Role of molecular reorientation in the vitrification of molecular liquids: A Monte Carlo study of the liquid and glassy states of 2,2-dimethylbutane

The liquid and the glassy phases of 2,2-dimethylbutane have been investigated by isothermal isobaric ensemble Monte Carlo simulation. Thermodynamic Properties and radial distribution functions for both the liquid and the glass have been obtained. The radial distribution functions have been classified into three types based on the accessibility of the group. It has been shown that the structure of the Iiquid and the glass can be understood in terms of the above classification of the radial distribution functions. Molecular reorientation plays an important role in the structural rearrangement accompanying glass formation. As much as 35% of the contribution to the increase in the intermolecular interaction energy on vitrification is due to the reorientation of the neighbouring pairs of molecules. The observed changes in the dimerisation energy and the bonding energy distribution function are consistent with the observed structural changes.

Syntheses, spectroscopy, structures, and conformations of .lambda.3-cyclotriphosphazanes: role of negative hyperconjugation

The reactions of As-chlorocyclotriphosphazane [EtNPCl], with phenols or trifluoroethanol yield the respective aryloxy- or trifluoroethoxy-containingX 3-cyclotriphosphazanes [EtNP(OR)]3 (R = C6H4Br-4 (2),C 6H5 (3C,6 H3-Mez-3,5 (4), C6H3Mez-2,6 (5), CH2CF3 (6)) as their cis-transisomericmixtures. The products have beencharacterized by IRand NMRspectroscopy. Thecrystalstructuresofboth thecis (2a) and trans(2b) isomer_softhep-bromophenoxy derivative have been determined by X-ray diffraction. Crystal data for 2a: triclinic, P1, a = 9.872(4) A, b = 13.438(6) A, c = 13.548(8) A, CY = 117.02(5)', 0 = 96.00(6)', y = 105.38(4)O, Z = 2, final R = 0.080. Crystal data for 2b: monoclinic, P21/n, a = 12.721(6) A, b = 13.468(7) A, c = 17.882(5) A, /3 = 101.62(3)O, Z = 4, final R = 0.066. The cis isomer exhibits a chair-triaxial conformation and the trans isomer a boat-triaxial conformation. Conformational preferences of X3-cyclotriphosphazanes have been probed by both MNDO and ab initio calculations on model systems [HNPXIp (X = H, F). In addition to vicinal lone pair repulsions, negative hyperconjugative interactions involving the nitrogen lone pairs and adjacent P-X Q* orbitals are found to be important (especially when X is an electronegative substituent) in determining the conformational preferences of X3-cyclotriphosphazanes. The calculations also show that the axial - equatorial conversion at phosphorus has a large activation barrier in these systems

Synthesis, spectral characterisation and single-crystal structure of a bicyclic tetraphosphapentazane tetraoxide, N5P4ET5O4(OC6H3Me2-2,6)2

Reaction of the bicyclic phosphazane N5P4Et5Cl2 with 2,6-dimethylphenol and subsequent oxidation of the product by aqueous hydrogen peroxide yields N5P4Et5O4(OC6H3Me2-2,6)2 in 85% yield. Its structure has been established by NMR spectroscopy and single-crystal X-ray diffraction. The compound crystallises in the monoclinic space group C2/c with a= 21.245(5), b= 10.879(2), c= 16.450(6)Å, ?= 123.94(2)°, Z= 4, R= 0.066. The structural features are compared with those of bicyclic ?5-phosphazenes of type N5P4R3(NR1R2)5(NHR3)(R1,R3= Me or Et, R2= H or Me). The observed conformation of the N3P3 rings in the present compound is mainly dictated by the maximisation of the stabilising influence of �negative hyperconjugative interactions� between the nitrogen lone pairs and the adjacent P�X ?* orbitals.

