Hydrogen-bonding in the structures of the hydrated proton-transfer compounds of isonipecotamide with the isomeric indole-2 and indole-3-carboxylic acids

The structures of two hydrated proton-transfer compounds of 4-piperidinecarboxamide (isonipecotamide) with the isomeric heteroaromatic carboxylic acids indole-2-carboxylic acid and indole-3-carboxylic acid, namely 4-carbamoylpiperidinium indole-2-carboxylate dihydrate (1) and 4-carbamoylpiperidinium indole-3-carboxylate hemihydrate (2) have been determined at 200 K. Crystals of both 1 and 2 are monoclinic, space groups P21/c and P2/c respectively with Z = 4 in cells having dimensions a = 10.6811(4), b = 12.2017(4), c = 12.5456(5) Å, β = 96.000(4)o (1) and a = 15.5140(4), b = 10.2908(3), c = 9.7047(3) Å, β = 97.060(3)o (2). Hydrogen-bonding in 1 involves a primary cyclic interaction involving complementary cation amide N-H…O(carboxyl) anion and anion hetero N-H…O(amide) cation hydrogen bonds [graph set R22(9)]. Secondary associations involving also the water molecules of solvation give a two-dimensional network structure which includes weak water O-H…π interactions. In the three-dimensional hydrogen-bonded structure of 2, there are classic centrosymmetric cyclic head-to-head hydrogen-bonded amide-amide interactions [graph set R22(8)] as well as lateral cyclic amide-O linked amide-amide extensions [graph set R24(8)]. The anions and the water molecule, which lies on a twofold rotation axis, are involved in secondary extensions.

Effects of ions and atomic hydrogen in plasma-assisted growth of single-walled carbon nanotubes

The growth of single-walled carbon nanotubes (SWCNTs) in plasma-enhanced chemical vapor deposition (PECVD) is studied using a surface diffusion model. It is shown that at low substrate temperatures (≤1000 K), the atomic hydrogen and ion fluxes from the plasma can strongly affect nanotube growth. The ion-induced hydrocarbon dissociation can be the main process that supplies carbon atoms for SWCNT growth and is responsible for the frequently reported higher (compared to thermal chemical vapor deposition) nanotube growth rates in plasma-based processes. On the other hand, excessive deposition of plasma ions and atomic hydrogen can reduce the diffusion length of the carbon-bearing species and their residence time on the nanotube lateral surfaces. This reduction can adversely affect the nanotube growth rates. The results here are in good agreement with the available experimental data and can be used for optimizing SWCNT growth in PECVD.

Helical conformations of three crystalline pentapeptide fragments of suzukacillin, a membrane channel forming polypeptide

The crystal structures of three pentapeptide fragments of suzukacillin-A have been determined. Boc-Aib-Pro-Val-Aib-Val-OMe (peptide 1–5) adopts a distorted helical conformation, stabilized by three intramolecular hydrogen bonds (two 5→1, one 4→1). Boc-Ala-Aib-Ala-Aib-Aib-OMe (peptide 6–10) and Boc-Leu-Aib-Pro-Val-Aib-OMe (peptide 16–20) adopt 310 helical structures stabilized by three and two 4→1 intramolecular hydrogen bonds, respectively. These structures provide substantial support for a largely helical conformation for the suzukacillin membrane channel.

Experimental investigation of catalytic and non-catalytic surface reactions on SiO2 thin films with shock heated oxygen gas

The present study is to investigate the interaction of strong shock heated oxygen on the surface of SiO2 thin film. The thermally excited oxygen undergoes a three-body recombination reaction on the surface of silicon dioxide film. The different oxidation states of silicon species on the surface of the shock-exposed SiO2 film are discussed based on X-ray Photoelectron Spectroscopy (XPS) results. The surface morphology of the shock wave induced damage at the cross section of SiO2 film and structure modification of these materials are analyzed using scanning electron microscopy and ion microscopy. Whether the surface reaction of oxygen on SiO2 film is catalytic or non-catalytic is discussed in this paper.

Novel correlations in two dimensions: Two-body problem

We discuss a many-body Hamiltonian with two- and three-body interactions in two dimensions introduced recently by Murthy, Bhaduri and Sen. Apart from an analysis of some exact solutions in the many-body system, we analyse in detail the two-body problem which is completely solvable. We show that the solution of the two-body problem reduces to solving a known differential equation due to Heun. We show that the two-body spectrum becomes remarkably simple for large interaction strengths and the level structure resembles that of the Landau levels. We also clarify the 'ultraviolet' regularization which is needed to define an inverse-square potential properly and discuss its implications for our model.

