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- All Subjects: Chemistry
- Creators: Arizona State University
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Description
We studied the relationship between the polarizability and the molecular conductance
that arises in the response of a molecule to an external electric field. To illustrate
the plausibility of the idea, we used Simmons' tunneling model, which describes image
charge and dielectric effects on electron transport through a barrier. In such a
model, the barrier height depends on the dielectric constant of the electrode-molecule-electrode junction, which in turn can be approximately expressed in terms of the
molecular polarizability via the classical Clausius-Mossotti relation. In addition to
using the tunneling model, the validity of the relationships between the molecular
polarizability and the molecular conductance was tested by comparing calculated
and experimentally measured conductance of different chemical structures ranging
from covalent bonded to non-covalent bonded systems. We found that either using
the tunneling model or the first-principle calculated quantities or experimental data,
the conductance decreases as the molecular polarizability increases. In contrast to
this strong correlation, our results showed that in some cases there was a weaker or
none correlation between the conductance and other molecular electronic properties
including HOMO-LUMO gap, chemical geometries, and interactions energies. All
these results together suggest that using the molecular polarizability as a molecular
descriptor for conductance can offer some advantages compared to using other
molecular electronic properties and can give additional insight about the electronic
transport property of a junction.
These results also show the validity of the physically intuitive picture that to a first
approximation a molecule in a junction behaves as a dielectric that is polarized in the
opposite sense of the applied bias, thereby creating an interfacial barrier that hampers
tunneling. The use of the polarizability as a descriptor of molecular conductance offers
signicant conceptual and practical advantages over a picture based in molecular
orbitals. Despite the simplicity of our model, it sheds light on a hitherto neglected
connection between molecular polarizability and conductance and paves the way for
further conceptual and theoretical developments.
The results of this work was sent to two publications. One of them was accepted
in the International Journal of Nanotechnology (IJNT) and the other is still under
review in the Journal of Physical Chemistry C.
that arises in the response of a molecule to an external electric field. To illustrate
the plausibility of the idea, we used Simmons' tunneling model, which describes image
charge and dielectric effects on electron transport through a barrier. In such a
model, the barrier height depends on the dielectric constant of the electrode-molecule-electrode junction, which in turn can be approximately expressed in terms of the
molecular polarizability via the classical Clausius-Mossotti relation. In addition to
using the tunneling model, the validity of the relationships between the molecular
polarizability and the molecular conductance was tested by comparing calculated
and experimentally measured conductance of different chemical structures ranging
from covalent bonded to non-covalent bonded systems. We found that either using
the tunneling model or the first-principle calculated quantities or experimental data,
the conductance decreases as the molecular polarizability increases. In contrast to
this strong correlation, our results showed that in some cases there was a weaker or
none correlation between the conductance and other molecular electronic properties
including HOMO-LUMO gap, chemical geometries, and interactions energies. All
these results together suggest that using the molecular polarizability as a molecular
descriptor for conductance can offer some advantages compared to using other
molecular electronic properties and can give additional insight about the electronic
transport property of a junction.
These results also show the validity of the physically intuitive picture that to a first
approximation a molecule in a junction behaves as a dielectric that is polarized in the
opposite sense of the applied bias, thereby creating an interfacial barrier that hampers
tunneling. The use of the polarizability as a descriptor of molecular conductance offers
signicant conceptual and practical advantages over a picture based in molecular
orbitals. Despite the simplicity of our model, it sheds light on a hitherto neglected
connection between molecular polarizability and conductance and paves the way for
further conceptual and theoretical developments.
The results of this work was sent to two publications. One of them was accepted
in the International Journal of Nanotechnology (IJNT) and the other is still under
review in the Journal of Physical Chemistry C.
