Stereochemistry of peptides containing 1-aminocyclopentane carboxylic acid (Acc5). Solution and solid state conformations of Boc-Acc5-Acc5-NHMe.

The conformational analysis of a protected homodipeptide of 1-aminocyclopentanecarboxylic acid (Acc5) has been carried out. 1H-nmr studies establish a ?-turn conformation for Boc-Acc5-Acc5-NHMe in chloroform and dimethylsulfoxide solutions involving the methylamide NH in an intramolecular hydrogen bond. Supportive evidence for the formation of an intramolecular hydrogen bond is obtained from ir studies. X-ray diffraction studies reveal a type III ?-turn conformation in the solid state stabilized by a 4 ? 1 hydrogen bond between the Boc CO and methylamide NH groups. The ?,? values for both Acc5 residues are close to those expected for an ideal 310-helical conformation (?? ± 60°, ?? ±30°).

Stereochemically constrained peptides. Theoretical and experimental studies on the conformations of peptides containing 1-aminocyclohexane carboxylic acid

Conformational energy calculations on the model system N-acetyl- 1 -aminocyclohexanecarboxylic acid N'methylamide (Ac-Acc6-NHMe), using an average geometry derived from 13 crystallographic observations, establish that the Acc6 residue is constrained to adopt conformations in the helical regions of In contrast, the a,a-dialkylated residue with linear hydrocarbon side chains, a,a-di-n-propylglycine favors fully extended backbone structures (6 1= $ = 180'). The crystal structures of two model peptides, Boc-(Acc6),-OMe (type 111 @-turn at -Acc6(1)-Acc6(2)-) and Boc-Pro-Acc6-Ala-OMe (type I1 P-turn at -Pro-Acc6-), establish that Acc6 residues can occupy either position of type 111 P-turns and the i + 2 position of type I1 @-turns. The stereochemical rigidity of these peptides is demonstrated in solution by NMR studies, which establish the presence of one intramolecular hydrogen bond in each peptide in CDCI, and (CDJ2S0. Nuclear Overhauser effects permit characterization of the @-turn conformations in solution and establish their similarity to the solid-state structures. The implications for the use of Acc6 residues in conformational design are considered.

Conformations of dehydrophenylalanine containing peptides. NMR studies on three tripeptides with a central dehydrophenylalanyl residue.

Three tripeptides containing a central Z-dehydrophenylalanine residue (Δz-Phe), Boc-L-Phe-Δz-Phe-X-OMe (X = L-Val 1, L-Leu 2 and X = L-Ala 3) have been synthesized and their solution conformations investigated by 270 MHz 1H NMR spectroscopy. In all three peptides, conformations involving the X residue NH in an intramolecular hydrogen bond were favoured in CDCl3 solutions. Studies of the nuclear Overhauser effect (NOE) provided support for a Type II β turn conformation in these peptides with Phe and Δz-Phe occupying the i + 1 and i + 2 positions, respectively. Significantly different conformations lacking any intramolecular hydrogen bonds were observed for peptide 1 in (CD3)2SO. NOE results were consistent with a significant population of molecules having semi-extended conformations (ø > 100°) at the Δz-Phe residue.

A MAS NMR investigation of aluminosilicate, silicophosphate, and aluminosilicophosphate gels and the evolution of crystalline structures on heating the gels

Gels of various composition containing SiO2, Al2O3, and P2O5 have been investigated by employing high resolution magic-angle-spinning (MAS) 27Al, 29Si, and 31P NMR spectroscopy. Changes occurring in the NMR spectra as the gels are progressively heated have been examined to understand the nature of structural changes occurring during the crystallization of the gels. 27Al resonance is sensitive to changes in the coordination number even when the Al concentration is as low as 1 mol%. As the percentage of Al increases, the hydroxyl groups tend to be located on the Al sites while Si remains as SiO4/2 (Q4). Mullite is the major phase formed at higher temperature in the aluminosilicate gels. In the case of the silicophosphate gels, Si is present in the form of Q4 and Q3 species. There is a change in the coordination of Si from four to six as the gel is heated. The formation of six-coordinated Si is facilitated even at lower temperatures (~673 K) when the P2O5 content is high. The phosphorus atoms present as orthophosphoric acid units in the xerogels change over to metaphosphate-like units as the gel is heated to higher temperatures. In aluminosilicophosphates, Si is present as Q4 and Q3 species while P is present as metaphosphate units; Al in these gels seems to be inducted into the tetrahedral network positions.

