How does contrasting dependence of impurity-atom diffusivity on the density of host disordered medium arise?

We report results of molecular dynamics investigations into neutral impurity diffusing within an amorphous solid as a function of the size of the diffusant and density of the host amorphous matrix. We find that self diffusivity exhibits an anomalous maximum as a function of the size of the impurity species. An analysis of properties of the impurity atom with maximum diffusivity shows that it is associated with lower mean square force, reduced backscattering of velocity autocorrelation function, near-exponential decay of the intermediate scattering function (as compared to stretched-exponential decay for other sizes of the impurity species) and lower activation energy. These results demonstrate the existence of size-dependent diffusivity maximum in disordered solids. Further, we show that the diffusivity maximum is observed at lower impurity diameters with increase in density. This is explained in terms of the Levitation parameter and the void structure of the amorphous solid. We demonstrate that these results imply contrasting dependence of self diffusivity (D) on the density of the amorphous matrix, p. D increases with p for small sizes of the impurity but shows an increase followed by a decrease for intermediate sizes of the impurity atom. For large sizes of the impurity atom, D decreases with increase in p. These contrasting dependence arises naturally from the existence of Levitation Effect.

Dipolar reorientation and phase-transition in mixed alkali-halide crystals

We show that the results of Lüty and Ortiz-Lopez relating the cyanide reorientation rates to the high-temperature phase diagrams of alkali-halide-alkali-cyanide mixed crystals can be understood within simple mean-field theory.

Adsorption isotherms for neutral organic compounds - A hierarchy in modelling: Part V. Models for the inner layer potential difference in the presence of dipolar adsorption

The relations for the inner layer potential &fference (E) in the presence of adsorbed orgamc molecules are derived for three hterarchlcal models, m terms of molecular constants like permanent &pole moments, polarlzablhtles, etc It is shown how the experimentally observed patterns of the E vs 0 plots (hnear m all ranges of $\sigma^M$, non-linear in one or both regions of o M, etc ) can be understood in a serm-quantltatlve manner from the simplest model in our hierarchy, viz the two-state site panty version Two-state multi-site and three-state (sxte panty) models are also analysed and the slope (3E/80),,M tabulated for these also The results for the Esm-Markov effect are denved for all the models and compared with the earlier result of Parsons. A comparison with the GSL phenomenologlcal equation is presented and its molecular basis, as well as the hmltatlons, is analysed. In partxcular, two-state multa-slte and three-state (site panty) models yield E-o M relations that are more general than the "umfied" GSL equation The posslblhty of vaewlng the compact layer as a "composite medium" with an "effective dlelectnc constant" and obtaimng novel phenomenological descnptions IS also indicated.

Direct estimation of an element of order matrix from H-1 NMR spectra of strongly dipolar coupled spins

NMR spectra of molecules oriented in thermotropic liquid crystalline media provide information on the molecular structure and order. The spins are generally strongly dipolar coupled and the spectral analyse require the tedious and time consuming numerical iterative calculations. The present study demonstrates the application of multiple quantum spin state selective detection of single quantum transitions for mimicking the homonuclear decoupling and the direct estimation of an element of ordering matrix. This information is utilized to estimate the nearly accurate starting dipolar couplings for iterative calculations. The studies on the spectra of strongly dipolar coupled five and six interacting spin systems are reported.

A 13C-NMR study of non-planar distortions in amides

The technique of 13C-NMR spectroscopy of oriented systems to problems of biological importance has been suggested and used to investigate non-planar distortions in substituted amides—models for peptides. The studies in conjunction with the proton magnetic resonance data on 5N-[13C]methyl[13C]formamide oriented in a nematic solvent provide all the direct dipolar couplings between the interacting nuclei in the system. When the 13C- and the 1H-NMR experiments are performed under non-identical conditions, 22 different direct dipolar couplings are obtained. It is demostrated that they can be used to determine unambiguously non-planar distortions around the nitrogen atom together with other geometrical data and the molecular order.