ContributorsVatan Meidanshahi, Reza (Author) / Mujica, Vladimiro (Thesis advisor) / Chizmeshya, Andrew (Committee member) / Richert, Ranko (Committee member) / Arizona State University (Publisher)
Created2014
Description
MAX phases are an intriguing class of materials with exotic combinations of properties, essentially turning them into metallic ceramics. Despite this unique feature, no commercialization has been accomplished yet. Looking at the state of the art within the MAX phase community, almost all published studies can be summarized using the term “traditional high temperature synthesis”. Contrasting the scientific interest that has been on the rise especially since the discovery of MXenes, the synthetic spectrum has been largely the same as it has been over the past decades.Herein, the newly-emerging sol-gel chemistry is being explored as an alternative non-conventional synthetic approach. Building on the successful sol-gel synthesis of Cr2GaC, this study focuses around the expansion of sol-gel chemistry for MAX phases. Starting with a thorough mechanistic investigation into the reaction pathway of sol-gel synthesized Cr2GaC, the chemical understanding of this system is drastically deepened. It is shown how the preliminary nano-structured metal-oxide species develop into bulk oxides, before the amorphous and disordered
graphite partakes in the reaction and reduces the metals into the MAX phase.
Furthermore, the technique is extended to the two Ge- based MAX phases V2GeC and Cr2GeC, a critical step needed to prove the viability and applicability of the newly developed technique. Additionally, by introducing Mn into the Cr-Ga-C system, a Mn-doping was achieved, and for the first time for (Cr1–xMnx)2GaC, a unit cell increase could be recorded. Based on magnetometry measurements, the currently widely accepted assumption of statistically distributed Mn in the M-layer is challenged.
The versatility of wet chemistry is explored using the model system Cr2GaC. Firstly, the MAX phase can be obtained in a microwire shape leveraging the branched biopolymer dextran, eliminating the need for any post-synthesis machining. Via halide intercalation, the electrical transport properties could be purposefully engineered.
Secondly, leveraging the unique and linear biopolymer chitosan, Cr2GaC was obtained as thick films and dense microspheres, drastically opening potential areas of application for MAX phases. Lastly, hollow microspheres with diameters of tens of μm were synthesized via carboxymethylated dextran. This shape once more opens the door to very specific applications requiring sophisticated structures.
ContributorsSiebert, Jan (Author) / Birkel, Christina (Thesis advisor) / Gould, Ian (Committee member) / Kouvetakis, John (Committee member) / Arizona State University (Publisher)
Created2022
Description
The discovery of DNA helical structure opened the door of modern molecular biology. Ned Seeman utilized DNA as building block to construct different nanoscale materials, and introduced a new field, know as DNA nanotechnology. After several decades of development, different DNA structures had been created, with different dimension, different morphology and even with complex curvatures. In addition, after construction of enough amounts DNA structure candidates, DNA structure template, with excellent spatial addressability, had been used to direct the assembly of different nanomaterials, including nanoparticles and proteins, to produce different functional nanomaterials. However there are still many challenges to fabricate functional DNA nanostructures. The first difficulty is that the present finite sized template dimension is still very small, usually smaller than 100nm, which will limit the application for large amount of nanomaterials assembly or large sized nanomaterials assembly. Here we tried to solve this problem through developing a new method, superorigami, to construct finite sized DNA structure with much larger dimension, which can be as large as 500nm. The second problem will be explored the ability of DNA structure to assemble inorganic nanomaterials for novel photonic or electronic properties. Here we tried to utilize DNA Origami method to assemble AuNPs with controlled 3D spacial position for possible chiral photonic complex. We also tried to assemble SWNT with discrete length for possible field effect transistor device. In addition, we tried to mimic in vivo compartment with DNA structure to study internalized enzyme behavior. From our results, constructed DNA cage origami can protect encapsulated enzyme from degradation, and internalized enzyme activity can be boosted for up to 10 folds. In summary, DNA structure can serve as an ideal template for construction of functional nanomaterials with lots of possibilities to be explored.
