Poland

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Functionality

Properties calculated:

  • Atomic charges and bond orders.

  • Geometries: local and global minima, transition states.

  • Thermodynamics properties: enthalpy, entropy, free energy and heat capacity.

  • Molecular orbitals and orbital energies.

  • Spectra: IR, UV-VIS.

  • NMR chemical shifts.

  • Electrical properties: dipole, quadrupole, and octupole moments; polarizability and hyperpolarizability.

  • Electrostatic potentials and isopotentials.

  • Susceptibility for electrophilic, nucleophilic and radical attack.

  • QSAR/QSPR properties.

  • Proteins and enzymes properties: sequence analysis, solvent accessible surface, ligand pocket surface.

Types of calculations:

  • Single-point calculations.

  • Geometry optimization.

  • Reaction modeling and localization of transition states.

  • Potential energy maps.

  • Vibrational frequencies and spectra.

  • Excited states calculations.

  • Molecular dynamics simulations.

  • Conformational analysis.

  • Automatic proteins sequence alignment (Needleman-Wunsch algorithm).

  • Docking and scoring a ligand into an active site.

Computational methods:

  • Molecular mechanics: MM2, MM3, and Amber.

  • The semiempirical methods: MNDO, MINDO/3, AM1, PM3, PM5, Iterative Extended Hückel, INDO/1, INDO2, CNDO/1, CNDO/2, RM1, PDDG/MNDO, PDDG/PM3, ZINDO/S, CNDO/S, CNDO/S2, CNDO/S3, and CNDO/2.

  • DFT energy functionals: D-VWN, D-PW92, B88-PW91, PW91-PW91, B88-P86, B88-LYP.

  • DFT basis sets: DZVP, TZVP, 3-21G, 3-21G*, 6-31G, 6-31G*, 6-31G**.

  • Solvent models: COSMO and Onsager.