Effects of As(III) binding on alpha-helical structure

As(III) displays a wide range of effects in cellular chemistry. Surprisingly, the structural consequences of arsenic binding to peptides and proteins are poorly understood. This study utilizes model alpha-helical peptides containing two cysteine (Cys) residues in various sequential arrangements and spatial locations to study the structural effects of arsenic binding. With i, and i + 1, i + 2, or i + 3 arrangements, CD spectroscopy shows that As(III) coordination causes helical destabilization when Cys residues are located at central or C-terminal regions of the helix. Interestingly, arsenic binding to i, i + 3 positions results in the elimination of helical structure and the formation of a relatively stable alternate fold. In contrast, helical stabilization is observed for peptides containing i, i + 4 Cys residues, with corresponding pseudo pairwise interaction energies (Delta G(pw) degrees) of -1.0 and -0.7 kcal/mol for C-terminal and central placements, respectively. Binding affinities and association rate constants show that As(III) binding is comparatively insensitive to the location of the Cys residues within these moderately stable helices. These data demonstrate that As(III) binding can be a significant modulator of helical secondary structure.     

Photoinduced axial ligation and deligation dynamics of nonplanar nickel dodecaarylporphyrins

The ground- and excited-state metal-ligand dynamics of nonplanar nickel(II) 2,3,5,7,8,10,12,13,15,17,18,20-dodecaphenylporphyrin (NiDPP) and two fluorinated analogues (NiF(20)DPP and NiF(28)DPP) have been investigated using static and time-resolved absorption spectroscopy in toluene and in ligating media that differ in basicity, aromaticity, and steric encumbrance. Because of the electronic and steric consequences of nonplanarity, NiDPP does not bind axial ligands in the ground state, but metal coordination does occur after photoexcitation with multistep dynamics that depend on the properties of the ligand. Following the structural relaxations that occur in all nickel porphyrins within approximately 10 ps, ligand binding to photoexcited NiDPP is progressively longer in pyridine, piperidine, and 3,5-lutidine (25-100 ps) but does not occur at all in 2,6-lutidine in which the ligating nitrogen is sterically encumbered. The transient intermediate that is formed, which nominally could be either a five- or six-coordinate species, also has a ligand-dependent lifetime (200-550 ps). Decay of this intermediate occurs partially via ligand release to re-form the uncoordinated species, in competition with binding of the second axial ligand and/or conformational/electronic relaxations (of a six-coordinate intermediate) to give the ground state of the bis-ligated photoproduct. The finding that the photoproduct channel principally depends on ligand characteristics along with the time-evolving spectra suggests that the transient intermediate may involve a five-coordinate species. In contrast to NiDPP, the fluorinated analogues NiF(20)DPP and NiF(28)DPP do coordinate axial ligands in the ground state but eject them after photoexcitation. Collectively, these results demonstrate the sensitivity with which the electronic and structural characteristics of the macrocycle, substituents, and solvent (ligands) can govern the photophysical and photochemical properties of nonplanar porphyrins and open new avenues for exploring photoinduced ligand association and dissociation behavior.     

Adsorption of organic substances on broken clay surfaces: a quantum chemical study

Hydrogen-bonded interactions between local defect structures on broken clay surfaces modeled as molecular clusters and the organic molecules acetic acid, acetate, and N-methylacetamide (NMA) have been investigated. Density functional theory and polarized basis sets have been used for the computation of optimized interaction complexes and formation energies. The activity of the defect structures has been characterized as physical or chemical in terms of the strength of the hydrogen bonds formed. Chemical defects lead to significantly enhanced interactions with stronger hydrogen bonds and larger elongation of OH bonds in comparison to the physical defects. The type of interaction with the defect structure significantly influences the planarity of the model peptide bond in NMA. Both cases, enhancement of the planarity by increase of the CN double bond character and strong deviations from planarity, are observed.     

Interesting fluorescence properties of C60-centered dendritic adduct with twelve symmetrically attached pyrenes

A C60-centered dendritic adduct with 12 symmetrically attached pyrene species was synthesized and found to have relatively simple fluorescence emission kinetics, in particular, the mono-exponential decay of the significant pyrene excimer emission.     

In situ Fe K-edge X-ray absorption fine structure of a nitrosyl adduct of iron phthalocyanine irreversibly adsorbed on a high area carbon electrode in an acidic electrolyte

Key aspects of the microenvironment surrounding the Fe center in the nitrosyl adduct of iron phthalocyanine, [Fe(Pc)(NO)], have been elucidated from the analysis of the Fe K-edge extended X-ray absorption fine structure (EXAFS) of the material adsorbed on the surface of a high area carbon electrode recorded in situ, in 0.5 M H(2)SO(4). Statistical best fits to the EXAFS data place the Fe center in a five-coordinated square pyramidal configuration shifted away from the Pc plane toward the axially bound NO bent at an angle of ca. 40 degrees with respect to the normal to the Pc plane. This environment is analogous to that of Fe in the nitrosyl adduct of crystalline [Fe(TPP)], where TPP = meso-tetraphenylporphyrinato(2-), determined from X-ray diffraction.     

Diamond and diamond-like carbon from a preceramic polymer

The synthesis of poly(hydridocarbyne), one of a class of carbon-based random network polymers and a structural isomer of polyacetlyene, is reported. The network backbone of this polymer is primarily composed of tetrahedrally hybridized carbon atoms, each bearing one hydride substituent and linked via three carbon-carbon single bonds into a three-dimensional random network of fused rings. This atomic-level carbon network backbone confers unusual properties on the polymer, including facile thermal decomposition to form diamond or diamond-like carbon high-quality films at atmospheric pressure, by direct deposition or by chemical vapor deposition (CVD), without the use of hydrogen or any other reagent.     