X-Ray Structure Of A Ternary Metal-Complex - Copper(Ii) Inosine 5'-Monophosphate Imidazole - Metal-Binding To The N(7) Atom Of The Nucleotide In A Mixed-Ligand System Containing An Aromatic Amine

A ternary metal-nucleotide complex, Na2[Cu(5’-IMP)2(im)o,8(H20)l,2(H20)2h]as~ 1be2e.n4 pHr2ep0a,r ed and its structure analyzed by X-ray diffraction (5’-IMP = inosine 5’-monophos hate; im = imidazole). The complex crystallizes in space group C222, with a = 8.733 (4) A, b = 23.213 (5) A, c = 21.489 (6) 1, and Z = 4. The structure was solved by the heavy-atom method and refined by full-matrix least-squares technique on the basis of 2008 observed reflections to a final R value of 0.087. Symmetry-related 5’-IMP anions coordinate in cis geometry through the N(7) atoms of the bases. The other cis positions of the coordination plane are statistically occupied by nitrogen atoms of disordered im groups and water oxygens with occupancies 0.4 and 0.6, respectively. Water oxygens in axial positions complete the octahedral coordination of Cu(I1). The complex is isostructural with C~S-[P~(S’-IMP),(NH~)~a] m”,o del proposed for Pt(I1) binding to DNA. The base binding observed in the present case is different from the typical ”phosphate only” binding shown from earlier studies on metal-nucleotide complexes containing various other ?r-aromatic amines.

In vitro demonstration of the heavy-atom effect for photodynamic therapy

Photodynamic therapy (PDT) is an emerging treatment modality for a range of disease classes, both cancerous and noncancerous. This has brought about an active pursuit of new PDT agents that can be optimized for the unique set of photophysical characteristics that are required for a successful clinical agent. We now describe a totally new class of PDT agent, the BF2-chelated 3,5-diaryl-1H-pyrrol-2-yl-3,5-diarylpyrrol-2-ylideneamines (tetraarylazadipyrromethenes). Optimized synthetic procedures have been developed to facilitate the generation of an array of specifically substituted derivatives to demonstrate how control of key therapeutic parameters such as wavelength of maximum absorbance and singlet-oxygen generation can be achieved. Photosensitizer absorption maxima can be varied within the body's therapeutic window between 650 and 700 nm, with high extinction coefficients ranging from 75,000 to 85,000 M(-1) cm(-1). Photosensitizer singlet-oxygen generation level was modulated by the exploitation of the heavy-atom effect. An array of photosensitizers with and without bromine atom substituents gave rise to a series of compounds with varying singlet-oxygen generation profiles. X-ray structural evidence indicates that the substitution of the bromine atoms has not caused a planarity distortion of the photosensitizer. Comparative singlet-oxygen production levels of each photosensitizer versus two standards demonstrated a modulating effect on singlet-oxygen generation depending upon substituent patterns about the photosensitizer. Confocal laser scanning microscopy imaging of 18a in HeLa cervical carcinoma cells proved that the photosensitizer was exclusively localized to the cellular cytoplasm. In vitro light-induced toxicity assays in HeLa cervical carcinoma and MRC5-SV40 transformed fibroblast cancer cell lines confirmed that the heavy-atom effect is viable in a live cellular system and that it can be exploited to modulate assay efficacy. Direct comparison of the efficacy of the photosensitizers 18b and 19b, which only differ in molecular structure by the presence of two bromine atoms, illustrated an increase in efficacy of more than a 1000-fold in both cell lines. All photosensitizers have very low to nondeterminable dark toxicity in our assay system.