ContributorsZhao, Zhao (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Seo, Dong-Kyun (Committee member) / Arizona State University (Publisher)
Created2013
Description
Deoxyribonucleic acid (DNA), a biopolymer well known for its role in preserving genetic information in biology, is now drawing great deal of interest from material scientists. Ease of synthesis, predictable molecular recognition via Watson-Crick base pairing, vast numbers of available chemical modifications, and intrinsic nanoscale size makes DNA a suitable material for the construction of a plethora of nanostructures that can be used as scaffold to organize functional molecules with nanometer precision. This dissertation focuses on DNA-directed organization of metallic nanoparticles into well-defined, discrete structures and using them to study photonic interaction between fluorophore and metal particle. Presented here are a series of studies toward this goal. First, a novel and robust strategy of DNA functionalized silver nanoparticles (AgNPs) was developed and DNA functionalized AgNPs were employed for the organization of discrete well-defined dimeric and trimeric structures using a DNA triangular origami scaffold. Assembly of 1:1 silver nanoparticle and gold nanoparticle heterodimer has also been demonstrated using the same approach. Next, the triangular origami structures were used to co-assemble gold nanoparticles (AuNPs) and fluorophores to study the distance dependent and nanogap dependencies of the photonic interactions between them. These interactions were found to be consistent with the full electrodynamic simulations. Further, a gold nanorod (AuNR), an anisotropic nanoparticle was assembled into well-defined dimeric structures with predefined inter-rod angles. These dimeric structures exhibited unique optical properties compared to single AuNR that was consistent with the theoretical calculations. Fabrication of otherwise difficult to achieve 1:1 AuNP- AuNR hetero dimer, where the AuNP can be selectively placed at the end-on or side-on positions of anisotropic AuNR has also been shown. Finally, a click chemistry based approach was developed to organize sugar modified DNA on a particular arm of a DNA origami triangle and used them for site-selective immobilization of small AgNPs.
ContributorsPal, Suchetan (Author) / Liu, Yan (Thesis advisor) / Yan, Hao (Thesis advisor) / Lindsay, Stuart (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2012
Description
Healthy mitochondria are essential for cell survival. Described herein is the synthesis of a family of novel aminoquinone antioxidants designed to alleviate oxidative stress and prevent the impairment of cellular function. In addition, a library of bleomycin disaccharide analogues has also been synthesized to better probe the tumor targeting properties of bleomycin. The first study involves the synthesis of a benzoquinone natural product and analogues that closely resemble the redox core of the natural product geldanamycin. The synthesized 5-amino-3-tridecyl-1,4-benzoquinone antioxidants were tested for their ability to protect Friedreich's ataxia (FRDA) lymphocytes from induced oxidative stress. Some of the analogues synthesized conferred cytoprotection in a dose-dependent manner in FRDA lymphocytes at micromolar concentrations. The biological assays suggest that the modification of the 2-hydroxyl and N-(3-carboxypropyl) groups in the natural product can improve its antioxidant activity and significantly enhance its ability to protect mitochondrial function under conditions of oxidative stress. The second project focused on the synthesis of a library of bleomycin disaccharide-dye conjugates and monitored their cellular uptake by fluorescence microscopy. The studies reveal that the position of the carbamoyl group plays an important role in modulating the cellular uptake of the disaccharide. It also led to the discovery of novel disaccharides with improved tumor selectivity.
