Current Search:  Computational Chemistry (x)

View All Items

  • CSV Spreadsheet
(1 - 4 of 4)
Modeling Transport and Protein Adsorption in Microfluidic Systems
Title
Modeling Transport and Protein Adsorption in Microfluidic Systems.
Creator
Finch, Craig, Hickman, James, Kincaid, John, Lin, Kuo-Chi, Behal, Aman, Cho, Hyoung, University of Central Florida
Abstract / Description
This work describes theoretical advances in the modeling and simulation of microfluidic systems and demonstrates the practical application of those techniques. A new multi-scale model of the adsorption of hard spheres was formulated to bridge the gap between simulations of discrete particles and continuum fluid dynamics. A whispering gallery mode (WGM) biosensor was constructed and used to measure the kinetics of adsorption for two types of proteins on four different surfaces. Computational...
Show moreThis work describes theoretical advances in the modeling and simulation of microfluidic systems and demonstrates the practical application of those techniques. A new multi-scale model of the adsorption of hard spheres was formulated to bridge the gap between simulations of discrete particles and continuum fluid dynamics. A whispering gallery mode (WGM) biosensor was constructed and used to measure the kinetics of adsorption for two types of proteins on four different surfaces. Computational fluid dynamics was used to analyze the transport of proteins in the flow cell of the biosensor. Kinetic models of protein adsorption that take transport limitations into account were fitted to the experimental data and used to draw conclusions about the mechanisms of adsorption. Transport simulations were then applied to the practical problem of optimizing the design of a microfluidic bioreactor to enable (")plugs(") of fluid to flow from one chamber to the next with minimal dispersion. Experiments were used to validate the transport simulations. The combination of quantitative modeling and simulation and experiments led to results that could not have been achieved using either approach by itself. Simulation tools that accurately predict transport and protein adsorption will enable the rational design of microfluidic devices for biomedical applications.
Show less
Date Issued
2011
Identifier
CFE0004474, ucf:49313
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0004474
Catalyst Design and Mechanism Study with Computational Method for Small Molecule Activation
Title
Catalyst Design and Mechanism Study with Computational Method for Small Molecule Activation.
Creator
Liu, Muqiong, Zou, Shengli, Harper, James, Dixon, Donovan, Chen, Gang, Feng, Xiaofeng, University of Central Florida
Abstract / Description
Computational chemistry is a branch of modern chemistry that utilizes the computers to solve chemical problems. The fundamental of computational chemistry is Schr(&)#246;dinger equation. To solve the equation, researchers developed many methods based on Born-Oppenheimer Approximation, such as Hartree-Fock method and DFT method, etc. Computational chemistry is now widely used on reaction mechanism study and new chemical designing.In the first project described in Chapter 3, we designed...
Show moreComputational chemistry is a branch of modern chemistry that utilizes the computers to solve chemical problems. The fundamental of computational chemistry is Schr(&)#246;dinger equation. To solve the equation, researchers developed many methods based on Born-Oppenheimer Approximation, such as Hartree-Fock method and DFT method, etc. Computational chemistry is now widely used on reaction mechanism study and new chemical designing.In the first project described in Chapter 3, we designed phosphine oxide modified Ag3, Au3 and Cu3 nanocluster catalysts with DFT method. We found that these catalysts were able to catalyze the activation of H2 by cleaving the H-H bond asymmetrically. The activated catalyst-2H complex can be further used as reducing agent to hydrogenate CO molecule to afford HCHO. The mechanism study of these catalysts showed that the electron transfer from electron-rich metal clusters to O atom on the phosphine oxide ligand is the major driving force for H2 activation. In addition, different substituent groups on phosphine oxide ligand were tested. Both H affinity of metal and the substituent groups on ligand can both affect the activation energy.Another project described in Chapter 4 is the modelling of catalyst with DFT. We chose borane/NHC frustrated Lewis pair (FLP) catalyzed methane activation reaction as example to establish a relationship between activation energy and catalysts' physical properties. After performing simulation, we further proved the well-accepted theory that the electron transfer is the main driving force of catalysis. Furthermore, we were able to establish a linearivrelationship for each borane between activation energy and the geometrical mean value of HOMO/LUMO energy gap (?EMO). Based on that, we introduced the formation energy of borane/NHC complex (?EF) and successfully established a generalized relationship between Ea and geometrical mean value of ?EMO and ?EF. This model can be used to predict reactivity of catalysts.
Show less
Date Issued
2018
Identifier
CFE0007343, ucf:52112
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0007343
Quantum Chemical Studies for the Engineering of Metal Organic Materials
Title
Quantum Chemical Studies for the Engineering of Metal Organic Materials.
Creator
Rivera Jacquez, Hector, Masunov, Artem, Balaeff, Alexander, Harper, James, Heider, Emily, Zou, Shengli, Kaden, William, University of Central Florida
Abstract / Description
Metal Organic Materials (MOM) are composed of transition metal ions as connectors and organic ligands as linkers. MOMs have been found to have high porosity, catalytic, and optical properties. Here we study the gas adsorption, color change, and non-linear optical properties of MOMs. These properties can be predicted using theoretical methods, and the results may provide experimentalists with guidance for rational design and engineering of novel MOMs. The theory levels used include semi...
