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HyperChem 6 FEATURE SUMMARY What is HyperChem? HyperChem is a sophisticated molecular modeling environment that is known for its quality, flexibility, and ease of use. Uniting 3D visualization and animation with quantum chemical calculations, molecular mechanics, and dynamics, HyperChem puts more molecular modeling tools at your fingertips than any other Windows program. What is new in HyperChem 6?

HyperChem 6 is a full 32-bit application, developed for the more powerful Windows 95, 98, NT and Windows 2000 operating systems. HyperChem 6 represents a major advance over earlier releases, with new visualization capabilities and important new customization tools. HyperChem 6 provides a more powerful and flexible molecular workspace than ever before. The new features of HyperChem 6 can be grouped into 5 categories:. The ChemPlus product has been integrated into HyperChem Professional.

The Molecular Presentations module has been dropped and in its place a new module, Polymer Builder, has been added. The modules integrated into HyperChem 6 still have a degree of separation form the core code and should be thought of as an integral part of HyperChem even though they integrate via Hypercube's module concept.

The integrated modules are:. RMS Fitting. Conformation Search.

Protein Sequence Editor. Polysaccharide Builder. Polymer Builder (New).

QSAR Properties. Script Editor. Raytraced Renderings New scientific methods are often associated with HyperChem's back ends.

Changes to the capability of these back ends involve new molecular mechanics methods, new quantum mechanics methods and new calculated properties form either of these technologies. New Force Fields HyperChem Release 6 adds significant new capability to the AMBER method of molecular mechanics by including up-to-date modifications of this force field. AMBER code now supports 5 parameter sets with their associated functional forms:. Amber 2. Amber 3.

Amber for saccharides. Amber 94. Amber 96 Default Parameter Scheme for AMBER and OPLS HyperChem Release 6 extends Hypercube's default parameter scheme, as previously implemented for MM+ to AMBER and OPLS. Thus any AMBER or OPLS computation can now continue computing with default parameters, when explicit parameters are missing from the relevant parameter file. The normal AMBER and OPLS parameter scheme fails when explicit parameters associated with 'atom types' are not available. With default parameters, no calculation fails for lack of parameters.

ESR Spectra Release 6 now makes available, for open shell systems, calculated values of Hyperfine Coupling constants characterizing the ESR spectra of the system. Electric Polarizabilities Polarizability tensors can now be computed in release 6. Some of the major new utilities in release 6 are: Save as HTML This feature allow you to calculate properties such as vibrational spectra or the orbitals of a molecule and save the results as an HTML file, which can be published on your web site using a free Active-X control distributed with HyperChem 6. This enables easy sharing of scientific data with colleagues across the world via your web site, where, for example, once can view an animation of the normal modes you computed or rotate computed molecular orbitals around for views from different angles. Plots of Potential Energy Release 6 allows you to select one or two structural features (bond length, torsion angle etc.) and request a plot of the potential energy as a function of either a single structural feature (2D plot) or two structural features (3D plot).

Protein Design Previous versions of HyperChem only allowed protein modifications that were point mutations. These mutation operations replaced a single amino acid with an alternative amino acid. In Release 6, it is possible to cut and paste any amino acid sequence. That is a piece can be cut out, a piece inserted, or a sequence of one length replaced by a new sequence of a different length.

Annealing operations are, of course, required for the rest of the protein to adapt to these modifications. Electric Fields It is now possible to superimpose an applied electric field on any calculation. For example, a charged system will now drift in the workspace during a molecular dynamics run if an external electric field has been applied. Studying molecular behavior in an electric field is now possible. The major new module in Release 6 is that associated with Annotations. HyperChem 6 defines a new plane for the workspace that is distinct from the molecular plane that has always been used to draw molecules, build 3D structures, and rotate and visualize molecules.

This new plane is the Annotation plane containing text annotations that can be used to describe the contents of the molecular plane. Annotations While it has always been possible to copy the rendering of molecules in HyperChem into a file or onto the clipboard and then transfer the rendering into a drawing or painting program to prepare overhead transparencies or other presentation material, directly creating such material without leaving HyperChem is now possible. An annotation in HyperChem is a length of text that can be placed anywhere in the workspace. Because the text can have attributes such as a font, a color, and a size, it is possible to create annotations such as arrows, lines, circles, rectangles and any number of other drawing primitives. Annotating the molecules that are being modeled in HyperChem allows you to print the workspace and more easily describe to others the results of your modeling.

