Hyperchem 8 1b422s

HyperChem 8.0 Professional Edition ===============================

FIXES and CHANGES to 8.0.7 in 8.0.8 ======================= 1. This version has the installation of a set of Windows runtime software modules that enable certain XP machines, such as some netbooks, to run HyperChem correctly. 2. A bug in 2D Potential Plots that essentially made them unavailable has been fixed. 3. Raytracing didn't work in 8.0.7 as HCRay.ini didn't properly point to Povray - fixed.

FIXES and CHANGES to 8.0.6 in 8.0.7 ======================= 1. This version has full compatibility with respect to Windows Vista and Windows 7. 2. A newer Windows 7 compatible version of Povray (3.6) has been added for raytracing. 3. HyperNMR has been rebuilt to function in 64-bit and Windows 7 environments. 4. Better RM1 parameters consistent with authors of RM1 are included. 5. The interface for Mopac2007 has been replaced by one for Mopac2009 and now includes a transition state interface. 6. Linux versions of the various backends are on the CD and can be used with the Network dialog box to farm out computations to various Linux servers connected to a Client HyperChem. 7. Hardlock (Dongle) licensing now works with 64-bit operating systems. 8. Errors in Equilibrium Constant calculation were fixed. 9. Errors in printing were fixed.

FIXES and CHANGES to 8.0.5 in 8.0.6 =======================

1. The new annotation graphics in 8.0.5 introduced a bug in the particle-in-box capability for regions of constant potential (linear potentials were OK). This problem is fixed in 8.0.6. 2. The new annotation graphics in 8.0.5 resulted in the tying of dotted lines for aromatic bonds to the dotted lines for annotation lines. Thus, aromatic bonds were not displayed correctly unless dotted lines were chosen for annotations. This is fixed in 8.0.6 where the two types of dotted lines are disassociated.

FIXES and CHANGES to 8.0.4 in 8.0.5 ======================= 1. The previous change from "current selection" to a named selection for the quantum region in calculations is now correctly reflected when asking for orbital and density plots. 2. The restraint of many HSVs having to be less than 32767 is now released. 3. Problems drawing (artifical white background) for Vista and certain graphics cards or graphics drivers is now fixed. 4. Annotations and certain isosurface plotting options which previously used older Microsoft graphics are now fully OpenGL. This eliminates some problems with "flashing" and the rendering of these on Vista and certain graphics cards or graphics drivers. These changes result in smoother, better, fully OpenGL compatible graphics everywhere in HyperChem. 5. Improvements to the vibrational analysis in HyperMM+ and HyperNewton allow proper investigation of the symmetry of normal modes. 6. A number of new script variables and commands have been added. 7. An RM1 option has been added to TNDO to go along with CNDO/INDO-based TNDO.

FIXES and CHANGES to 8.0.3 in 8.0.4

======================= 1. The hsv.h, hsv.bas, hsv.fi are now corretly installed and consistent with Release 8.0.3 or 8.0.4. 2. The script command "name-selection XXX" where XXX is POINT, LINE or PLANE has been fixed. 3. The New80.exe file, allowing the installing of a apart from , is now part of the standard install. 4. The softlock version of HyperChem now only looks at the hard drive and not the ethernet card. This elimnates some problems associated with losing ones license when the network configuration is changed. 5. A bug with linear (not constant) potentials in the Particle-in-a-Box annotations is fixed. 6. A bug associated with displaying electrostatic potentials for very large molecules has been fixed. 7. Some additional sample scripts have been added to the CDK directory.

FIXES and CHANGES to 8.0.2 in 8.0.3 ======================= 1. FIXEDATOMS was not always assigned nor released properly in scripts. It now is. 2. MECHANICALATOMS was not always assigned nor released properly in scripts. It now is. 3. The script color-secondary-selection didn't work properly - fixed. 4. Memory is not always released because of new Undo operation in Release 8. Memory may not be recovered until a "New" menu operation takes place. For memory critical applications that delete large numbers of atoms a script variable "undo-disabled" is now available.