Quantum theoretical study of molecular mechanisms of mutation and cancer - A review

Several endogenous and exogenous chemical species, particularly the so-called reactive oxygen species (ROS) and reactive nitrogen oxide species (RNOS), attack deoxyribonucleic acid (DNA) in biological systems producing DNA lesions which hamper normal cell functioning and cause various diseases including mutation and cancer. The guanine (G) base of DNA among all the bases is most susceptible and certain modified guanines get involved in mispairing with other bases during DNA replication. The biological system repairs the abnormal base pairs, but those that are still left cause mutation and cancer. Anti-oxidants present in biological systems can scavenge the ROS and RNOS. Thus three types of molecular events occur in biological media: (i) DNA damage, (ii) DNA repair, and (iii) prevention of DNA damage by scavenging ROS and RNOS. Quantum mechanical methods may be used to unravel molecular mechanisms of such phenomena. Some recent quantum theoretical results obtained on these problems are reviewed here.

Chain Length Effects on Helix-Hairpin Distribution in Short Peptides with Aib-(D)Ala and Aib-Aib Segments

The Aib-(D)Ala dipeptide segment has a tendency to form both type-I'/III' and type-I/III beta-turns. The occurrence of prime turns facilitates the formation of beta-hairpin conformations, while type-I/III turns can nucleate helix formation. The octapeptide Boc-Leu-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-OMe (1) has been previously shown to form a beta-hairpin in the crystalline state and in solution. The effects of sequence truncation have been examined using the model peptides Boc-Phe-Val-Aib-Xxx-Leu-Phe-NHMe (2, 6), Boc-Val-Aib-Xxx-Leu-NHMe (3, 7), and Boc-Aib-Xxx-NHMe (4, 8), where Xxx = (D)Ala, Aib. For peptides with central Aib-Aib segments, Boc-Phe-Val-Aib-Aib-Leu-Phe-NHMe (6), Boc-Val-Aib-Aib-Leu-NHMe (7), and Boc-Aib-Aib-NHMe (8) helical conformations have been established by NMR studies in both hydrogen bonding (CD(3)OH) and non-hydrogen bonding (CDCl(3)) solvents. In contrast, the corresponding hexapeptide Boc-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-NHMe (2) favors helical conformations in CDCl(3) and beta-hairpin conformations in CD(3)OH. The beta-turn conformations (type-I'/III) stabilized by intramolecular 4 -> 1 hydrogen bonds are observed for the peptide Boc-Aib-(D)Ala-NHMe (4) and Boc-Aib-Aib-NIiMe (8) in crystals. The tetrapeptide Boc-Val-Aib-Aib-Leu-NHMe (7) adopts an incipient 3(10)-helical conformation stabilized by three 4 -> 1 hydrogen bonds. The peptide Boc-Val-Aib-(D)Ala-Leu-NHMe (3) adopts a novel et-turn conformation, stabilized by three intramolecular hydrogen bonds (two 4 -> 1 and one 5 -> 1). The Aib-L(D)Ala segment adopts a type-I' beta-turn conformation. The observation of an NOE between Val (1) NH <-> HNCH(3) (5) in CD(3)OH suggests, that the solid state conformation is maintained in methanol solutions. (C) 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 744-756, 2011.

Sodium-ion battery cathodes Na2FeP2O7 and Na2MnP2O7: diffusion behaviour for high rate performance

Na-ion batteries are currently the focus of significant research activity due to the relative abundance of sodium and its consequent cost advantages. Recently, the pyrophosphate family of cathodes has attracted considerable attention, particularly Li2FeP2O7 related to its high operating voltage and enhanced safety properties; in addition the sodium-based pyrophosphates Na2FeP2O7 and Na2MnP2O7 are also generating interest. Herein, we present defect chemistry and ion migration results, determined via atomistic simulation techniques, for Na2MP2O7 (where M = Fe, Mn) as well as findings for Li2FeP2O7 for direct comparison. Within the pyrophosphate framework the most favourable intrinsic defect type is found to be the antisite defect, in which alkali-cations (Na/Li) and M ions exchange positions. Low activation energies are found for long-range diffusion in all crystallographic directions in Na2MP2O7 suggesting three-dimensional (3D) Na-ion diffusion. In contrast Li2FeP2O7 supports 2D Li-ion diffusion. The 2D or 3D nature of the alkali-ion migration pathways within these pyrophosphate materials means that antisite defects are much less likely to impede their transport properties, and hence important for high rate performance.

