Investigating Diproline Segments in Proteins: Occurrences, Conformation and Classification

The covalent linkage between the side-chain and the backbone nitrogen atom of proline leads to the formation of the five-membered pyrrolidine ring and hence restriction of the backbone torsional angle phi to values of -60 degrees +/- 30 degrees for the L-proline. Diproline segments constitute a chain fragment with considerably reduced conformational choices. In the current study, the conformational states for the diproline segment ((L)Pro-(L)Pro) found in proteins has been investigated with an emphasis on the cis and trans states for the Pro-Pro peptide bond. The occurrence of diproline segments in turns and other secondary structures has been studied and compared to that of Xaa-Pro-Yaa segments in proteins which gives us a better understanding on the restriction imposed on other residues by the diproline segment and the single proline residue. The study indicates that P(II)-P(II) and P(II)-alpha are the most favorable conformational states for the diproline segment. The analysis on Xaa-Pro-Yaa sequences reveals that the XaaPro peptide bond exists preferably as the trans conformer rather than the cis conformer. The present study may lead to a better understanding of the behavior of proline occurring in diproline segments which can facilitate various designed diproline-based synthetic templates for biological and structural studies. (C) 2011 Wiley Periodicals, Inc. Biopolymers 97: 54-64, 2012.

Phenylboronic acids in crystal engineering: Utility of the energetically unfavorable syn,syn-conformation in co-crystal design

Phenylboronic acids can exist, in principle, in three different conformers (syn,syn; syn,anti and anti,anti) with distinct energy profiles. In their native state, these compounds prefer the energetically favored syn, anti-conformation. In molecular complexes, however, the functionality exhibits conformational diversity. In this paper we report a series of co-crystals, with N-donor compounds, prepared by a design strategy involving the synthons based on the syn, syn-conformation of the boronic acid functionality. For this purpose, we employed compounds with the 1,2-diazo fragment (alprazolam, 1H-tetrazole, acetazolamide and benzotriazole), 1,10-phenanthroline and 2,2'-bipyridine for the co-crystallization experiments. However, our study shows that the mere presence of the 1,2-diazo fragment in the coformer does not guarantee the successful formation of co-crystals with a syn, syn-conformation of the boronic acid. [GRAPHICS] The -B(OH)(2) fragment makes unsymmetrical O-H center dot center dot center dot N heterosynthons with alprazolam (ALP) and 1,10-phenanthroline (PHEN). In the co-crystals of phenylboronic acids with 1H-tetrazole (TETR) and 2,2'-bipyridine (BPY), the symmetrical boronic acid dimer is the major synthon. In the BPY complex, boronic acid forms linear chains and the pyridine compound interacts with the lateral OH of boronic acid dimers that acts as a connector, thus forming a ladder structure. In the TETR complex, each heterocycle interacts with three boronic acids. While two boronic acids interact using the phenolic group, the third molecule generates O-H center dot center dot center dot N hydrogen bonds using the extra OH group, of -B(OH)(2) fragment, left after the dimer formation. Thus, although molecules were selected retrosynthetically with the 1,2-diazo fragment or with nearby hetero-atoms to induce co-crystal formation using the syn,syn-orientation of the -B(OH)(2) functionality, co-crystal formation is in fact selective and is probably driven by energy factors. Acetazolamide (ACET) contains self-complementary functional groups and hence creates stable homosynthons. Phenylboronic acids being weak competitors fail to perturb the homosynthons and hence the components crystallize separately. Therefore, besides the availability of possible hydrogen bond acceptors in the required position and orientation, the ability of the phenyl-boronic acid to perturb the existing interactions is also a prerequisite to form co-crystals. This is illustrated in the table below. In the case of ALP, PHEN and BPY, the native structures are stabilized by weak interactions and may be influenced by the boronic acid fragment. Thus phenylboronic acids can attain co-crystals with those compounds, wherein the cyclic O-H center dot center dot center dot N hydrogen bonds are stronger than the individual homo-interactions. This can lower the lattice energy of the molecular complex as compared with the individual crystals. [GRAPHICS] Phenylboronic acids show some selectivity in the formation of co-crystals with N-heterocycles. The differences in solubility of the components fall short to provide a possible reason for the selective formation of co-crystals only with certain compounds. These compounds, being weak acids, do not follow the Delta pK(a) analysis and hence fail to provide any conclusive observation. Theoretical results show that of the three conformers possible, the syn,anti conformer is the most stable. The relative stabilities of the three conformers syn,anti,syn,syn and anti,anti are 0.0, 2.18 and 3.14 kcal/mol, respectively. The theoretical calculations corroborate the fact that only energetically favorable synthons can induce the formation of heterosynthons, as in ALP and PHEN complexes. From a theoretical and structural analysis it is seen that phenylboronic acids will form interactions with those molecules wherein the heterocyclic and acidic fragments can interrupt the homosynthons. However, the energy profile is shallow and can be perturbed easily by the presence of competing functional groups (such as OH and COOH) in the vicinity. [GRAPHICS] .

Conformation-Changing Aggregation in Hydroxyacetone: A Combined Low-Temperature FTIR, Jet, and Crystallographic Study

Aggregation in hydroxyacetone (HA) is studied using low-temperature FTIR, supersonic jet expansion, and X-ray crystallographic (in situ cryocrystallization) techniques. Along with quantum chemical methods (MP2 and DFT), the experiments unravel the conformational preferences of HA upon aggregation to dinners and oligomers. The O-H center dot center dot center dot O=C intramolecular hydrogen bond present in the gas-phase monomer partially opens upon aggregation in supersonic expansions, giving rise to intermolecular cooperatively enhanced O-H center dot center dot center dot O-H hydrogen bonds in competition with isolated O-H center dot center dot center dot O=C hydrogen bonds. On the other hand, low-temperature IR studies on the neat solid and X-ray crystallographic data reveal that HA undergoes profound conformational changes upon crystallization, with the HOCC dihedral angle changing from similar to 0 degrees in the gas phase to similar to 180 degrees in the crystalline phase, hence giving rise to a completely new conformation. These conclusions are supported by theoretical calculations performed on the geometry derived from the crystalline phase.