5. The default values for plotting orbitals etc. did not reflect new use of the MECHANICALATOMS named selection rather than current selection. Fixed. 6. MM/QM operations were not always using new MECHANICALATOMS rather than current selection to distinguish quantum region. Fixed. 7. Protein "Turn" in HIN files was not properly recognized - Fixed. 8. Some anomalies in differential rendering of neighboring atoms were fixed. Affected primarily "tube" and "ball and cylinder" renderings on adjacent atoms. 9. An older hcqmart.dll was getting installed affecting rendering of some semi-empirical obitals and densities. 10.Selection of residues based on their name was broken - Fixed. 11.A new chem.tpl file addresses some anomalies in positioning of HG in Leucine and HE in Arginine. 12 Made scripts produce 0.0 rather than 0 for output of floats (e.g. for third party fortran programs). 13.Made consistent when using scripts to read/write coordinates when have lone pair atoms.

ADDITIONS in 8.0.3 ================== 1. New script variables are available in 8.0.3: undo-disabled -saves some meory point-to-point -new geometric variables point-to-line point-to-plane line-to-line line-to-plane plane=to-plane

vibrational-energy -new energies rotational-energy translational-energy vibrational-entropy rotational-entropy translational entropy system-temperature -as opposed to dynamics temperature 2. Selection of tube-rendered atoms was made easier by coloring half bond.

Fixes and Chabges to 8.0.1 in 8.0.2 =======================

1. All basis set files (many missing in 8.0.1) are now included in the install. 2. A new version (no functionality change) of HCSugar.EXE is included in the install. This fixes an ID problem so that it can be executed properly by 8.0 3. A fix to HCConformation.EXE eliminates false error message about problems with "Unable to vary acyclic torsion". 4. Fix to HyperChem that retreats to allowing HyperChem to name HIN files with any extension. This eliminates false error messages about *.$$$ files from modules that interact with HyperChem using such HIN files. 5. Fix to retaining restraints properly in HIN file. 8.0.1 had a problem coming from new universal double precision that restraints not read out of HIN file correctly (difference between %lf and %f).

6. Fix to problem in playback of dynamics that sometimes didn't show plot because mod of period was not working correctly. 7. Fix reading and writing of ISIS sketch files. These are binary files and must use floats not doubles. Change to universal double prcision broke these.

HyperChem 8.00 Professional: An update to HyperChem 7.52 Professional ===================================================================== Known Problems

(1) VISTA ONLY - Microsoft no longer s the help engine that HyperChem uses for its help capability and thus does not include it with Vista. It can, however, be ed for Microsoft. Without this Help does not function on Vista machines. The file to down load is WinHlp32.exe from www.microsoft.com/s - search for winhlp32.exe. Network s may wish to explore the winhlp32.exe issues further at .microsoft.com/kb/917607. The warning about macros can be eliminated with information described there.

(2) VISTA ONLY - Some graphics cards still do not have great vista drivers. If using Vista be sure you have a recent driver from the card manufacturer. A problem has been seen on Intel Mobile ggraphics involving drawing with "sticks". This was solved by a newer driver on other machines.

(3) Some time the Particle-in-a-box seems to appear when unasked. A simple File/New will eliminate this.

(4) Some graphics cards don't show annotations properly. Need to use a better graphics card or driver.

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Changes in HyperChem 8.0

* double precision everywhere

* geometries (PLANE to PLANE, etc.)

* Substituents (Methyl, Amide, etc.)

* color of drawing icons, etc.

* add c,n,o to toolbar

* using periodic table easier (focus is at main window)

* improvements to printing (hdc rendering)

* rendering of POINT, LINE, and PLANE

* Calculation of Entropies, Free Energies, and Heat Capacities.