Do we see what we should see? Describing non-covalent interactions in protein structures including precision

The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and alpha-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

Physical investigations of small particles : (I) aerosol particle charging and flux enhancement and (II) whispering gallery mode sensing

Part I

Particles are a key feature of planetary atmospheres. On Earth they represent the greatest source of uncertainty in the global energy budget. This uncertainty can be addressed by making more measurement, by improving the theoretical analysis of measurements, and by better modeling basic particle nucleation and initial particle growth within an atmosphere. This work will focus on the latter two methods of improvement.

Uncertainty in measurements is largely due to particle charging. Accurate descriptions of particle charging are challenging because one deals with particles in a gas as opposed to a vacuum, so different length scales come into play. Previous studies have considered the effects of transition between the continuum and kinetic regime and the effects of two and three body interactions within the kinetic regime. These studies, however, use questionable assumptions about the charging process which resulted in skewed observations, and bias in the proposed dynamics of aerosol particles. These assumptions affect both the ions and particles in the system. Ions are assumed to be point monopoles that have a single characteristic speed rather than follow a distribution. Particles are assumed to be perfect conductors that have up to five elementary charges on them. The effects of three body interaction, ion-molecule-particle, are also overestimated. By revising this theory so that the basic physical attributes of both ions and particles and their interactions are better represented, we are able to make more accurate predictions of particle charging in both the kinetic and continuum regimes.

The same revised theory that was used above to model ion charging can also be applied to the flux of neutral vapor phase molecules to a particle or initial cluster. Using these results we can model the vapor flux to a neutral or charged particle due to diffusion and electromagnetic interactions. In many classical theories currently applied to these models, the finite size of the molecule and the electromagnetic interaction between the molecule and particle, especially for the neutral particle case, are completely ignored, or, as is often the case for a permanent dipole vapor species, strongly underestimated. Comparing our model to these classical models we determine an “enhancement factor” to characterize how important the addition of these physical parameters and processes is to the understanding of particle nucleation and growth.

Part II

Whispering gallery mode (WGM) optical biosensors are capable of extraordinarily sensitive specific and non-specific detection of species suspended in a gas or fluid. Recent experimental results suggest that these devices may attain single-molecule sensitivity to protein solutions in the form of stepwise shifts in their resonance wavelength, \lambda_{R}, but present sensor models predict much smaller steps than were reported. This study examines the physical interaction between a WGM sensor and a molecule adsorbed to its surface, exploring assumptions made in previous efforts to model WGM sensor behavior, and describing computational schemes that model the experiments for which single protein sensitivity was reported. The resulting model is used to simulate sensor performance, within constraints imposed by the limited material property data. On this basis, we conclude that nonlinear optical effects would be needed to attain the reported sensitivity, and that, in the experiments for which extreme sensitivity was reported, a bound protein experiences optical energy fluxes too high for such effects to be ignored.

Thermodynamic and kinetic behavior of an argon plasma jet. Decomposition of nitric oxide between 1300 - 1750 degrees K in an argon plasma

In the first part of the study, an RF coupled, atmospheric pressure, laminar plasma jet of argon was investigated for thermodynamic equilibrium and some rate processes.

Improved values of transition probabilities for 17 lines of argon I were developed from known values for 7 lines. The effect of inhomogeneity of the source was pointed out.

The temperatures, T, and the electron densities, n_e , were determined spectroscopically from the population densities of the higher excited states assuming the Saha-Boltzmann relationship to be valid for these states. The axial velocities, v_z, were measured by tracing the paths of particles of boron nitride using a three-dimentional mapping technique. The above quantities varied in the following ranges: 10¹² ˂ n_e ˂ 10¹⁵ particles/cm³, 3500 ˂ T ˂ 11000 °K, and 200 ˂ v_z ˂ 1200 cm/sec.

The absence of excitation equilibrium for the lower excitation population including the ground state under certain conditions of T and n_e was established and the departure from equilibrium was examined quantitatively. The ground state was shown to be highly underpopulated for the decaying plasma.

