Surface Enhanced/Quenched Fluorescence near a nanorod
Shengli Zou and Yadong Zhou
University of Central Florida
Using a developed model, we showed that surface enhanced fluorescence for molecules or quantum dots near a cylindrical nanorod can not be predicted using the conventional method. We studied the position dependence of the emitter near the nanorod and also investigated the emission wavelength and incident polarization dependence of the enhanced fluorescence signals. The model was also verified by comparing the calculated the enhancement factors of surface enhanced Raman scattering with those measured in the experiments.
A molecular simulation investigation of PEGDA nanogels
Shalini J. Rukmani1, Ping Lin2, Coray M. Colina1,2
1. Department of Materials Science and Engineering, University of Florida, Gainesville, 32611, USA
2. Department of Chemistry, University of Florida, Gainesville, 32611, USA
PEG (polyethylene glycol) based nanogels have been widely used in biomedical applications due to several attractive properties including biocompatibility and versatile end group chemistry. In this work, we studied the effect of varying cross-linking densities and topological features on the structural properties of PEGDA (PEG-diacrylate) nanogels using atomistic molecular dynamics simulations. Topology diagrams were constructed to study the distribution of cross-linked junctions and meshes formed in these networks. It was found that the radius of gyration, average mesh sizes and hydrophilicity decreased as a function of the cross-linking density. The shapes of these nanogels for different topologies were characterized by calculating the aspect ratios based on the gyration tensor. Nanogel structures with higher cross-linking densities showed a globular shape while structures with lower cross-linking density showed shape anisotropy. The connectivity and distribution of the cross-linked junctions played a major role in determining the size, shape anisotropy and hydrophilicity of PEGDA nanogels.
Conformational free energy calculations with the confinement method
Arjan van der Vaart
University of South Florida, Department of Chemistry
The confinement method is a robust and conceptually simple free energy simulation method that allows for the calculation of conformational free energy differences between highly dissimilar states. We have developed protocols to make the calculations more accurate and efficient. Moreover, we have developed a simple method to allow accurate treatment in explicit water. Together, these improvements allow for the treatment of conformational changes in complex systems.
Accuracy of density functional theory for predicting kinetics of methanol synthesis from CO and CO2 hydrogenation on copper
Maliheh Shaban Tameh, Albert Dearden, and Chen Huang
Department of Scientific Computing, Florida State University
Methanol synthesis is an important industrial process to produce methanol which is the building block for synthesizing many other chemicals and is also used in fuel cells. Despite extensive research on methanol synthesis, the active sites for this catalytic process are still under debates. Density functional theory (DFT) is widely used to gain insight into the kinetics of heterogeneous catalysis with atomistic resolution, however its accuracy heavily depends on the approximated exchange-correlation (XC) functionals. In this work, we examine the effect of XC functionals on the prediction of the kinetics of methanol synthesis on copper surface by using XC functionals of three different levels of accuracy: Perdew-Burke-Ernzerhof (PBE) XC functional, Heyd-Scuseria-Ernzerhof (HSE) hybrid XC functional, and the exact exchange and random phase approximation (RPA) correlation functional. Microkinetic modeling based on PBE and HSE predicts that the turnover frequencies of methanol are two orders of magnitude faster than the RPA predictions. PBE predicts that CO is the carbon source which is contradictory to the previous isotope-labeling experiments which suggested that CO2 is the carbon source. This contradiction indicates that metallic copper is not the active site. A different picture is obtained with RPA calculations which show that both CO and CO2 contribute to the methanol production, therefore suggesting that we cannot rule out the possibility that metallic copper is the active site in industrial methanol synthesis. Our results suggest that sufficiently accurate XC functionals are needed to achieve predictive computational modeling of methanol synthesis in which competing processes, such as CO and CO2 hydrogenation, exist.
