Matching Items (8)
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- All Subjects: Physical Chemistry
- Creators: Mujica, Vladimiro
Description
Molecular dynamics simulations were used to study properties of water at the interface with nanometer-size solutes. We simulated nonpolar attractive Kihara cavities given by a Lennard-Jones potential shifted by a core radius. The dipolar response of the hydration layer to a uniform electric field substantially exceeds that of the bulk. For strongly attractive solutes, the collective dynamics of the hydration layer become slow compared to bulk water, as the solute size is increased. The statistics of electric field fluctuations at the solute center are Gaussian and tend toward the dielectric continuum limit with increasing solute size. A dipolar probe placed at the center of the solute is sensitive neither to the polarity excess nor to the slowed dynamics of the hydration layer. A point dipole was introduced close to the solute-water interface to further study the statistics of electric field fluctuations generated by the water. For small dipole magnitudes, the free energy surface is single-welled, with approximately Gaussian statistics. When the dipole is increased, the free energy surface becomes double-welled, before landing in an excited state, characterized again by a single-welled surface. The intermediate region is fairly broad and is characterized by electrostatic fluctuations significantly in excess of the prediction of linear response. We simulated a solute having the geometry of C180 fullerene, with dipoles introduced on each carbon. For small dipole moments, the solvent response follows the results seen for a single dipole; but for larger dipole magnitudes, the fluctuations of the solute-solvent energy pass through a second maximum. The juxtaposition of the two transitions leads to an approximately cubic scaling of the chemical potential with the dipole strengh. Umbrella sampling techniques were used to generate free energy surfaces of the electric potential fluctuations at the heme iron in Cytochrome B562. The results were unfortunately inconclusive, as the ionic background was not effectively represented in the finite-size system.
ContributorsFriesen, Allan Dwayne (Author) / Matyushov, Dmitry V (Thesis advisor) / Angell, C Austen (Thesis advisor) / Beckstein, Oliver (Committee member) / Mujica, Vladimiro (Committee member) / Arizona State University (Publisher)
Created2012
Description
Waste heat energy conversion remains an inviting subject for research, given the renewed emphasis on energy efficiency and carbon emissions reduction. Solid-state thermoelectric devices have been widely investigated, but their practical application remains challenging because of cost and the inability to fabricate them in geometries that are easily compatible with heat sources. An intriguing alternative to solid-state thermoelectric devices is thermogalvanic cells, which include a generally liquid electrolyte that permits the transport of ions. Thermogalvanic cells have long been known in the electrochemistry community, but have not received much attention from the thermal transport community. This is surprising given that their performance is highly dependent on controlling both thermal and mass (ionic) transport. This research will focus on a research project, which is an interdisciplinary collaboration between mechanical engineering (i.e. thermal transport) and chemistry, and is a largely experimental effort aimed at improving fundamental understanding of thermogalvanic systems. The first part will discuss how a simple utilization of natural convection within the cell doubles the maximum power output of the cell. In the second part of the research, some of the results from the previous part will be applied in a feasibility study of incorporating thermogalvanic waste heat recovery systems into automobiles. Finally, a new approach to enhance Seebeck coefficient by tuning the configurational entropy of a mixed-ligand complex formation of copper sulfate aqueous electrolytes will be presented. Ultimately, a summary of these results as well as possible future work that can be formed from these efforts is discussed.
ContributorsGunawan, Andrey (Author) / Phelan, Patrick E (Thesis advisor) / Buttry, Daniel A (Committee member) / Mujica, Vladimiro (Committee member) / Chan, Candace K. (Committee member) / Wang, Robert Y (Committee member) / Arizona State University (Publisher)
Created2015
Description
Non-photochemical quenching (NPQ) is a photoprotective regulatory mechanism essential to the robustness of the photosynthetic apparatus of green plants. Energy flow within the low-light adapted reaction centers is dynamically optimized to match the continuously fluctuating light conditions found in nature. Activated by compartmentalized decreases in pH resulting from photosynthetic activity during periods of elevated photon flux, NPQ induces rapid thermal dissipation of excess excitation energy that would otherwise overwhelm the apparatus’s ability to consume it. Consequently, the frequency of charge separation decreases and the formation of potentially deleterious, high-energy intermediates slows, thereby reducing the threat of photodamage by disallowing their accumulation. Herein is described the synthesis and photophysical analysis of a molecular triad that mimics the effects of NPQ on charge separation within the photosynthetic reaction centers. Steady-state absorption and emission, time-resolved fluorescence, and transient absorption spectroscopies were used to demonstrate reversible quenching of the first singlet excited state affecting the quantum yield of charge separation by approximately one order of magnitude. As in the natural system, the populations of unquenched and quenched states and, therefore, the overall yields of charge separation were found to be dependent upon acid concentration.
ContributorsPahk, Ian (Author) / Gust, Devens (Thesis advisor) / Gould, Ian (Committee member) / Mujica, Vladimiro (Committee member) / Arizona State University (Publisher)
Created2015
Description
Studying charge transport through single molecules is of great importance for unravelling charge transport mechanisms, investigating fundamentals of chemistry, and developing functional building blocks in molecular electronics.