ContributorsMathilakathu Madathil, Manikandadas (Author) / Hecht, Sidney M. (Thesis advisor) / Rose, Seth (Committee member) / Woodbury, Neal (Committee member) / Arizona State University (Publisher)
Created2013
Description
ABSTRACT Manipulation of biological targets using synthetic or naturally occurring organic compounds has been the focal point of medicinal chemistry. The work described herein centers on the synthesis of organic small molecules that are targeted either to cell surface receptors, to the ribosomal catalytic center or to human immunodeficiency virus reverse transcriptase. Bleomycins (BLMs) are a family of naturally occurring glycopeptidic antitumor agents with an inherent selectivity towards cancer cells. DeglycoBLM, which lacks the sugar moiety of bleomycin, has much lower cytotoxicity in cellular assays. A recent study using microbbuble conjugates of BLM and deglycoBLM showed that BLM was able to selectively bind to breast cancer cells, whereas the deglyco analogue was unable to target either the cancer or normal cells. This prompted us to further investigate the role of the carbohydrate moiety in bleomycin. Fluorescent conjugates of BLM, deglycoBLM and the BLM carbohydrate were studied for their ability to target cancer cells. Work presented here describes the synthesis of the fluorescent carbohydrate conjugate. Cell culture assays showed that the sugar moiety was able to selectively target various cancer cells. A second conjugate was prepared to study the importance of the C-3 carbamoyl group present on the mannose residue of the carbohydrate. Three additional fluorescent probes were prepared to improve the uptake of this carbohydrate moiety into cancer cells. Encouraged by the results from the fluorescence experiments, the sugar moiety was conjugated to a cytotoxic molecule to selectively deliver this drug into cancer cells. The nonsense codon suppression technique has enabled researchers to site specifically incorporate noncanonical amino acids into proteins. The amino acids successfully incorporated this way are mostly α-L-amino acids. The non-α-L-amino acids are not utilized as substrates by ribosome catalytic center. Hoping that mutations near the ribosome peptidyltransferase site might alleviate its bias towards α-L-amino acids, a library of modified ribosomes was generated. Analogues of the naturally occurring antibiotic puromycin were used to select promising candidates that would allow incorporation of non-α-L-amino acids into proteins. Syntheses of three different puromycin analogues are described here. The reverse transcriptase enzyme from HIV-1 (HIV-1 RT) has been a popular target of HIV therapeutic agents due to its crucial role in viral replication. The 4-chlorophenyl hydrazone of mesoxalic acid (CPHM) was identified in a screen designed to find inhibitors of strand transfer reactions catalyzed by HIV-1 RT. Our collaborators designed several analogues of CPHM with different substituents on the aromatic ring using molecular docking simulations. Work presented here describes the synthesis of eight different analogues of CPHM.
ContributorsPaul, Rakesh (Author) / Hecht, Sidney M. (Thesis advisor) / Moore, Ana L (Committee member) / Rose, Seth D (Committee member) / Arizona State University (Publisher)
Created2013
Description
Chimeric antigen receptor (CAR) T-cell therapies present transformative potentials for progressive and refractory cancer treatment. However, therapy-associated neuronal toxicities, cytokine release syndromes, relapse rates, and the complex responses of patients and medical management have increased the cost of patient care. Prompt point-of-care (POC) quantification of circulating CAR T-cells and associated cytokines could enhance safety, simplify patients' management, and decrease patient care costs. While effective, existing standard detection methods, such as Enzyme-Linked Immunosorbent Assay (ELISA), quantitative Polymerase Chain Reaction(qPCR), and Flow cytometry, are not conducive to quick POC testing due to their complexity and expense. This research introduces a centrifuge-free Rapid Optical Imaging (ROI)-based platform to quantify CAR T-cells and therapy-related cytokine (Interleukin-6) from a single drop of whole blood. Through machine learning, label-free ROI-based CAR T-cell detection has been improved for accuracy compared with fluorescent staining results, and the morphological characteristics of CAR-T cells have been applied to attribute for differentiation and reduce false positives. This multi-layered microfluidic chip integrates cell and cytokines separation, collection, and detection steps, reducing the need for centrifugation or staining procedures. The microfluidic channel system separates white blood cells from whole blood after red blood cell agglutination and membrane filtration. The non-agglutinated samples are then extracted into a subchannel with a functionalized sensor surface for CAR-T-specific detection. Calibration curves were established using blood samples spiked with varying CAR-T cell concentrations. Another subchannel, featuring dual-layer membrane filtration, has been designed for cytokine detection using gold nanoparticle-labeled detection antibodies. Cytokine concentrations are digitally measured by tracking the number of gold nanoparticles in designated zones. This platform aims to offer a rapid and cost-efficient prognostic tool for timely assessment of key molecular and cellular biomarkers of CAR-T therapy patients, facilitating timely and evidence-based treatment adjustments.
