HyperChem

HyperChem is a molecular modelling environment that unite 3D visualization and animation with quantum chemical calculations, molecular mechanics and dynamics. As per today, the latest version is HyperChem 8.0.10. The features on HyperChem are:

A Chemical Substituent Operation

HyperChem has the ability to create a three-dimensional molecular structure by just drawing it and applying the modal builder. This involves the usual chemical idea of chemical substituents, R. In HyperChem these substituents replace any selected Hydrogen atom. Thus H->R has become a standard operation for a variety of common R-groups, including Phenyl (Ph). It is expected that a near term release of HyperChem will even allow users to define their own R groups. In any event it is now easier and faster to create molecules from standard components. Starting with H2 or CP, for example, one could create any organic molecule with a few clicks rather than having to draw the whole molecule.

Calculation of Entropies and Free Energies
Calculating entropies, of course, requires more effort than just the "simple" energy. However, with the computation of vibrational and rotational spectra comes the possibility of computing the energy (E), entropy (S), and Helmholtz free energy (A=E-TS). Temperature is now a more fundamental quantity in HyperChem than before as are the thermodynamic quantities that depend on it.

Calculation of Heat Capacities
As with Energy, Entropy, and Free Energy, it is now possible to calculate Heat Capacities. These are now routinely computed along with the other thermodynamic quantities that depend upon the temperature.

Calculation of Zero-Point Energies

At zero degrees Kelvin, the energy is the dominant quantity of interest but does not only have an electronic component. Until now vibrational analysis has not reported the zero-point energy of vibration. These now are a part of any vibrational analysis.

Computation of Rate Constants

May molecular modeling programs have little to say about rate constants which are obviously an important quantity in chemistry. HyperChem makes a start at making reactivity a mainstream molecular modeling activity. While only computing rate constants using the simplest Transition State Theory it is a beginning towards being a fundamental component of the whole of chemistry rather than only what computational chemists are best at.

HyperChem computes partition functions for reactants A and B (in biomolecular reactions) or just A (in unimolecular reactions) and then computes the partition function for the Transition State. The input to these calculations are the structure of each of these species (created in HyperChem and then stored in HIN files) as well as the energy, and vibrational and rotational spectra of the species (created in HyperChem and then stored in EXT files).

These quantities can come from external third party packages as well (as described in the Third Party Interface Section above. The partition functions simply require the vibrational spectra (frequencies only) and rotatational spectra (moments of inertia only) from an EXT file created by HyperChem or elsewhere. A calculation of the rate constant as a function of temperature is then made and becomes available as a simple plot for placing into Power Point, etc.). In addition, the Arrhenius parameters can be extracted from the variation of the rate constant as a function of temperature. If desired, and the the corresponding energies are available for the products (not just the reactants and transition state), a plot of the energy of reactants, transition state, and products is available.

Computation of Equilibrium Constants

Since free energies are now available in HyperChem, a similar simple capability for calculating equilibrium constants as a function of temperature to that described for rate constants above is now available. The Helmholtz free energy A as a function of temperature is calculated from the electronic, vibrational, rotational, and translational components of the energy and entropy. The equilibrium constant for the reaction is then just the appropriate exp(- A/kT).

New Semi-empirical Method, RM1

The RM1 method is essentially an extensive re-parameterization of AM1. The results given by this method are expected to be better than those from AM1 or PM3.   The elements available are still only those that have been available with AM1 and unfortunately are still a relatively small set of atoms not including any transition metals.

Since free energies are now available in HyperChem, a similar simple capability for calculating equilibrium constants as a function of temperature to that described for rate constants above is now available. The Helmholtz free energy A as a function of temperature is calculated from the electronic, vibrational, rotational, and translational components of the energy and entropy. The equilibrium constant for the reaction is then just the appropriate exp(- A/kT).

Further Capabilities for MP2 Perturbation Energies

HyperChem has had available the computation of second-order correlation energies via the MP2 method. These are given a more prominent position in that any single point energy used, for example, by optimization, by potential plots, by rate constants, by molecular dynamics, etc., can now include the MP2 energy as well as the SCF energy. Previously, the check box for MP2 only showed that correlation energy as a property of the SCF calculation. Now that check box will use SCF MP2 results as the energy for subsequent computations. The MP2 result is considerably more reliable in many circumstances that SCF Hartree-Fock result and with advances in desktop computation speeds it seems appropriate to give MP2 a more prominent role.

The MP2 gradients, unfortunately are still computed numerically rather than analytically so these calculations are certainly not as fast as pure SCF calculations. One also should be conscious that the check box for MP2 will be used universally and slow down what previously might have been only SCF computations.

Separation of Configuration from Single Points

In a corresponding move to that for MP2 replacing SCF, a more prominent role for Configuration Interaction (CI) is expected in the future. In addition, CI was somewhat hidden in nested dialog boxes for Single Point calculations so that it was not always clear that CI was turned on. This option has now been made explicit with a Single Point CI menu item for clarity and future additions to this capability.

Display of Line Width Envelopes for IR and UV Spectra

HyperChem has performed IR and UV computations for many years. These spectra are displayed as stick drawings with individual intensities shown on the plot. The similar display of NMR spectra over the years has had "line width" capability of assigning a line width to each spectral line (the same line width for each frequency) and then summing them up to obtain an envelope that simulates what the experimental spectrum might look like. No line widths are computed - only a slider is made available to simulate increasing global line widths. Release 8 makes this same facility available for IR and UV spectra that has been available for NMR spectra. The line width is initially set to zero but a simple slider changes the appearance of the spectra to the satisfaction of the user.

Separation of MM-QM Capabilities from Current Selection

HyperChem for many years (the first wide spread implementation) had the capability of performing MM-QM calculations, i.e. calculations that on a large system treat part of the molecule with quantum mechanics (QM) and the remaining part of the molecule with molecular mechanics (MM). This capability operated via the current selection. If a subset selection was invoked at the time a quantum calculation was requested, the selected portion of the molecule was treated via quantum mechanics and the remaining portion via molecular mechanics. That is, the charges of the MM par were included in the core Hamiltonian of the quantum part.

While convenient, this use of "current selection" has proved limiting in that "current selection" meant something different during pure MM calculations. There it meant atoms that were allowed to move rather than remain fixed in space. This also made it impossible to fix atoms in space during quantum calculations.

Vibrational Analysis for Molecular Mechanics
It is available across the board with any of the "Energy Engines" available in HyperChem. With vibrational analysis and rotational moments of inertia, it is now possible to calculate Entropies and Free Energies across the board as well.
It may still be possible to spend lots of computational time performing vibrational analysis, particularly for large molecules since second derivatives are still not computed analytically for any of the methods. It is a goal for HyperChem in the future to speed up those methods that depend upon second derivatives of the energy such as vibrational analysis. This ought to be, in principal, relatively easy for molecular mechanics.

Applied Electric Fields for Molecular Mechanics
Electric fields are now available in the workspace for any of the "Compute Engines". Previously, the ability to apply an electric field was restricted to quantum mechanical methods. In molecular mechanics, the electric field interacts with the atom charges on each of the atoms. For MM , which has options for either atom charges or bond dipoles, the electric field interacts only with the atomic charges.

Source: Hypercube