Probing molecular shape. 1. Conformational studies of 5-hydroxyhexahydropyrimidine and related compounds

Understanding the factors that determine molecular shape enables scientists to begin to understand and tailor molecular properties and reactivity. Many biomolecules and bioactive compounds contain aliphatic heterocyclic rings whose conformations play a major role in their biological activity. The interplay of a number of factors, both steric and electronic, is examined for 5-hydroxyhexahydropyrimidine (1) and related compounds with use of spectroscopy and molecular modeling.     

Investigating the specific interactions between carbonic anhydrase and a sulfonamide inhibitor by single-molecule force spectroscopy

In this communication, we report on the interaction landscape of an active site-specific enzyme-inhibitor complex by single-molecule force spectroscopy. Electrostatic immobilization was employed to orient a carbonic anhydrase enzyme on a positively charged surface so its active site is pointing upward. This approach to immobilization effectively increases the number of specific interactions measured between the zinc ion of the active site on carbonic anhydrase and a sulfonamide inhibitor tethered to an atomic force microscope (AFM) probe. Further, it reduces the time required for data collection and thereby minimizes the possible mechanical damage to the probe and contamination of the enzyme surface. The rupture force measured at various loading rates is interpreted in terms of a single energy barrier for the carbonic anhydrase enzyme-sulfonamide inhibitor complex from which the kinetic and thermodynamic parameters were estimated on the basis of microscopic models and were compared to the Bell-Evans model. The dissociation rate for the enzyme-inhibitor complex was found to be significantly faster (~35 times) than the natural spontaneous dissociation rate.     

Bioreductive activation and drug chaperoning in cobalt pharmaceuticals

The potential for cobalt(III) complexes in medicine, as chaperones of bioactive ligands, and to target tumours through bioreductive activation, has been examined over the past 20 years. Despite this, chemical properties such as reduction potential and carrier ligands required for optimal tumour targeting and drug delivery have not been optimised. Here we review the chemistry of cobalt(III) drug design, and recent developments in the understanding of the cellular fate of these drugs.     

IR/Raman spectroscopy and DFT calculations of cyclic di‐amino acid peptides. Part III: comparison of solid state and solution structures of cyclo(L‐Ser‐L‐Ser)

B3‐LYP/cc‐pVDZ calculations of the gas‐phase structure and vibrational spectra of the isolated molecule cyclo(L ‐Ser‐L ‐Ser), a cyclic di‐amino acid peptide (CDAP), were carried out by assuming C₂ symmetry. It is predicted that the minimum‐energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L ‐seryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol⁻¹) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X‐ray crystallographic structure of cyclo(L ‐Ser‐L ‐Ser), shows that the DKP ring displays a near‐planar conformation, with both the two L ‐seryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier‐transform infrared (FT‐IR) spectra of solid state and aqueous solution samples of cyclo(L ‐Ser‐L ‐Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid‐state samples show characteristic amide I vibrations which are split (Raman: 1661 and 1687 cm⁻¹, IR: 1666 and 1680 cm⁻¹), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ∼30 cm⁻¹, which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm⁻¹. The occurrence of this cis amide II mode at a wavenumber above 1500 cm⁻¹ concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C^α atoms, and is also indicative of a relatively unstrained DKP ring. Copyright © 2009 John Wiley & Sons, Ltd.     

Surface complexation of Pb(II) on amorphous iron oxide and manganese oxide: spectroscopic and time studies

Hydrous Fe and Mn oxides (HFO and HMO) are important sinks for heavy metals and Pb(II) is one of the more prevalent metal contaminants in the environment. In this work, Pb(II) sorption to HFO (Fe(2)O(3) x nH(2)O, n=1-3) and HMO (MnO(2)) surfaces has been studied with EXAFS: mononuclear bidentate surface complexes were observed on FeO(6) (MnO(6)) octahedra with PbO distance of 2.25-2.35 Angstrom and PbFe(Mn) distances of 3.29-3.36 (3.65-3.76) Angstrom. These surface complexes were invariant of pH 5 and 6, ionic strength 2.8 x 10(-3) to 1.5 x 10(-2), loading 2.03 x 10(-4) to 9.1 x 10(-3) mol Pb/g, and reaction time up to 21 months. EXAFS data at the Fe K-edge revealed that freshly precipitated HFO exhibits short-range order; the sorbed Pb(II) ions do not substitute for Fe but may inhibit crystallization of HFO. Pb(II) sorbed to HFO through a rapid initial uptake ( approximately 77%) followed by a slow intraparticle diffusion step ( approximately 23%) resulting in a surface diffusivity of 2.5 x 10(-15) cm(2)/s. Results from this study suggest that mechanistic investigations provide a solid basis for successful adsorption modeling and that inclusion of intraparticle surface diffusion may lead to improved geochemical transport depiction.     

