This book is a basic reference providing concise, accurate definitions of the key terms and concepts of organic chemistry. Not simply a listing of organic compounds, structures, and nomenclatures, the book is organized into topical chapters in which related terms and concepts appear in close proximity to one another, giving context to the information and helping to make fine distinctions more understandable. Areas covered include: bonding, symmetry, stereochemistry, types of organic compounds, reactions, mechansims, spectroscopy, and photochemistry.

True adventures of youth with a mission.

Recent scientific efforts aim to blend light harvesting with the fuel forming catalysis, as a novel method to store the energy captured from the Sun. Our approach is to construct an efficient photoelectrochemical cell using earth-abundant materials. The proposed system contains bioinspired metal-free hydride donors suitable for fuel forming reductions and a p-type semiconductor that serve as a light harvester and source of electrons. In this thesis, we investigate fundamental steps that determine the efficiency of the photoelectrochemical cell: photoreduction of NAD+ dyes by p-GaP semiconductor and the hydricity of NADH analogs. First, thermodynamics for photo-induced electron transfer from p-GaP to NAD+ dyes are evaluated using steady-state UV/Vis absorption and cyclic voltammetry experiments. Photoelectrochemical measurement conducted on p-GaP electrodes immersed in aqueous electrolytes and dye show sensitization for only two dyes. Pump-probe measurements reveal that the "inefficient" dyes have short-lived excited states, inhibiting the successful charge transfer into p-GaP surface. This work provides an insight on timescales of hole-injection rates during dye-sensitization processes. Furthermore, we evaluate the hydricity for model NADH analogs using experimental methods and calculations. The obtained hydricity values display a strong dependence on structural and electronic properties of the model compounds. When compared with metal-based analogs, NADH analogs show similar hydride donor ability. However, the high reduction potentials for metal-free hydride donors hinder their applicability in the catalysis. This work offers a reasonable explanation on why NADH analogs have not been utilized in fuel forming catalysis and provides the answers how to overcome these limitations..

This work presents supramolecular fluorescent probes capable of specific detection of carbonic anhydrases (CAs), a biologically and clinically important family of metalloenzymes implicated in certain pathological health conditions in humans. The probes, comprising 1,3,4-thiadiazol-5-yl-2-sulfonamide high-affinity moiety, were employed in fluorescence titrations with CAs and showed highly variable analyte-dependent change in fluorescence intensity. Moreover, the probes were utilized in competitive fluorescence-based assay to investigate affinity of model carbonic anhydrase inhibitors towards CAs. The probes were utilized in a competitive sensor array using simple instrumentation under high throughput screening settings. The excellent capability of recognizing a large number of structurally distinct CAIs at various concentrations was demonstrated in qualitative as well as quantitative assays. The throughput, sensitivity and limit of detection surpass the current state-of-the-art methods that generally require enzyme-linked immunosorbent assay based protocols and/or computational modeling. This study opens a new avenue for the development of simple high-throughput assays for the drug development and drugs candidates structure optimization in the near future. To the best of our knowledge, this study presents the first supramolecular fluorescence-based assay for carbonic anhydrase inhibitors.

We present the formulation and study of light-responsive materials based on carboxylate-containing polysaccharides. The functional groups in these natural polymers allow for strong interactions with transition metal ions such as Fe(III). The known photochemistry of hydroxycarboxylic acids in natural waters inspired us in exploring the visible light induced photochemistry of the carboxylates in these polysaccharides when coordinated to Fe(III) ions. Described in this dissertation are the design and characterization of the Fe(III)-polysaccharide materials, specifically the mechanistic aspects of the photochemistry and the effects that these reactions have on the structure of the polymer materials. We present a study of the quantitative photochemistry of different polysaccharide systems, where the presence of uronic acids was important for the photoreaction to take place. Alginate (Alg), pectate (Pec), hyaluronic acid (Hya), xanthan gum (Xan), and a polysaccharide extracted from the Noni fruit (NoniPs), were among the natural uronic acid-containing polysaccharide (UCPS) systems we analyzed. Potato starch, lacking of uronate groups, did not present any photochemistry in the presence of Fe(III); however, we were able to induce a photochemical response in this polysaccharide upon chemical manipulation of its functional groups. Important structure-function relationships were drawn from this study. The uronate moiety present in these polysaccharides is then envisioned as a tool to induce response to light in a variety of materials. Following this approach, we report the formulation of materials for controlled drug release, able to encapsulate and release different drug models only upon illumination with visible light. Furthermore, hybrid hydrogels were prepared from UPCS and non-responsive polymers. Different properties of these materials could be tuned by controlling the irradiation time, intensity and location. These hybrid gels were evaluated as scaffolds for tissue engineering showing great promise, as changes in the behavior of the growing cells were observed as a result of the photochemical treatment of the material. We present these natural and readily available, polysaccharide-based, metal-coordination materials as convenient building blocks in the formulation of new stimuli responsive materials. The photochemical methods developed here can be used as convenient tools for creating advanced materials with tailored patterns and gradients of mechanical properties.