* Calculation of zero point vibrational energy

* Better integration of Temperature into Program

* Calculation of Particle-in-Box energies and wavefunctions

* undo and redo added

* Recent file List Added

* Modelbuilder button on toolbar

* CI made clearer by being separated from Single Point

* fixes for Vista

* Added batch for native

* Third-party Interfaces - interctive, batch, and input only

* added line width envelope for IR and UV spectra

* added named selections for fixed and quantum

* made selection of surface renderings better behaved

* vibrations for molecular mechanics

* calculation or rate constants

* calculation of equilibrium constants

* expanded use of MP2

* imposed electric fields for molecular mechanics

* better clarification and ands use of units (kcal/mol, etc)

Changes in HyperChem 7.52

FUNCTIONALITY CHANGES

* Enhanced smoothness of secondary structure rendering. The display of secondary structures has better resolution particularly for highly-curved backbones.

* Beta Sheet displays now include an arrow showing N to C direction.

* Stereo display of molecules has returned with enhanced options. This was temporarily lost in going to OpenGL rendering but is now available again. Options for creating hard copy stereo images are particularly improved.

* Transparent isosurfaces. These were missing in the first OpenGL versions but have returned with OpenGL quality.

* Specific secondary structures, such as "Helix4", can now be selected. Previously only "All Helices" was available.

* Secondary structures can now be interactively selected by explicitly clicking on them with the mouse.

* When all atoms are hidden it now chooses a box for isosurface computation that includes the size of the whole molecule whereas before the box was only chosen based on visible atoms.

* New scripting of dot surfaces - apply-dots and hide-dots.

* Thick line drawing applied to bond drawing no longer applies to isosurface meshes.

* Maximum number of secondary structures in PDB files has increased.

BUGS FIXED

* A bug that gave the wrong value of dipole moments when computed from molecular mechanics has been fixed.

* A bug in the rendering of "Balls" has been fixed. This rendering appeared

on some but not all platforms. This rendering differs from K in that it includes "sticks" leading to a "ball and stick" rendering when the ball radius is small.

* A bug such that right mouse button (as opposed to left mouse button) rotation and translation moved only atoms but not secondary structures has been fixed.

* A bug that slighly affected convenient closing of secondary structure color preference sheet has been fixed.

* A bug that showed duplicate labels when rotating certain isosurfaces has been fixed.

* Using RenderUsingOpenGl=No in Registry to revert to older graphics no longer results in optimization crashing.

* Render-method script no longer applies only to current on-screen rendering but also to next use of variable such as in the rendering dialog box.

* Scripts to rotate and translate molecules now apply to associated secondary structure rendering as well as to the atoms.

* A bug that left off last residue when applying special coloring to a beta sheet connected to a coil has been fixed.

* A bug in showing the previous "average value" of a quantity averaged

during a molecular dynamics playback has been fixed.

* Redundant and non-functioning Help Menu Items have been removed.

* A bug that resulted in Hyperfine constants not being computed for DFT has been fixed.

* A bug that allowed only reading and not writing of XYZ files has been fixed.

HyperChem 7.51 Professional: An update to HyperChem 7.5 Professional ====================================================================

HyperChem 7.51 New Features

* Different rendering quality is possible for static and rotating molecules. This allows one to use a faster, lower quality rendering while rotating or moving a molecule, and a higher quality for a non=moving molecule.

* Alpha cylinder rendering now has the option to be capped.

* Ball and cylinder renderings now have the option to scale the balls by their Van der Waals radii. Previously all balls were the same size.

* The width as well as the thickness of ribbons can now be modified.

Changes to HyperChem 7.5

* The red to green to blue rendering of isosurfaces has been reversed to use red as the positive potential and blue as the negative potential.

* Isolated atom rendering has been changed to fix certain display problems.

* The tube display of double and triple bonds has modified (improved).

* Protein data bank files now use *.PDB as well as *.ENT for file extensions.