Release 6 contains a number of features associated with creating and manipulating these annotations. Because they exist in a plane or layer that is independent of the molecular or modeling plane, they augment rather than collide with the modeling of earlier versions of HyperChem. At the same time by being able to show or print both planes at the same time, a rich set of annotation options is possible.

While that is not the primary intent, HyperChem could now be used to prepare illustrations independent of chemistry and molecular modeling. A number of other improvements have been implemented in HyperChem 6 that do not fall under the above topics: Charge and Multiplicity are Saved The total charge and spin multiplicity are now stored in the HIN file and are restored when a molecular HIN file is read. Earlier, these had to be set interactively for any new molecule in the workspace. Drawing Constraints It is now possible to constrain your drawing of 2D molecules so that the the resultant drawn molecule has uniform bond lengths and angles and resembles a standard 2D molecular representation as might be seen in textbooks.

These constraints have no effect on the subsequent 2D to 3D model building. Formal Charge is Now Defined Release 6 introduces the concept of a formal charge on an atom. This has always been missing in HyperChem. The formal charge primarily affects the model builder’s creation of a 3D structure from a 2D drawing. Now, for example, if the formal charge on a Nitrogen atom is set to +1, the model builder applied to the Nitrogen atom will create NH4+ rather than NH3 as in previous releases of HyperChem. When formal charges are zero, the model builder operates as it always has.

This features improves HyperChem’s basic understanding of chemistry. Label Enhancements A number of new labels have been defined for atoms. These labels are updated dynamically (during optimizations, for example) and include:.

Spin population - the total excess of alpha spin electrons over beta spin electrons on an atom. RMS gradient - a measure of the force on an atom. Custom text - arbitrary text that can be used to label an atom. Graphical Display of Gradients It is now possible to visualize the gradient (force) on any atom as a vector. Any set of atoms can display these vectors.

Bond Labels A new set of dynamically updated labels are now available for bonds as well as atoms and residues. These bond labels can be one of:. Bond length. Bond order - as calculated quantum mechanically Current Properties Now Available in GUI In Release 6 a number of calculated properties, such as the energy, are permanently available in dialog boxes, i.e.

They are in the graphical user interface rather than are just seen temporarily on the status line as they are computed. Earlier, these had to be retrieved from the log file if the status line was updated or changed. Enhanced Selection Capability HyperChem operations depend to a great extent on one’s ability to select a subset of atoms. Many ways have been available to select a subset but Release 6 further expands these selection options considerably. For example, it is now possible to select atoms based on the range of various computed quantities such as their atomic charge or atomic gradient. Thus, for example, one can now select all atoms with a charge between -0.1 and 0.1.

The atom selection options are now organized as either a selection based on a 'string' property of an atom, such as the atom type (e.g. CH), or a 'number' property such as the atom charge described above. Whether you use HyperChem's many internal features or build a live link with your other chemistry programs, the benefit of working with HyperChem 6 is that you are free to focus on the things that you do best. HyperChem does the rest. HyperChem 6 Feature Summary Structure Input and Manipulation Building molecules with HyperChem is simple: just choose an element from the periodic table, and click and drag with the mouse to sketch a structure. Mouse control of rotation around bonds, stereochemistry, and 'rubber banding' of bonds makes changing structures easy. Extensive selection, highlighting, and display capabilities make it easy to focus on areas of interest in complex molecules.

Select, rotate, translate, and resize structures with convenient mouse controlled tools. Modify settings to control operation of tools. Convert rough sketches into 3D structures with HyperChem's model builder. Apply builder constraints easily: specify bond lengths, bond angles, torsion angles, or the bonding geometry about a selected atom. Specify atom type, atom charge, formal charge and atomic mass.

Build clusters and complex molecular assemblies; move individual atoms and molecules as easily as you move groups. Build peptides and nucleic acids from amino acid and nucleotide residue libraries. Mutate residues and build large molecules incrementally (make changes at any point).

Add a periodic box of pre-equilibrated water molecules for aqueous solvation studies. Periodic boundary conditions can be used with other solvent systems, or without solvents. Import structures from standard file formats: Brookhaven PDB, ChemDraw CHM, MOPAC Z-matrix, MDL MOL and ISIS Sketch, and Tripos MOL2 files. Molecular Display.

