Conformational analysis of D-pantothenic acid

The conformational analysis of d-pantothenic acid using classical semiempirical methods has been carried out. The pantothenic acid molecule can exist in the neutral form (I) or in the ionised form (II) with a deprotonated negatively charged carboxyl group. The neutral molecule as well as the anion is highly flexible and has an ensemble of several allowed conformations rather than one or two unique conformations. The distribution of allowed conformations indicate that the β-alanine as well as the pantoic acid part of the molecule prefers partially folded conformations. The conformation of the former is greatly affected by the ionisation state of the carboxyl group whereas that of the latter is not. Possibility of intramolecular hydrogen bonding in different allowed conformations has also been explored. A bifurcated hydrogen bond involving a carboxyl (or carboxylate) oxygen atom and a hydroxyl oxygen atom, as acceptors, and the amide nitrogen atom as the donor occurs frequently in both I and II. Amongst the two crystal structures containing pantothenic acid reported so far, the conformation of the molecule in l-lysine d-pantothenate lies in the allowed region and is stabilised by a bifurcated intramolecular hydrogen bond, whereas that in the calcium bromide salt falls in a disallowed region, presumably due to the requirement of tridentate metal coordination.

Redox-linked proton transfer by cytochrome c oxidase

The respiratory chain is found in the inner mitochondrial membrane of higher organisms and in the plasma membrane of many bacteria. It consists of several membrane-spanning enzymes, which conserve the energy that is liberated from the degradation of food molecules as an electrochemical proton gradient across the membrane. The proton gradient can later be utilized by the cell for different energy requiring processes, e.g. ATP production, cellular motion or active transport of ions. The difference in proton concentration between the two sides of the membrane is a result of the translocation of protons by the enzymes of the respiratory chain, from the negatively charged (N-side) to the positively charged side (P-side) of the lipid bilayer, against the proton concentration gradient. The endergonic proton transfer is driven by the flow of electrons through the enzymes of the respiratory chain, from low redox-potential electron donors to acceptors of higher potential, and ultimately to oxygen. Cytochrome c oxidase is the last enzyme in the respiratory chain and catalyzes the reduction of dioxygen to water. The redox reaction is coupled to proton transport across the membrane by a yet unresolved mechanism. Cytochrome c oxidase has two proton-conducting pathways through which protons are taken up to the interior part of the enzyme from the N-side of the membrane. The K-pathway transfers merely substrate protons, which are consumed in the process of water formation at the catalytic site. The D-pathway transfers both substrate protons and protons that are pumped to the P-side of the membrane. This thesis focuses on the role of two conserved amino acids in proton translocation by cytochrome c oxidase, glutamate 278 and tryptophan 164. Glu278 is located at the end of the D-pathway and is thought to constitute the branching point for substrate and pumped protons. In this work, it was shown that although Glu278 has an important role in the proton transfer mechanism, its presence is not an obligatory requirement. Alternative structural solutions in the area around Glu278, much like the ones present in some distantly related heme-copper oxidases, could in the absence of Glu278 support the formation of a long hydrogen-bonded water chain through which proton transfer from the D-pathway to the catalytic site is possible. The other studied amino acid, Trp164, is hydrogen bonded to the ∆-propionate of heme a3 of the catalytic site. Mutation of this amino acid showed that it may be involved in regulation of proton access to a proton acceptor, a pump site, from which the proton later is expelled to the P-side of the membrane. The ion pair that is formed by the ∆-propionate of heme a3 and arginine 473 is likely to form a gate-like structure, which regulates proton mobility to the P-side of the membrane. The same gate may also be part of an exit path through which water molecules produced at the catalytically active site are removed towards the external side of the membrane. Time-resolved optical and electrometrical experiments with the Trp164 to phenylalanine mutant revealed a so far undetected step in the proton pumping mechanism. During the A to PR transition of the catalytic cycle, a proton is transferred from Glu278 to the pump site, located somewhere in the vicinity of the ∆-propionate of heme a3. A mechanism for proton pumping by cytochrome c oxidase is proposed on the basis of the presented results and the mechanism is discussed in relation to some relevant experimental data. A common proton pumping mechanism for all members of the heme-copper oxidase family is moreover considered.

