All Alchemy
Alchemy 2000 we tested Version 2.05 is a graphic interface for running molecular mechanics and semiempirical calculations. Calculations can be done with the built-in Tripos force field or by calling the MM3 or MOPAC programs, which are included with the package. Alchemy is designed by Tripos and sold by SciVision. Molecules can be built using a two-dimensional sketch mode and are then converted to three-dimensional geometries by the program. It is also possible to build molecules in the...
Yaehmop For Linux System
YAeHMOP stands for yet another extended Huckel molecular orbital package. The package has two main executables and a number of associated utilities. The bind program does molecular and crystal band structure extended Huckel calculations. The viewkel program is used for displaying results. We tested Version 3.0 of bind and Version 2.0 of viewkel. The bind program requires an ASCII input and generates one or more ASCII output files. The molecular geometry can be defined as a Z-matrix, Cartesian...
Notation
Most calculations today are done by choosing an existing segmented GTO basis set. These basis sets are identified by one of a number of notation schemes. These abbreviations are often used as the designator for the basis set in the input to ab initio computational chemistry programs. The following is a look at the notation for identifying some commonly available contracted GTO basis sets. The smallest basis sets are called minimal basis sets. The most popular minimal basis set is the STO 3G...
Zindo
The Zerner's INDO method ZINDO is also called spectroscopic INDO INDO S . This is a reparameterization of the INDO method specifically for the purpose of reproducing electronic spectra results. This method has been found to be useful for predicting electronic spectra. ZINDO is also used for modeling transition metal systems since it is one of the few methods parameterized for metals. It predicts UV transitions well, with the exception of metals with unpaired electrons. However, its use is...
A ChemSketch and the ACD Software Suite
ChemSketch we tested Version 4.01 is a graphic interface that can be used as the front end for a host of programs sold by Advanced Chemistry Development. Both free and commercial versions are available. It is a two-dimensional structure drawing program primarily designed for organic molecules. Although the drawing mode is essentially a two-dimensional drawing routine, it is also possible to rotate the molecule in three dimensions. The program automatically keeps track of the number of hydrogens...
A PC Model
PC Model we tested Version 7.00 is a molecular mechanics program with a graphic user interface. It can also be used as a graphic interface for AMPAC, MOPAC, and Gaussian. Separately sold modules are available for displaying orbitals and vibrational modes for these programs as well as Hondo and Jaguar. It is able to read and write a variety of chemical-structure data file formats. The native file format can hold many structures that can be used for either batch processing or displaying an...
A Molpro
MOLPRO we tested Version 98.1 is an ab initio program designed for performing complex calculations. This program is often used for calculations that present technical difficulties or are very sensitive to electron correlation. A few portions of the code have been parallelized. Calculations that can be performed are HF, CI, MRCI, FCI, CC, DFT, MCSCF, CASSCF, ACPF, CEPA, valence bond, and many variations of these. Perturbation theory calculations can be done from single- and multiple-determinant...
A Moe
MOE Version 2000.02 stands for molecular operating environment. The developers of this package took the unique approach of creating a programming language for writing molecular modeling software. The package currently includes molecular mechanics, dynamics, periodic boundary conditions, QSAR, a combinatorial builder, and many functions ideal for protein modeling, including multiple-sequence alignment and homology model building. Functions are also available for computing polymer properties and...
A Molden
Molden we tested Version 3.6 is a molecular display program. It can display molecular geometries read from a number of molecular file formats. Various views of the wave function can be displayed from the output of the Gaussian and GAMESS programs. Some functionality is available from MOPAC and AMPAC files. Conversion programs are available to import wave functions from ADF, MOLPRO, ACES II, MOLCAS, DALTON, Jaguar, and HONDO. Molden can display molecular geometries in a variety of formats,...
