Microsoft Windows 7 and Vista Compatibility

Microsoft Windows 7 and Vista involves extensive new and modified features. HyperChem 8 has been prepared to provide reliable computation in this new environment. In some cases, however, manufacturers’ graphics drivers (OpenGL drivers) have not proved to yet be up to the earlier standards of Windows XP. Where problems have been seen, installation of a new driver from the graphics card manufacturer has often eliminated any problem. To use HyperChem effectively, one should have a good graphics card and a compatible newer driver. Any graphics hardware should be sufficient to run HyperChem. However, inexpensive machines will often have graphics hardware, included on the motherboard, that results in relatively slow manipulation of large molecules, compared to that with a modern 3rd-party graphics card.

HyperChem 8 has the capability of being a graphics and GUI provider (including the displaying of results) for a number of third party software packages. These packages may include other ab initio and semi-empirical packages such as GAMESS and MOPAC2009. Included with HyperChem 8 is the copyrighted source code for a number of these interfaces. A standard menu item in HyperChem, “Third-Party Interfaces” executes a standard HyperChem Command Language (HCL) script installed with the product. This script has the pre-defined name, thirdparty.scr. This script can be modified by users to add other third-party applications but comes included with a variety of evolving interfaces. These interfaces uses the elegant “open architecture” features of HyperChem that allow software outside HyperChem to interact and read/write information to/from HyperChem. The interface software is copyrighted “Open Source” software that any HyperChem user can modify to improve the interface or to create a new interface to his/her own software. The interfaces generally allow a user, for example, to run a GAMESS job from within HyperChem, and get back the results for display. The first level of interface, that is included to begin with in HyperChem 8, allows a user to display optimized structures, vibrational spectra and animations of normal modes plus 3D renderings of orbitals, electron densities, and electrostatic potentials. It is to be expected that these interfaces evolve to become richer as users and members of Hypercube, Inc. contribute to their capability.

New Batch Capabilities

HyperChem has traditionally operated in a purely interactive mode where a calculation (a back end, e.g. HyperNewton) is connected in a “live fashion” to HyperChem (the front end). This has been the case even when the back end resided on another machine on the network. This is not a terrible limitation since once can run many HyperChem front ends simultaneously if one likes. With HyperChem 8, however, one now has the choice of running a calculation interactively or in Batch mode. In Batch mode the computation is severed and carries on by itself while HyperChem is free to read in a new molecule or continue on in any way it pleases, including spawning more batched jobs. The back ends have been instructed by the front end that they are indeed batch processes and instead of sending their results live to the front end, they create a *.ext file that can be read at any later time into the HyperChem front end to display the results just as if the calculation was run interactively.

Universal Use of Double Precision

Because of Hypercube, Inc. long history, there has been a legacy history of using single precision floating point to save time when double precision was not absolutely necessary. Thus, until now coordinates of molecules at the front end (i.e. HyperChem) were single precision while coordinates at the back end (e.g. HyperGauss) were double precision where they needed to be. This saved time for graphical and communication operations where precision was not critical. However, small discrepancies between the front end and back end coordinates were occasionally noticeable such as when restarting an optimization. The optimization lost some precision when results were sent back to the front end. With faster graphics and faster machines, HyperChem is now universally double precision.

Undo and Redo Capabilities for Model Building

A feature that has occasionally been adamantly requested in HyperChem is now available. This is an “undo” operation for molecular manipulations. Thus one can delete atoms, draw atoms, etc. and decide that these changes are undesirable and Undo them. Along with undo is a “redo” when the undo is decided as undesirable! These features are common in many programs but not in molecular modeling. They are now available in Release 8. Naturally one cannot undo everything so this capability is restricted to changes in the molecular structure of the molecules in the workspace.

Easy Access to Molecules via a Recent File List

Another feature that is common in many Windows programs that has been missing in HyperChem is the ability to see a list of recent Geometric Measurement Involving Points, Lines, and Planes file openings and closing so that one doesn’t have to go searching again through the file system to read in a molecule that one recent read. This “File List” is now available in HyperChem and is four files long.

Geometric Measurement Involving Points, Lines, and Planes

HyperChem has long had the idea of a POINT, LINE, or PLANE. If one selects a set of atoms (all or any subset of the workspace) one can define POINT, LINE, or PLANE. The POINT is the center of mass of the selection. The LINE is the principal axis of the selection and the PLANE is a plane through the center of mass perpendicular to the tertiary axis. Thus PLANE is, for example, the plane of a Benzene molecule. With HyperChem one can now visualize these geometric features and make associated measurements. Thus, one can ask about the variables associated with the selection that previously created POINT, LINE and PLANE and the current selection. Thus measurements are available of the distance between two POINTs, the distance of a POINT to a LINE or a PLANE, the angle between two LINES or a LINE and a PLANE or the angle between two PLANES.