Position preference and diffusion path of an oxygen ion in apatite-type lanthanum silicate La9.33Si6O26: A density functional study

Using density functional theory, we investigated the position preference and diffusion mechanisms of interstitial oxygen ions in lanthanum silicate La9.33Si6O26, which is an apatite-structured oxide and a promising candidate electrolyte material for solid oxide fuel cells. The reported lanthanum vacancies were explicitly taken into account by theoretically determining their arrangement with a supercell model. The most stable structures and the formation energies of oxygen interstitials were determined for each charged state. It was found that the double-negatively charged state is stable over a wide range of the Fermi level, and that the excess oxygen ions form split interstitials with the original oxygen ions, while the neutral and the single-negatively charged states preferably form molecular oxygen. These species were found near the lanthanum vacancy site. The theoretically determined migration pathway along the c-axis essentially follows an interstitialcy mechanism. The obtained migration barrier is sensitive to the charge state, and is also affected by the lanthanum vacancy. The barrier height of the double-negatively charged state was calculated to be 0.58 eV for the model structure, which is consistent with the measured activation energy.

Melting of an Anchored Bilayer: Molecular Dynamics Simulations of the Structural Transition in (CnH2n+1NH3)(2)PbI4 (n=12, 14, 16, 18)

The thermally driven Structural phase transition in the organic-inorganic hybrid perovskite (CnH2n+1NH3)(2)PbI4 has been investigated using molecular dynamics (MD) simulations. This system consists of positively charged alkyl-amine chains anchored to a rigid negatively charged PbI4 sheet with the chains organized as bilayers with a herringbone arrangement. Atomistic simulations were performed using ail isothermal-isobaric ensemble over a wide temperature range from 65 to 665 K for different alkyl chain lengths, n = 12, 14, 16, and 18. The simulations are able to reproduce the essential Features of the experimental observations of this system, including the existence of a transition, the linear variation of the transition temperature with alkyl chain length, and the expansion of the bilayer thickness at the transition. By use of the distance fluctuation Criteria, it is Shown that the transition is associated With a Melting of the alkyl chains of the anchored bilayer. Ail analysis of the conformation of the alkyl chains shows increased disorder in the form of gauche defects above due melting transition. Simulations also show that the melting transition is characterized by the complete disappearance of all-trans alkyl chains in the anchored bilayer, in agreement with experimental observations. A conformationally disordered chain has a larger effective cross-sectional area, and above due transition a uniformly tilted arrangement of the anchored chains call no longer be Sustained. At the melt the angular distribution of the orientation of the chains are 110 longer uniform; the chains are splayed allowing for increased space for individual chains of the anchored bilayer. This is reflected in a sharp rise in the ratio of the mean head-to-head to tail-to-tail distance of the chains of the bilayer at the transition resulting in in expansion of the bilayer thickness. The present MD simulations provide a simple explanation as to how changes in conformation of individual alkyl-chains gives rise to the observed increase in the interlayer lattice spacing of (CnH2n+1NH3)(2)PbI4 at the melting transition.