ContributorsYu, Nanxi (Author) / Wang, Shaopeng SW (Thesis advisor) / Forzani, Erica EF (Thesis advisor) / Borges, Chad CB (Committee member) / Liu, Yan YL (Committee member) / Arizona State University (Publisher)
Created2023
Description
In this thesis, applications of sparsity, specifically sparse-tensors are motivated in physics.An algorithm is introduced to natively compute sparse-tensor's partial-traces, along with direct implementations in popular python libraries for immediate use. These applications include the infamous exponentially-scaling (with system size) Quantum-Many-Body problems (both Heisenberg/spin-chain-like and Chemical Hamiltonian models). This sparsity aspect is stressed as an important and essential feature in solving many real-world physical problems approximately-and-numerically. These include the original motivation of solving radiation-damage questions for ultrafast light and electron sources.
ContributorsCandanedo, Julio (Author) / Beckstein, Oliver (Thesis advisor) / Arenz, Christian (Thesis advisor) / Keeler, Cynthia (Committee member) / Erten, Onur (Committee member) / Arizona State University (Publisher)
Created2023
Description
Banded iron formations (BIFs) are among the earliest possible indicators for oxidation of the Archean biosphere. However, the origin of BIFs remains debated. Proposed formation mechanisms include oxidation of Fe(II) by O2 (Cloud, 1973), photoferrotrophy (Konhauser et al., 2002), and abiotic UV photooxidation (Braterman et al., 1983; Konhauser et al., 2007). Resolving this debate could help determine whether BIFs are really indicators of O2, biological activity, or neither.
To examine the viability of abiotic UV photooxidation of Fe, laboratory experiments were conducted in which Fe-bearing solutions were irradiated with different regions of the ultraviolet (UV) spectrum and Fe oxidation and precipitation were measured. The goal was to revisit previous experiments that obtained conflicting results, and extend these experiments by using a realistic bicarbonate buffered solution and a xenon (Xe) lamp to better match the solar spectrum and light intensity.
In experiments reexamining previous work, Fe photooxidation and precipitation was observed. Using a series of wavelength cut-off filters, the reaction was determined not to be caused by light > 345 nm. Experiments using a bicarbonate buffered solution, simulating natural waters, and using unbuffered solutions, as in prior work showed the same wavelength sensitivity. In an experiment with a Xe lamp and realistic concentrations of Archean [Fe(II)], Fe precipitation was observed in hours, demonstrating the ability for photooxidation to occur significantly in a simulated natural setting.
These results lead to modeled Fe photooxidation rates of 25 mg Fe cm-2 yr-1—near the low end of published BIF deposition rates, which range from 9 mg Fe cm-2 yr-1 to as high as 254 mg Fe cm-2 yr-1 (Konhauser et al., 2002; Trendall and Blockley, 1970). Because the rates are on the edge and the model has unquantified, favorable assumptions, these results suggest that photooxidation could contribute to, but might not be completely responsible for, large rapidly deposited BIFs such those in the Hamersley Basin. Further work is needed to improve the model and test photooxidation with other solution components. Though possibly unable to fully explain BIFs, UV light has significant oxidizing power, so the importance of photooxidation in the Archean as an environmental process and its impact on paleoredox proxies need to be determined.
To examine the viability of abiotic UV photooxidation of Fe, laboratory experiments were conducted in which Fe-bearing solutions were irradiated with different regions of the ultraviolet (UV) spectrum and Fe oxidation and precipitation were measured. The goal was to revisit previous experiments that obtained conflicting results, and extend these experiments by using a realistic bicarbonate buffered solution and a xenon (Xe) lamp to better match the solar spectrum and light intensity.
