The decay rates for molecules at rough surfaces are studied via an island surface model, with particular emphasis on the effect due to the distribution of surface roughness. Two extreme cases are studied when the surface islands distribute themselves evenly and when they coalesce to form local clusters at the molecule-substrate interface. The optical properties of the interfacial layer in these two cases are described by the Maxwell-Garnett and the fractal-cluster models, respectively. Among other results, it is found that both enhancement and suppression of the surface-induced decay rates are possible due to the presence of roughness, with more dramatic suppression taking place when the surface islands coalesce to form clusters.

Thesis (Ph.D.)--Chemical Engineering, Georgia Institute of Technology, 2009. / Committee Chair: Peter Ludovice; Committee Member: Amyn Teja; Committee Member: Arthur Ragauskas; Committee Member: William Koros; Committee Member: Yulin Deng.

Thesis (Ph.D)--Chemical Engineering, Georgia Institute of Technology, 2009. / Committee Chair: Ludovice, Pete; Committee Member: Grover, Martha; Committee Member: Jones, Christopher; Committee Member: Realff, Matthew; Committee Member: Sherrill, David. Part of the SMARTech Electronic Thesis and Dissertation Collection.

University of Macau / Institute of Chinese Medical Sciences

A thesis submitted to the Faculty of Science University of the Witwatersrand in fulfillment of the requirements for the degree of Doctor of Philosophy. Johannesburg, 1998. / Conformational analysis of portions of functionally-active and functionally-inactive signal peptides (incorporating the wild-type and mutants thereof) has been performed using a variety of computational prediction techniques based on both statistics and molecular mechanics. Molecular mechanics conformational studies are generally plagued by the problem of combinatorial explosion; this problem was addressed with a systematic searching procedure as well as a recently developed genetic algorithm, both utilising tile ECEPP/3 force field. The genetic algorithm, in combination with a gradient minimiser, proved to be successful in finding low-energy conformations for each peptide sequence studied. Analysis was performed in both simulated hydrophobic and hydrophilic environments, under distance-constraints. The molecular mechanics results and statistical predictions generated from the study were compared With existing experimental observations. The reliability of statistical predictions proved to be dependent on prediction method; the more consistent predictions were produced by methods based on membrane proteins, as opposed to those based on globular proteins. The physical property of hydrophobicity of signal peptide sequences, explored in these statistical predictions, was determined to be an important factor in relating sequence to functional activity. Molecular mechanics calculations produced either interrupted or non interrupted a-helical secondary structures both for functionally-efficient and for functionally-inefficient signal peptides, indicating that cc-helixformation alone cannot be correlated with protein export competence. It was concluded from our overall results that both a-helicity and hydrophobicity are required for the efficient functioning of signal peptides. / AC2017

No description available.

Simulations were used to assist in both the optimization and experimental support of polymer-supported immobilized homogeneous catalysts. This work is a starting point for using molecular modeling to assist in the design of immobilized homogeneous catalysts, where the broader impact is the use of such catalysts which offer high reactivity and selectivity while also providing improved separability and recyclability over heterogeneous catalysts. ROMP poly(norbornene) was examined because it was hypothesized that one of its isomeric configurations might have a helical conformation like vinylic PNB. Alpha shapes were used to determine the accessibility of these polymers with an approximated catalyst group attached to the backbone. The polymer size, reactant size, catalyst size, and linker length were all varied. The simulations were validated by reproducing the expected trends of a random coil for accessibility across the range of the varied properties. Structural analysis of the final conformations showed that these structures were all random coils. It was found that the assumption that the backbone cyclopentane ring was a non-rotatable bond was invalid, which was most likely the largest contributing factor in the lack of a helical structure. It was also found that increasing the size of the virtual catalyst group caused this polymer to have a regions with a local helical conformation. The backbone cyclopentane ring of ROMP PNB was stiffened by adding a dicarboximide group to the ring. The simulation results showed that the TR configuration produced a broad helical conformation. This helix is broad, so its radius of gyration is indistinguishable from that of an equivalent random coil with less than 100 repeat units. Additionally, accessibility did not properly capture this structural difference, but that was mainly because these simulations were pre-optimized for accessibility by having a long linker length and relatively small polymer dimensions. Co(III)salen catalysts were simulated to determine a way to use simulations to optimize polymer supports for these catalysts. The supports examined were an oligomer synthesized by Jacobsen, poly(cyclooctene) polymerized as a macrocycle, and PCO polymerized as a straight chain polymer. The MMFF94 force field was extended to accommodate cobalt terms based on the ESFF force field, X-ray diffraction structures, and ab initio quantum calculations. In order to compare the supports, the individual catalyst efficiency and the overall catalyst efficiency were combined into a "reaction score." The results showed that the PCO macrocycle was the optimal support in the range of 3-5 repeat units, which was consistent with experimental work.