A Chemical Substituent Operation

One of the most elegant features of HyperChem is the ability to create a three-dimensional molecular structure by just drawing it and applying the model builder. This remains true. However, with HyperChem 8, another rapid drawing capability is available. 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.

Revised Toolbar with Easier Access to Model Building

Model building in HyperChem normally involves the selection of an element, often Carbon, to draw a skeleton of the molecule which is then possibly modified with the addition of some Nitrogens, Oxygens or more rarely other elements, and then performing a model build without “Explicit Hydrogen”. This adds the requisite Hydrogens automatically. This operation is now easier as the selection of Carbon, Nitrogen, Oxygen, and the subsequent Model Building have been added to the toolbar. It is still possible to do everything as before. The new toolbar elements just make common operations faster.

Calculation of Entropies and Free Energies

All previous versions of HyperChem really only dealt with Energy (Enthalpy?) rather than Free Energy. This is in some sense a historical association with Quantum Chemistry which has traditionally focussed on these to the detriment of Entropy and other thermodynamic variables. 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). These calculations are now available in HyperChem 8 as a function of Temperature. 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

Computational Chemistry and been better at Structure and Thermodynamics than at Kinetics. May molecular modeling programs have little to say about rate constants which are obviously an important quantity in chemistry. With Release 8, 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 8 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

A new semi-empirical method is available in 8.0.  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. the reference is: Gerd B. Rocha, Ricardo O. Freire, Alfredo M. Simas, James J. P. Stewart,: RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I, Journal of Computational Chemistry, Vol. 27, 10, 1101-1111, 2006.

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. With Release 8 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 Interaction 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.

With release 8 a “named selection” is used to distinguish QM atoms from MM atoms in a MM-QM computation. The new pre-defined named selection is called “MECHANICAL ATOMS”. Such a selection of atoms will become the MM atoms of any quantum calculation.

Separation of Fixed Atoms from Current Selection

This new option related the one just described above. Atoms subset selected in a pure MM calculation were previously the only ones allowed to move. While convenient, this was limiting. Now a new pre-named selection, “FIXED ATOMS” is used to specify that any atoms in either a MM or QM calculation are fixed in Cartesian space and not allowed to move in optimizations, molecular dynamics, Monte Carlo, etc. This capability is not new in MM but does allow a whole new capability in Quantum Mechanical calculation.

These fixed atoms need not have their gradients calculated in any computation and as such this new option ought to speed up calculations. In addition there may be situations where one wants to leave a portion of a molecule fixed and only allow optimization, dynamics, etc. on a portion of the molecule. As with MECHANICAL ATOMS, one ought to be careful now that FIXED ATOMS are not set when you don’t want that option. These two options are now less visible that when they involved the current selection.

Vibrational Analysis for Molecular Mechanics

Until Release 8, vibrational analysis was restricted to one of the quantum mechanical methods. Now 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.

Ability to Explore “Particle-in-a Box” Wave Functions

A new capability that might be thought to be somewhat disjoint from the rest of HyperChem is its new ability to perform calculations of the energies and wavefunctions for relatively arbitrary shaped “Particles in a Box”. This capability is likely to be extended later to include hydrogenic wavefunctions (sperical harmonics) as well as anharmonic and harmonic wavefunctions simple diatomics. These capabilites are part of a standard Physical Chemistry curriculum and are targets for HyperChem to enhance its applicability in the educational experience.

The particle in a box functionality is implemented as an Annotation to keep it separate from the normal molecular modeling functions. The box is a box with infinite walls. Later it may be useful to extend this capability to finite boxes involving continuum (scattering) functions. A dialog box allows auser to choose the width and scale of the box and the number (n) of partitons of the box into either constant or linear potentials. The bottom of the box is drawn by the user in a very constrained way until the whole bottom, for the n partitions, is complete. At that point, the wave functions and energies levels are presented. These are simply annotations and can be treated exactly as any other annotation. The various components of the box can be deleted, as with other annotations. Selecting the dialog box again draws the walls for a new box to be drawn. Selecting New eliminates the box along with all other elements of the workspace.