Mulliken Population Analysis
One of the original and still most widely used population analysis schemes is the Mulliken population analysis. The fundamental assumption used by the Mulliken scheme for partitioning the wave function is that the overlap between two orbitals is shared equally. This does not completely reflect the electronegativity of the individual elements. However, it does give one a means for partitioning a wave function and has been found to be very effective for small basis sets. For large basis sets,...
Basic Theory
The premise behind DFT is that the energy of a molecule can be determined from the electron density instead of a wave function. This theory originated with a theorem by Hoenburg and Kohn that stated this was possible. The original theorem applied only to finding the ground-state electronic energy of a molecule. A practical application of this theory was developed by Kohn and Sham who formulated a method similar in structure to the Hartree-Fock method. In this formulation, the electron density...
Ab initio Methods Lvq
Ab initio methods pose problems due a whole list of technical difficulties. Most of these stem from the large number of electrons and low-energy excited state. Core potentials are often used for heavier elements to ease the computational requirements and account for relativistic effects. Convergence problems are very common due to the number of orbitals available and low-energy excited states. The most difficult calculations are generally those with open-shell systems and an unfilled...
Molecular Mechanics Methods
In the past, when molecular mechanics methods were used for transition metals, it was by having a set of parameters for the metal that were parameterized specifically for one class of compounds. There have been a number of full periodic table force fields created, with the most successful being the UFF force field. All the full periodic molecular mechanics methods still give completely unreasonable results for certain classes of compounds. One reason for these difficulties is that metals have...
Molecular Mechanics Prediction
Traditionally, molecular mechanics has not been the method of choice for predicting transition structures. However, since it is the only method viable for many large molecules, some efforts have been made to predict transition structures. Since the bonds are explicitly defined in molecular mechanics methods, it is not possible to simply find a point that is an energy maximum, except for conformational intermediates. Some force fields, such as MMX, have atom types designated as...
A Mopac
MOPAC we tested Versions 6 and 2000 stands for molecular orbital package. It is one of the most widely used semiempirical software packages and is designed for robustness and a wide range of functionality. Programs that can be used as a graphic interface for MOPAC are WinMOPAC from Fujitsu, Alchemy from SciVision, PC Model from Serena Software, Chem3D from CambridgeSoft, and HyperChem from HyperCube Inc. The earlier versions of MOPAC were available at little or no cost. Many graphic interface...
Hardsphere Collision Theory
The simplest approach to computing the pre-exponential factor is to assume that molecules are hard spheres. It is also necessary to assume that a reaction will occur when two such spheres collide in order to obtain a rate constant k for the reactants B and C as follows k _ Nan rB rc 2 where rB and rc are radii of molecules with masses mB and mc. To a first approximation, the activation energy can be obtained by subtracting the energies of the reactants and transition structure. The hard-sphere...
Lowdin Population Analysis
The Lowdin population analysis scheme was created to circumvent some of the unreasonable orbital populations predicted by the Mulliken scheme, which it does. It is different in that the atomic orbitals are first transformed into an orthogonal set, and the molecular orbital coefficients are transformed to give the representation of the wave function in this new basis. This is less often used since it requires more computational work to complete the orthogonalization and has been incorporated...
Semiempirical Methods
Semiempirical calculations are set up with the same general structure as a HF calculation in that they have a Hamiltonian and a wave function. Within this framework, certain pieces of information are approximated or completely omitted. Usually, the core electrons are not included in the calculation and only a minimal basis set is used. Also, some of the two-electron integrals are omitted. In order to correct for the errors introduced by omitting part of the calculation, the method is...
Simulation Of Molecules
In order to analyze the vibrations of a single molecule, many molecular dynamics steps must be performed. The data are then Fourier-transformed into the frequency domain to yield a vibrational spectrum. A given peak can be selected and transformed back to the time domain. This results in computing the vibra- tional motion at that frequency. Such a technique is one of the most reliable ways to obtain the very-low-frequency or anharmonic motions of large molecules. Another reason for simulating...