Introduction to HyperChem Standard
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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- · 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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· 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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During simulations, display and average kinetic, potential, and total energy, as well as values of user-specified bond lengths, bond angles, or torsion angles.
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