X-ray studies on crystalline complexes involving amino acids and peptides. XXXIII. Crystal structures of L- and DL-arginine complexed with oxalic acid and a comparative study of amino acid oxalic acid complexes

The DL- and L-arginine complexes of oxalic acid are made up of zwitterionic positively charged amino acid molecules and semi-oxalate ions. The dissimilar molecules aggregate into separate alternating layers in the former. The basic unit in the arginine layer is a centrosymmetric dimer, while the semi-oxalate ions form hydrogen-bonded strings in their layer. In the L-arginine complex each semi-oxalate ion is surrounded by arginine molecules and the complex can be described as an inclusion compound. The oxalic acid complexes of basic amino acids exhibit a variety of ionization states and stoichiometry. They illustrate the effect of aggregation and chirality on ionization state and stoichiometry, and that of molecular properties on aggregation. The semi-oxalate/oxalate ions tend to be planar, but large departures from planarity are possible. The amino acid aggregation in the different oxalic acid complexes do not resemble one another significantly, but the aggregation of a particular amino acid in its oxalic acid complex tends to have similarities with its aggregation in other structures. Also, semi-oxalate ions aggregate into similar strings in four of the six oxalic acid complexes. Thus, the intrinsic aggregation propensities of individual molecules tend to be retained in the complexes.

Study of Ion Transport in Lithium Perchlorate-Succinonitrile Plastic Crystalline Electrolyte via Ionic Conductivity and in Situ Cryo-Crystallography

Ion transport mechanism in lithium perchlorate (LiClO4)-succinonitrile (SN), a prototype of plastic crystalline soft matter electrolyte is discussed in the context of solvent configurational isomerism and ion solvation. Contributions of both solvent configurational isomerism and ion solvation are reflected in the activation energy for ion conduction in 0-1 M LiClO4-SN samples. Activation energy due to solvent configurational changes, that is, trans-gauche isomerism is observed to be a function of salt content and decreases in presence of salt (except at high salt concentrations, e.g. 1 M LiClO4-SN). The remnant contribution to activation energy is attributed to ion-association. The X-ray diffraction of single crystals obtained using in situ cryo-crystallography confirms directly the observations of the ionic conductivity measurements. Fourier transform infrared spectroscopy and NMR line width measurements provide additional support to our proposition of ion transport in the prototype plastic crystalline electrolyte.

Crystalline A-DNA: The X-Ray Analysis of the Fragment d(G-G-T-A-T-A-C-C)

An A-DNA type double helical conformation was observed in the single crystal X-ray structure of the octamer d(G-G-T-A-T-A-C-C), 1, and its 5-bromouracil-containing analogue, 2. The structure of the isomorphous crystals (space group P61) was solved by a search technique based on packing criteria and R-factor calculations, with use of only low order data. At the present stage of refinement the R factors are 31 % for 1 and 28 % for 2 at a resolution of 2.25 A (0.225 nm). The molecules interact through their minor grooves by hydrogen bonding and base to sugar van der Waals contacts. The stable A conformation observed in the crystal may have some structural relevance to promoter regions where the T-A-T-A sequence is frequently found.

Pressure transitions and electron transport behaviour of crystalline Se-Te alloys

Pressure transitions of Se-Te alloys have been studied over the entire range of compositions. Conductivities have also been measured as a function of temperature and alloy composition. Transition pressures, activation barriers and isothermal conductivities exhibit distinct changes of slope in their variation as a function of composition at about 8 at % of Te. Transition pressures change slope at not, vert, similar 35% Te also. An attempt has been made to explain these observations on the basis of the size effect of Te which, in turn, affects the electron energy dispersions in the band structure.

x-ray studies on crystalline complexes involving amino-acids and peptides .10. head-to-tail sequences in the crystal-structure of l-lysine acetate

l-Lysine acetate crystallises in the monoclinic space group P21 with a = 5.411 (1), b = 7.562(1), c= l2.635(2) Å and β = 91.7(1). The crystal structure was solved by direct methods and refined to an R value of 0.049 using the full matrix least squares method. The conformation and the aggregation of lysine molecules in the structure are similar to those found in the crystal structure of l-lysine l-aspartate. A conspicuous similarity between the crystal structures of l-arginine acetate and l-lysine acetate is that in both cases the strongly basic side chain, although having the largest pK value, interacts with the weakly acidic acetate group leaving the α-amino and the α-carboxylate groups to take part in head-to-tail sequences. These structures thus indicate that electrostatic effects are strongly modulated by other factors so as to give rise to head-to-tail sequences which have earlier been shown to be an almost universal feature of amino acid aggregation in the solid state.

