Naomi L. Haworth

Electrostatic catalysis of a Diels–Alder reaction

It is often thought that the ability to control reaction rates with an applied electrical potential gradient is unique to redox systems. However, recent theoretical studies suggest that oriented electric fields could affect the outcomes of a range of chemical reactions, regardless of whether a redox system is involved. This possibility arises because many formally covalent species can be stabilized via minor charge-separated resonance contributors. When an applied electric field is aligned in such a way as to electrostatically stabilize one of these minor forms, the degree of resonance increases, resulting in the overall stabilization of the molecule or transition state. This means that it should be possible to manipulate the kinetics and thermodynamics of non-redox processes using an external electric field, as long as the orientation of the approaching reactants with respect to the field stimulus can be controlled. Here, we provide experimental evidence that the formation of carbon–carbon bonds is accelerated by an electric field. We have designed a surface model system to probe the Diels–Alder reaction, and coupled it with a scanning tunnelling microscopy break-junction approach. This technique, performed at the single-molecule level, is perfectly suited to deliver an electric-field stimulus across approaching reactants. We find a fivefold increase in the frequency of formation of single-molecule junctions, resulting from the reaction that occurs when the electric field is present and aligned so as to favour electron flow from the dienophile to the diene. Our results are qualitatively consistent with those predicted by quantum-chemical calculations in a theoretical model of this system, and herald a new approach to chemical catalysis.

Potential role of glutathione in evolution of thiol-based redox signaling sites in proteins

Cysteine is susceptible to a variety of modifications by reactive oxygen and nitrogen oxide species, including glutathionylation; and when two cysteines are involved, disulfide formation. Glutathione-cysteine adducts may be removed from proteins by glutaredoxin, whereas disulfides may be reduced by thioredoxin. Glutaredoxin is homologous to the disulfide-reducing thioredoxin and shares similar binding modes of the protein substrate. The evolution of these systems is not well characterized. When a single Cys is present in a protein, conjugation of the redox buffer glutathione may induce conformational changes, resulting in a simple redox switch that effects a signaling cascade. If a second cysteine is introduced into the sequence, the potential for disulfide formation exists. In favorable protein contexts, a bistable redox switch may be formed. Because of glutaredoxins similarities to thioredoxin, the mutated protein may be immediately exapted into the thioredoxin-dependent redox cycle upon addition of the second cysteine. Here we searched for examples of protein substrates where the number of redox-active cysteine residues has changed throughout evolution. We focused on cross-strand disulfides (CSDs), the most common type of forbidden disulfide. We searched for proteins where the CSD is present, absent and also found as a single cysteine in protein orthologs. Three different proteins were selected for detailed study—CD4, ERO1, and AKT. We created phylogenetic trees, examining when the CSD residues were mutated during protein evolution. We posit that the primordial cysteine is likely to be the cysteine of the CSD which undergoes nucleophilic attack by thioredoxin. Thus, a redox-active disulfide may be introduced into a protein structure by stepwise mutation of two residues in the native sequence to Cys. By extension, evolutionary acquisition of structural disulfides in proteins can potentially occur via transition through a redox-active disulfide state.

Tuning electron transfer through p-phenyleneethynylene molecular wires

Weak wire-like behavior-with a damping factor (beta) of 0.2 +/- 0.05 A(-1)--has been found in a series of C60-wire-exTTF systems (i.e., p-phenyleneethynylene): these results contrast with previous observations involving p-phenylenevinylene systems.

Conformational changes in redox pairs of protein structures

Disulfides are conventionally viewed as structurally stabilizing elements in proteins but emerging evidence suggests two disulfide subproteomes exist. One group mediates the well known role of structural stabilization. A second redox‐active group are best known for their catalytic functions but are increasingly being recognized for their roles in regulation of protein function. Redox‐active disulfides are, by their very nature, more susceptible to reduction than structural disulfides; and conversely, the Cys pairs that form them are more susceptible to oxidation. In this study, we searched for potentially redox‐active Cys Pairs by scanning the Protein Data Bank for structures of proteins in alternate redox states. The PDB contains over 1134 unique redox pairs of proteins, many of which exhibit conformational differences between alternate redox states. Several classes of structural changes were observed, proteins that exhibit: disulfide oxidation following expulsion of metals such as zinc; major reorganisation of the polypeptide backbone in association with disulfide redox‐activity; order/disorder transitions; and changes in quaternary structure. Based on evidence gathered supporting disulfide redox activity, we propose disulfides present in alternate redox states are likely to have physiologically relevant redox activity.

Heats of formation of phosphorus compounds determined by current methods of computational quantum chemistry

The heats of formation of a range of phosphorus containing molecules (P2, P4, PH, PH2, PH3, P2H2, P2H4, PO, PO2, PO3, P2O, P2O2, HPO, HPOH, H2POH, H3PO, HOPO, and HOPO2) have been determined by high level quantum chemical calculations. The equilibrium geometries and vibrational frequencies were computed via density functional theory, utilizing the B3LYP/6-31G(2df,p) functional and basis set. Atomization energies were obtained by the application of ab initio coupled cluster theory with single and double excitations from (spin)-restricted Hartree–Fock reference states with perturbative correction for triples [CCSD(T)], in conjunction with cc-pVnZ basis sets (n=T, Q, 5) which include an extra d function on the phosphorus atoms and diffuse functions on the oxygens, as recommended by Bauschlicher [J. Phys. Chem. A 103, 11126 (1999)]. The valence correlated atomization energies were extrapolated to the complete basis limit and corrected for core–valence (CV) correlation and scalar relativistic effects, as well ...