A molecular dynamics study of cage-to-cage migration in sodium Y zeolite: role of surface-mediated diffusion

The details of cage-to-cage migration have been obtained from an analysis of the molecular dynamics trajectory of a probe adsorbate. It is observed that particles utilize the region within a radius of 2 angstrom from the window center but with diffusion taking place predominantly at 1.6 angstrom from the window center and a potential energy of nearly -12 kJ/mol. A barrier of about 0.5 kJ/mol is observed for surface-mediated diffusion. Surprisingly, for diffusion without surface mediation for a particle going from one cage center to another, there is an attractive well near the window instead of a barrier. At low adsorbate concentrations and room temperature, the predominant mode for cage-to-cage migration is surface-mediated diffusion. The analysis suggests that particles slide along the surface of the inner walls of the alpha-cages during migration from one cage to another.

Diffusion coefficients for selected binary liquid systems: cyclohexanes and n-alkyl alcohols

In the present work the integral diffusion coefficients are estimated by using the diaphragm cell technique. The diffusion coefficients are measured at various compositions for two sets binary systems: one of cyclohexane and n-paraffinic alcohols and the other of methylcyclohexane and n-paraffinic alcohols. The alcohols used are seven members of homologous series of n-paraffinic alcohols from ethanol to octanol. The maximum possible error in the experimental diffusion coefficient could be 8% for both the cyclohexane-n-alkyl alcohol system and methylcyclohexane-n-alkyl alcohol system. A correlation for each of the two sets of binary systems is given. The maximum deviation in the correlations was less than 6.5 and 3.5% for cyclohexane-n-alkyl alcohols and methylcyclohexane-n-alkyl alcohols, respectively.

Mutual diffusion coefficients of some binary liquid systems: benzene-n-alkyl alcohol

The mutual diffusion coefficients for binary liquid systems of benzene-n-alkyl alcohol at various compositions have been determined by the diaphragm cell method at 28-degrees-C. The alcohols used were the members of n-paraffinic alcohols ranging from C1 to C8. The maximum possible experimental error is 14%. The data were fitted with a generalized correlation, giving the deviation from the experimental data to within 2.75%, on average.

On the models for deuterium long-range isotope effects in13C NMR spectroscopy

The long-range deuterium isotope effects on13C nuclear shielding are physically not yet completely understood. Two existing models for explaining these effects, vibrational and substituent, are compared here. The vibrational model is based on the Born-Oppenheimer approximation, but it can explain only one-bond deuterium effects. To the contrary, the substituent model may explain many long-range isotope effects, but it is controversial due to the assumption of some distinct electronic properties of isotopes. We explain how long-range deuterium isotope effects may be rationalized by the subtle electronic changes induced by isotope substitution, which does not violate the Born-Oppenheimer approximation.

Optimization of two-dimensional NMR by matched accumulation

It is well known that in the time-domain acquisition of NMR data, signal-to-noise (S/N) improves as the square root of the number of transients accumulated. However, the amplitude of the measured signal varies during the time of detection, having a functional form dependent on the coherence detected. Matching the time spent signal averaging to the expected amplitude of the signal observed should also improve the detected signal-to-noise. Following this reasoning, Barna et al. (J Magn. Reson.75, 384, 1987) demonstrated the utility of exponential sampling in one- and two-dimensional NMR, using maximum-entropy methods to analyze the data. It is proposed here that for two-dimensional experiments the exponential sampling be replaced by exponential averaging. The data thus collected can be analyzed by standard fast-Fourier-transform routines. We demonstrate the utility of exponential averaging in 2D NOESY spectra of the protein ubiquitin, in which an enhanced SIN is observed. It is also shown that the method acquires delayed double-quantum-filtered COSY without phase distortion.

Protonic conductivity of (NH4) 4Fe(CN)6·1.5H2O by complex admittance method

The protonic conductivity of ammonium ferrocyanide hydrate has been studied by the complex admittance method. The admittance plots show departures from ideal Debye behaviour. The values of ionic conductivity (sigma = 3.7 X 10(-5) (OMEGA-cm)-1) and diffusion coefficient (D = 3.8 X 10(-10) cm2/s) obtained at room temperature are consistent with the corresponding values estimated by an earlier NMR study.

Studies of phosphazenes. Part 33. Thermal rearrangement of alkoxy(p-methylphenoxy)cyclophosphazenes: a synthetic route to oxocyclophosphazanes, phosphazadienes and phosphaz-1-enes

The aryloxy(alkoxy)cyclotriphosphazenes N3P3(OR)6�m(OC6H4Me-p)n(R = Me, n= 1�3; R = Et or CH2Ph, n= 3) rearrange on heating to give trioxocyclotriphosphazanes; the di- and mono-methoxy derivatives, N3P3(OMe)6�n(OC6H4Me-p)n(n= 4 or 5), yield dioxophosphaz-1-enes and an oxophosphazadiene respectively. The 1H, 13C and 31P NMR data for the starting materials and the products are presented. No evidence has been found for partially rearranged products. The geometrical disposition of the aryloxy groups in the starting material is retained in the rearranged products. Some aspects of the mechanism of the thermal rearrangement are discussed.