Geometry and quadratic nonlinearity of charge transfer complexes in solution using depolarized hyper-Rayleigh scattering

We report large quadratic nonlinearity in a series of 1:1 molecular complexes between methyl substituted benzene donors and quinone acceptors in solution. The first hyperpolarizability, beta(HRS), which is very small for the individual components, becomes large by intermolecular charge transfer (CT) interaction between the donor and the acceptor in the complex. In addition, we have investigated the geometry of these CT complexes in solution using polarization resolved hyper-Rayleigh scattering (HRS). Using linearly (electric field vector along X direction) and circularly polarized incident light, respectively, we have measured two macroscopic depolarization ratios D = I-2 omega,I-X,I-X/I-2 omega,I-Z,I-X and D' = I-2 omega,I-X,I-C/I-2 omega,I-Z,I-C in the laboratory fixed XYZ frame by detecting the second harmonic scattered light in a polarization resolved fashion. The experimentally obtained first hyperpolarizability, beta(HRS), and the value of macroscopic depolarization ratios, D and D', are then matched with the theoretically deduced values from single and double configuration interaction calculations performed using the Zerner's intermediate neglect of differential overlap self-consistent reaction field technique. In solution, since several geometries are possible, we have carried out calculations by rotating the acceptor moiety around three different axes keeping the donor molecule fixed at an optimized geometry. These rotations give us the theoretical beta(HRS), D and D' values as a function of the geometry of the complex. The calculated beta(HRS), D, and D' values that closely match with the experimental values, give the dominant equilibrium geometry in solution. All the CT complexes between methyl benzenes and chloranil or 1,2-dichloro-4,5-dicyano-p-benzoquinone investigated here are found to have a slipped parallel stacking of the donors and the acceptors. Furthermore, the geometries are staggered and in some pairs, a twist angle as high as 30 degrees is observed. Thus, we have demonstrated in this paper that the polarization resolved HRS technique along with theoretical calculations can unravel the geometry of CT complexes in solution. (C) 2011 American Institute of Physics. doi:10.1063/1.3514922]

Amino acid selective unlabeling for sequence specific resonance assignments in proteins

Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative approach is the method of amino acid selective `unlabeling' or reverse labeling, which involves selective unlabeling of specific amino acid types against a uniformly C-13/N-15 labeled background. Based on this method, we present a novel approach for sequential assignments in proteins. The method involves a new NMR experiment named, {(CO)-C-12 (i) -N-15 (i+1)}-filtered HSQC, which aids in linking the H-1(N)/N-15 resonances of the selectively unlabeled residue, i, and its C-terminal neighbor, i + 1, in HN-detected double and triple resonance spectra. This leads to the assignment of a tri-peptide segment from the knowledge of the amino acid types of residues: i - 1, i and i + 1, thereby speeding up the sequential assignment process. The method has the advantage of being relatively inexpensive, applicable to H-2 labeled protein and can be coupled with cell-free synthesis and/or automated assignment approaches. A detailed survey involving unlabeling of different amino acid types individually or in pairs reveals that the proposed approach is also robust to misincorporation of N-14 at undesired sites. Taken together, this study represents the first application of selective unlabeling for sequence specific resonance assignments and opens up new avenues to using this methodology in protein structural studies.