Corrections to HyperChem 7.5

* Aromatic rings now displayed correctly

* Dipole moments now displayed correctly

* The Raytrace feature is now compatible with the latest version of POV-Ray.

* A bug in the QSAR module which incorrectly reported zero for the surface area of large molecules has been fixed.

* A bug associated with certain graphics hardware that caused HyperChem to

eventually use up all its resources and disable a proper display has been fixed.

* The menu item, "Display/Show Isosurface", that toggled isosurfaces has been fixed.

* The F2 key that recovered the last rendering only worked the first time. It has been fixed.

* A bug that sometimes caused the first displayed label to be colored differently from other labels has been fixed.

* A bug that sometimes caused isosurface renderings to scale down in size after bringing up "File/Preferences" has been fixed.

HyperChem 7.5 Professional: An update to HyperChem 7 Professional =================================================================

HyperChem 7.5 New Features

* The basic rendering model in HyperChem has been converted to a full new OpenGL model. This affects all the molecular rendering giving a generally higher quality of graphics throughout the product.

* It is now possible to color molecules, backgrounds, etc. using any of 16 million available colors rather than the traditional 8 standard colors

that HyperChem has used in the past.

* The rendering of molecules s different rendering for different parts of the same molecule. That is any atom can be rendered using any of the rendering molecules -- stick, balls, ball and stick, etc.

* A new "tube" rendering is now available for atoms.

* Extensive additions have been made to HyperChem's ability to deal with protein structures. HyperChem now s four secondary structure descriptions - helices, sheets, turns, and coils. The secondary structures can be individual selected, colored, and renderered using a new secondary structure rendering capability.

* HyperChem recognizes and s secondary structure information in its molecule files. Information from protein database (PDB) files is captured for and retained in HIN files. The peptide builder s this new capability and adds a secondary structure description to all residues.

* Secondary structure rendering now includes ribbon lines, narrow ribbon sheets, thick ribbon sheets, encoming helical cylinders and a coil rendering. These new renderings can be selected for any secondary structure or part of a secondary structure. They can be colored globally or colored differently for specific residues.

* In addition to alpha helices and beta sheets, the peptide builder now s beta turns, parallel and anti-parallel beta sheets, left-handed

alpha helices, 310-helices, and pi-helices.

* A rapid new method is available for calculating and displaying the electron density and electrostatic potential of molecules. For example, the new method makes it practical to very quickly display the electron density of large proteins.

HyperChem 7.1 Professional: An update to HyperChem 7 Professional ==================================================================

1. Changes to HyperChem 7

* A large set of tutorials has been added to the product. These tutorials use videos to explain various operation in HyperChem. The videos (AVI files) are invoked by clicking on an HTML link in a new HTML Help engine and tutorial interface. The tutorials can be invoked directly from HyperChem and installed with HyperChem or they may be left on the installation CD-ROM (they occupy more than 200 MBytes) and played off the CD-ROM from HyperChem or played completely independently of HyperChem.

* The Select... Dialog was fixed to allow the selection of single character atom types.

* A previously undocumented script command, re-bond-system, had a bug that caused the hin file to be incorrectly written when the file is saved. This

bug had been fixed. This new script command will completely remove all the bonding information of a molecular system, and add bonds where appropriate based on a simple set of rules of atom distances. Because there is not a rigorous procedure for determining bonding rules, this tool is not designed to be applicable to all systems and all bonding conditions. The best use of the re-bond-system script command may be when replaying dynamics simulations. Setting the re-bond-system command to execute at every timestep (using the chem_dynamics.scr file) will allow you to visualize chemical bonding changes during dynamics playback. The script file chem_dynamics.scr is executed at every step during dynamics simulations playback.

* The atom-labels script command gave the wrong labels for mass, basis set and chirality. These have been fixed and new labels have been added. The available options for the atom-labels script command are:

None, Symbol, Name, Number, Type, Charge, Spin, Mass, BasisSet, Chirality, RMSGradient and Custom

* A erroneous warning produced by the factory-settings script command has been eliminated.

