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HyperChem Standard Features
Results with HyperChem Standard
System Requirements
Academic and Commercial Pricing
HyperChem 5.1 for Digital ALPHA Purchase HyperChem Standard Online

Introduction to HyperChem Standard

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

 

HyperChem Standard Features

 
Structure Input and Manipulation
Molecular Display
Computational Chemistry
Computational Methods
Structure Input and Manipulation

Building molecules with HyperChem is simple: just choose an element from the periodic table, then 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 nterest in complex molecules.

· Select, rotate, translate, and resize structures with convenient mouse-controlled tools. Modify settings to control operation of tools.
· Convert rough 2D 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, 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)
· A periodic box of pre-equilibrated water molecules can be added 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.
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Molecular Display

· Display strucures 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.
· Select and name sets of atoms for custom display or monitoring of properties.
· Display protein backbones using ribbons, with optional display of sidechains.
· Highlight potential hydrogen bond interactions.
· Display dipole moment vectors.
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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.
· Transition state searching locates the metastable structures corresponding to transition states using either Eigenvector Following or Synchronous Transit methods. Molecular properties are then calculated.
Two methods for the location of transition states are implemented in HyperChem 5. Both rely upon the location of a maximum on the potential energy surface

· 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 dissipative 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.

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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, MINDO3, MNDO, MNDO/d, AM1, PM3 (including transition metals), ZINDO/1 and ZINDO/S.
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.
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Results with HyperChem Standard 

DISPLAY
Rendering choices:
Ball-and-stick
Fused CPK spheres with optional shading/ highlighting.
VDW dots, sticks, sticks and dots;
Cylinders
Ribbon rendering for protein backbones, with optional sidechain display.
3-D Isosurfaces or 2-D contour plots of:
Total charge density
Molecular orbitals
Spin density
Electrostatic potential (ESP) contour plot
ESP mapped onto 3-D charge density isosurface
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.
SAVE RESULTS
Use Import/Export option to save results of quantum mechanics calculations or to view results generated by other programs.
PREDICT
Relative stabilities of isomers
Heats of formation
Activation energies
Atomic charges
HOMO-LUMO energy gap
Ionization potentials
Electron affinities
Dipole moments
Electronic energy levels
MP2 electron correlation energy
CI excited state energy
Transition state structures and properties
Non-bonded interaction energy
UV-VIS absorption spectra
IR absorption spectra
Isotope effects on vibrations
Collision effects on structural properties
Stability of clusters
SIMULATE
Docking interactions
Temperature effects on molecular motion
Reactive collisions - record in AVI format for playback
Solvent effects on structure and dynamics
Intermolecular interactions in clusters
HyperChem Standard is available for both standalone and networked installations.
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System Requirements
· PC running Windows 95/98 or Windows NT
· At least 8 Mb of RAM (16 recommended)
· At least 15 Mb of available hard disk space
· PC with math coprocessor
· VGA or better graphics adapter
· mouse or other pointing device

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