No description available.

The circadian oscillator of the cyanobacterium Synechococcus elongatus is composed of only three proteins, KaiA, KaiB, and KaiC, which together with ATP can generate a self-sustained ~24 hour oscillation of KaiC phosphorylation for several days. KaiA induces KaiC to autophosphorylate whereas KaiB blocks the stimulation of KaiC by KaiA, which allows KaiC to autodephosphorylate. We propose and support a model in which the C-terminal loops of KaiC, the “A-loops”, are the master switch that determines overall KaiC activity. When the A-loops are in their buried state, KaiC is an autophosphatase. When the A-loops are exposed, however, KaiC is an autokinase. The data suggest that KaiA stabilizes the exposed state of the A-loops through direct binding. We also show evidence that if KaiA cannot stabilize the exposed state KaiC remains hypophosphorylated. We propose that KaiB inactivates KaiA by preventing it from stabilizing the exposed state of the A-loops. Thus, KaiA and KaiB likely act by shifting the dynamic equilibrium of the A-loops between exposed and buried states, which shifts the balance of autokinase and autophosphatase activities of KaiC. A-loop exposure likely moves the ATP closer to the sites of phosphorylation and we show evidence in support of how this movement may be accomplished. Density functional theory calculations of isolated Watson–Crick A:U and A:T base pairs predict that adenine 13C2 trans-hydrogen bond deuterium isotope shifts due to isotopic substitution at the pyrimidine H3, 2hΔ13C2, are sensitive to the hydrogen-bond distance between the N1 of adenine and the N3 of uracil or thymine, which supports the notion that 2hΔ13C2 is sensitive to hydrogen-bond strength. Calculated 2hΔ13C2 values at a given N1–N3 distance are the same for isolated A:U and A:T base pairs. Replacing uridine residues in RNA with 5-methyl uridine and substituting deoxythymidines in DNA with deoxyuridines do not statistically shift empirical 2hΔ13C2 values. Thus, we show experimentally and computationally that the C7 methyl group of thymine has no measurable affect on 2hΔ13C2 values. Furthermore, 2hΔ13C2 values of modified and unmodified RNA are more negative than those of modified and unmodified DNA, which supports our hypothesis that RNA hydrogen bonds are stronger than those of DNA. It is also shown here that 2hΔ13C2 is context dependent and that this dependence is similar for RNA and DNA.

Use of hydrogen bonding as internuclear connecting information to better determine molecular structure or dynamics.

The main focus of this thesis is on the ring conformations of carbohydrate molecules; how the conformational equilibria and the rates of the associated interconversions are affected by the molecular constitution and their surroundings. The conformational equilibria of a group of amine linked pseudodisaccharides, designed as potential glycosidase inhibitors, comprising α-D-altrosides are described in Chapter 3. The OS2 conformation was largely populated, and the ring conformation was found to depend on the charge of the amine functionality. The conformations of β-D-xylopyranoside derivatives with naphthyl-based aglycones, which are potential anti-cancer agents, are described in chapter 4. Solvent dependent flexibility was observed. Intramolecular hydrogen bonds were concluded to be involved in the stabilization of 1C4 conformers in non-hydrogen bonding solvents of low polarity. Chapter 5 describes the first measurements of the conformational exchange rates of mannuronic acid ester derivatives between the 4C1 and 1C4 conformations, through DNMR measurements. The relative reactivity of glycosyl triflates as electrophiles in glycosylation reactions were investigated with NMR-based competition experiments. In Chapter 6, investigations of ruthenium-catalyzed epimerizations of the allylic alcohols of glycal derivatives, and stereoselective synthesis of esters through a DYKAT protocol, are described. The kinetics of the epimerizations were elaborated through different NMR-spectroscopic methods. Chapter 7 describes additions of NMR chemical shift data of mono- and oligosaccharides to database of the computer program CASPER, and applications thereof. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Submitted. Paper 5: Manuscript.</p>

No description available.

Pulsed-beam Fourier transform microwave spectroscopy (PBFTMS) was used to determine the rotational structure of N-hydroxypyridine-2(1H)-thione. PBFTMS was also used to determine the rotational structure of a hydrogen dimer between propiolic acid and formic acid. Rotational constants and quadrupole coupling constants were determined. Calculations (MP2/DFT) were utilized in predicting the isotopic structures. Isotopic data (D, and ¹³C) and normal isotopomers collected were used in establishing of key structural parameters such as bond length and bond angles.