* The New.exe utility has been updated. Now the HyperChem 7 installation saves default registry settings in the HKEY_LOCAL_MACHINE portion of the Windows Registry. When HyperChem is installed on a multi- system, the New.exe utility should be executed for each , so that the s registry values may be initialized. The New.exe utility copies the

settings from HKEY_LOCAL_MACHINE to HKEY_CURRENT_.

* The Quench Rotation about Center of Mass operation in the Set Velocity dialog box and the associated reporting of rotational velocity and energy was not working properly and has been fixed.

HyperChem 7.03 Professional: An update to HyperChem 7 Professional ==================================================================

1. Changes to HyperChem 7

* A Charmm improper torsions bug that routinely caused Charmm22 force field calculations to crash has been fixed

* Software-licensed server software (SentinelLM software) updated

2. Updates to HyperChem 7

* HyperChem can now run with in an environment where the \Hyper7 folder is set as read-only.

* Raytrace and the Crystal Builder use the ChemTempPath setting for temporary files

* NMR uses the NMRTempPath setting in the win.ini file for temporary files

3. Addition to HyperChem 7

* Sample HyperChem scripts and Excel macros have been placed in the \Samples\Scripts folder

HyperChem 7.02 Professional: An update to HyperChem 7 Professional ==================================================================

1. Changes to HyperChem 7

* Improper Torsions

With Release 6, a small error related to improper torsions (keeping carbonyl groups planar, for example) crept into HyperChem. This error has kept a number of optimizations of proteins (or nucleic acids) from sometimes converging as tightly, ie. beyond ~0.01, as one might have liked. This error only affected HyperNewton not HyperMM+. This small error was never noticed until now but has been corrected in Release 7.02.

* ZINDO/s Chlorine parameters

* New improper torsions for Amber 94 and Charmm22 force fields

* Amber94/96 *.par file update

* NMRParmPath correctly set by install

* Eliminate total number of atoms ceiling

* Eliminate PocketPC HIN file 4K maximum

HyperChem 7.01 Professional: An update to HyperChem 7 Professional ==================================================================

1. Addition to HyperChem 7

* Pocket HyperChem Server

This Release of HyperChem now allows HyperChem to act as a server for Pocket PC's running Pocket HyperChem. To Place HyperChem in "Server Mode", check the appropriate box in the Network Options dialog box accessed through the Setup\Network menu item. To return to "Interactive Mode" just click on the Cancel menu.

To use HyperChem as a server for calculations from a Pocket PC or other handheld device you need to have purchased the appropriate version of Pocket HyperChem (1.1 or greater).

* Amber 99 Parameters

This Release includes new Amber parameters labeled as Amber99. They are for use with the same Cornell et. al. force field (JACS, 117, 5159, 1995) as per Amber94 and Amber96 but with a newer set of parameters applicable to a broader range of molecules.

* New Semi-Empirical Parameters

PM3 parameters added for Li, B, Ca, Ru and Gd AM1 parameters added for Na, K and Sn MNDO and MNDO/d parameters added for Na and K

2. Corrections to HyperChem 7

* Save As HTML...

The technology introduced in HyperChem Release 6 and continued in Release 7.0 for producing HTML files, using "Chemical Objects for the Web" (COW) files, enabling dynamic web display of molecules, orbitals, spectra, etc. was developed using Netscape plug-in technology so that web pages could be viewed with Netscape browsers as well as Microsoft browsers. Unfortunately, Microsoft decided with Service Pack 2 of Internet Explorer 5.5 and beyond to stop ing Netscape Plug-ins. Thus, with Release 7.0 of HyperChem this functionality was specifically broken for Internet Explorer 6.0, the current version of the Microsoft browser.

