HyperChem 7.0
Feature Summary
HyperChem Release 7, is a full 32-bit application, developed for the
Windows 95, 98, NT, 2000 and XP operating systems. HyperChem
Release 7 incorporates even more powerful computational chemistry
tools than ever before, as well as newly incorporated modules,
additional basis sets, new drawing capabilities and more.
What's New in HyperChem Release 7?

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.

NMR Simulation
The HyperNMR 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.
Based on 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 spectra.

Database Package
A full database capability is integrated into HyperChem 7. 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.

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 of HyperChem updates 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 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.

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 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.
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 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 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, 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
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 this drawing capability is 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, 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.

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, 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.