Evaluating the stability of disulfide bridges in proteins: a torsional potential energy surface for diethyl disulfide

Disulfide bonds formed by the oxidation of cysteine residues in proteins are the major form of intra- and inter-molecular covalent linkages in the polypeptide chain. To better understand the conformational energetics of this linkage, we have used the MP2(full)/6-31G(d) method to generate a full potential energy surface (PES) for the torsion of the model compound diethyl disulfide (DEDS) around its three critical dihedral angles (χ2, χ3, χ2′). The use of ten degree increments for each of the parameters resulted in a continuous, fine-grained surface. This allowed us to accurately predict the relative stabilities of disulfide bonds in high resolution structures from the Protein Data Bank. The MP2(full) surface showed significant qualitative differences from the PES calculated using the Amber force field. In particular, a different ordering was seen for the relative energies of the local minima. Thus, Amber energies are not reliable for comparison of the relative stabilities of disulfide bonds. Surprisingly, the surface did not show a minimum associated with χ2∼ − 60°, χ3∼90, χ2′∼ − 60°. This is due to steric interference between Hα atoms. Despite this, significant populations of disulfides were found to adopt this conformation. In most cases this conformation is associated with an unusual secondary structure motif, the cross-strand disulfide. The relative instability of cross-strand disulfides is of great interest, as they have the potential to act as functional switches in redox processes.

HIGH TORSIONAL ENERGY DISULFIDES: RELATIONSHIP BETWEEN CROSS-STRAND DISULFIDES AND RIGHT-HANDED STAPLES

Redox-active disulfides are capable of being oxidized and reduced under physiological conditions. The enzymatic role of redox-active disulfides in thiol-disulfide reductases is well-known, but redox-active disulfides are also present in non-enzymatic protein structures where they may act as switches of protein function. Here, we examine disulfides linking adjacent beta-strands (cross-strand disulfides), which have been reported to be redox-active. Our previous work has established that these cross-strand disulfides have high torsional energies, a quantity likely to be related to the ease with which the disulfide is reduced. We examine the relationship between conformations of disulfides and their location in protein secondary structures. By identifying the overlap between cross-strand disulfides and various conformations, we wish to address whether the high torsional energy of a cross-strand disulfide is sufficient to confer redox activity or whether other factors, such as the presence of the cross-strand disulfide in a strained beta-sheet, are required.

Estimating Relative Disulfide Energies: An Accurate Ab Initio Potential Energy Surface

Disulfide torsional energy, a good predictor of disulfide redox potential in proteins, may be estimated by interpolation on a potential energy surface (PES) describing the twisting of diethyl disulfide through its three central dihedral angles. Here we update PES calculations at the M05-2X level of theory with the 6-31G(d) basis set. Although the surface shows no qualitative differences from an earlier MP2(full) PES, energy differences greater than 1 kJ mol–1 were seen for conformations with χ2 between –60° and 30°, or with χ3 below 60° or above 130°. This is particularly significant for highly strained disulfides that are likely to be spontaneously reduced by mechanical means. In benchmarking against the high-level G3X method, M05-2X showed significantly reduced root mean squared deviation compared with MP2(full) (1.0 versus 2.0 kJ mol–1 respectively). Results are incorporated into a web application that calculates relative torsional energies from disulfide dihedral angles (http://www.sbinf.org/applications/pes.html).

An experimental and theoretical investigation of the triple fragmentation of CFClBr2 by photolysis near 250 nm

Abstract Photodissociation of CFClBr 2 + hν →CFCl has been shown to occur for λ 436±2 kJ mol −1 ). G3 Ab initio calculations were performed to provide estimates of Δ f H for CFClBr 2 , CFClBr, and CFCl, which were calculated to be −188±5, −43±5 and +30±5 kJ mol −1 , respectively. The dissociation energies (0 K) for sequentially breaking the C–Br bonds were calculated to be 257±5 and 183±5 kJ mol −1 , respectively. The energy required to break both C–Br bonds was calculated to be 440±5 kJ mol −1 , in excellent agreement with the experimental appearance threshold for CFCl. From the experimental appearance threshold, Δ f H (CFClBr 2 ) is estimated to be −184±5 kJ mol −1 .

The effect of leaving radical on the formation of tetrahydroselenophene by SHi ring closure: an experimental and computational study.

Competition kinetic studies augmented with laser-flash photolysis and high-level computational techniques [G3(MP2)-RAD], with [COSMO-RS, SMD] and without solvent correction, provide kinetic parameters for the ring closures of a series of 4-(alkylseleno)butyl radicals 1. At 22 °C rate constants (kc) that lie between 10(4)-10(7) s(-1) were determined experimentally and correlate with expectations based on leaving group ability. Activation energies (Eact) were determined to lie between 10.6 (R = Ph2CH) and 28.0 (R = n-Bu) kJ mol(-1), while log(A/s(-1)) values were generally between 9 and 10 in benzene. Computationally determined rate constants were in good-to-excellent agreement with those determined experimentally, with the COSMO-RS solvation model providing values that more closely resemble those from experiment than SMD.