The impact of Mn oxide coatings on Zn distribution

Zinc sorption to hydrous manganese oxide (HMO)-coated clay was investigated macroscopically, kinetically, and spectroscopically. Adsorption edges and isotherms revealed that the affinity and capacity of the HMO-coated montmorillonite was greater than that of montmorillonite, and when normalized to the oxide present, the coatings behaved similarly to the discrete Mn oxide. Over two pH conditions, 5 and 6, a linear relationship was observed for the isotherms; further analysis with X-ray absorption spectroscopy (XAS) resulted in one type of sorption configuration as a function of loading and ionic strength at pH 5. However, at a surface loading of 10(-3) mol(Zn) g(HMO-coatedclay)(-1) when the pH increased from 5 to 7, the first shell distance decreased slightly, while the atoms and coordination numbers remained the same; this change may be attributed to an increase in electrostatic interactions. After a contact time of 4 months where an additional 60% of the sites become occupied, the slower sorption process was modeled as intraparticle surface diffusion. Best fit diffusivities ranged from 10(-18) to 10(-17) cm2/s, where a slower process was observed for the coated surface as compared to the discrete oxide. Interestingly, the porosity of the Mn oxide coating appears to be influenced by the substrate during its growth, as its increase and shift to a smaller pore size distribution resulted in a diffusivity between that observed for discrete HMO and montmorillonite.     

The perception of entropy in rapidly moving sparse dot arrays: a nonlinear dynamic perspective

In visual fields composed of dots spatially randomly distributed but moving rigidly, the percept of coherent motion is lost once D_max is exceeded, resulting in an incoherent, random percept. We have investigated this transition both from a psychophysics perspective and in the development of a dynamic model of the visual system based on a spatially coupled array of nonlinear damped mass-springs cells. We present results of experiments using rigidly moving arrays of dots of different levels of sparseness and differing displacement magnitudes. Results show that the perception of randomness can be reliably judged and displays a transition from coherent to non-coherent motion as the motion amplitude is increased. Using standard psychophysical just noticeable difference (JND) judgements, we noted that the threshold JND was a function of displacement magnitude and sparseness and could not be explained by extant spatiotemporal filtering models. Our model qualitatively explains the important features of the data, reproducing the experimental D_max and entropy perception effects with increased stimuli motion amplitude at different spatial sparseness levels. We have then performed some numerical simulations of the model when the masses in the array are randomly distributed. Results show that sparseness plays different role if close or far from D_max in terms of motion coherence discrimination.     

Formation of N2O from a nickel nitrosyl: isolation of the cis-[N2O2]2- intermediate

Addition of 2,2'-bipyridine (bipy) to [Ni(NO)(bipy)][PF(6)] (1) results in formation of a rare five-coordinate nickel nitrosyl [Ni(NO)(bipy)(2)][PF(6)] (2). This complex exhibits a bent NO(-) ligand in the solid state. On standing in acetonitrile, 2 furnishes the NO coupled product, [Ni(κ(2)-O(2)N(2))(bipy)] (8) in moderate yield. Subsequent addition of 2 equiv of acetylacetone (H(acac)) to 8 results in formation of [Ni(acac)(2)(bipy)], N(2)O, and H(2)O. Preliminary mechanistic studies suggest that the N-N bond is formed via a bimetallic coupling reaction of two NO(-) ligands.     

Site-directed coordination chemistry with P22 virus-like particles

Protein cage nanoparticles (PCNs) are attractive platforms for developing functional nanomaterials using biomimetic approaches for functionalization and cargo encapsulation. Many strategies have been employed to direct the loading of molecular cargos inside a wide range of PCN architectures. Here we demonstrate the exploitation of a metal-ligand coordination bond with respect to the direct packing of guest molecules on the interior interface of a virus-like PCN derived from Salmonella typhimurium bacteriophage P22. The incorporation of these guest species was assessed using mass spectrometry, multiangle laser light scattering, and analytical ultracentrifugation. In addition to small-molecule encapsulation, this approach was also effective for the directed synthesis of a large macromolecular coordination polymer packed inside of the P22 capsid and initiated on the interior surface. A wide range of metals and ligands with different thermodynamic affinities and kinetic stabilities are potentially available for this approach, highlighting the potential for metal-ligand coordination chemistry to direct the site-specific incorporation of cargo molecules for a variety of applications.