Indiana University-Purdue University Indianapolis (IUPUI) / Molecular polarizability plays a significant role in chemistry, biology, and medicine. Classical prediction of polarizability often relies on atomic-type specific polarizability optimized for training set molecules, which limits the calculations to systems of similar chemical environment. Although ab initio (AI) quantum mechanical (QM) methods are more transferable in predicting molecular polarizability, their high computational costs especially when used with large basis sets for obtaining quantitatively reliable results make them less practical. To obtain accurate QM polarizability in an efficient manner, we have developed a dual-level approach, where the polarizability (α) obtained from the efficient semiempirical QM (SE) method is corrected using a set of element-base atomic polarizabilities derived from the atomic dipole interaction model (ADIM) to reproduce the density functional theory (DFT) results. We have optimized the atomic polarizability correction parameters for CHON-containing systems using a small training set of molecules and tested the resulting SE-ADIM model on the neutral drug-like molecules in the QM7B database. SE-ADIM corrected AM1 showed substantial improvement with its relative percent error (RPE) compared to B3LYP reduced from 33.81% to 3.35%. To further test its robustness for larger molecules in broader chemical bonding situations, we applied this method to a collection of drug molecules from the e-Drug3D database. For the 1004 molecules tested, our SE-ADIM model, which only contains four empirical parameters, greatly reduces the RPE in AM1 polarizability relative to B3LYP from 26.8% to 2.9%. Error decomposition shows consistent improvements across molecules with diverse bond saturations, molecular sizes, and charge states. In addition, we have applied AlphaML, a promising machine learning (ML) technique for predicting molecular polarizability, to the e-Drug3D dataset to compare its performance with our SE-ADIM correction of AM1. We found SE-ADIM performs competitively with AlphaML bolstering our confidence in the value of our method. Errors distinct to AlphaML were also discovered. We found four molecules for which AlphaML predicts negative molecular polarizabilities, all of which were peroxides. In contrast, SE-ADIM has no such issue with these molecules or this chemical type. Finally, to improve performance of SE-ADIM when correcting AM1 molecular polarizability calculations for charged molecules, we introduce a charge dependent polarizability (CDP) enabled SE-ADIM. Training the CDP enabled SE-ADIM with a single additional parameter, B, we were able to reduce error in AM1 molecular polarizability calculations of charged molecules relative to B3LYP from 29.57% to 5.16%. By contrast, SE-ADIM without CDP corrected AM1 relative to B3LYP had an RPE of 8.56%. The most benefit of CDP was evident within negatively charged molecules where AM1 error relative to B3LYP fell from 32.20% to 3.77% while SE-ADIM without CDP enabled error for these same negative molecules was 10.06%.

A combination of quantum chemical calculation and molecular dynamics simulation is applied to compute refractive indices of liquid-forming silicon oils. The densities of these species are obtained from molecular dynamics simulations based on the NPT ensemble while the molecular polarizabilities are evaluated by density functional theory. This procedure is shown to yield results well compatible with available experimental data, suggesting that it represents a robust and economic route for determining the refractive indices of liquid-forming organic complexes containing silicon.

Submitted by Jaqueline Silva (jtas29@gmail.com) on 2014-09-16T17:01:54Z No. of bitstreams: 2 Naves, Emílio Santiago-2014-tese.pdf: 587232 bytes, checksum: 384bbcad6790ecde844af07f4c8deed9 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Jaqueline Silva (jtas29@gmail.com) on 2014-09-16T17:02:18Z (GMT) No. of bitstreams: 2 Naves, Emílio Santiago-2014-tese.pdf: 587232 bytes, checksum: 384bbcad6790ecde844af07f4c8deed9 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-09-16T17:02:18Z (GMT). No. of bitstreams: 2 Naves, Emílio Santiago-2014-tese.pdf: 587232 bytes, checksum: 384bbcad6790ecde844af07f4c8deed9 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2013-11-08 / This work presents results for the dynamic (hyper)polarizabilities of ozone, sulfur dioxide, nitrous oxide and carbon dioxide molecules, with inclusion of vibrational corrections. The electronic contributions for the properties of interest were computed analytically at the single and double coupled cluster level through response theory. Ozone and sulfur dioxide were studied separately. For both systems, contributions of connected triple excitations were also estimated by the multiplicative correction scheme. The vibrational corrections were calculated by the perturbation theoretical method (PT). The zero-point vibrational average correction, calculated only for ozone and sulfur dioxide, proved to be small. Results also show that the pure vibrational correction is relevant for the following nonlinear optical processes: dc-Pockels effect, intensity dependent refractive index, and dc-Kerr effect. For the ozone molecule the dc-second harmonic generation effect also had a significant pure vibrational correction. In addition, pure vibrational correction was calculated according to a variational methodology proposed by our research group (VAR) for the four systems, and the results were compared with the corresponding PT results. A comparison between PT and VAR results shows that ozone is the system most sensitive to the method, while sulfur dioxide and carbon dioxide are the most well behaved. / Neste trabalho são apresentados resultados para as (hiper)polarizabilidades dinâmicas das moléculas de ozônio, dióxido de enxofre, óxido nitroso e dióxido de carbono, com inclusão de correções vibracionais. As contribuições eletrônicas das propriedades de interesse foram computadas analiticamente através da teoria de resposta no nível coupled cluster com substituições simples e duplas. O ozônio e o dióxido de enxofre foram estudados separadamente. Para ambos os sistemas, as contribuições das substituições triplas conexas também foram estimadas através do esquema de correção multiplicativa. As correções vibracionais foram calculadas por meio dométodo de perturbação teórica (PT). A correção da média vibracional de ponto zero, calculada apenas para o ozônio e o dióxido de enxofre, revelou-se pequena. Os resultados também mostram que a correção vibracional pura é relevante para os seguintes processos ópticos não lineares: efeito dc-Pockels, índice de refração dependente da intensidade e efeito dc-Kerr. Para a molécula de ozônio o efeito de geração de segundo harmônico dc também teve uma correção vibracional pura significativa. Em adição, a correção vibracional pura foi calculada segundo uma metologia variacional proposta pelo nosso grupo de pesquisa (VAR) para os quatro sistemas, e os resultados foram comparados com os respectivos resultados PT. Uma comparação entre os resultados PT e VAR mostra que o ozônio é o sistema mais sensível ao método, ao passo que o dióxido de enxofre e o dióxido de carbono são os mais bem comportados.

<p>Utilizing a genetic algorithm training of the atom dipole interaction model was performed to arrive at C,H, N, & O atomic polarizabilities that constitute a correction to semiempirical molecular polarizability calculations increasing the accuracy of these calculations to near parity with DFT at a fraction of the computational load.</p>