Display structures using ball and stick, fused CPK spheres, sticks, van der Waals dots, and sticks with vdW dots; switch easily between rendering styles. Specify shading and highlighting, stick width, and the radii of spheres. Stereo and perspective viewing are also available. Display a Ray Traced image of the molecules in the workspace. Select and name sets of atoms for custom display or monitoring of properties.

Set and display custom labels for atoms. Display bond labels showing the current bond length or the currently computed quantum mechanical bond order. Display protein backbones using ribbons, with optional display of sidechains. Highlight potential hydrogen bond interactions. Display dipole moment vectors and gradient vectors.

Computational Chemistry Use HyperChem to explore quantum or classical model potential energy surfaces with single point, geometry optimization, or transition state search calculations. Include the effects of thermal motion with molecular dynamics, Langevin dynamics or Metropolis Monte Carlo simulations. User defined structural restraints may be added. Types of Calculations. Single point calculations determine the molecular energy and properties for a given fixed geometry. Geometry optimization calculations employ energy minimization algorithms to locate stable structures. Five minimization algorithms are provided.

Vibrational frequency calculations find the normal vibrational modes of an optimized structure. The vibrational spectrum can be displayed and the vibrational motions associated with specific transitions can be animated.

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Transition state searching locates the metastable structures corresponding to transition states using either Eigenvector Following or Synchronous Transit methods. Molecular properties are then calculated. Molecular dynamics simulations compute classical trajectories for molecular systems. Quantum forces can be used to model reactive collisions. Heating, equilibration, and cooling periods can be employed for simulated annealing and for studies of other temperature dependent processes. Both constant energy and constant temperature simulations are available. Langevin dynamics simulations add frictional and stochastic forces to conventional molecular dynamics to model solvent collisional effects without inclusion of explicit solvent molecules.

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Metropolis Monte Carlo simulations sample configurations from a statistical ensemble at a given temperature and are useful for exploring the possible configurations of a system as well as for computing temperature dependent equilibrium averages. Computational Methods Ab Initio Quantum Mechanics. Choose from many commonly used basis sets (STO-1G to D95.) including the standard STO-3G, 3-21G, 6-31G., and 6-31G. basis sets. Extra basis functions ( s, p, d, sp, spd ) can be added to individual atoms or to groups of atoms.

Users can also define their own basis sets or modify existing basis sets easily using HyperChem's documented basis set file format. Semi-empirical Quantum Mechanics.

HyperChem offers ten semi-empirical molecular orbital methods, with options for organic and main-group compounds, for transition metal complexes, and for spectral simulation. Choose from Extended Huckel, CNDO, INDO, MINDO/3, MNDO, MNDO/d, AM1, PM3 (including transition metals), ZINDO/1 and ZINDO/S.

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Molecular Mechanics. Four force fields provide computationally convenient methods for exploring the stability and dynamics of molecular systems.

Added flexibility of user defined atom types and parameters. Choose from MM+, a general purpose force field, and three specialized biomolecule force fields: Amber, BIO+, and OPLS.

Mixed Mode Calculations. HyperChem allows you to perform quantum calculations on part of a molecular system, such as the solute, while treating the rest of the system classically. This boundary technique is available for all the quantum methods, with some limits for ab initio calculations.

Customize and Extend HyperChem with the Chemist's Developer Kit. Streamline HyperChem's menus.

Add new graphical and computational features; create custom menus for specific applications. Interface to Visual Basic, C, C and FORTRAN programs. Add dialog boxes as well as menu items.

For example, you could use HyperChem for visualization of structures and results from non-graphical quantum chemistry programs. Link HyperChem procedures to other Windows programs such as MS Word and Excel; direct selected results to these applications for convenient analysis and reporting.

Results with HyperChem Display. Rendering choices: Ball-and-stick, fused CPK spheres with optional shading and highlighting. Also vdW dots, cylinders and overlapping spheres.

Ribbon rendering for protein backbones, with optional sidechain display. 3D Isosurfaces or 2D contour plots of: total charge density, molecular orbitals, spin density, electrostatic potential (ESP), ESP mapped onto 3D charge density surface. Isosurface rendering choices: wire mesh, Jorgensen-Salem, transparent and solid surfaces, Gouraud shaded surface. User specified grid and isosurface value. During simulations, display and average kinetic, potential, and total energy, as well as values of user specified bond lengths, bond angles, or torsion angles.

Animate vibrational modes.