An integrated graph-theoretic and geometric approach to the analysis of aqueous solvation of atomic ions is presented. This analysis makes use of a novel data-mining tool, moleculaRnetworks, to process data from molecular dynamics simulations. The workings and structure of this tool are discussed, along with the development and testing of its PageRank algorithm-based rapid solvation polyhedra classifier. The ability to classify instantaneous solvation polyhedra enables a finely detailed understanding of shell structure-behavior relationships, as water molecules simultaneously rearrange about ions, exchange with the bulk, and rearrange their hydrogen-bond network. The application of the tool to cation systems, including lithium, sodium, potassium, magnesium, calcium, and lanthanum, yields new insight into the mechanisms of water exchange about these ions. It is shown that in order for exchange events to occur, the solvation shell must "preorganize" to admit or expel a molecule of water: this preorganization is reflected in the mechanistic preference for each ion. The application of the tool to anion systems, including fluoride, chloride, and bromide, reveals that these ions have an extended effect on the reorientation ability of water molecules beyond their first solvation shell. Finally, when both ions are present, as in the potential of mean force simulation between lanthanum and chloride, structural rearrangements can be seen as the ions break through the barrier to form the contact ion pair. Taken together, these results show the utility of the moleculaRnetworks tool in broadening our understanding of aqueous ion solvation.

This work presents findings from experiments carried out using the neutron Laue method in tandem with laboratory source X-ray diffraction to characterise a series of organic molecular complexes which exhibit interesting, and potentially “tunable”, temperature dependent charge transfer effects, such as proton migration and proton disorder within hydrogen bonded networks. These subtle processes are studied by variable temperature neutron diffraction studies, allowing the positional and anisotropic displacement parameters of the hydrogen atoms to be refined accurately and their evolution with temperature followed. The hydrogen atom behaviour is found to be influenced by the local environment, including weak intermolecular interactions in the vicinity of the hydrogen bond under study. Complexes of urea and methyl substituted ureas with small organic acids are presented, which show robust and reproducible structural motifs. In favourable circumstances, these contain short, strong hydrogen bonds (SSHBs) within which the proton may undergo temperature dependent migration. By synthesising a number of complexes containing SSHBs, potential routes to the design of proton migration complexes are found, which utilise crystal engineering principles and pKa matching. Variable temperature studies conducted on these complexes also show unusual thermal expansion properties and phase transitions in urea-acid complexes which do not display proton migration. Systems containing hydrogen bonded dimers of 3,5-dinitrobenzoic acid are also studied, and shown to contain temperature proton disorder within moderate strength hydrogen bonds linking the dimers. The presence and potential onset temperature of any disorder is found to be influenced by interactions around the acid dimers and potential routes to controlling proton disorder are discussed. Complexes of the proton sponge, 1,8-bis(dimethylamino)napthalene (DMAN), with organic acids are also presented, in which the structures have been determined using neutron diffraction. DMAN readily accepts a proton from the acid co-molecules used in forming the complexes, forming a strong intramolecular SSHB within the protonated DMAN. Strong intermolecular hydrogen bonds are also induced between the acid molecules in many cases. The neutron studies presented here investigate the effect of weak interactions on the behaviour of hydrogen atoms located within these SSHBs, and also indicate over what distance such interactions significantly affect the hydrogen atom behaviour.

Squaramides (3,4-diaminocyclobutene-1,2-diones) are known to be strong hydrogen bond donors, and recently have been demonstrated to show unusual responses to anions and the potential to adopt secondary structures. In the first part of the project, a small molecule version of a fluorene-based poly(squaramide) was synthesized to gain insights into the mechanism of the “turn-on” fluorescence response of the polymer in the presence of mono-basic phosphate anions. In the second part, mono and dipyridyl squaramides are examined. Pyridyl squaramides were discovered to form strong intramolecular hydrogen bonds, making the folding process more favorable than their urea counterparts. They are particularly interesting as their urea analogues are capable of taking up helical conformations when folded. The folding properties of these pyridyl squaramides in a range of solvents, and the influence of added anions on the folding process, are described herein.

Squaramides (3,4-diaminocyclobutene-1,2-diones) are known to be strong hydrogen bond donors, and recently have been demonstrated to show unusual responses to anions and the potential to adopt secondary structures. In the first part of the project, a small molecule version of a fluorene-based poly(squaramide) was synthesized to gain insights into the mechanism of the “turn-on” fluorescence response of the polymer in the presence of mono-basic phosphate anions. In the second part, mono and dipyridyl squaramides are examined. Pyridyl squaramides were discovered to form strong intramolecular hydrogen bonds, making the folding process more favorable than their urea counterparts. They are particularly interesting as their urea analogues are capable of taking up helical conformations when folded. The folding properties of these pyridyl squaramides in a range of solvents, and the influence of added anions on the folding process, are described herein.