Session VI

Wednesday, May 24th

Session VI


YAeHMOP in Avogadro: An Open-Source, User-Friendly Tool for Quick Extended Hückel Calculations of Periodic Systems

Patrick Avery, Herbert Ludowieg, Jochen Autschbach and Eva Zurek

University at Buffalo, Department of Chemistry

The open-source molecular editor, Avogadro, has recently been interfaced with Greg Landrum's YAeHMOP (Yet Another extended Hückel Molecular Orbital Package) program. With the Avogadro interface, a user is now able to perform quick extended Hückel calculations of the following kinds: band structure, density of states, projected density of states, and crystal orbital overlap population (COOP). All of these calculations can be done on periodic systems of one, two, or three dimensions.  An overview of the calculations and some demonstration will be given in this presentation.


Nonlinear optical property prediction using a Padé approximant based finite field method

Anand Patel, Ahmed A.K. Mohammed, Peter A. Limacher and Paul W. Ayers

McMaster University, Department of Chemistry and Chemical Biology

Computing accurate nonlinear optical (NLO) properties is of great interest to the fields of organic chemistry, spectroscopy and materials science, among others. Of the available tools to determine these properties, the finite field (FF) method is one of the most computationally inexpensive. However, the accuracy of traditional FF methods are highly dependent on the external electric fields at which the calculation is performed. Thus, we propose a modified FF method that uses a Padé approximant to compute NLO properties, rather than the previously used Taylor polynomial. As previously done for the polynomial-based FF method, the new Padé approximant based method must be tuned for accuracy, by taking three factors into account: the number of fields, the distribution of these fields, and the field strengths used. Once optimized, this new FF method was found to be more robust than the polynomial-based FF method, but is slightly less accurate overall. Despite the loss of accuracy, the robustness and ease of implementation make this method a viable option to implement in new quantum chemistry software packages. 


Magnetic Resonance Properties of Uranyl Carbonate Complexes in Water

Alex Marchenko, and Jochen Autschbach

University at Buffalo, Department of Chemistry

The structural dynamics, magnetic resonance chemical shifts, and quadrupolar relaxation rates of dioxouranate(VI), tris(carbonato)dioxouranate(VI), and hexakis(carbonato)tris[dioxouranate(VI)] are investigated using Car-Parrinello molecular dynamics and ab initio calculations. Magnetic resonance properties are computed on clusters extracted from the dynamics trajectory. Coordination by water at the uranium center of the first complex causes a decrease of about 25% in the chemical shift compared to models without the presence of explicit water molecules. The influence of water on oxygen and carbon chemical shifts of ligand carbonates is less pronounced. For the third complex, the trend in the two carbon chemical shifts is correctly reproduced. Relaxation rate data support the broad chemical shift ranges observed experimentally. Comparison between relaxation rate data for water including versus water free models suggests that ligand motion in the second and third complexes has a larger influence on chemical shifts than water coordination. Overall, excellent agreement with respect to available experimental data in this work lays the foundation for on-going work where experimental data is not available.


Investigation of mesoscale drug molecule distribution and solubility using surfactant and lipid bilayer membrane

Syeda Nusrat Muhith, Leela Rakesh1 and Anja Mueller2

 1Department of Mathematics, Center for Applied Mathematics & Polymer Fluid Dynamics, Central Michigan University, Mt. Pleasant, Michigan 48859

2Department of Chemistry, Central Michigan University, Mt. Pleasant, Michigan 48859

"Dissipative Particle Dynamics (DPD) method is employed to investigate the effect of drug distribution and solubility in the presence of surfactant and lipid bilayer membrane. DPD is a coarse-grained simulation technique, where several atoms are united into a single bead particle for the simulation. Due to conservation of momentum among the dissipative particles used in DPD simulation, the disparity of hydrodynamic time and length scales can be achieved to a greater extent than molecular dynamics [1]. Following the procedures given in one of the author’s article along with the literatures cited in the article and using the theory of solutions of Flory-Huggins interaction parameters, the new bead system parameters are computed for the present simulation. The result from these literatures is reproduced for standardizing our current research study where the surfactant has turned the water- impermeable lipid bilayer membrane into water-permeable. Also, it is found that increase in percentage of surfactant, ruptures the lipid bilayer. Similar study is carried out in water and drug-surfactant mesostructured system, which manifests, with increase in hydrophobic portion of surfactant, solubility of drugs improves with increase in surfactant percentage. However, at smaller hydrophobic portion in surfactant, percentage of surfactant does not influence the solubility of drug in aqueous media significantly. Furthermore, using DPD method, interaction between water, polysaccharide mixtures, lipid bilayers and drug will also be investigated to understand the solubility of drug in the matrix and explore further applications.


1. N. Thota and J. Jiang, J. Frontiers in Materials, 2015, 2, 64.


Superconducting Phases of Phosphorus Hydride Under Pressure: Stabilization via Mobile Molecular Hydrogen

Tiange Bi, Daniel P. Miller, Andrew Shamp and Eva Zurek

University at Buffalo, Department of Chemistry

At 80 GPa phases with the PH2 stoichiometry, which are composed of simple cubic like phosphorus layers capped with hydrogen atoms and layers of H2 molecules, are predicted to be important species contributing to the recently observed superconductivity in compressed phosphine. The electron phonon coupling in these phases results from the motions of the phosphorus atom and the hydrogens bound to them. The role of the mobile H2 layers is to decrease the Coulomb repulsion between the negatively charged hydrogen atoms capping the phosphorus layers. An insulating PH5 phase, whose structure and bonding is reminiscent of diborane, is also predicted to be metastable at this pressure.