METHODS FOR DETERMINING THE STRUCTURE OF MOLECULES

The molecular geometry can be determined by various spectroscopic methods and diffraction methods. IR, Microwave and Raman spectroscopy can give information about the molecule geometry from the details of the vibrational and rotational absorbances detected by these techniques. X-ray crystallography, neutron diffraction and electron diffraction (GED) can give molecular structure for crystalline solids based on the distance between nuclei and concentration of electron density. Gas electron diffraction can be used for small molecules in a gas phase. NMR and FRET methods can be used to determine complentary information including relative distances, dihedral angles, angles, and connectivity. Molecular geometries are best determined at low temperature because at higher temperatures the molecular structure is averaged over more accessible geometries. Larger molecules often exist in multiple stable geometries (conformational isomerism) that are close in energy to the potential energy surface. Geometries can also be computed by ab initio quantum chemistry methods to high accuracy. The term ab initio indicates that the calculation is from the first principles and that no empirical data used. Robert Parr claims in an interview that the term was first used in a letter to him by David Craig and was put into the manuscript of their paper on the excited states of benzene published in 1950.The simplest type of ab initio electronic structure calculation is the Hartree-Fock (HF) scheme, in which the instantaneous Coulombic electron-electron repulsion is not specifically taken into account. Only its average effect (mean field) is included into the calculation. This is a variational procedure. Therefore the obtained approximate energies, expressed in terms of the system wave function, are always equal to or greater than the exact energy, and tend to a limiting value called the Hartree-Fock limit as the size of the basis is increased. Many types of calculations begin with a Hartree-Fock calculation and subsequently correct for electron-electron repulsion, referred to also as electronic correlation. Moller-Plesset perturbation theory (MPn) and coupled cluster theory (CC) are examples of these post-Hartree-Fock methods. In some cases, particularly for bond breaking processes, the Hartree-Fock method is inadequate and this single-determinant reference function is not a good basis for post-Hartree-Fock methods. It is then necessary to start with a wave function that includes more than one determinant such as multi-configurational self-consistent field (MCSCF) and the methods have been developed that use these multi-determinant references for improvements.

The position of each atom is determined by the nature of the chemical bonds by which it is connected to its neighboring atoms. The molecular geometry can be described by the positions of these atoms in space, evoking bond lengths of two joined atoms, bond angles of three connected atoms, and torsion angles (dihedral angles) of three consecutive bonds.