First, a study of the thermoelectric effect in single DNA molecules is reported. By varying the molecular length and sequence, the charge transport in DNA was tuned to either a hopping- or tunneling-dominated regimes. In the hopping regime, the thermoelectric effect is small and insensitive to the molecular length. Meanwhile, in the tunneling regime, the thermoelectric effect is large and sensitive to the length. These findings indicate that by varying its sequence and length, the thermoelectric effect in DNA can be controlled. The experimental results are then described in terms of hopping and tunneling charge transport models.
Then, I showed that the electron transfer reaction of a single ferrocene molecule can be controlled with a mechanical force. I monitor the redox state of the molecule from its characteristic conductance, detect the switching events of the molecule from reduced to oxidized states with the force, and determine a negative shift of ~34 mV in the redox potential under force. The theoretical modeling is in good agreement with the observations, and reveals the role of the coupling between the electronic states and structure of the molecule.
Finally, conclusions and perspectives were discussed to point out the implications of the above works and future studies that can be performed based on the findings.
First, a study of the thermoelectric effect in single DNA molecules is reported. By varying the molecular length and sequence, the charge transport in DNA was tuned to either a hopping- or tunneling-dominated regimes. In the hopping regime, the thermoelectric effect is small and insensitive to the molecular length. Meanwhile, in the tunneling regime, the thermoelectric effect is large and sensitive to the length. These findings indicate that by varying its sequence and length, the thermoelectric effect in DNA can be controlled. The experimental results are then described in terms of hopping and tunneling charge transport models.
Then, I showed that the electron transfer reaction of a single ferrocene molecule can be controlled with a mechanical force. I monitor the redox state of the molecule from its characteristic conductance, detect the switching events of the molecule from reduced to oxidized states with the force, and determine a negative shift of ~34 mV in the redox potential under force. The theoretical modeling is in good agreement with the observations, and reveals the role of the coupling between the electronic states and structure of the molecule.
Finally, conclusions and perspectives were discussed to point out the implications of the above works and future studies that can be performed based on the findings.
ContributorsLi, Yueqi, Ph.D (Author) / Tao, Nongjian (Thesis advisor) / Buttry, Daniel (Committee member) / Mujica, Vladimiro (Committee member) / Arizona State University (Publisher)
Created2017
Description
This thesis is devoted to the theoretical and computational study of electron transport in molecular junctions where one or more hydrogen bonds are involved in the process. While electron transport through covalent bonds has been extensively studied, in recent work the focus has been shifted towards hydrogen-bonded systems due to their ubiquitous presence in biological systems and their potential in forming nano- junctions between molecular electronic devices and biological systems.
This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junc- tion significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction.
In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH···O, OH···O, and NH···N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has fo- cused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance de- scriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular descrip- tion of conductance that is not based on the conventional view of molecular orbitals as transport channels. My findings suggest that the hydrogen-bond networks are crucial in understanding the conductance of these junctions.
A broader impact of this work pertains the fact that characterizing transport through hydrogen bonding networks may help in developing faster and cost-effective approaches to personalized medicine, to advance DNA sequencing and implantable electronics, and to progress in the design and application of new drugs.
This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junc- tion significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction.
In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH···O, OH···O, and NH···N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has fo- cused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance de- scriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular descrip- tion of conductance that is not based on the conventional view of molecular orbitals as transport channels. My findings suggest that the hydrogen-bond networks are crucial in understanding the conductance of these junctions.
A broader impact of this work pertains the fact that characterizing transport through hydrogen bonding networks may help in developing faster and cost-effective approaches to personalized medicine, to advance DNA sequencing and implantable electronics, and to progress in the design and application of new drugs.
ContributorsWimmer, Michael (Author) / Mujica, Vladimiro (Thesis advisor) / Wolf, George (Committee member) / Chizmeshya, Andrew (Committee member) / Arizona State University (Publisher)
Created2017
Description
Understanding charge transport in single molecules covalently bonded to electrodes is a fundamental goal in the field of molecular electronics. In the past decade, it has become possible to measure charge transport on the single-molecule level using the STM break junction method. Measurements on the single-molecule level shed light on charge transport phenomena which would otherwise be obfuscated by ensemble measurements of groups of molecules. This thesis will discuss three projects carried out using STM break junction. In the first project, the transition between two different charge transport mechanisms is reported in a set of molecular wires. The shortest wires show highly length dependent and temperature invariant conductance behavior, whereas the longer wires show weakly length dependent and temperature dependent behavior. This trend is consistent with a model whereby conduction occurs by coherent tunneling in the shortest wires and by incoherent hopping in the longer wires. Measurements are supported with calculations and the evolution of the molecular junction during the pulling process is investigated. The second project reports controlling the formation of single-molecule junctions by means of electrochemically reducing two axial-diazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in-situ between the molecule and gold electrodes. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond. Finally, the third project investigates the role that molecular conformation plays in the conductance of oligothiophene single-molecule junctions. Ethyl substituted oligothiophenes were measured and found to exhibit temperature dependent conductance and transition voltage for molecules with between two and six repeat units. While the molecule with only one repeat unit shows temperature invariant behavior. Density functional theory calculations show that at higher temperatures the oligomers with multiple repeat units assume a more planar conformation, which increases the conjugation length and decreases the effective energy barrier of the junction.