Bulk heterojunction organic solar cells (BHJ OSCs) have been recognized as one of the most promising next generation green technology alternatives to inorganic solar cells because of the low-cost, lightweight, flexibility. Specifically, the use of small molecules instead of polymers as donors in BHJ OSC have been developed very fast recently because small molecules can be facilely synthesized and easily purified, and have a determined molecular structure without batch-to-batch variations. To date, those among the most efficient small molecules were constructed as acceptor-donor-acceptor (A-D-A) structural configuration from electron-rich units such as benzodithiophene (BDT), dithienosilole (DTS), oligothiophene units, and electron-deficient units such as benzothiadiazole (BT), diketopyrrolopyrrole (DPP), isoindigo (IID) and perylenediimide (PDI). Surprisingly, porphyrins were rarely studied either in polymers or π-conjugated small molecules as donor materials, though they have unique chemistry together with excellent photochemical and electrochemical properties, such as facile functionalization of the periphery and the variation of the central atom (metal ions), strong UV-visible absorption, ultrafast photoinduced charge separation in porphyrin-fullerene systems. In this research work, we design, synthesize and characterize new porphyrin-based small molecules with acceptor-donor-acceptor (A-D-A) configuration for bulk heterojunction organic solar cells, and investigate their structure-property relationships, specifically the effect of peripheral and backbone alkyl side-chains, π-conjugated linkers as well as electron-deficient ending units on the charge mobility, film morphology and solar cell performances. In Chapter 1, a general review on the historic and recent development of BHJ OSCs was given first, including the major components and working principle of OSC, the versatile organic semiconductors and their performances in OSCs. In chapter 2, six A-D-A structural porphyrin small molecules were designed and synthesized, in which different peripheral alkyl substitutions are attached to the meso-position of porphyrin core (CS-I, CS-II, CS-III, CS-4, CS-5 and CS-6), and 3-ethylrhodanine is used as terminal group. Their UV-visible absorption in solid, energy level, blend film morphology, charge mobility and cell performance are dependent on the different peripheral substitutions. The active layer consists of these six small molecules as donor materials and PC71BM as the acceptor material with an optimized film thickness. Although all six molecules show similar optical spectrum in solutions, the introduction of linear alkyl side chains can promote thin-film nanostructural order, especially shown to shorten π-π stacking distances between backbones and increase the correlation lengths of both π-π stacking and lamellar spacing, leading to higher efficiency in this serial. Among them, the highest power conversion efficiency of 9.09% has been achieved by CS-4 based devices. In chapter 3, another two new A-D-A porphyrin small molecules (PTTR and PTTCNR) have been developed, which are similar in structure to CS-I, II and III, except that the linker is phenylethynyl in CS-I, II and III, whereas it is terthiophenylethynyl in PTTR and PTTCNR. The highest power conversion efficiency of 8.21% is achieved by PTTCNR, corresponding to a JSC of 14.30 mA cm−2, VOC of 0.82 V, and FF of 70.01%. The excellent device performances can be ascribed to the conjugated structure of porphyrin with 3,3''-dihexyl-terthiophene and the aliphatic 2-octylundecyl peripheral substitutions, which not only effectively increase the solar flux coverage between the conventional Soret and Q bands of porphyrin unit, but also optimize molecular packing through polymorphism associated with side-chain and the π-conjugated backbones, and form the blend films with [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) characteristics of bi-continuous, interpenetrating networks required for efficient charge separation and transportation.;In chapter 4, we designed and synthesized a new dimeric porphyrin donor molecule (CS-DP) containing A-π2-D-π1-D-π2-A architecture by coupling of two zinc porphyrin cores through ethynyl linker. Interestingly, it can harvests the photons up to deep near-infrared (NIR) region in the absorption spectrum. From the past decades, it has been found that developing donor molecules with the absorption spectral in NIR region is a challenging key factor to get the high performance BHJ OSCs. Solar cell devices employing CS-DP as a donor exhibit a highest power conversion efficiency of 8.23%, corresponding to JSC = 15.14 mA cm-2, VOC = 0.781 mV and FF = 69.8% under AM 1.5G solar radiation. The high efficiency of this molecule is attributed to a panchromatic IPCE action spectrum from 300 nm to 1000 nm. Also, this performance is best for the reported deep NIR organic solar cells based on single small molecule and PC71BM system so far. We envision that this new small bandgap dimeric porphyrin is very promising to use in ternary and multi-junction applications as well as NIR photodetectors. In chapter 5, a series of new A-D-A structural porphyrin small molecules (CS-10, CS-11 and CS-12) have been prepared, that contain the same meso-thienyl-thioalkyl substituted porphyrin core and 3-ethylrhodanine ending unit, but varies with different numbers of phenylethynyl linker. Using them as donors for solution-processed organic solar cells, the device based on CS-10 featuring single phenyl ethynyl π-linker exhibits high power conversion efficiency (PCE) of 7.0%. The results indicate that meso-thienyl-thioalkyl substitution and controlled π-linker length is beneficial to tune the optoelectronic properties, film morphology and consequently performance of porphyrin-based BHJ OSCs. In chapter 6, two symmetrical tetra-meso-substituted porphyrin molecules (ZnP and CuP) have been prepared in gram-scale through the direct condensation of pyrrole and 4-[bis(4-methoxyphenyl)amino]benzaldehyde. Its Zn(II) and Cu(II) complexes exhibit excellent thermal and electrochemical stability, specifically, high hole mobility and very favorable energetics for hole extraction that render them attractive for implementation as new hole transporting materials in organometallic halide perovskite solar cells (PSCs). As expected, the use of ZnP as HTM in PSCs affords a competitive PCE of 17.78%, which is comparable to the most powerful HTM of Spiro-OMeTAD (18.59%) under the same working conditions. Meanwhile, the metal centers affect somewhat the photovoltaic performances that CuP as HTM produces a relative lower PCE of 15.36%. Notably, the perovskite solar cells employing ZnP show longer stability than that of Spiro-OMeTAD. Moreover, the two porphyrin-based HTMs can be prepared from relatively cheap raw materials with a facile synthetic route. The results demonstrate that ZnP and CuP can be a new class of HTMs for efficient and stable perovskite solar cells. To the best of our knowledge, this is the highest performance for porphyrin-based perovskite solar cells with PCE > 17%. The dissertation was completed with conclusions and outlooks in chapter 7.