Structure and Dynamics of Coil-like Molecules by Residual Dipolar Couplings

Nuclear magnetic resonance (NMR) spectroscopy provides us with many means to study biological macromolecules in solution. Proteins in particular are the most intriguing targets for NMR studies. Protein functions are usually ascribed to specific three-dimensional structures but more recently tails, long loops and non-structural polypeptides have also been shown to be biologically active. Examples include prions, -synuclein, amylin and the NEF HIV-protein. However, conformational preferences in coil-like molecules are difficult to study by traditional methods. Residual dipolar couplings (RDCs) have opened up new opportunities; however their analysis is not trivial. Here we show how to interpret RDCs from these weakly structured molecules. The most notable residual dipolar couplings arise from steric obstruction effects. In dilute liquid crystalline media as well as in anisotropic gels polypeptides encounter nematogens. The shape of a polypeptide conformation limits the encounter with the nematogen. The most elongated conformations may come closest whereas the most compact remain furthest away. As a result there is slightly more room in the solution for the extended than for the compact conformations. This conformation-dependent concentration effect leads to a bias in the measured data. The measured values are not arithmetic averages but essentially weighted averages over conformations. The overall effect can be calculated for random flight chains and simulated for more realistic molecular models. Earlier there was an implicit thought that weakly structured or non-structural molecules would not yield to any observable residual dipolar couplings. However, in the pioneering study by Shortle and Ackerman RDCs were clearly observed. We repeated the study for urea-denatured protein at high temperature and also observed indisputably RDCs. This was very convincing to us but we could not possibly accept the proposed reason for the non-zero RDCs, namely that there would be some residual structure left in the protein that to our understanding was fully denatured. We proceeded to gain understanding via simulations and elementary experiments. In measurements we used simple homopolymers with only two labelled residues and we simulated the data to learn more about the origin of RDCs. We realized that RDCs depend on the position of the residue as well as on the length of the polypeptide. Investigations resulted in a theoretical model for RDCs from coil-like molecules. Later we extended the studies by molecular dynamics. Somewhat surprisingly the effects are small for non-structured molecules whereas the bias may be large for a small compact protein. All in all the work gave clear and unambiguous results on how to interpret RDCs as structural and dynamic parameters of weakly structured proteins.

Unusual Anisotropic Effects from 1,3-Dipolar Cycloadducts of 4-Azidomethyl Coumarins

4-Bromomethylcoumarins (1) reacted with sodium azide in aqueous acetone to give 4-azidomethyl-coumarins (2), which underwent 1,3-dipolar cycloaddition with acetylenic dipolarophiles to give triazoles (3). These triazoles (3) have been found to exhibit interesting variations in the chemical shifts of C-3-H and C-4-methylene protons. Protonation studies indicate that the shielding effect of the C-3-H of coumarin is due to pi-electrons of the triazole ring, further supported by diffraction and computational studies.

Expanding the Peptide beta-Turn in alpha gamma Hybrid Sequences: 12 Atom Hydrogen Bonded Helical and Hairpin Turns

Hybrid peptide segments containing contiguous alpha and gamma amino acid residues can form C-12 hydrogen bonded turns which may be considered as backbone expanded analogues of C-10 beta-turns) found in alpha alpha segments. Exploration of the regular hydrogen bonded conformations accessible for hybrid alpha gamma sequences is facilitated by the use of a stereochemically constrained gamma amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn), in which the two torsion angles about C-gamma-C-beta (theta(1)) and C-beta-C-alpha (theta(2)) are predominantly restricted to gauche conformations. The crystal structures of the octapeptides Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (1) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (2) reveal two distinct conformations for the Aib-Gpn segment. Peptide 1 forms a continuous helix over the Aib(2)-Aib(6) segment, while the peptide 2 forms beta-hairpin structure stabilized by four cross-strand hydrogen bonds with the Aib-Gpn segment forming a nonhelical C-12 turn. The robustness of the helix in peptide 1 in solution is demonstrated by NMR methods. Peptide 2 is conformationally fragile in solution with evidence of beta-hairpin conformations being obtained in methanol. Theoretical calculations permit delineation of the various C-12 hydrogen bonded structures which are energetically feasible in alpha gamma and gamma alpha sequences.