Rates of recombination between electrons and ions were obtained by solving the steady-state equation of continuity for electrons. The observed rates were consistent with a dissociative-molecular ion mechanism with a steady-state assumption for the molecular ions.

In the second part of the study, decomposition of NO was studied in the plasma at lower temperatures. The mole fractions of NO denoted by x_NO were determined gas-chromatographically and varied between 0.0012 ˂ x_NO ˂ 0.0055. The temperatures were measured pyrometrically and varied between 1300 ˂ T ˂ 1750°K. The observed rates of decomposition were orders of magnitude greater than those obtained by the previous workers under purely thermal reaction conditions. The overall activation energy was about 9 kcal/g mol which was considerably lower than the value under thermal conditions. The effect of excess nitrogen was to reduce the rate of decomposition of NO and to increase the order of the reaction with respect to NO from 1.33 to 1.85. The observed rates were consistent with a chain mechanism in which atomic nitrogen and oxygen act as chain carriers. The increased rates of decomposition and the reduced activation energy in the presence of the plasma could be explained on the basis of the observed large amount of atomic nitrogen which was probably formed as the result of reactions between excited atoms and ions of argon and the molecular nitrogen.

两种银莲花属植物的化学成分研究

本学位论文由5 章组成。第1 章报道了两头尖中三萜皂苷类化合物的全扫描电喷雾多级质谱分析及银莲花素A 的电喷雾质谱裂解规律；第2 和3 章报道了两种银莲花属药用植物化学成分的研究结果；第4 章报道了银莲花素A 的化学结构修饰及其对一种蛋白酪氨酸磷酸酯酶（PTP-1B）的抑制活性；第5 章综述了电喷雾质谱在皂苷类化合物结构鉴定中的应用进展。 第1 章报道了运用全扫描电喷雾多级质谱对两头尖中三萜皂苷类化合物的快速定性检测，共检测出18 个准分子离子峰，根据多级质谱数据并结合文献报道，对其中的15 个准分子离子峰进行了归属，并区分了一些同分异构体；更有意思的是，发现了3 个未见文献报道的三萜皂苷类化合物。根据它们的多级质谱数据，对其结构分别进行了初步解析。本章同时对银莲花素A 特殊的质谱裂解途径通过衍生物制备及其质谱分析进行了确认。 第2 和3 章，分别报道了两头尖和打破碗花花中水溶性多糖苷的分离纯化和结构鉴定。采用D101 大孔树脂和反复硅胶柱层析等分离手段，从两头尖水溶性部分分离得到8 个三萜皂苷类化合物，通过红外、电喷雾质谱和核磁共振等现代谱学方法，并结合传统的化学手段鉴定了它们的结构，其中4 个化合物为新化合物，分别命名为多被银莲花皂苷19、多被银莲花皂苷20、多被银莲花皂苷21和多被银莲花皂苷22。从打破碗花花水溶性部位分离得到6 个三萜皂苷类化合物，通过现代谱学手段，并结合传统的化学方法对它们进行了鉴定，其中1 个为新化合物，命名为打破碗花花苷H。 第4 章报道了以银莲花素A 及其同系物为先导化合物，进行化学结构修饰并对修饰产物进行广泛的生物活性筛选，发现在银莲花素A 及其同系物的结构中引入一些酸性基团后，其生物活性发生了变化，一些修饰产物显示出很强的PTP-1B 抑制作用，提示这些化合物有可能用于治疗II 型糖尿病。 第5 章综述了电喷雾多级质谱用于皂苷类化合物结构鉴定的研究进展。 This dissertation composes of five chapters. The first chapter elaborates the detection and qualification of the triterpenoidal saponins in Anemone raddeana by positive and negative full scan ESI-MSn. This part also reports the special fragmentation pathway of Raddeanin A by ESI-MS/MS. The second and third chapters present the phytochemical investigation of two medicinal plants from Anemone. The fourth part dwells on the structure modification of Raddeanin A and their inhibitory activity against PTP-1B. The last part is a review on the progress in the application of ESI-MSn in the structure identification of saponins. The first chapter reports the application of full scan ESI-MSn for fast analysis of triterpenoid saponins in Anemone raddeana. Eighteen quasi- molecular ion peaks were detected in the positive full scan ESI-MS and fifteen of them were identified by analysis of their tandem mass spectral data in the negative ion mode. Several isomers were differentiated. More interesting, three unreported triterpenoid saponins in this medicinal plant were detected and their structures were deduced according to the dissociation pathway of the known triterpenoidal saponins. This chapter also confirms the special fragmentation pathway of Raddeanin A by its derivative and the mass spectral analysis. The second and third chapters expatiate on the isolation and identification of the chemical constituents from A. raddeana and A. hupehensis. Eight compounds were isolated from the roots and stems of A. raddeana by methanol extraction and repeated column chromatography (including D101 and silica gel), and their structures were determined on the basis of IR, ESI-MS, NMR and chemical methods (including acid hydrolysis and alkaline saponification). Among them, four are new triterpenoid saponins and named as Raddeanoside R19, Raddeanoside R20, Raddeanoside R21 and Raddeanoside R22. Six compounds were isolated from the whole plants of A. hupehensis by the same methods as above, and their structures were also determined with the same way. One of them was confirmed to be new triterpenoid saponins and named as hupehensis saponin H. In the fourth chapter, in order to look for new active compounds, the structure of Raddeanin A and its analogs were modified. It was found that the modified products exhibited obvious inhibitory activity against PTP-1B when several acid groups were introduced. The fifth chapter summarizes the progress on the application of ESI-MSn in the structure identification of saponins.