Phospholipid cytochrome c interactions

The ability of the peripherally associated membrane protein cytochrome c (cyt c) to bind phospholipids in vitro was studied using fluorescence spectroscopy and large unilamellar liposomes. Previous work has shown that cyt c can bind phospholipids using two distinct mecha- nisms and sites, the A-site and the C-site. This binding is mediated by electrostatic or hydrophobic interactions, respectively. Here, we focus on the mechanism underlying these interactions. A chemically modified cyt c mutant Nle91 was used to study the ATP-binding site, which is located near the evolutionarily invariant Arg 91 on the protein surface. This site was also demonstrated to mediate phospholipid binding, possibly by functioning as a phospholipid binding site. Circular dichroism spectroscopy, time resolved fluorescence spectroscopy of zinc- porphyrin modified [Zn2+-heme] cyt c and liposome binding studies of the Nle91 mutant were used to demonstrate that ATP induces a conformational change in membrane- bound cyt c. The ATP-induced conformational changes were mediated by Arg 91 and were most pronounced in cyt c bound to phospholipids via the C-site. It has been previously reported that the hydrophobic interaction between phospho- lipids and cyt c (C-site) includes the binding of a phospholipid acyl chain inside the protein. In this mechanism, which is known as extended phospholipid anchorage, the sn-2 acyl chain of a membrane phospholipid protrudes out of the membrane surface and is able to bind in a hydrophobic cavity in cyt c. Direct evidence for this type of bind- ing mechanism was obtained by studying cyt c/lipid interaction using fluorescent [Zn2+- heme] cyt c and fluorescence quenching of brominated fatty acids and phospholipids. Under certain conditions, cyt c can form fibrillar protein-lipid aggregates with neg- atively charged phospholipids. These aggregates resemble amyloid fibrils, which are involved in the pathogenesis of many diseases. Congo red staining of these fibers con- firmed the presence of amyloid structures. A set of phospholipid-binding proteins was also found to form similar aggregates, suggesting that phospholipid-induced amyloid formation could be a general mechanism of amyloidogenesis.

Recombination and trapping in n-type cobalt-doped germanium

The role of cobalt centers in promoting the recombination and trapping processes in n-type germanium has been investigated. Data on lifetime measurements carried out by the steadystate photoconductivity and photo-magneto-electric methods in the temperature range 145 to 300°K on n-type germanium samples containing cobalt in the concentration range 1·1013 to 5.·014/cm3 are presented. The results are analysed on the basis of Sah-Shockley's multi-level formula to yield the capture cross-sections Sp= (hole capture cross-section at doubly negatively charged center) and Sn-(electron capture cross-section at singly negatively charged center) and temperature dependence. It is found that Sp= is (22 ± 6). 10-16 cm2 and Sn- is ∼ 0·1. 10-16 cm2 at 145°K. Sp= varies (n = 3·5 to 4·5) in the range 145-220°K; above 225°K the index 'n' tends to a smaller value. Sn- is practically temperature independent below 180°K and increases with increase of temperature above 180°K. The value of Sp= and its temperature variation lead one to the conclusion that during capture at attractive centers, the phonon cascade mechanism is responsible for the dissipation of the recombination energy.

Electron-hole recombination in cobalt-doped p-type germanium

The recombination properties of cobalt centers in p-type germanium containing cobalt in the concentration range 1014 to 1016 atoms/cm3 have been investigated. The measurement of lifetime has been carried out by steady-state photoconductivity and photo-magneto-electric methods in the temperature range 145 to 300°K. The cross-sections Sno (electron capture cross-section at neutral centers). Sn- (electron capture cross-section at singly negatively charged centers) and their temperature variations have been estimated by the analysis of the lifetime data on the basis of Sah-Shockley's multi-level formula. The value of Sno is (15±5).10-16 cm2 and is temperature independent. The value of Sn- is ≈4·10-16 cm2 around 225°K and it increases with increase of temperature. The possible mechanisms for capture at neutral and repulsive centers are discussed and a summary of the capture cross-sections for cobalt centers is given. A comparison of the cross-section values of cobalt and their temperature variations with those of the related impurities-manganese, iron and nickel-in germanium has been made.

Effect of electric field on ammonium perchlorate decomposition

A novel method of detecting the charge-carrying species in inorganic decomposable salts is described. In ammonium perchlorate it is observed that the charge-carrying species at temperatures 150 and 230°C are oppositely charged; i.e., they are negatively charged (ClO−4 ions) at 230°C and positively charged (H+ or NH+4) at 150°C.

Effect of electric field on ammonium perchlorate decomposition

A novel method of detecting the charge-carrying species in inorganic decomposable salts is described. In ammonium perchlorate it is observed that the charge-carrying species at temperatures 150 and 230°C are oppositely charged; i.e., they are negatively charged (ClO−4 ions) at 230°C and positively charged (H+ or NH+4) at 150°C.