Dynamic nature of proteins - interpretation of residual dipolar couplings

Protein conformations and dynamics can be studied by nuclear magnetic resonance spectroscopy using dilute liquid crystalline samples. This work clarifies the interpretation of residual dipolar coupling data yielded by the experiments. It was discovered that unfolded proteins without any additional structure beyond that of a mere polypeptide chain exhibit residual dipolar couplings. Also, it was found that molecular dynamics induce fluctuations in the molecular alignment and doing so affect residual dipolar couplings. The finding clarified the origins of low order parameter values observed earlier. The work required the development of new analytical and computational methods for the prediction of intrinsic residual dipolar coupling profiles for unfolded proteins. The presented characteristic chain model is able to reproduce the general trend of experimental residual dipolar couplings for denatured proteins. The details of experimental residual dipolar coupling profiles are beyond the analytical model, but improvements are proposed to achieve greater accuracy. A computational method for rapid prediction of unfolded protein residual dipolar couplings was also developed. Protein dynamics were shown to modulate the effective molecular alignment in a dilute liquid crystalline medium. The effects were investigated from experimental and molecular dynamics generated conformational ensembles of folded proteins. It was noted that dynamics induced alignment is significant especially for the interpretation of molecular dynamics in small, globular proteins. A method of correction was presented. Residual dipolar couplings offer an attractive possibility for the direct observation of protein conformational preferences and dynamics. The presented models and methods of analysis provide significant advances in the interpretation of residual dipolar coupling data from proteins.

Single atom (Pd/Pt) supported on graphitic carbon nitride as efficient photocatalyst for visible-light reduction of carbon dioxide

Reducing carbon dioxide (CO2) to hydrocarbon fuel with solar energy is significant for high-density solar energy storage and carbon balance. In this work, single palladium/platinum (Pd/Pt) atoms supported on graphitic carbon nitride (g-C3N4), i.e. Pd/g-C3N4 and Pt/g-C3N4, acting as photocatalysts for CO2 reduction were investigated by density function theory (DFT) calcu-lations for the first time. During CO2 reduction, the individual metal atoms function as the active sites, while g-C3N4 provides the source of hydrogen (H*) from hydrogen evolution reaction. The complete, as-designed photocatalysts exhibit excellent activity in CO2 reduction. HCOOH is the preferred product of CO2 reduction on the Pd/g-C3N4 catalyst with a rate-determining barrier of 0.66 eV, while the Pt/g-C3N4 catalyst prefers to reduce CO2 to CH4 with a rate-determining barrier of 1.16 eV. In addition, depositing atom catalysts on g-C3N4 significantly enhances the visible light absorption, rendering them ideal for visible light reduction of CO2. Our findings open a new avenue of CO2 reduction for renewable energy supply.

The effect of halogen atom on the molecular quadratic nonlinearity of half sandwich complexes in the presence of an acceptor

Half sandwich complexes of the type [CpM(CO)(n)X] {X=Cl, Br, I; If, M=Fe, Ru; n=2 and if M=Mo; n=3} and [CpNiPPh3X] {X=Cl, Br, I} have been synthesized and their second order molecular nonlinearity (beta) measured at 1064 nm in CHCl3 by the hyper-Rayleigh scattering technique. Iron complexes consistently display larger beta values than ruthenium complexes while nickel complexes have marginally larger beta values than iron complexes. In the presence of an acceptor ligand such as CO or PPh3, the role of the halogen atom is that of a pi donor. The better overlap of Cl orbitals with Fe and Ni metal centres make Cl a better pi donor than Br or I in the respective complexes. Consequently, M-pi interaction is stronger in Fe/Ni-Cl complexes. The value of beta decreases as one goes down the halogen group. For the complexes of 4d metal ions where the metal-ligand distance is larger, the influence of pi orbital overlap appears to be less important, resulting in moderate changes in beta as a function of halogen substitution. (C) 2006 Elsevier B.V. All rights reserved.