concept of a formal charge
on an atom. This has always been missing in HyperChem. The formal charge
primarily affects the model builders creation of a 3D structure from a
2D drawing. Now, for example, if the formal charge on a Nitrogen atom is
set to +1, the model builder applied to the Nitrogen atom will create NH4+
rather than NH3 as in previous releases of HyperChem. When formal charges
are zero, the model builder operates as it always has. This features improves
HyperChems basic understanding of chemistry.
A number of new labels have been defined for atoms. These
labels are updated dynamically (during optimizations, for example) and
Graphical Display of Gradients
Spin population - the total excess of alpha spin electrons
over beta spin electrons on an atom.
RMS gradient - a measure of the force on an atom.
Custom text - arbitrary text that can be used to label an
It is now possible to visualize the gradient (force) on
any atom as a vector. Any set of atoms can display these vectors.
A new set of dynamically updated labels are now available
for bonds as well as atoms and residues. These bond labels can be one of:
Bond order - as calculated quantum mechanically
Current Properties Now Available in GUI
In Release 6 a number of calculated properties, such as
the energy, are permanently available in dialog boxes, i.e. they are in
the graphical user interface rather than are just seen temporarily on the
status line as they are computed. Earlier, these had to be retrieved from
the log file if the status line was updated or changed.
Enhanced Selection Capability
HyperChem operations depend to a great extent on ones
ability to select a subset of atoms. Many ways have been available to select
a subset but Release 6 further expands these selection options considerably.
For example, it is now possible to select atoms based on the range of various
computed quantities such as their atomic charge or atomic gradient. Thus, for example, one can now select all atoms with a charge between -0.1 and 0.1.
The atom selection options are now organized as either
a selection based on a "string" property of an atom, such as the atom type
(e.g. CH), or a "number" property such as the atom charge described above.
Whether you use HyperChem's many internal features or
build a live link with your other chemistry programs, the benefit of working
with HyperChem 6 is that you are free to focus on the things that you do
best. HyperChem does the rest.
HyperChem 6 Feature Summary
Structure Input and Manipulation
Building molecules with HyperChem is simple: just choose
an element from the periodic table, and click and drag with the mouse to
sketch a structure. Mouse control of rotation around bonds, stereochemistry,
and "rubber banding" of bonds makes changing structures easy. Extensive
selection, highlighting, and display capabilities make it easy to focus
on areas of interest in complex molecules.
Select, rotate, translate, and resize structures with convenient
mouse controlled tools. Modify settings to control operation of tools.
Convert rough sketches into 3D structures with HyperChem's
Apply builder constraints easily: specify bond lengths, bond
angles, torsion angles, or the bonding geometry about a selected atom.
Specify atom type, atom charge, formal charge and atomic
Build clusters and complex molecular assemblies; move individual
atoms and molecules as easily as you move groups.
Build peptides and nucleic acids from amino acid and nucleotide
Mutate residues and build large molecules incrementally (make
changes at any point).
Add a periodic box of pre-equilibrated water molecules for
aqueous solvation studies. Periodic boundary conditions can be used with
other solvent systems, or without solvents.
Import structures from standard file formats: Brookhaven
PDB, ChemDraw CHM, MOPAC Z-matrix, MDL MOL and ISIS Sketch, and Tripos
Display structures using ball and stick, fused CPK spheres,
sticks, van der Waals dots, and sticks with vdW dots; switch easily between
Specify shading and highlighting, stick width, and the radii
of spheres. Stereo and perspective viewing are also available.
Display a Ray Traced image of the molecules in the
Select and name sets of atoms for custom display or monitoring
Set and display custom labels for atoms.
Display bond labels showing the current bond length or the
currently computed quantum mechanical bond order.
Display protein backbones using ribbons, with optional display
Highlight potential hydrogen bond interactions.
Display dipole moment vectors and gradient vectors.
Use HyperChem to explore quantum or classical model potential
energy surfaces with single point, geometry optimization, or transition
state search calculations. Include the effects of thermal motion with molecular
dynamics, Langevin dynamics or Metropolis Monte Carlo simulations. User
defined structural restraints may be added.