ContributorsHines, Thomas (Author) / Tao, Nongjian (Thesis advisor) / Li, Jian (Thesis advisor) / Mujica, Vladimiro (Committee member) / Allee, David (Committee member) / Arizona State University (Publisher)
Created2013
Description
Molecular structures and dynamics in amorphous materials present unique experimental challenges compared with the characterization of crystalline solids. Liquids and glassy solids have many applications in industry such as ionic liquids for fuel cells or biomolecule stabilizing agents, enhancing pharmaceuticals dissolution rates, and modified high performance biopolymers like silk for textile, biomedical, drug delivery, among many others. Amorphous materials are metastable, with kinetic profiles of phase transitions depending on relaxation dynamics, thermal history, plus factors such as temperature, pressure, and humidity. Understanding molecular structure and phase transitions of amorphous states of small molecules and biopolymers is broadly important for realizing their applications. The structure of liquid and glassy states of the drugs carbamazepine (CBZ) and indomethacin (IMC) were studied with solid-state nuclear magnetic resonance (ssNMR) spectroscopy, high energy X-ray diffraction, Fourier Infrared Transform Spectroscopy (FTIR), differential scanning calorimetry (DSC), and Empirical Potential Structure Refinement (EPSR). Both drugs have multiple crystalline polymorphs with slow dissolution kinetics, necessitating stable glassy or polymer dispersed formulations. More hydrogen bonds per CBZ molecule and a larger distribution of oligomeric states in the glass versus the liquid than expected. The chlorobenzyl ring of crystalline and glassy IMC measured with ssNMR were surprisingly found to have similar mobility. Crucially, humidity strongly affects glass structure, highlighting the importance of combining modeling techniques like EPSR with careful sample preparation for proper interpretation. Highly basic protic ionic liquids with low ∆pKa were synthesized with metathesis rather than proton transfer and characterized using NMR and dielectric spectroscopy. Finally, the protein secondary structure of spider egg sac silk was studied using ssNMR, FTIR, and scanning electron microscopy. Tubuliform silk found in spider egg sacs has extensive β-sheet domains which form nanocrystallites within an amorphous matrix. Structural predictions and spectroscopic measurements of tubuliform silk solution are mostly α-helical, with the mechanism of structural rearrangement to the β-sheet rich fiber unknown. The movement of spiders during egg silk spinning make in situ experiments difficult practically. This work is the first observation that tubuliform silk of Argiope aurantia after liquid crystalline spinning exits the spinneret as a predominantly (~70%) β-sheet fiber.
ContributorsEdwards, Angela Diane (Author) / Yarger, Jeffery L (Thesis advisor) / Liu, Yan (Committee member) / Mujica, Vladimiro (Committee member) / Arizona State University (Publisher)
Created2022
Description
The movement of energy within a material is at the heart of numerous fundamental properties of chemistry and physics. Studying the process of photo-absorption in real time provides key insights into how energy is captured, stabilized, and dissipated within a material. The work presented in this thesis uses ultrafast time-of-flight mass spectrometry and computational modeling to observe and understand the properties of photo-excited states within molecules and clusters. Experimental results provide direct measurement of excited state lifetimes, while computational modeling provides a more thorough understanding of the movement of energy within an excited state. Excited state dynamics in covalent molecules such as n-butyl bromide (C4H9Br), presented in Chapter 4, demonstrate the significance of IVR of photo-excited states. Exciting to the high energy Rydberg manifold leads to predissociation into fragments of various lengths and degrees of saturation but the predissociation process is disrupted by energy redistribution into hot vibrational states. Experimental lifetimes show that IVR occurs over rapidly (~ 600 fs) leaving less energy for bond dissociation. Additionally, a long-lived feature in the dynamics of C4H9+ shows evidence of ion-pair formation – a known phenomenon which creates a stable A+/B- pair separated by several angstroms and occurring at energies lower than direct ionization. The results of this research show the dynamics of energy transfer into bond fragmentation, kinetic energy, and vibrational motion.
Metal-oxide clusters are unique materials which are representative of bulk materials but with quantized excited states instead of bands and as such can be used as atomically precise analogs to semiconducting materials. Excited state lifetimes and theoretical descriptors of electron-hole interactions of titanium oxide clusters, presented in Chapter 5, shows the significance of structure and oxidation of charge-transfer materials. Modeling the excited states of the photo-generated electrons and holes provides a window into the dynamics of charge-transfer and electron-hole separation and recombination in bulk materials. Furthermore, changes in the oxidation of the cluster have a dramatic impact on the nature of excited states and overall cluster properties. Such changes are analogous to oxygen defects in bulk materials and are critical for understanding reaction chemistry at defect sites.
ContributorsHeald, Lauren (Author) / Sayres, Scott G (Thesis advisor) / Seo, Dong-Kyun (Committee member) / Mujica, Vladimiro (Committee member) / Arizona State University (Publisher)
Created2022