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's new in Version 7.5
Open GL Rendering
The basic rendering modeling in HyperChem has been converted to a full
new OpenGL model. This affects all the molecular rendering, giving a generally
higher quality of graphics throughout the product.
Image Gallery - click to enlarge
Custom Color Support
It is now possible to color molecules, backgrounds, etc. using any of
16 million available colors rather than the traditional 8 standard colors
that HyperChem has used in the past.
The rendering of molecules supports different rendering for different
parts of the same molecule. That is any atom can be rendered using any
of the rendering molecules -- stick, balls, ball and stick, etc.
Tube Rendering of Atoms
A new "tube" rendering is now available for atoms.
Manipulate Protein Structures
Extensive additions have been made to HyperChem's ability to deal with
protein structures. HyperChem now supports four secondary structure descriptions
- helices, sheets, turns, and coils. The secondary structures can be individual
selected, colored, and rendered using a new secondary structure rendering
Support for Secondary Structure Information in Protein Data Bank files
HyperChem recognizes and supports secondary structure information in its
molecule files. Information from protein database (PDB) files is captured
for and retained in HIN files. The peptide builder supports this new capability
and adds a secondary structure description to all residues.
Protein Secondary Structure Rendering
Secondary structure rendering now includes ribbon lines, narrow ribbon
sheets, thick ribbon sheets, encompassing helical cylinders and a coil
rendering. These new renderings can be selected for any secondary structure
or part of a secondary structure. They can be colored globally or colored
differently for specific residues.
Enhanced Protein Builder Capability
In addition to alpha helices and beta sheets, the peptide builder now
supports beta turns, parallel and anti-parallel beta sheets, left-handed
alpha helices, 310-helices, and pi-helices.
Large Molecule Electron Density Approximation
A rapid new method is available for calculating and displaying the electron
density and electrostatic potential of molecules. For example, the new
method makes it practical to very quickly display the electron density
of large proteins.
Density Functional Package
|| Density Functional
Theory (DFT) has been added as a basic computational engine to complement
Molecular Mechanics, Semi-Empirical Quantum Mechanics and Ab Initio
Quantum Mechanics. This new computational method comes with
full capabilities including first and second derivatives so that
all the capabilities of other earlier engines are also available
with DFT. These include
geometry optimization, infrared and optical spectra, molecular dynamics,
Monte Carlo, etc.
A full complement of
exchange and correlation functions is available, including eight
exchange functionals and eight correlation functionals that can
be combined in any fashion.
Also included are four combination or hybrid functions,
such as the popular B3-LYP or Becke-97 methods.
A choice of various integration grids, controlling the
method’s accuracy, is available to the user.
package has been integrated into the core of HyperChem. This
package allows for the simulation of NMR spectra. An accurante
semi-empirical tailored specifically to NMR allows rapid interactive
computation of NMR shielding constants (chemical shifts) and coupling
constants for molecules as large as proteins. Basedon a solution
of the quantum mechanical coupled-Hartree-Fock equations rather
than simple database lookup, this package allows full exploration
of NMR parameters in any situation, such as a new or novel chemical
environment where simple database interpolation is impossible.
When appropriate, the NMR parameters
can be integrated into a spin Hamiltonian to predict and display
the full one-dimensional NMR spectra. The spectra can be
manipulated to add line widths so as to simulate experimental
Charmm Protein Simulations
A full database
capability is integrated into HyperChem 7.5.
This includes database search and retrieval of molecules
for subsequent molecular modeling calculations as well as the
storing of computed properties and optimized structures of your
molecules in a new database.
Included with the product is a sample database of 10,000
molecules that have previously been optimized with HyperChem.
The sample database that is included is representative
of common chemical compounds and can be used in a variety of ways
associated with research in computational chemistry.
Database retrieval is simple and interactive
and a variety of methods can be used to search a database, including
a search for 2D or 3D structure. In conjunction with HyperChem’s
scripting capability, a generic search based on appropriate computed
properties is possible.
That is, a question such as, “Give me all molecules whose
stored or computed value of X is between x-d and x+d” is possible.