Computer modelling studies on the mechanism of action of ribonuclease T1

The mechanism of action of ribonuclease (RNase) T1 is still a matter of considerable debate as the results of x-ray, 2-D nmr and site-directed mutagenesis studies disagree regarding the role of the catalytically important residues. Hence computer modelling studies were carried out by energy minimisation of the complexes of RNase T1 and some of its mutants (His40Ala, His40Lys, and Glu58Ala) with the substrate guanyl cytosine (GpC), and of native RNase T1 with the reaction intermediate guanosine 2',3'-cyclic phosphate (G greater than p). The puckering of the guanosine ribose moiety in the minimum energy conformer of the RNase T1-GpC (substrate) complex was found to be O4'-endo and not C3'-endo as in the RNase T1-3'-guanylic acid (inhibitor/product) complex. A possible scheme for the mechanism of action of RNase T1 has been proposed on the basis of the arrangement of the catalytically important amino acid residues His40, Glu58, Arg77, and His92 around the guanosine ribose and the phosphate moiety in the RNase T1-GpC and RNase T1-G greater than p complexes. In this scheme, Glu58 serves as the general base group and His92 as the general acid group in the transphosphorylation step. His40 may be essential for stabilising the negatively charged phosphate moiety in the enzyme-transition state complex.

Synthesis of graphene oxide-intercalated alpha-hydroxides by metathesis and their decomposition to graphene/metal oxide composites

Graphene oxide-intercalated alpha-metal hydroxides were prepared using layers from the delaminated colloidal dispersions of cetyltrimethylammonium-intercalated graphene oxide and dodecylsulfate-intercalated alpha-hydroxide of nickel/cobalt as precursors. The reaction of the two dispersions leads to de-intercalation of the interlayer ions from both the layered solids and the intercalation of the negatively charged graphene oxide sheets between the positively charged layers of the alpha-hydroxide. Thermal decomposition of the intercalated solids yields graphene/nanocrystalline metal oxide composites. Electron microscopy analysis of the composites indicates that the nanoparticles are intercalated between graphene layers. (C) 2010 Elsevier Ltd. All rights reserved.

DNA Compaction by a Dendrimer

At physiological pH, a PAMAM dendrimer is positively charged and can effectively bind negatively charged DNA. Currently, there has been great interest in understanding this complexation reaction both for fundamental (as a model for complex biological reactions) as well as for practical (as a gene delivery material and probe for sensing DNA sequence) reasons. Here, we have studied the complexation between double-stranded DNA (dsDNA) and various generations of PAMAM dendrimers (G3-05) through atomistic molecular dynamics simulations in the presence of water and ions. We report the compaction of DNA on a nanosecond time scale. This is remarkable, given the fact that such a short DNA duplex with a length close to 13 nm is otherwise thought to be a rigid rod. Using several nanoseconds long MD simulations, we have observed various binding modes of dsDNA and dendrimers for various generations of PAMAM dendrimers at varying charge ratios, and it confirms some of the binding modes proposed earlier. The binding is driven by the electrostatic interaction, and the larger the dendrimer charge, the stronger the binding affinity. As DNA wraps/binds to the dendrimer, counterions originally condensed onto DNA (Na+) and the dendrimer (Cl-) get released. We calculate the entropy of counterions and show that there is gain in entropy due to counterion release during the complexation. MD simulations demonstrate that, when the charge ratio is greater than 1 (as in the case of the G5 dendrimer), the optimal wrapping of DNA is observed. Calculated binding energies of the complexation follow the trend G5 > 04 > 03, in accordance with the experimental data. For a lower-generation dendrimer, such as G3, and, to some extent, for G4 also, we see considerable deformation in the dendrimer structure due to their flexible nature. We have also calculated the various helicoidal parameters of DNA to study the effect of dendrimer binding on the structure of DNA. The B form of the DNA is well preserved in the complex, as is evident from various helical parameters, justifying the use of the PAMAM dendrimer as a suitable delivery vehicle.