Amber‐Woody Scent: Alcohols with Divergent Structure Present Common Olfactory Characteristics and Sharp Enantiomer Differentiation

Only one out of the four possible trans isomers of the important perfumery alcohol Norlimbanol^® ( 1 ) possesses a very strong amber‐woody smell, the isomer 1A with (1′R,3S,6′S) absolute configuration. Its enantiomer 1B is almost odorless and devoid of amber‐woody character, whereas the diastereoisomers 1C and 1D are considerably weaker and perceptible only by the most‐sensitive persons. The same is true for a whole series of perceptual analogs of 1 , including β‐alkoxy alcohols. These ethers belong to two structural classes: [(2,2,6‐trimethylcyclohexyl)oxy]‐ (see 3, 4 , and 16 ) or {[2‐(tert‐butyl)cyclohexyl]oxy}alkan‐2‐ol derivatives (see 19 and 20 ; Table). A superimposition model allowing for good overlap of the respective hydroxylated side chains offers a tentative explanation for the shared perceptual characteristics of the two classes (Fig. 5). The lipophilic cyclohexane moieties present only a minimal overlap in this model, suggesting that quite larger molecules might possess the same smell. (S)‐Configured β‐alkoxy alcohols can conveniently be obtained on a larger scale by enantioselective reduction of the corresponding ketones (Scheme 9).     

Radical para-benzoic acid derivatives: transmission of ferromagnetic interactions through hydrogen bonds at long distances

Investigation of the transmission of magnetic interactions through hydrogen bonds has been carried out for two different benzoic acid derivatives which bear either a tert-butyl nitroxide (NOA) or a poly(chloro)triphenylmethyl (PTMA) radical moiety. In the solid state, both radical acids formed dimer aggregates by the complementary association of two carboxylic groups though hydrogen bonding. This association ensured that atoms with most spin density are separated from one another by more than 15 A. Thus, no competing through-space magnetic exchange interactions are expected in these dimers and, hence, they provide good models to investigate whether noncovalent hydrogen bonds play a role in the long-range transmission of magnetic interactions. The nature of the magnetic exchange interaction and their strengths within similar dimer aggregates in solution was assessed by electron spin resonance (ESR) spectroscopy. In the case of radical NOA, low-temperature ESR experiments showed a weak ferromagnetic interaction between the two radicals in the dimer aggregates (which have the same geometry as in the solid state). In contrast, the corresponding solution ESR study performed with radical PTMA did not lead to any conclusive results, as aggregates were formed by noncovalent interactions other than hydrogen bonds. However, the bulkiness of the poly(chloro)triphenylmethyl radical prevented interdimer contacts in the solid state between regions of high spin density. Hence, solid-state measurements of the alpha phase of PTMA radical provided evidence of the intradimer interaction to confirm the transmission of a weak ferromagnetic interaction through the carboxylic acid bridges, as found for the NOA radical. Moreover, crystallization of the PTMA radical in presence of ethanol to form the beta phase of PTMA radical prevented the dimer formation; this resulted in the suppression of this interaction and provides further evidence of the magnetic exchange mechanism through noncovalent hydrogen bonds at long distances.     

Discovery of a new phosphotyrosine mimetic for PTP1B using breakaway tethering

Protein tyrosine phosphatases play important roles in many signaling cascades involved in human disease. The identification of druglike inhibitors for these targets is a major challenge, and the discovery of suitable phosphotyrosine (pY) mimetics remains one of the key difficulties. Here we describe an extension of tethering technology, "breakaway tethering", which is ideally suited for discovering such new chemical entities. The approach involves first irreversibly modifying a protein with an extender that contains both a masked thiol and a known pY mimetic. The extender is then cleaved to release the pY mimetic, unmasking the thiol. The resulting protein is screened against a library of disulfide-containing small molecule fragments; any molecules with inherent affinity for the pY binding site will preferentially form disulfides with the extender, allowing for their identification by mass spectrometry. The ability to start from a known substrate mimimizes perturbation of protein structure and increases the opportunity to probe the active site using tethering. We applied this approach to the anti-diabetic protein PTP1B to discover a pY mimetic which belongs to a new molecular class and which binds in a novel fashion.     

Aggregation and reactivity of the cesium enolate of 6-phenyl-alpha-tetralone: comparison with the lithium enolate

The cesium enolate of 6-phenyl-alpha-tetralone (CsPAT) has a lambda(max) in THF at about 387 nm, but the variation with concentration is too small for application of singular value decomposition. Proton-transfer studies with several indicators show that CsPAT forms monomer-tetramer mixtures with a tetramerization equilibrium constant, K(1,4) = 2.3 x 10(11) M(-3). The pK of the monomer is 23.39 on a scale where fluorene is assigned 22.9 (per hydrogen). For comparison, the lithium enolate, LiPAT, is also a monomer-tetramer with K(1,4) = 4.7 x 10(10) M(-3) and a monomer pK = 14.22. HMPA in large amounts promotes dissociation to monomer with both enolates. Ion-pair S(N)2 initial rates were measured for CsPAT with several alkyl halides and with methyl tosylate and compared with other rates with LiPAT. In all cases, the enolate monomers are much more reactive than the aggregates. Reaction of CsPAT with alkyl halides is generally C-alkylation but HMPA promotes increasing amounts of O-alkylation. A new indicator, 11-methyl-11H-benzo[b]fluorene, has a pK on the cesium scale of 23.39.