Entrance channel dependence of the correlation function of IMFs in Ar-36+Sn-112,Sn-124 at 35MeV/u

The reduced velocity correlation functions of the Intermediate Mass Fragments (IMFs) were measured in the reactions of Ar-36+ Sn-112,Sn-124 at 35MeV/u. The anti-correlation at small reduced velocities is more pronounced in Ar-36+ Sn-124 system than that in Ar-36+ Sn-112 system. The difference of the correlation functions between the two reactions is mainly contributed by the particle pairs with high momenta. A three-body Coulomb repulsive trajectory code (MENEKA) is employed to calculate the emission time scale of IMFs for-the both systems. The time scale is 150fm/c in the Ar-36+ Sn-112 system and 120fm/c in the Ar-36+ Sn-124 system, respectively. A calculation based on an Isospin dependence Quantum Molecular Dynamics code (IQMD) reveals that the emission time spectrum of IMFs is shifted slightly leftwards in Ar-36+ Sn-124 compared with that in the Ar-16+ Sn-112 system, indicating a shorter emission time scale. Correspondingly, the central density of the hot nuclei decreases faster in Ar-36+ Sn-124 than in Ar-36+ Sn-112

Investigation of two-proton emission from excited states of the odd-Z nucleus P-28 by complete-kinematics measurements

An experiment to study exotic two-proton emission from excited levels of the odd-Z nucleus P-28 was performed at the National Laboratory of Heavy Ion Research-Radioactive Ion Beam Line (HIRFL-RIBLL) facility. The projectile P-28 at the energy of 46.5 MeV/u was bombarding a Au-197 target to populate the excited states via Coulomb excitation. Complete-kinematics measurements were realized by the array of silicon strip detectors and the CsI + PIN telescope. Two-proton events were selected and the relativistic-kinematics reconstruction was carried out. The spectrum of relative momentum and opening angle between two protons was deduced from Monte Carlo simulations. Experimental results show that two-proton emission from P-28 excited states less than 17.0 MeV is mainly two-body sequential emission or three-body simultaneous decay in phase space. The present simulations cannot distinguish these two decay modes. No obvious diproton emission was found.

Charge transfer across the water/nitrobenzene interface by three-electrode system

A droplet of aqueous solution containing a certain molar ratio of redox couple is first attached onto a platinum electrode surface, then the resulting drop electrode is immersed into the organic solution containing very hydrophobic electrolyte. Combined with reference and counter electrodes, a classical three-electrode system has been constructed, Ion transfer (IT) and electron transfer (ET) are investigated systematically using three-electrode voltammetry. Potassium ion transfer and electron transfer between potassium ferricyanide in the aqueous phase and ferrocene in nitrobenzene are observed with potassium ferricyanide/potassium ferrocyanide as the redox couple. Meanwhile, the transfer reactions of lithium, sodium, potassium, proton and ammonium ions are obtained with ferric sulfate/ferrous sulfate as the redox couple. The formal transfer potentials and the standard Gibbs transfer energy of these ions are evaluated and consistent with the results obtained by a four-electrode system and other methods.