Temperature and concentration dependence of adsorption properties of methane in NaY: a molecular dynamics study

Molecular dynamics calculations on methane sorbed in NaY (Si/Al = 3.0) employing realistic methane-methane and methane-zeolite intermolecular potential functions at different temperatures (50, 150, 220, and 300 K) and concentrations (2, 4, 6, and 8 molecules/cage) are reported. The thermodynamic results are in agreement with the available experimental data. Guest-guest and guest-host radial distribution functions (rdfs), energy distribution functions, distribution of cage occupancy, center-of-cage-center-of-mass (coc-com) rdfs, velocity autocorrelation functions for com and angular motion and the Fourier transformed power spectra, and diffusion coefficients are presented as a function of temperature and concentration. At 50 K, methane is localized near the adsorption site. Site-site migration and essentially free rotational motion are observed at 150 K. Molecules preferentially occupy the region near the inner surface of the alpha-cage. The vibrational frequencies for the com of methane shift toward higher values with decreasing temperature and increasing adsorbate concentration. The observed frequencies for com motion are 36, 53, and 85 cm-1 and for rotational motion at 50 K, 95 and 150 cm-1 in agreement with neutron scattering data. The diffusion coefficients show a type I behavior as a function of loading in agreement with NMR measurements. Cage-to-cage diffusion is found to be always mediated by the surface.

Large-amplitude chirped coherent phonons in tellurium mediated by ultrafast photoexcited carrier diffusion

We report femtosecond time-resolved reflectivity measurements of coherent phonons in tellurium performed over a wide range of temperatures (3-296 K) and pump-laser intensities. A totally symmetric A(1) coherent phonon at 3.6 THz responsible for the oscillations in the reflectivity data is observed to be strongly positively chirped (i.e., phonon time period decreases at longer pump-probe delay times) with increasing photoexcited carrier density, more so at lower temperatures. We show that the temperature dependence of the coherent phonon frequency is anomalous (i.e, increasing with increasing temperature) at high photoexcited carrier density due to electron-phonon interaction. At the highest photoexcited carrier density of (1.4 x 10(21) cm(-3) and the sample temperature of 3 K, the lattice displacement of the coherent phonon mode is estimated to be as high as similar to 0.24 angstrom. Numerical simulations based on coupled effects of optical absorption and carrier diffusion reveal that the diffusion of carriers dominates the nonoscillatory electronic part of the time-resolved reflectivity. Finally, using the pump-probe experiments at low carrier density of 6 x 10(18) cm(-3), we separate the phonon anharmonicity to obtain the electron-phonon coupling contribution to the phonon frequency and linewidth.

Impurity diffusion in bismuth single-crystals

Measurements of impurity diffusion of 86Rb, 90Sr, 133Ba, and 137Cs in single crystal Bi were carried out. Diffusion samples were prepared from single crystal Bi by ion implantation. About 1012-1013 ions were implanted, resulting in surface activities approx =104 cpm. After implantation, specimens were annealed for specified times at 220-265 deg C, and tracer penetration profiles were determined by an electrolytic method. A typical penetration profile for 137Cs in Bi showed a linear relationship for log C vs x in with Fick's law for volume diffusion. Laws of grain boundary diffusion were not obeyed and the order of magnitude of the penetration distances was much less than on a grain boundary mechanism. Results were interpreted in terms of a modified Fischer analysis using a kinetic trapping term. Effective half lengths for trapping at a twin boundary were determined for each impurity.

An Investigation Of Alkali Aluminosilicate Glasses By Si-29 And Al-27 Magic-Angle-Spinning Nmr-Spectroscopy

Alkali aluminosilicate glasses prepared by the gel and the melt routes have been investigated by Si-29 and Al-27 MAS NMR spectroscopy. It is found that Al has a tetrahedral coordination in the gel glasses modified with equivalent proportions of alkalis unlike in a pure aluminosilicate glass where Al has both four and six coordinations. Silicon is present as Q4 units in all the 5M2O 5Al2O3 9OSiO2 ( M = Li, Na and K) gel glasses studied whereas it is present in Q2 or Q3 species in the lithium aluminosilicate glasses of compositions 40Li2O x Al2O3 (1-x)SiO2 (1 less-than-or-equal-to x less-than-or-equal-to 15) and xLi2O 10Al2O3 (1-x)SiO2 (20 less-than-or-equal-to x less-than-or-equal-to 40). The combination of Q2 and Q3 is also found in certain sodium aluminosilicate glasses, but they change to Q2 and Q1 as the concentration of SiO2 decreases.