Submitted in fulfillment of the requirement for the degree Master of Applied Sciences in Chemistry, Durban University of Technology, Durban, South Africa, 2017. / In this study, molecular modeling was used to investigate the intermolecular interactions between the functional monomer and ketoprofen which is an acidic pharmaceutical that possesses anti-inflammatory and analgesic activities. Ketoprofen is widely employed in medical care for treating musculoskeletal injury. This led to rational design of a molecularly imprinted polymer (MIP) that is selective to ketoprofen. Density functional theory (DFT) at B3LYP/6-31 level was used to investigate the intermolecular interaction between functional monomers and ketoprofen. Binding energy, ΔE, was used as an indication of the strength of the interaction that occurs between functional monomers and ketoprofen. 2-vinylpyridine (2-VP) as one of the functional monomers gave the lowest binding energy when compared to all the functional monomers investigated. Monomer-template interactions were further experimentally investigated using spectroscopic techniques such as Ultraviolet-visible and Fourier transform infrared (FTIR). A selective MIP for ketoprofen was synthesized using 2-vinylpyridine, ethylene glycol dimethacrylate, 1,1’-azobis(cyclohexanecarbonitrile), toluene/acetonitrile (9:1, v/v), and ketoprofen as a functional monomer, cross-linker, initiator, porogenic mixture, and template, respectively. The polymerization was performed at 60 °C for 16 h, and thereafter the temperature was increased to 80 °C for 24 h to achieve a solid monolith polymer. The non-imprinted polymer (NIP) was synthesized in a similar manner with the omission of ketoprofen. Characterization with thermogravimetric analysis (TGA) and powder X-ray diffraction (XRD) showed that the synthesized polymers were thermally stable and amorphous. Morphology of the particles were clearly visible, with MIP showing rough and irregular surface compared to NIP on the scanning electron microscopy (SEM). The characterization of the prominent functional groups on both MIP and NIP were performed using FTIR and nuclear magnetic resonance (NMR). The existence of hydroxyl was observed in the MIP; this was due to the presence of ketoprofen in the cavity. Prominent carbonyl group was an indication of the cross-linker present in both polymers. The synthesized MIP was applied as a selective sorbent in the solid-phase extraction of ketoprofen from the water. The extracted ketoprofen was monitored by high performance liquid chromatography (HPLC) coupled with UV/Vis detector. Several parameters were investigated for maximum recovery of ketoprofen from the spiked deionized water. The optimum method involved the conditioning of 14 mg MIP sorbent with 5 mL of methanol followed by equilibrating with 5 mL of deionized water adjusted to pH 2.5. Thereafter, 50 mL sample (pH 5) was loaded into the cartridge containing MIP sorbent followed by washing and eluting with 1% TEA/H2O and 100% methanol, respectively. Eluted compounds were quantified with HPLC. MIP was more selective to ketoprofen in the presence of other structural related competitors. The analytical method gave detection limits of 0.23, 0.17, and 0.09 mg L-1 in wastewater influent, effluent, and deionized water, respectively. The recovery for the wastewater influent and effluent spiked with 5 µg L-1 of ketoprofen was 68%, whereas 114% was obtained for deionized water. The concentrations of ketoprofen in the influent and effluent samples were in the ranges of 22.5 - 34.0 and 1.14 - 5.33 mg.L-1, respectively. The relative standard deviation (RSD) given as ± values indicates that the developed analytical method for the analysis of ketoprofen in wastewater was rapid, affordable, accurate, precise, sensitive, and selective. / M

