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.
HyperChem is a full 32-bit application, developed for the Windows 95, 98, NT, ME, 2000, XP, and Vista operating systems. HyperChem Release 8.0 incorporates even more powerful computational chemistry tools than ever before, as well as supporting multiple third-party applications. Its drawing and rendering capabilities andease of use are standards for the industry.
Features of HyperChem
Structure Input and ManipulationBuilding 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.
- Replace any selected Hydrogen with a variety of substituents including your own custom substituent.
- 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 salvation 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.
- Display structures using ball and stick, fused CPK spheres, sticks, ball and cylinder, or tubes
- Add van der Waals dots to any rendering.
- Use any rendering on any atom in the same molecule.
- Specify stick or cylinder width, and the radii of spheres.
- Stereo and perspective viewing are available as well as a quality setting.
- 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, beta sheets, random coils, cylinders, etc. with optional display of side chains.
- Highlight potential hydrogen bond interactions.
- Display dipole moment vectors and gradient vectors.
Use HyperChem to explore quantum or classical model potential energy surfaces with single point, geometry optimization, or transition state searchcalculations . 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.
- 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.
- 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.
- Excited states via singly-excited configuration interaction (CI).
Computational Methods
Density Functional Theory (DFT)- Choose from a large variety of exchange and correlation functionals.
- Choose from a variety of integration grids
- All the options of Ab Initio calculations and basis functions.
- 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.
- HyperChem offers eleven 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, RM1, PM3 (including transition metals), ZINDO/1 and ZINDO/S.
- 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.
- 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.
- 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
DisplayRendering choices: Stick, Ball-and-stick, fused CPK spheres, Ball and Cylinder, Tubes with optional dot surfaces.
New Force Fields
HyperChem added significant new capability to the AMBER method of molecular mechanics by including up-to-date modifications of this force field. AMBER code supports 5 parameter sets with their associated functional forms:
- Amber 2
- Amber 3
- Amber for saccharides
- Amber 94
- Amber 96
- Amber 99
Any molecular mechanics computation can continue computing with default parameters, when explicit parameters are missing from the relevant parameter file. The normal MM2, AMBER, Charmm 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
Calculated values of Hyperfine Coupling constants are also available, for characterizing the ESR spectra of open shell systems.
Electric Polarizabilities
Computation of polarizability tensors is available.
Plots of Potential Energy
You can 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
You can 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 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.
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.
HyperChem 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.
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 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.
Graphical Display of Gradients
It is possible to visualize the gradient (force) on any atom as a vector. Any set of atoms can display these vectors.
Bond Labels
A set of dynamically updated labels are available for bonds as well as atoms and residues. These bond labels can be one of:
- Bond length
- Bond order - as calculated quantum mechanically
HyperChem operations depend to a great extent on one’s ability to select a subset of atoms. For example, it is 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 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 Release 7 is that you are free to focus on the things that you do best. HyperChem does the rest.
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