Hypercube, Inc. is making an effort to recover this technology by using ActiveX controls rather than Netscape plug-ins. This release of HyperChem contains a new ActiveX control, IEHin32Control.dll, that replaces much of the previous functionality for Internet Explorer 6.0, i.e NPHin32.dll. The Save As HTML dialog box now allows you to create HTML pages for the new control as well as the older plug-in. Unfortunately, the new ActiveX control does not yet allow display of Spectra but only of molecules, orbitals, and normal modes.

Both the Newer, ActiveX Version and the Older, Plug-in version are available in HyperChem 7.01. The newer ActiveX control works with any version of Internet Explorer, including Internet Explorer 6.0 and later. The older plugin version works with Netscape 4 and Netscape 6 (Mozilla) and Internet Explorer 5.0, and 5.5, but does not work with Internet Explorer 5.5 SP2 or later.

The Save As HTML feature of HyperChem can only create pages compatible with one version or the other. HTML pages that work in the plug-in version will not work in the ActiveX version or vice versa, even though the COW files are identical.

* The default bond order for Amber and Charmm has been corrected. The default bond order (for default parameters) was always a single bond.

* Potential energy plotting should now work as d. The graph32.ocx file was not properly ed on installation.

* HyperChem sometimes gave an error when reading older *.hin files created with the HyperChem modules. HyperChem has been set to disregard final zero in "mol 1 0" entries in hin files.

* Molecular mechanics calculations did not work correctly if the last quantum mechanical optimization method was conjugate directions. The optimization method is now reset.

* Molecular mechanics calculations failed when HyperChem was configured with the default registry values. The MechanicsComponentFlags value is now properly set on exiting HyperChem.

* In certain rare circumstances, the reported energy was corrupted but was immediately obvious as an invalid value. This associated bug has been fixed.

* HyperChem Data 'Get Record from HyperChem' function gave an error when no database is open. The function is no longer available without an open database.

3. Updates to HyperChem 7

* Amino acid template entries have been corrected for Amber 94 and 96 zwitterions. Previously, the template charges were zero.

* HyperChem on-line help has been updated to include images of dialog boxes.

4. Known bug in HyperChem 7

* QSAR Surface Area (grid) returns zero values for surface area on small proteins of > 80 residues. QSAR should be used for modest-sized molecules only.

HyperChem 7 Professional ========================

Contents

Installation Windows NT, 2000 and XP Installation HyperChem 7 & Computational Chemistry Discussion Pages Report Bugs What's New in HyperChem Release 7

1. Installation

The HyperChem 7 installation is started by executing setup.exe from the HyperChem 7 CD. When installing a purchased copy of HyperChem, select 'Purchased Product' from the installation options and choose the HyperChem version corresponding to the purchased license type.

HyperChem 7 Evaluation Installation

HyperChem Release 7 includes a 30-day evaluation license. Please install the Evaluation version of HyperChem 7. After the installation, the HyperChem Client Activator will start. You will have the option to 'Evaluate' the software during the Evaluation period. If you which to install the standalone or network versions, please [email protected].

2. Windows NT, 2000 and XP Installation

HyperChem must be installed with privileges under Windows NT, 2000 and XP. Before using HyperChem as a , run:

C:\Hyper7\Program\New.exe

after logging on as a to set up the HyperChem Registry.

3. HyperChem 7 & Computational Chemistry Discussion Pages

To participate in the HyperChem 7 and Computational Chemistry discussion pages, please visit http://www.hyper.com/Discussion. You may report bugs in the software, suggest new features or share ideas on topics in HyperChem 7 specific and general computational chemistry.

4. Report Bugs

Please Report bugs and other comments to Hypercube, Inc.

Phone: Fax:

(352) 371 7744 (352) 371 3662

Email:

mailto:[email protected]

Web Site:

http://www.hyper.com/

Discussion:

http://www.hyper.com/Discussion

5. 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 .

NMR Simulation

The HyperNMR package has been integrated into the core of HyperChem. This package allows for the simulation of NMR spectra. An accurate 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 coupledHartree-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 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 s, 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 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 s 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 , 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.