The molecular modeling of several drugs in complexes with deoxyribonucleic acid (DNA) was undet1aken. Selected bis-lexitropsins, based upon NMR and modeling studies of bis-distamycin A, were modeled with an oligonucleotide d(CGAACA TGTTCG)2 using MidasPlus and AMBER 4.0. Intercalators ethidium, ellipticinc. mitoxantrone, and bisantrene were modeled with an oligonucleotide d(CGCG)~ using SpartanPlus and DOCK 4.0. The binding site was prepared from an x-ray study of this oligonucleotide interacting with ditercalinium, a bis-intercalator. The purpost: of this study was to estimate the conformation and orientation of the molecules in tht:ir rt:spcctive binding sites. The mndding study of the bis-lexitropsins showed good agreement with previous modeling studies on distamycin and would be further enhanced by acquisition and interpretation ofNOESY NMR data. The computer modeling study shows that one of the bis-lexitropsins (pyrrole-pyrrole-imidazole, PPI) forms several hydrogen bonds between subunits, which may make it less effective for binding DNA. The other bis-lexitropsin (pyrrole-imidazole-pyrrole, PIP) also forms some interactions between dimers, but is mainly occupied with binding to the DNA and therefore has a more favorable interaction energy for binding to the chosen sequence. The intercalators were similarly agreeable with previous models. Bisantrene has the most favorable interaction energy. It threads its sidechain through the DNA so that while the planar aromatic ring system stacks between base pairs, there is one sidechain in the major groove and one in the minor groove. These extra interactions between the drug and DNA help the interaction to be more favorable.