On Two-User Gaussian Multiple Access Channels With Finite Input Constellations

Constellation Constrained (CC) capacity regions of two-user Single-Input Single-Output (SISO) Gaussian Multiple Access Channels (GMAC) are computed for several Non-Orthogonal Multiple Access schemes (NO-MA) and Orthogonal Multiple Access schemes (O-MA). For NO-MA schemes, a metric is proposed to compute the angle(s) of rotation between the input constellations such that the CC capacity regions are maximally enlarged. Further, code pairs based on Trellis Coded Modulation (TCM) are designed with PSK constellation pairs and PAM constellation pairs such that any rate pair within the CC capacity region can be approached. Such a NO-MA scheme which employs CC capacity approaching trellis codes is referred to as Trellis Coded Multiple Access (TCMA). Then, CC capacity regions of O-MA schemes such as Frequency Division Multiple Access (FDMA) and Time Division Multiple Access (TDMA) are also computed and it is shown that, unlike the Gaussian distributed continuous constellations case, the CC capacity regions with FDMA are strictly contained inside the CC capacity regions with TCMA. Hence, for finite constellations, a NO-MA scheme such as TCMA is better than FDMA and TDMA which makes NO-MA schemes worth pursuing in practice for two-user GMAC. Then, the idea of introducing rotations between the input constellations is used to construct Space-Time Block Code (STBC) pairs for two-user Multiple-Input Single-Output (MISO) fading MAC. The proposed STBCs are shown to have reduced Maximum Likelihood (ML) decoding complexity and information-losslessness property. Finally, STBC pairs with reduced sphere decoding complexity are proposed for two-user Multiple-Input Multiple-Output (MIMO) fading MAC.

Friction and wear behaviour of continuous fibre as cast Kevlar-phenolic resin composite

A compression moulded Kevlar-phenolic resin composite consisting of 30 wt% continuous fibres was slid against a steel disc such that the fibre axis was normal to the sliding plane. The sliding experiments were conducted in a normal pressure range of 0.47–4.27 MPa and at a sliding speed of 0.5 ms–1. The initial sliding interaction is abrasive. With further sliding, as patches of polymer transfer film develop on the polymer pin and counterface, the interaction becomes adhesive and steady-state friction is established. The wear resistance of the polymer was found to be related to the stability of this film.

Friction and wear of PTFE — a review

Polytetrafluoroethylene (PTFE) is an important engineering material. When rubbed or slid against a hard surface, PTFE exhibits a low coefficient of friction but a high rate of wear. These unique properties of the polymer have encouraged many mechanistic and physical examinations of the processes involved in the friction and wear of this polymer. A section of such work carried out over the past 30 years is reviewed here. When rubbed against a hard surface, the PTFE chain undergoes scission, creating active groups which chemically react with the counterface. This results in strong adhesion and a coherent transfer film. Further interaction between the bulk polymer and the transfer film gives rise to anisotropic deformation of the unit cell, which results in closeness of adjacent chains and easy shear between chains. Sliding brings about growth in as well as reorientation of crystallites situated in a very thin subsurface region of the bulk polymer. Such structural rearrangement facilitates the joining of adjacent aligned crystallites to form films and ribbons which emerge as debris.

Reactions of the hexachlorocyclodiphosphazane [MeNPCl3]2 with primary aromatic amines: formation of highly basic bisphosphinimines

Reactions of hexachlorocyclodiphosphazane [MeNPCl3]2 with primary aromatic amines afforded the bisphosphinimine hydrochlorides [(RNH)2(RN)PN(Me)P(NHMe)(NHR)2]+Cl- (R = Ph 1, C6H4Me-4 2 or C6H4OMe-4 3). Dehydrochlorination of 2 and 3 by methanolic KOH yielded highly basic bisphosphinimines [(RNH)2(RN)PN(Me)P(NMe)(NHR)2] (R = C6H4Me-4 4 or C6H4OMe-4 5). Compounds 1-5 have been characterised by elemental analysis and IR and NMR (H-1, C-13, P-31) spectroscopy. The structure of 2 has been confirmed by single-crystal X-ray diffraction. The short P-N bond lengths and the conformations of the PN, units can be explained on the basis of cumulative negative hyperconjugative interactions between nitrogen lone pairs and adjacent P-N sigma* orbitals. Ab initio calculations on the model phosphinimine (H2N)3P=NH and its protonated form suggest that (amino)phosphinimines would be stronger bases compared to many organic bases such as guanidine.

Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S

Two fragments of pancreatic ribonuclease A, a truncated version of S-peptide (residues 1-15) and S-protein (residues 21-124), combine to give a catalytically active complex. We have substituted the wild-type residue at position 13, methionine (Met), with norleucine (Nle), where the only covalent change is the replacement of the sulfur atom with a methylene group. The thermodynamic parameters associated with the binding of this variant to S-protein, determined by titration calorimetry in the temperature range 10-40 degrees C, are reported and compared to values previously reported [Varadarajan, R., Connelly, P. R., Sturtevant, J. M., & Richards, F. M. (1992) Biochemistry 31, 1421-1426] for other position 13 analogs. The differences in the free energy and enthalpy of binding between the Met and Nle peptides are 0.6 and 7.9 kcal/mol at 25 degrees C, respectively. These differences are slightly larger than, but comparable to, the differences in the values for the Met/Ile and Met/Leu pairs. The structure of the mutant complex was determined to 1.85 Angstrom resolution and refined to an R-factor of 17.4% The structures of mutant and wild-type complexes are practically identical although the Nle side chain has a significantly higher average B-factor than the corresponding Met side chain. In contrast, the B-factors of the atoms of the cage of residues surrounding position 13 are all somewhat lower in the Nle variant than in the Met wild-type. Thus, the large differences in the binding enthalpy appear to reside entirely in the difference in chemical properties or dynamic behavior of the -S- and -CH2- groups and not in differences in the geometry of the side chains or the internal cavity surface. In addition, a novel method of obtaining protein stability data by means of isothermal titration calorimetry is introduced.

Reversible Insertion of a Trivalent Cation onto MnO2 Leading to Enhanced Capacitance

Supercapacitor properties of MnO2 are studied generally in aqueous alkali metal salt solutions, often in a Na salt solution. During electrochemical discharge-charge processes, Na+ ions from the electrolyte get reversibly inserted/deinserted on the surface of MnO2 particles, which leads to redox reaction between MnOONa and MnO2. In the present study, it has been shown that MnO2 exhibits enhanced capacitance behaviour in a rare earth metal salt solution, namely, La(NO3)(3) solution in comparison with NaNO3 and Mg(NO3)(2) aqueous solutions. The specific capacitance increases with an increase in charge on the solution cation (Na+, Mg2+ and La3+). It is proposed that the number of surface sites for adsorption of cations remains unaltered in all solutions. The surface insertion of cation facilitates the reduction of Mn4+ in MnO2 to Mn3+ equivalent to the charge present on the cation. As the specific capacitance is related to the quantity of charge that is exchanged between the solid MnO2 and the aqueous solution, the trivalent cation (La3+) provides greater specific capacitance than in Mg(NO3)(2) and NaNO3 electrolytes. Accordingly, the number of Mn(IV)/Mn(III) redox pairs involved in the neighbourhood of the adsorption site is one, two and three when Na+, Mg2+ and La3+ ions, respectively, are adsorbed. (C) 2011 The Electrochemical Society. DOI: 10.1149/1.3565177] All rights reserved.

Design of logical topologies for wavelength-routed optical networks

his paper studies the problem of designing a logical topology over a wavelength-routed all-optical network (AON) physical topology, The physical topology consists of the nodes and fiber links in the network, On an AON physical topology, we can set up lightpaths between pairs of nodes, where a lightpath represents a direct optical connection without any intermediate electronics, The set of lightpaths along with the nodes constitutes the logical topology, For a given network physical topology and traffic pattern (relative traffic distribution among the source-destination pairs), our objective is to design the logical topology and the routing algorithm on that topology so as to minimize the network congestion while constraining the average delay seen by a source-destination pair and the amount of processing required at the nodes (degree of the logical topology), We will see that ignoring the delay constraints can result in fairly convoluted logical topologies with very long delays, On the other hand, in all our examples, imposing it results in a minimal increase in congestion, While the number of wavelengths required to imbed the resulting logical topology on the physical all optical topology is also a constraint in general, we find that in many cases of interest this number can be quite small, We formulate the combined logical topology design and routing problem described above (ignoring the constraint on the number of available wavelengths) as a mixed integer linear programming problem which we then solve for a number of cases of a six-node network, Since this programming problem is computationally intractable for larger networks, we split it into two subproblems: logical topology design, which is computationally hard and will probably require heuristic algorithms, and routing, which can be solved by a linear program, We then compare the performance of several heuristic topology design algorithms (that do take wavelength assignment constraints into account) against that of randomly generated topologies, as well as lower bounds derived in the paper.