Show moreMetal Organic Materials (MOM) are composed of transition metal ions as connectors and organic ligands as linkers. MOMs have been found to have high porosity, catalytic, and optical properties. Here we study the gas adsorption, color change, and non-linear optical properties of MOMs. These properties can be predicted using theoretical methods, and the results may provide experimentalists with guidance for rational design and engineering of novel MOMs. The theory levels used include semi-empirical quantum mechanical calculations with the PM7 Hamiltonian and, Density Functional Theory (DFT) to predict the geometry and electronic structure of the ground state, and Time Dependent DFT (TD-DFT) to predict the excited states and the optical properties.The molecular absorption capacity of aldoxime coordinated Zn(II) based MOMs (previously measured experimentally) is predicted by using PM7 Theory level. The 3D structures were optimized with and without host molecules inside the pores. The absorption capacity of these crystals was predicted to be 8H2 or 3N2 per unit cell. When going beyond this limit, the structural integrity of the bulk material becomes fractured and microcrystals are observed both experimentally and theoretically.The linear absorption properties of Co(II) based complexes are known to change color when the coordination number is altered. In order to understand the mechanism of this color change TD-DFT methods are employed. The chromic behavior of the Co(II) based complexes studied was confirmed to be due to a chain in coordination number that resulted in lower metal to ligand distances. These distances destabilize the occupied metal d orbitals, and as a consequence of this, the metal to ligand transition energy is lowered enough to allow the crystals to absorb light at longer wavelengths.Covalent organic frameworks (COFs) present an extension of MOM principles to the main group elements. The synthesis of ordered COFs is possible by using predesigned structures andcarefully selecting the building blocks and their conditions for assembly. The crystals formed by these systems often possess non-linear optical (NLO) properties. Second Harmonic Generation (SHG) is one of the most used optical processes. Currently, there is a great demand for materials with NLO optical properties to be used for optoelectronic, imaging, sensing, among other applications. DFT calculations can predict the second order hyperpolarizability ?2 and tensor components necessary to estimate NLO. These calculations for the ?2 were done with the use of the Berry's finite field approach. An efficient material with high ?2 was designed and the resulting material was predicted to be nearly fivefold higher than the urea standard.Two-photon absorption (2PA) is another NLO effect. Unlike SHG, it is not limited to acentric material and can be used development of in vivo bio-imaging agents for the brain. Pt(II) complexes with porphyrin derivatives are theoretically studied for that purpose. The mechanism of 2PA enhancement was identified. For the most efficient porphyrin, the large 2PA cross-section was found to be caused by a HOMO-LUMO+2 transition. This transition is strongly coupled to 1PA allowed Q-band HOMO-LUMO states by large transition dipoles. Alkyl carboxyl substituents delocalize the LUMO+2 orbital due to their strong ?-acceptor effect, enhancing transition dipoles and lowering the 2PA transition to the desirable wavelengths range.The mechanism 2PA cross-section enhancement of aminoxime and aldoxime ligands upon metal addition of is studied with TD-DFT methods. This mechanism of enhancement is found to be caused by the polarization of the ligand orbitals by the metal cation. After polarization an increase in ligand to ligand transition dipole moment. This enhancement of dipole moment is related to the increase in 2PA cross-sections.
Show less
Date Issued
2015
Identifier
CFE0005990, ucf:50777
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0005990
THEORETICAL TAILORING OF PERFORATED THIN SILVER FILMS FOR AFFINITY SURFACE PLASMON RESONANCE BIOSENSOR APPLICATIONS
Title
THEORETICAL TAILORING OF PERFORATED THIN SILVER FILMS FOR AFFINITY SURFACE PLASMON RESONANCE BIOSENSOR APPLICATIONS.
Creator
Gongora Jr., Renan, Zou, Shengli, University of Central Florida
Abstract / Description
Metallic films, in conjunction with biochemical-targeted probes, are expected to provide early diagnosis, targeted therapy and non-invasive monitoring for epidemiology applications. The resonance wavelength peaks, both plasmonic and Wood-Rayleigh Anomalies (WRAs), in the scattering spectra are affected by the metallic architecture. As of today, much research has been devoted to extinction efficiency in the plasmonic region. However, Wood Rayleigh Anomalies (WRAs) typically occur at...
Show moreMetallic films, in conjunction with biochemical-targeted probes, are expected to provide early diagnosis, targeted therapy and non-invasive monitoring for epidemiology applications. The resonance wavelength peaks, both plasmonic and Wood-Rayleigh Anomalies (WRAs), in the scattering spectra are affected by the metallic architecture. As of today, much research has been devoted to extinction efficiency in the plasmonic region. However, Wood Rayleigh Anomalies (WRAs) typically occur at wavelengths associated with the periodic distance of the structures. A significant number of papers have already focused on the plasmonic region of the visible spectrum, but a less explored area of research was presented here; the desired resonance wavelength region was 400-500nm, corresponding to the WRA for the silver film with perforated hole with a periodic distance of 400nm. Simulations obtained from the discrete dipole approximation (DDA) method, show sharp spectral bands (either high or low scattering efficiencies) in both wavelength regions of the visible spectrum simulated from Ag film with cylindrical hole arrays In addition, surprising results were obtained in the parallel scattering spectra,where the electric field is contained in the XY plane, when the angle between the metallic surface and the incident light was adjusted to 14 degrees; a bathochromic shift was observed for the WRA peak suggesting a hybrid resonance mode. Metallic films have the potential to be used in instrumental techniques for use as sensors, i.e. surface plasmon resonance affinity biosensors, but are not limited to such instrumental techniques. Although the research here was aimed towards affinity biosensors, other sensory designs can benefit from the optimized Ag film motifs. The intent of the study was to elucidate metal film motifs, when incorporated into instrumental analysis, allowing the quantification of genetic material in the visible region. Any research group that routinely benefits from quantification of various analytes in solution matrices will also benefit from this study, as there are a bewildering number of instrumental sensory methods and setups available.
Show less
Date Issued
2014
Identifier
CFH0004538, ucf:45155
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFH0004538