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HyperChem PRO 8 |
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 model builder.
- Replace any
selected Hydrogen with a variety of substituents including your own
custom substituent.
- 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
salvation 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 MOL2 files.
Molecular
Display
- Display
structures using ball and stick, fused CPK spheres, sticks, ball and
cylinder, or tubes
- Add van der
Waals dots to any rendering.
- Use any
rendering on any atom in the same molecule.
-
Specify stick or cylinder width, and the radii of spheres.
- Stereo and
perspective viewing are available as well as a quality setting.
- 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 atoms.
- Display
bond labels showing the current bond length or the currently
computed quantum mechanical bond order.
- Display
protein backbones using ribbons, beta sheets, random coils,
cylinders, etc. with optional display of side chains.
- Highlight
potential hydrogen bond interactions.
- Display
dipole moment vectors and gradient vectors.
Computational Chemistry
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
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.
- Excited
states via singly-excited configuration interaction (CI).
Computational Methods
Density Functional Theory (DFT)
- Choose from a large variety of exchange and
correlation functionals.
- Choose from a variety of integration grids
- All the options of Ab Initio calculations
and basis functions (see below).
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 eleven 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, RM1, PM3
(including transition metals), ZINDO/1 and ZINDO/S.
Molecular
Mechanics
- 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 programs.
- Link
HyperChem procedures to other Windows
programs such as MS Word and Excel; direct selected results to these
applications for convenient analysis and reporting.
Results with HyperChem
Display
Rendering choices: Stick,
Ball-and-stick, fused CPK spheres, Ball and Cylinder, Tubes with
optional dot surfaces.
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 MM+, AMBER, Charmm, and OPLS
Any molecular mechanics
computation can continue computing with default parameters, when
explicit parameters are missing from the relevant parameter file. The
normal MM2, AMBER, Charmm 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.
ESR
Spectra
Calculated values of Hyperfine
Coupling constants are also available, for characterizing the ESR
spectra of open shell systems.
Electric
Polarizabilities
Computation of polarizability
tensors is available.
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).
Protein
Design
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.
Electric
Fields
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.
Annotations
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.
Drawing
Constraints
It is 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 building.
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.
Bond
Labels
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 mechanically
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.
What Was New in HyperChem 7.0 and 7.5
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
combinations 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.
Charmm Protein Simulations
The Bio force field in
HyperChem represents a version of
the Chemistry at Harvard using Molecular Mechanics (Charmm) force
field. Release 7.5 of
HyperChem updated this force field with new functional
terms and new parameters to represent the latest science from the Charmm
community.
The new parameter sets for Charmm-19 represent new parameters for the
bio force field of earlier versions of HyperChem, but parameter sets
Typed Neglect of Differential Overlap (TNDO)
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 mechanics.
HyperChem 7.5
included 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.
Molecules in Magnetic
Fields
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
7.5 added 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 the Geometry of Excited
States
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.
Optimization
of MP2 Correlated Geometries
A relatively 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.
New Rendering of Aromatic
Rings
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
7.5, it was made possible to represent aromatic rings as a more
conventional ring with a circle in the middle of it, rather than a ring
with dotted bonds.
Drawing Program
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
7.5 this drawing capability was extended to lines, ellipses (circles),
and rectangles (squares). These elements can be colored, filled or
unfilled, dotted, etc.
They are included in the latest HIN file standard so that HyperChem
can be used as a simple drawing program.
Interactive Examination
and Manipulation of Parameters
Molecular mechanics 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
chemical computations. It has always been possible to edit the
text-based parameter files and re-compile them. With
HyperChem
7.5, it was made 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.
Enhanced Polymer Builder
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.
New Basis Sets
In conjunction with the new DFT capability of
HyperChem
7.5, 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.
New User Colors
When HyperChem was developed back in the 1980s for the
first version of Windows, it was restricted to a total of 8 standard
colors. Since many shades of these 8 are available for shaded models of
molecules and orbitals, it has not been a debilitating limitation.
However, it does not allow pastels and specific colors that a a
particular user might desire. With Release 7.5 the limitation to 8
colors was relaxed to essentially permit you to use any of the 16
million (24 bit) colors available with most graphics cards.
Rather than forcing a user to continually decide on
these 24 bits, Release 7.5 introduced the concept of "User Colors" that
you can set to any of the 16 million choices and then reuse easily. This
is done by adding to the standard 8 Windows colors, 4 user-definable
colors referred to as user1, user2, user3, and user4. HyperChem 7.5
provided an easy way for you to define and retain, and remember these
colors.
Different Rendering for
Different Atoms
While Hypercube, Inc.’s version of HyperChem for Unix (SGI)
allowed this, until now the Windows version of HyperChem required you to
use the same rendering for every atom in the system. With Release 7.5,
you could now choose to mix renderings and any of the various atom
renderings can be used with any atom. A new tube rendering is now
available so that any atom in the system can now be rendered as:
• Sticks
• Balls and Sticks
• Balls and Cylinders
• Overlapping CPK Spheres
• Tubes
In addition, any atom can have a dot surface added to
its rendering. The radii of all balls, spheres, cylinders, and tubes can
be varied.
Protein Capabilities
Release 7.5 added significant new capability for dealing
with peptides and proteins, particularly as related to Protein Data Bank
(PDB) files. The new features are:
• Peptide builder knows further secondary structure,
such as 3-10 helix, for example.
• Protein secondary structure is part of each residues
definition. Each residue can be helix, sheet, turn or random coil.
• Protein secondary structure is automatically extracted
from PDB files and automatically retained in corresponding HIN files.
• You can make a selection based upon protein secondary
structure.
• Secondary structures, such as helices and sheets, can
be rendered in a variety of new ways. There are now two main rendering
motifs - rendering of atoms and rendering of secondary structures.
• Selection can be used to arbitrarily color secondary
structure renderings.
Secondary Structure
Renderings
HyperChem has always contained a relative primitive
ribbon rendering of proteins. That is, the earlier rendering consisted
of parallel lines along the backbone. With Release 7.5 and the
introduction of OpenGL into HyperChem, a number of other more
sophisticated solid ribbon-like renderings were made available. These
consist of:
• Ribbon lines.
• Thin solid ribbons.
• Thick solid ribbons.
• Cylinders - normally representing the position of head
and tail of helices.
• A tubular coil rendering - normally representing
random coil secondary structures.
The properties of these protein secondary structure
renderings, such as thickness (or radius) can be manipulated to suite
your personal taste. They can be colored in arbitrary ways. A default
secondary structure rendering is based of the actual secondary structure
(such as cylinders for helices). However, you can customize the
secondary structure rendering (for example, using a tubular coil
rendering for helices rather than a cylinder).
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