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.
- • 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.
Molecular Display
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
- • 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 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.
- 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).