Typed Neglect of Differential Overlap (TNDO)
Bio+ force field in HyperChem represents a version of the Chemistry
at HARvard using Molecular Mechanics (Charmm) force field. Release 7 of HyperChem updates this
force field with new functional terms and new parameters to represent
the latest science from the Charmm community.
new parameter sets for Charmm-19 represent new parameters for
the bio+ force field of earlier versions of HyperChem, but parameter
sets Charmm-22 and beyond represent a newer force field implemented
in HyperChem 7 that includes a Urey-Bradley term describing interactions
between the two terminal atoms of a 3-atom bond angle.
Molecules in Magnetic Fields
The Typed Neglect
of Differential Overlap method is a new semi-empirical method
that merges ideas from molecular mechanics and semi-empirical
quantum mechanics. It is designed as a generic semi-empirical
method capable of high accuracy when combined with the appropriate
parameters. It uses
the molecular mechanics idea of atom “typing” to describe the
chemical environment of an atom in a molecule with different types
being given different parameters.
This is the key idea that gives molecular mechanics its
validity and accuracy in the absence of any quantum mechanical
capability. TNDO combines atom typing a basic
quantum mechanical method and allows a rapid semi-empirical method
to offer reliable results.
The deficiency is the need to develop parameter sets for
different types (different classes of molecules) as in molecular
7 includes on a first step in this parameter generation but considerable
research effort on the part of Hypercube, Inc., HyperChem users,
and the general research community is needed to have parameter
sets that cover a wide range of chemical situations. Hypercube’s web site will collect
these parameter sets.
Optimization of the Geometry of Excited States
||It is now possible
to explore the structure and reactivity of molecular systems in
a uniform magnetic field.
HyperChem 6 added an optional external electric field to
the workspace and HyperChem 7 adds an optional external magnetic
field. The effect of
magnetic fields is relatively unknown but this feature allows interactive
exploration of how magnetic fields affect chemical behavior.
Two terms in
the Hamiltonian are included.
The first is the interaction of the magnetic field with
the orbital angular momentum of electrons and the second is the
Zeeman interaction of the magnetic field with the electrons’ spin.
This later term is only present with open-shell systems
or calculations that use the Unrestricted Hartree-Fock calculations.
Optimization of MP2 Correlated Geometries
||A new optimization
method, Conjugate Directions, has been added.
This method allows geometry optimization using only energies
without the necessity of computing gradients (first derivatives). This opens up the possibility of
optimizing structures for a number of new situations. In particular, any state of a Configuration
Interaction calculation can be optimized. These include excited states for
the first time.
New Rendering of Aromatic Rings
accurate and relatively simple way of including electron correlation
in ab initio calculations is Moller-Plesset second-order perturbation
theory (MP2). Previously, HyperChem users could
calculate MP2 energies only but now, using the Conjugate Directions
optimizer mentioned above, they can calculate the optimized geometry
of a structure using MP2 theory.
||While HyperChem is
fundamentally a molecular modeling program, not a drawing program,
it is convenient to have available the ability to easily create
annotations of molecular structures and drawings that one can use
in presentations. A principal deficiency in this regard
has been the lack of a “pretty picture” of aromatic rings since
HyperChem represents these with dotted lines, as is convenient for
most situations where one is fundamentally interested in modeling
not drawing. With HyperChem
7, it is now possible to represent aromatic rings as a more conventional
ring with a circle in the middle of it, rather than a ring with
Interactive Examination and Manipulation of Parameters
In the evolution of adding
convenient drawing capabilities, as just mentioned, HyperChem
6 added the concept of annotations where text (essentially) could
be add to the workspace to annotate chemical structures.
These “text” annotations could include many symbols (such
as arrows) using various fonts.
With HyperChem 7 this drawing capability is extended to
lines, ellipses (circles), and rectangles (squares). These elements can be colored, filled
or unfilled, dotted, etc.
are included in the latest HIN file standard so that HyperChem
can be used as a simple drawing program.
