Atomic decomposition of molecular properties

Abstract: In this thesis, new methodology of computing properties aimed for multipleapplications is developed. We use quantum mechanics to compute propertiesof molecules, and having these properties as a basis, we set up equations basedon a classical reasoning. These approximations are shown to be quite good inmany cases, and makes it possible to calculate linear and non-linear propertiesof large systems.The calculated molecular properties are decomposed into atomic propertiesusing the LoProp algorithm, which is a method only dependent on the overlapmatrix. This enables the expression of the molecular properties in the two-site atomic basis, giving atomic, and bond-centric force-fields in terms of themolecular multi-pole moments and polarizabilities. Since the original LoProptransformation was formulated for static fields, theory is developed which makesit possible to extract the frequency-dependent atomic properties as well. Fromthe second-order perturbation of the electron density with respect to an externalfield, LoProp is formulated to encompass the first order hyperpolarizability.The original Applequist formulation is extended into a quadratic formula-tion, which produces the second-order shift in the induced dipole moments of thepoint-dipoles from the hyperpolarizability. This enables the calculation of a to-tal hyperpolarizability in systems consisting of interacting atoms and molecules.The first polarizability α and the first hyperpolarizability β obtained via theLoProp transformation are used to calculate this response with respect to anexternal field using the quadratic Applequist equations.In the last part, the implemented analytical response LoProp procedureand the quadratic Applequist formalism is applied to various model systems.The polarizable force-field that is obtained from the decomposition of the staticmolecular polarizability α is tested by studying the one-photon absorption spec-trum of the green fluorescent protein. From the frequency dispersion of thepolarizability α(ω), the effect of field perturbations is evaluated in classicaland QM/MM applications. Using the dynamical polarizabilities, the Rayleigh-scattering of aerosol clusters consisting of water and cis–pinonic acid moleculesis studied. The LoProp hyperpolarizability in combination with the quadraticApplequist equations is used to test the validity of the model on sample wa-ter clusters of varying sizes. Using the modified point-dipole model developedby Thole, the hyper-Rayleigh scattering intensity of a model collagen triple-helix is calculated. The atomic dispersion coefficients are calculated from thedecomposition of the real molecular polarizability at imaginary frequencies. Fi-nally, using LoProp and a capping procedure we demonstrate how the QM/MMmethodology can be used to compute x-ray photoelectron spectra of a polymer.