Types of Calculations
Single point calculations determine the molecular energy
and properties for a given fixed geometry.
Geometry optimization calculations employ energy minimization
algorithms to locate stable structures. Five minimization algorithms are
Vibrational frequency calculations find the normal vibrational
modes of an optimized structure. The vibrational spectrum can be displayed
and the vibrational motions associated with specific transitions can be
Transition state searching locates the metastable structures
corresponding to transition states using either Eigenvector Following or
Synchronous Transit methods. Molecular properties are then calculated.
Molecular dynamics simulations compute classical trajectories
for molecular systems. Quantum forces can be used to model reactive collisions.
Heating, equilibration, and cooling periods can be employed for simulated
annealing and for studies of other temperature dependent processes. Both
constant energy and constant temperature simulations are available.
Langevin dynamics simulations add frictional and stochastic
forces to conventional molecular dynamics to model solvent collisional
effects without inclusion of explicit solvent molecules.
Metropolis Monte Carlo simulations sample configurations
from a statistical ensemble at a given temperature and are useful for exploring
the possible configurations of a system as well as for computing temperature
dependent equilibrium averages.
Ab Initio Quantum Mechanics
Choose from many commonly used basis sets (STO-1G to D95**)
including the standard STO-3G, 3-21G, 6-31G*, and 6-31G** basis sets
Extra basis functions ( s, p, d, sp, spd ) can be added to
individual atoms or to groups of atoms.
Users can also define their own basis sets or modify existing
basis sets easily using HyperChem's documented basis set file format.
Semi-empirical Quantum Mechanics
HyperChem offers ten semi-empirical molecular orbital methods,
with options for organic and main-group compounds, for transition metal
complexes, and for spectral simulation.
Choose from Extended Huckel, CNDO, INDO, MINDO/3, MNDO, MNDO/d,
AM1, PM3 (including transition metals), ZINDO/1 and ZINDO/S.
Four force fields provide computationally convenient methods
for exploring the stability and dynamics of molecular systems.
Added flexibility of user defined atom types and parameters.
Choose from MM+, a general purpose force field, and three
specialized biomolecule force fields: Amber, BIO+, and OPLS.
Mixed Mode Calculations
HyperChem allows you to perform quantum calculations on part
of a molecular system, such as the solute, while treating the rest of the
system classically. This boundary technique is available for all the quantum
methods, with some limits for ab initio calculations.
Customize and Extend HyperChem with the Chemist's Developer
Results with HyperChem
Streamline HyperChem's menus. Add new graphical and computational
features; create custom menus for specific applications.
Interface to Visual Basic, C, C++ and FORTRAN programs. Add
dialog boxes as well as menu items. For example, you could use HyperChem
for visualization of structures and results from non-graphical quantum
Link HyperChem procedures to other Windows programs such
as MS Word and Excel; direct selected results to these applications for
convenient analysis and reporting.
Rendering choices: Ball-and-stick, fused CPK spheres with
optional shading and highlighting. Also vdW dots, cylinders and overlapping
Ribbon rendering for protein backbones, with optional sidechain
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++,
Send HyperChem results to MS Word or Excel
Interface with other desktop programs
Relative stabilities of isomers
Heats of formation
HOMO-LUMO energy gap
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
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 (HyperChem Suite only).
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 New Modules in HyperChem 6
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
Run POV-Ray to generate high quality images in any of several
graphic file formats supported by POV-Ray.
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
Have the corresponding atoms be all atoms, or selected atoms
Designate the corresponding atoms by their numbering within
a molecule, or by the order in which you select them.
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
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
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.
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
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
Control which crystal face you view, by specifying Miller
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.
With Sugar Builder you can construct polysaccharides from
individual saccharide components. The Sugar Builder's features include
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
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
Construct polymers from other, possibly non-saccharide, components
using the user-defined component dialog box.
Link polysaccharide strands, with full specification of site
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).
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
Select the torsion angles you wish to vary using HyperChem's
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 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
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
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
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.
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
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.
Download the 20
day evaluation copy of HyperChem Release 6