HyperChem 7.0
Feature Summary What's New in HyperChem Release 7?
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.