Calorimetric, infrared and ESR studies of the plastically crystalline state of organic compounds

Enthalpy changes of the crystal-plastic and plastic-liquid transitions are related to the temperature range of stability of the plastic phase. Thermodynamics of the plastic state of binary mixtures have been examined. Infrared correlation times, τc, and activation energies have been measured for a few molecules in the plastic state. Molecular tumbling times, τt, have also been measured employing ESR spectra of a spin-probe. Plots of log τc(τt) 1/T are continuous through the plastic-liquid transition. Activation energies for molecular motion seem to vary in the same direction as the ΔH of the plastic-crystal transition. Infrared correlation times of solute molecules in binary solutions in the plastic and the liquid states show interesting variations with solute concentration.

X-ray Studies on Crystalline Complexes Involving Amino Acids and Peptides. XIII. Effect of Chirality on Molecular Aggregation: The Crystal Structures of L-Arginine D-Aspartate and L-Arginine D-Glutamate Trihydrate

The crystal structures of (1) L-arginine D-asparate, C6HIsN40~.C4H6NO4 [triclinic, P1, a=5.239(1), b=9.544(1), c=14.064(2)A, a=85"58(1), /3=88.73 (1), ~/=84.35 (1) °, Z=2] and (2) L-arginine D-glutamate trihydrate, C6H15N40~-.CsHsNO4.3H20 [monoclinic, P2~, a=9.968(2), b=4.652(1), c=19.930 (2) A, fl = 101.20 (1) °, Z = 2] have been determined using direct methods. They have been refined to R =0.042 and 0.048 for 2829 and 2035 unique reflections respectively [I>2cr(I)]. The conformations of the two arginine molecules in the aspartate complex are different from those observed so far in the crystal structures of arginine, its salts and complexes. In both complexes, the molecules are organized into double layers stacked along the longest axis. The core of each double layer consists of two parallel sheets made up of main-chain atoms, each involving both types of molecules. The hydrogen bonds within each sheet and those that interconnect the two sheets give rise to EL-, DD- and DE-type head-to-tail sequences. Adjacent double layers in (1) are held together by side-chain-side-chain interactions whereas those in (2) are interconnected through an extensive network of water molecules which interact with sidechain guanidyl and carboxylate groups. The aggregation pattern observed in the two LD complexes is fundamentally different from that found in the corresponding EL complexes.

An infrared spectroscopic study of the phase transitions of crystalline aromatic donor-acceptor complexes involving a pseudoplastic state

Variable temperature i.r. spectroscopic studies of weak pi-donor-pi-acceptor complexes in the crystalline state indicate that the complexes undergo order-disorder transitions, the disorder being caused by molecular motion. Thermodynamic data on the phase transitions along with the spectral data suggest that the high-temperature crystalline forms of the complexes are likely to be pseudoplastic.

X-ray studies on crystalline complexes involving amino acids and peptides. Part XIV: Closed conformation and head-to-tail arrangement in a new crystal form of L-histidine L-aspartate monohydrate

A new form of L-histidine L-aspartate monohydrate crystallizes in space group P22 witha = 5.131(1),b = 6.881(1),c= 18.277(2) Å,β= 97.26(1)° and Z = 2. The structure has been solved by the direct methods and refined to anR value of 0.044 for 1377 observed reflections. Both the amino acid molecules in the complex assume the energetically least favourable allowed conformation with the side chains staggered between the α-amino and α-scarboxylate groups. This results in characteristic distortions in some bond angles. The unlike molecules aggregate into alternating double layers with water molecules sandwiched between the two layers in the aspartate double layer. The molecules in each layer are arranged in a head-to-tail fashion. The aggregation pattern in the complex is fundamentally similar to that in other binary complexes involving commonly occurring L amino acids, although the molecules aggregate into single layers in them. The distribution of crystallographic (and local) symmetry elements in the old form of the complex is very different from that in the new form. So is the conformation of half the histidine molecules. Yet, the basic features of molecular aggregation, particularly the nature and the orientation of head-to-tail sequences, remain the same in both the forms. This supports the thesis that the characteristic aggregation patterns observed in crystal structures represent an intrinsic property of amino acid aggregation.

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.