This dissertation consists of two parts that together broadly aim to understand the relationship between the structure and function of protein. Part I is a study of the Fe-S cluster assembly system U-type scaffold protein, SufU, from the Gram positive bacterium Bacillus subtilis. The conformational changes of the protein, upon interaction with two different metals, Zn2+ and Fe3+, were investigated. The results indicate that purified SufU that had been stripped of its bound Zn2+ undergoes conformational changes upon reconstitution with Zn2+ ions, but there is no evidence of such changes upon the addition of Fe3+ ions. Thus, B. subtilis SufU discriminates between Zn2+ and Fe3+, and preferentially binds Zn2+ ions. Similar results have been reported for two other U-type proteins, namely, Escherichia coli IscU and Streptococcus mutans SufU, which suggests that these properties are widespread among U-type proteins. Part II is an investigation of the role of the post-translation acetylation modification of the Rhodobacter sphaeroides Puc1B protein. Together with PucA, PucB comprises the structural component of one of two light harvesting (LH) complexes that deliver photons to the photosynthesis reaction center. Rba. sphaeroides encodes two such sets of PucB and A proteins; Puc1B and Puc1A, and Puc2B and Puc2A. While the amino acid sequence of Puc1B differs by only 3 residues from Puc2B, mass spectrometry data indicate that only the former is acetylated. The findings presented here indicate that acetylation is important for efficient assembly of LH2. The specificity required to acetylate Puc1B, and not Puc2B, evokes an enzyme-catalyzed process, which raises the possibility that Puc1B acetylation is a regulated event, and the rate of acetylation of Puc1B might then govern the rate of LH2 assembly.

The need for a detailed mechanistic understanding of the photoisomerization of retinal chromophore (retinal protonated Schiff base, rPSB) is becoming increasingly important, not only due to its fundamental importance in vision but also owing to the growing number of applications in various fields. The development of microbial rhodopsin based fluorescent probes and actuators essential in neuroscience, synthetic bio-mimetic molecular switches and motors useful in material science and synthetic biology are examples of such applications. The work presented in this dissertation is devoted to unveil and understand a novel mechanistic factor with significant impact on the photoisomerization of rPSB-like systems. This factor corresponds to the interaction between the first electronic excited state and higher states (usually the second excited state) occurring during the excited state lifetime or, in other words, along the excited state photoisomerization coordinate. This "electronic state mixing" effect is studied by employing different computer tools including hybrid quantum mechanics/molecular mechanics (QM/MM) methods. The investigated systems include representative animal and microbial rhodopsins, bio-mimetic N-alkyl-indanylidene-pyrrolinium (NAIP) molecular switches and a recently reported water soluble rhodopsin mimic. Our results unveil two type of effects due to changes in the electronic mixing: an impact on the excited state lifetime and an impact on vibrational coherence as we now briefly describe. The impact on excited state lifetime is first demonstrated by uncovering the variation of rPSB photoisomerization speed in different environments is due to an increase or decrease of electronic state mixing and that this effect can be controlled by the electrostatic field of the environment. This leads us to hypothesize that animal rhodopsins, which isomerize within 200 fs, have been evolved to minimize the electronic state mixing such that biological functions are carried out in a timely manner. We then show that electronic state mixing can be used as a design principle to achieve artificial rPSBs with a longer excited state lifetime useful for producing rhodopsin based fluorescent probes. In this context, we demonstrate that minor electron donating or withdrawing chemical substitutions can cause an increase or decrease in the photoisomerization speed of rPSB. We have also investigated the photocycle and the electronic state mixing of a water-soluble artificial rhodopsin mimic. The room temperature photodynamics simulations of this system suggests that molecules of a light excited population which decay early or later is possibly modulated by electronic state mixing. The impact of electronic state mixing on vibrational coherence is mainly investigated focusing on synthetic molecular switches. Accordingly, we show how electronic state mixing induced by steric effects can be used to control the vibrational coherence of NAIP molecular switches. On this basis, we propose that vibrational coherence may be engineered into other synthetic molecular devices by modulating steric and electronic effects.

The development of efficient, durable, and low-cost oxygen evolution and oxygen reduction reaction (OER and ORR) catalysts is crucial for several energy storage applications. Here we propose that the metal-free catalysis can be achieved by organic motifs that catalyze OER through alcohol and peroxide intermediates. Particularly, we studied the most difficult step of proposed catalytic cycle for OER: the O-O bond formation. To identify ideal catalytic motifs for this step, we synthesized a series of covalently linked dimers, named DPE, XAN, and BP, investigated their structure using DFT calculations, NMR, and X-ray spectroscopy and identified the efficiency of peroxide formation from their alcohols. This work has shown, for the first time, that the O-O bond can be formed by the oxidation of two organic alcohols, showing a proof-of-principle chemical reactivity that can be utilized for future metal-free graphenic OER catalysts. Remarkably, we are presenting for the first time that even monomeric model MONO upon oxidation formed alkoxy radicals who coupled to make peroxide bond. Furthermore, we show evidence that dimeric model BP formed significantly more peroxide, while DPE and XAN produced no peroxides, demonstrating that choice of right linker is vital for design of efficient catalyst. Spacer should be designed on a way that O-O distance is appropriate for O-O bond formation. Additionally, it also must possess some degree of rigidity to force two -OH groups in close proximity, but still to attain enough flexibility to accommodate dynamically changed distances between active centers over an entire catalytic cycle.