Basis set dependence of the molecular electrostatic potential topography. A case study of substituted benzenes

The basis set dependence of the topographical structure of the molecular electrostatic potential (MESP), as well as the effect of substituents on the MESP distribution, has been investigated with substituted benzenes as test cases. The molecules are studied at HF-SCF 3�21G and 6�31G** levels, with a further MESP topographical investigation at the 3�21G, double-zeta, 6�31G*, 6�31G**, double-zeta polarized and triple-zeta polarized levels. The MESP critical points for a 3�21G optimized/6�31G** basis are similar to the corresponding 6�31G** optimized/6�31G** ones. More generally, the qualitative features of the MESP topography computed at the polarized level are independent of the level at which optimization is carried out. For a proper representation of oxygen lone pairs, however, optimization using a polarized basis set is required. The nature of the substituent drastically changes the MESP distribution over the phenyl ring. The values and positions of MESP minima indicate the most active site for electrophilic attack. This point is strengthened by a study of disubstituted benzenes.

Important role of the amino acid attached to tRNA in formylation and in initiation of protein synthesis in Escherichia coli

In attempts to convert an elongator tRNA to an initiator tRNA, we previously generated a mutant elongator methionine tRNA carrying an anticodon sequence change from CAU to CUA along with the two features important for activity of Escherichia coli initiator tRNA in initiation. This mutant tRNA (Mi:2 tRNA) was active in initiation in vivo but only when aminoacylated with methionine by overproduction of methionyl-tRNA synthetase. Here we show that the Mi:2 tRNA is normally aminoacylated in vivo with lysine and that the tRNA aminoacylated with lysine is a very poor substrate for formylation compared with the same tRNA aminoacylated with methionine. By introducing further changes at base pairs 4:69 and 5:68 in the acceptor stem of the Mi:2 tRNA to those found in the E. coli initiator tRNA, we show that change of the U4:A69 base pair to G4:C69 and overproduction of lysyl-tRNA synthetase and methionyl-tRNA transformylase results in partial formylation of the mutant tRNA and activity of the formyllysyl-tRNAs in initiation of protein synthesis. Thus, the G4:C69 base pair contributes toward formylation of the tRNA and protein synthesis in E. coli can be initiated with formyllysine. We also discuss the implications of these and other results on recognition of tRNAs by E. coli lysyl-tRNA synthetase and on competition in cells among aminoacyl-tRNA synthetases.

Microstructure of copolyperoxides of alpha-methylstyrene with styrene and methyl methacrylate

This paper reports a study on the microstructure of two series of copolyperoxides of alpha-methylstyrene, with styrene and with methylmethacrylate. The copolyperoxides were synthesized by the free radical-initiated oxidative copolymerization of the vinyl monomer pairs. The copolyperoxide compositions obtained from the H-1 and C-13 NMR spectra led to the determination of the reactivity ratios. The product of the reactivity ratios indicates that alpha-methylstyrene forms a block copolyperoxide with styrene and a random copolyperoxide with methylmethacrylate. Microstructural parameters like average sequence length, run number, etc. have been determined for the latter copolyperoxide from analysis of its C-13 NMR spectrum. The aromatic quaternary and carbonyl carbons were found to be sensitive to triad sequences. The end groups of the copolyperoxides have been identified by H-1 NMR as well as FTIR spectroscopic techniques. The thermal degradation of the copolyperoxides has been studied by differential scanning calorimetry, which confirms the alternating peroxide units in the copolyperoxide chain.