TD-DFT Calculations to Assign Ground and Excited State Electronic Structures of DioxoCr(VI) sites
David Jeffcoat, Albert Stiegman
Florida State University
Assignment of the excited states was facilitated using time-dependent density functional theory (TD-DFT) calculations performed on cluster models. All of the observed electronic transitions and their energies are accounted for by dioxoCr(VI) sites. The lowest energy observed excitation at 22 800 cm–1 populates a singlet excited state, while the emitting state is the corresponding triplet state, accessed by intersystem crossing from the singlet state. Spectroscopic bands observed at 29 100, 36 900, and 41 500 cm–1 were assigned, based on the TD-DFT calculation, to spin-allowed transitions that are consistent with emission polarization anisotropy measurements.
Mechanistic studies of hydrogen evolution reactions over low-dimensional, Pt-free transition metal catalysts
Abdulrahiman Nijamudheen,a,b Srimanta Pakhira,a,b Carlos I. Aguirre-Velez,a,b and Jose L. Mendoza-Cortesa,b,c
a. Department of Chemical & Biomedical Engineering, Florida A&M University, and Florida State University, Joint College of Engineering, Tallahassee FL, 32310, USA
b. Scientific Computing Department, Materials Science and Engineering Program, High-Performance Material Institute, Florida State University, Tallahassee FL, 32310, USA.
c. Condensed Matter Theory, National High Magnetic Field Laboratory, Florida State University, Tallahassee FL, 32310, USA.
Low-dimensional Pt-free catalysts are attractive candidate materials for performing hydrogen evolution reactions (HER). In this regard, transition metal dichalcogenides and phosphides have been proposed as efficient catalysts. Experiments indicate that S doping can be used to enhance the HER efficiency of MoP. In fact, S-doped MoP shows superior catalytic activities than other conventional transition metal dichalcogenide catalysts. We use hybrid density functional theory methods to understand the electronic structure and catalytic properties of MoS2, MoP, and S-doped MoP (MoPS). By studying the detailed mechanisms and kinetics for the reactions over various systems, we explain how S doping increases the activity of MoP. The current theoretical study establishes the HER mechanisms over doped and undoped catalysts under different electrochemical conditions. Based on our calculations, we propose a number of design principles for improving the catalytic activities of low-dimensional Pt-free HER catalysts.
Investigating plasticization and swelling in polymers of intrinsic microporosity (PIM-1) from atomistic molecular simulations
Grit Kupgan1, Alexander Demidov2, Coray M. Colina1,2
1Department of Materials Science and Engineering, University of Florida, Gainesville, FL, 32611, USA
2Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
Polymers of intrinsic microporosity (PIMs) are a promising class of polymeric membranes for gas separation. Their design is based on their semi-rigid and contorted backbones, yielding polymers with high free volume architectures. Although PIMs have gained significant attention recently, they can be subjected to undesirable plasticization. Plasticization is defined as the rearrangement of polymers chains due to local swelling of microstructure by condensable penetrants. Understanding the effect of plasticization on polymers is crucial since the process can significantly deteriorate the performance of these materials. In this work, we investigated the plasticization behavior in PIM-1 using atomistic molecular simulations. PIM-1 was constructed with Polymatic which is based on a simulated polymerization approach. To account for plasticization and swelling, a hybrid approach is implemented using Monte Carlo (GCMC) and molecular dynamics (NPT). An open-source python package, Pysimm, was used to communicate simulation data between Cassandra and LAMMPS software. When the systems are equilibrated based on proposed convergence criteria, structural and adsorption properties of the simulated samples can be probed at various loading while considering the flexibility of the polymer. This approach allows the study of the effects of plasticization on the performance of PIM-1 for their industrial employment in membrane and pressure swing adsorption applications. Our results showed that the gas loading has a major impact on most structural and adsorption properties. From MC/MD simulation, we found that gas loading can initiate swelling within PIM-1 around ~3 mmol/g at 300 K. Moreover, we found that plasticization does not always result in the decline of material’s performance.