In experiments reexamining previous work, Fe photooxidation and precipitation was observed. Using a series of wavelength cut-off filters, the reaction was determined not to be caused by light > 345 nm. Experiments using a bicarbonate buffered solution, simulating natural waters, and using unbuffered solutions, as in prior work showed the same wavelength sensitivity. In an experiment with a Xe lamp and realistic concentrations of Archean [Fe(II)], Fe precipitation was observed in hours, demonstrating the ability for photooxidation to occur significantly in a simulated natural setting.
These results lead to modeled Fe photooxidation rates of 25 mg Fe cm-2 yr-1—near the low end of published BIF deposition rates, which range from 9 mg Fe cm-2 yr-1 to as high as 254 mg Fe cm-2 yr-1 (Konhauser et al., 2002; Trendall and Blockley, 1970). Because the rates are on the edge and the model has unquantified, favorable assumptions, these results suggest that photooxidation could contribute to, but might not be completely responsible for, large rapidly deposited BIFs such those in the Hamersley Basin. Further work is needed to improve the model and test photooxidation with other solution components. Though possibly unable to fully explain BIFs, UV light has significant oxidizing power, so the importance of photooxidation in the Archean as an environmental process and its impact on paleoredox proxies need to be determined.
ContributorsCastleberry, Parker (Author) / Anbar, Ariel D (Thesis advisor) / Herckes, Pierre (Committee member) / Lyons, James (Committee member) / Arizona State University (Publisher)
Created2017
Description
Late first row transitional metals have attracted attention for the development of sustainable catalysts due to their low cost and natural abundance. This dissertation discusses the utilization of redox-active ligands to overcome one electron redox processes exhibited by these base metals. Previous advances in carbonyl and carboxylate hydrosilylation using redox active ligand-supported complexes such as (Ph2PPrPDI)Mn and (Ph2PPrDI)Ni have been reviewed in this thesis to set the stage for the experimental work described herein.The synthesis and electronic structure of late first row transition metal complexes featuring the Ph2PPrPDI chelate was pursued. Utilizing these complexes as catalysts for a variety of reactions gave a recurring trend in catalytic activity. DFT calculations suggest that the trend in activity observed for these complexes is associated with the ease of phosphine arm dissociation.
Furthermore, the synthesis and characterization of a phosphine-substituted aryl diimine ligand, Ph2PPrADI-H was explored. Addition of Ph2PPrADI-H to CoCl2 resulted in C-H activation of the ligand backbone and formation of [(Ph2PPrADI)CoCl][Co2Cl6]0.5. Reduction of [(Ph2PPrADI)CoCl][Co2Cl6]0.5 afforded the precatalyst, (Ph2PPrADI)Co, that was found to effectively catalyze carbonyl hydrosilylation. At low catalyst loading, TOFs of up to 330 s-1 could be achieved, the highest ever reported for metal-catalyzed carbonyl hydrosilylation.
This dissertation also reports the first cobalt catalyzed pathway for dehydrocoupling diamines or polyamines with polymethylhydrosiloxanes to form crosslinked copolymers. At low catalyst loading, (Ph2PPrADI)Co was found to catalyze the dehydrocoupling of 1,3-diaminopropane and TMS-terminated PMHS with TOFs of up to 157 s-1, the highest TOF ever reported for a Si-N dehydrocoupling reaction. Dehydrocoupling of diamines with hydride-terminated polydimethylsiloxane yielded linear diamine siloxane copolymers as oils.
Finally, dehydrocoupling between diamines and organosilanes catalyzed by a manganese dimer complex, [(2,6-iPr2PhBDI)Mn(μ-H)]2, has allowed for the preparation of silane diamine copolymers. Exceptional solvent absorption capacity was demonstrated by the solid networks, which were found to absorb up to 7 times their own weight. Furthermore, degradation of these networks revealed that their Si-N backbones are easily hydrolysable when exposed to air. The use of lightly crosslinked copolymers as coatings was also studied using SEM analysis.
ContributorsSharma, Anuja (Author) / Trovitch, Ryan J. (Thesis advisor) / Seo, Dong-Kyun (Committee member) / Moore, Gary F. (Committee member) / Arizona State University (Publisher)
Created2024