A simulation study of the mixing, atomic flow and velocity profiles of crystalline materials during sliding

Self-contained Non-Equilibrium Molecular Dynamics (NEMD) simulations using Lennard-Jones potentials were performed to identify the origin and mechanisms of atomic scale interfacial behavior between sliding metals. The mixing sequence and velocity profiles were compared via MD simulations for three cases, viz.: sell-mated, similar and hard-softvcrystal pairs. The results showed shear instability, atomic scale mixing, and generation of eddies at the sliding interface. Vorticity at the interface suggests that atomic flow during sliding is similar to fluid flow under Kelvin-Helmholtz instability and this is supported by velocity profiles from the simulations. The initial step-function velocity profile spreads during sliding. However the velocity profile does not change much at later stages of the simulation and it eventually stops spreading. The steady state friction coefficient during simulation was monitored as a function of sliding velocity. Frictional behavior can be explained on the basis of plastic deformation and adiabatic effects. The mixing layer growth kinetics was also investigated.

Evidence of episodic brittle faulting in the cratonic part of the Peninsular India and its implications for seismic hazard in slow deforming regions

The region around Waclakkancheri, in the province of Kerala, India, which lies in the vicinity of Palghat-Cauvery ;hear zone (within the Precambrian crystalline terrain), has been a site of microseismic activity since 1989. Earlier studies had identified a prominent WNW-ESE structure overprinting on the E-W trending lineaments associated with Palghat-Cauvery shear zone. We have mapped this structure, located in a chamockite quarry near Desamangalam, Waclakkancheri, which we identify as a ca. 30 km-long south dipping reverse fault. This article presents the characteristics of this fault zone exposed on the exhumed crystalline basement and discusses its significance in understanding the earthquake potential of the region. This brittle deformation zone consists of fracture sets with small-scale displacement and slip planes with embedded fault gouges. The macroscopic as well as the microscopic studies of this fault zone indicate that it evolved through different episodes of faulting in the presence of fluids. The distinct zones within consolidated gouge and the cross cutting relationship of fractures indicate episodic fault activity. At least four faulting episodes can be recognized based on the sequential development of different structural elements in the fault rocks. The repeated ruptures are evident along this shear zone and the cyclic behavior of this fault consists of co-seismic ruptures alternating with inter-seismic periods, which is characterized by the sealed fractures and consolidated gouge. The fault zone shows a minimum accumulated dip/oblique slip of 2.1 m in the reverse direction with a possible characteristic slip of 52 cm (for each event). The ESR dating of fault gouge indicates that the deformation zone records a major event in the Middle Quaternary. The empirical relationships between fault length and slip show that this fault may generate events M >= 6. The above factors suggest that this fault may be characterized as potentially active. Our study offers some new pointers that can be used in other slow deforming cratonic hinterlands in exploring the discrete active faults.

Quasi Crystalline A1-Mn Alloys: Pressure Induced Crystallization and Structural Studies

Irreversible, Pressure induced, quasicrystal-to-crystal transitions are observed for the first time in melt spun alloys at 4.9 GPa for Al 78 Mn22 and 9.3 GPa for Al86 Mn14 by monitoring the electrical resistivities of these alloys as a function of pressure. Electron diffraction and x-ray measurements are used to show that these quasicrystalline phases have icosohedral point group symmetry. The crystalline phases which appear at high pressures are identified as h.c.p. for Al78 Mn22 and orthorhombic for Al86 Mn14.

High pressure induced crystallization of rapidly solidified Al---Fe and Al---Mn quasi-crystalline alloysstar

The presence of phases showing icosahedral point symmetry was reported by Shechtman, Blech, Gratias and Cahn in rapidly quenched alloys of Al---Mn, Al---Fe and Al---Cr, and subsequently many other splat-cooled alloys with the i phase have been reported. In this paper we present the first results of high pressure experiments carried out on Al---Fe and Al---Mn quasi-crystals. The experiments performed at room temperature showed irreversible quasi-crystal-to-crystal transitions in Al---Mn and Al---Fe alloys. The transition pressures are 49 kbar for Al78Mn22, 93 kbar for Al86Mn14, 79 kbar for Al86Fe14, 54 kbar for Al82Fe18 and 108 kbar for Al75Fe25. The high pressure phases are found to be the equilibrium phases.

Electrical transport in layered crystalline semiconductors GeS doped with Ag, P impurities at high pressure

A study of the transport properties of layered crystalline semiconductors GeS (undoped and doped with Ag, P impurity) under quasihydrostatic pressure using Bridgman anvil system is made for the first time. Pressure-induced effects in undoped crystals reveal initial rise in resistivity followed by two broad peaks at higher pressures. Silver doping induces only minor changes in the behaviour except removing the second peak. Phosphorous impurity is found to have drastic effect on the transport properties. Temperature dependence of the resistivity exhibits two activation energies having opposite pressure coefficients. Results are discussed in the light of intrinsic features of the layered semiconductors.