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.
- 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.