Electrochemical preparation of few layer-graphene nanosheets via reduction of oriented exfoliated graphene oxide thin films in acetamide-urea-ammonium nitrate melt under ambient conditions

Electrochemical reduction of exfoliated graphene oxide, prepared from pre-exfoliated graphite, in acetamide-urea-ammonium nitrate ternary eutectic melt results in few layer-graphene thin films. Negatively charged exfoliated graphene oxide is attached to positively charged cystamine monolyer self-assembled on a gold surface. Electrochemical reduction of the oriented graphene oxide film is carried out in a room temperature, ternary molten electrolyte. The reduced film is characterized by atomic force microscopy (AFM), conductive AFM, Fourier-transform infrared spectroscopy and Raman spectroscopy. Ternary eutectic melt is found to be a suitable medium for the regulated reduction of graphene oxide to reduced graphene oxide-based sheets on conducting surfaces. (C) 2010 Elsevier B.V. All rights reserved.

Composition Driven Monolayer to Bilayer Transformation in a Surfactant Intercalated Mg-Al Layered Double Hydroxide

The structure and organization of dodecyl sulfate (DDS) surfactant chains intercalated in an Mg-Al layered double hydroxide (LDH), Mg(1-x)Alx(OH)(2), with differing Al/Mg ratios has been investigated. The Mg-Al LDHs can be prepared over a range of compositions with x varying from 0.167 to 0.37 and therefore provides a simple system to study how the organization of the alkyl chains of the intercalated DDS anions change with packing density; the Al/Mg ratio or x providing a convenient handle to do so. Powder X-ray diffraction measurements showed that at high packing densities (x >= 0.3) the alkyl chains of the intercalated dodecyl sulfate ions are anchored on opposing LDH sheets and arranged as bilayers with an interlayer spacing of similar to 27 angstrom. At lower packing densities (x < 0.2) the surfactant chains form a monolayer with the alkyl chains oriented flat in the galleries with an interlayer spacing of similar to 8 angstrom. For the in between compositions, 0.2 <= x < 0.3, the material is biphasic. MD simulations were performed to understand how the anchoring density of the intercalated surfactant chains in the Mg-Al LDH-DDS affects the organization of the chains and the interlayer spacing. The simulations are able to reproduce the composition driven monolayer to bilayer transformation in the arrangement of the intercalated surfactant chains and in addition provide insights into the factors that decide the arrangement of the surfactant chains in the two situations. In the bilayer arrangement, it is the dispersive van der Waals interactions between chains in opposing layers of the anchored bilayer that is responsible for the cohesive energy of the solid whereas at lower packing densities, where a monolayer arrangement is favored, Coulomb interactions between the positively charged Mg-Al LDH sheets and the negatively charged headgroup of the DDS anion dominate.

Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures

DNA three-way junctions (TWJs) are important intermediates in various cellular processes and are the simplest of a family of branched nucleic acids being considered as scaffolds for biomolecular nanotechnology. Branched nucleic acids are stabilized by divalent cations such as Mg2+, presumably due to condensation and neutralization of the negatively charged DNA backbone. However, electrostatic screening effects point to more complex solvation dynamics and a large role of interfacial waters in thermodynamic stability. Here, we report extensive computer simulations in explicit water and salt on a model TWJ and use free energy calculations to quantify the role of ionic character and strength on stability. We find that enthalpic stabilization of the first and second hydration shells by Mg2+ accounts for 1/3 and all of the free energy gain in 50% and pure MgCl2 solutions, respectively. The more distorted DNA molecule is actually destabilized in pure MgCl2 compared to pure NaCl. Notably, the first shell, interfacial waters have very low translational and rotational entropy (i.e., mobility) compared to the bulk, an entropic loss that is overcompensated by increased enthalpy from additional electrostatic interactions with Mg2+. In contrast, the second hydration shell has anomalously high entropy as it is trapped between an immobile and bulklike layer. The nonmonotonic entropic signature and long-range perturbations of the hydration shells to Mg2+ may have implications in the molecular recognition of these motifs. For example, we find that low salt stabilizes the parallel configuration of the three-way junction, whereas at normal salt we find antiparallel configurations deduced from the NMR. We use the 2PT analysis to follow the thermodynamics of this transition and find that the free energy barrier is dominated by entropic effects that result from the decreased surface area of the antiparallel form which has a smaller number of low entropy waters in the first monolayer.