Enhanced Polymer Builder
and semi-empirical methods use a large variety of parameters. In particular, the new TNDO method
lends itself to a variety of parameter sets for a variety of different
It has always been possible to edit the text-based parameter
files and re-compile them. With HyperChem 7, it is possible to see
parameters on-screen associated with selected atoms, bonds, torsions,
etc. These can then be immediately edited
if desired. In addition,
it is possible, interactively, to copy whole parameter sets making
it feasible to interactively explore different parameters sets in
an easy fashion.
New Basis Sets
||The polymer builder
has been enhanced to create branched polymers as well as linear
polymers. As TAIL is attached to HEAD, it
is possible to specify random attachment to either the new HEAD
or an old HEAD, creating a branch in the polymer. In addition to explicitly specifying
torsion angles for the HEAD to TAIL join, it is now possible to
specify torsion angles for the internal backbone of the monomer;
specifically, one can have these monomer backbone angles chosen
randomly or as originally specified in describing the monomer.
conjunction with the new DFT capability of HyperChem 7, a large
number of new basis sets have been added to the sets already included
with HyperChem. These
basis sets are available for either the ab initio module or the DFT module.
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 model builder.
- 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 mass.
- 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 residue libraries.
- 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
- Import structures from standard
file formats: Brookhaven PDB, ChemDraw CHM, MOPAC Z-matrix,
MDL MOL and ISIS Sketch, and Tripos MOL2 files.
- Display structures using ball and
stick, fused CPK spheres, sticks, van der Waals dots, and
sticks with vdW dots; switch easily between rendering styles.
- 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 workspace.
- Select and name sets of atoms for
custom display or monitoring of properties.
- Set and display custom labels for
- Display bond labels showing the
current bond length or the currently computed quantum mechanical
- Display protein backbones using
ribbons, with optional display of sidechains.
- Highlight potential hydrogen bond
- Display dipole moment vectors and
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 provided.
- 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 animated.
- 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
- 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
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
- 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
- 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 Kit
- 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 chemistry
- Link HyperChem procedures to other
Windows programs such as MS Word and Excel; direct selected
results to these applications for convenient analysis and
|Results with HyperChem
- 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
- 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
Customize and Automate
- Construct custom menus
- Automate routine operations
- Send selected data to files
- 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
- 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
- Non-bonded interaction energy
- UV-VIS absorption spectra
- IR absorption spectra
- Isotope effects on vibrations
- Collision effects on structural
- 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.
- Create Reaction Movies in
- Save as HTML page to store
and display teh structure, orbitals, IR and UV spectra
and IR spectra with normal modes.
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 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 provides additional
tools for manipulating strings of amino acids in HyperChem.
The Sequence Editor brings the following capabilities
- 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)
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
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
- 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
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
- 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,
- 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 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
- 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
- QSAR Properties can compute
the property for the current system in HyperChem, or
operate in standalone mode with HyperChem Input (HIN)
- 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
- 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
- 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.
New Force Fields
HyperChem added significant new capability
to the AMBER method of molecular mechanics by including up-to-date
modifications of this force field. AMBER code supports 5 parameter
sets with their associated functional forms:
- Amber 2
- Amber 3
- Amber for saccharides
- Amber 94
- Amber 96
- Amber 99
Default Parameter Scheme for AMBER
Any AMBER or OPLS computation can 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.
Calculated values of Hyperfine Coupling
constants are also available, for characterizing the ESR spectra
of open shell systems.
Computation of polarizability tensors is
Plots of Potential Energy
You can 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).
You can 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 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.
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.
HyperChem 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 modeling.
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 model
Graphical Display of Gradients
It is possible to visualize the gradient
(force) on any atom as a vector. Any set of atoms can
display these vectors.
A set of dynamically updated labels
are available for bonds as well as atoms and residues. These
bond labels can be one of:
- Bond length
- Bond order - as calculated quantum
Enhanced Selection Capability
HyperChem operations depend to a great
extent on one’s ability to select a subset of atoms. For
example, it is 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 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 Release 7 is that
you are free to focus on the things that you do best. HyperChem
does the rest.
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