Climate change and crop yields in the Indian Cardamom Hills, 1978-2007 CE

In this study we analyzed climate and crop yields data from Indian cardamom hills for the period 1978-2007 to investigate whether there were significant changes in weather elements, and if such changes have had significant impact on the production of spices and plantation crops. Spatial and temporal variations in air temperatures (maximum and minimum), rainfall and relative humidity are evident across stations. The mean air temperature increased significantly during the last 30 years; the greatest increase and the largest significant upward trend was observed in the daily temperature. The highest increase in minimum temperature was registered for June (0.37A degrees C/18 years) at the Myladumpara station. December and January showed greater warming across the stations. Rainfall during the main monsoon months (June-September) showed a downward trend. Relative humidity showed increasing and decreasing trends, respectively, at the cardamom and tea growing tracts. The warming trend coupled with frequent wet and dry spells during the summer is likely to have a favorable effect on insect pests and disease causing organisms thereby pesticide consumption can go up both during excess rainfall and drought years. The incidence of many minor pest insects and disease pathogens has increased in the recent years of our study along with warming. Significant and slight increases in the yield of small cardamom (Elettaria cardamomum M.) and coffee (Coffea arabica), respectively, were noticed in the recent years.; however the improvement of yield in tea (Thea sinensis) and black pepper (Piper nigrum L.) has not been seen in our analysis.

Volume change behaviour of expansive soils

Understanding the volume change behaviour of expansive soils/clays becomes a dire necessity to obtain engineering solutions to structures founded on these soils. Behaviour of expansive soils does not conform to the natural behaviour of fine grained soils. Most of the cases, the permissible heave/settlement forms the design criteria. The paper discusses the basic properties, the role of effective stress concept, basic mechanism in controlling the volume change behaviour, the role of double layer repulsion and its validity and certain basic considerations of footing resting on an expansive soil with respect to heave or settlement and the soil reinforcement as a possible engineering solution.

Optical properties change in Sb40S40Se20 thin films by light-induced effect

Thin films of Sb40Se20S40 with thickness 1000 nm were prepared by thermal evaporation technique. The amorphous nature of the thin films was verified by X-ray diffractometer. The chemical composition of the deposited thin films was examined by energy dispersive X-ray analysis (EDAX). The changes in optical properties due to the influence of laser radiation on amorphous thin films of Sb40Se20S40 glassy alloy were calculated from absorbance spectra as a function of photon energy in the wavelength region 450-900 nm. Analysis of the optical absorption data shows that the rule of non-direct transitions predominates. It has been observed that laser-irradiation of the films leads to a decrease in optical band gap while increase in absorption coefficient. The decrease in the optical band gap is explained on the basis of change in nature of films due to disorderness. The optical changes are supported by X-ray photoelectron spectroscopy and Raman spectroscopy. (C) 2012 Elsevier B.V. All rights reserved.

Synthesis and an Evaluation of Molecular Conformation and Crystal Packing in Two Substituted 4-Phenylquinolines

The title compounds, namely Methyl 2-methyl-4 -phenylquinoline-3-carboxylate (I), C18H15NO2, and (2E)-3-(3,4-dimethoxyphenyl)-1-(2-methyl-4 -phenylquinolin-3-yl)prop-2-en-1-one (II), C27H23NO3, comprising of the phenyl ring, exhibit differences in conformational behaviour with respect to the plane of the quinoline fragment. (I) contains the methyl ester moiety whereas (II) contains the chalcone fragment, consisting of a double bond and phenyl group containing dimethoxy groups as substituents. The dihedral angles between the phenyl group and the quinoline ring is 82.77 (7)A degrees in (I), and 79.02 (8)A degrees in (II) respectively. It is the weak C-H center dot center dot center dot O=C H-bond and C-H center dot center dot center dot pi interactions which dictate packing of molecules in (I). In (II), it is C-H center dot center dot center dot N and C-H center dot center dot center dot pi, involving the dimethoxy ring, which controls packing of molecules in the crystal lattice. In addition, pi center dot center dot center dot pi aromatic stacking interactions involving the quinoline fragment is present in all the molecules. The title compounds, namely methyl-2-methyl-4 -phenylquinoline-3-carboxylate (I), C18H15NO2, and (2E)-3-(3,4-dimethoxyphenyl)-1-(2-methyl-4 -phenylquinolin-3-yl)prop-2-en-1-one (II), C27H23NO3, comprising of the phenyl ring, exhibit differences in conformational behaviour with respect to the plane of the quinoline fragment. (I) contains the methyl ester moiety whereas (III) contains the chalcone fragment, consisting of a double bond and phenyl group containing dimethoxy groups as substituents. The dihedral angles between the phenyl group and the quinoline ring is 82.77 (7)A degrees in (I), and 79.02 (8)A degrees in (II) respectively. It is the weak C-H center dot center dot center dot O=C H-bond and C-H center dot center dot center dot pi interactions which dictate packing of molecules in (I). In (II), it is C-H center dot center dot center dot N and C-H center dot center dot center dot pi, involving the dimethoxy ring, which controls packing of molecules in the crystal lattice. In addition, pi center dot center dot center dot pi aromatic stacking interactions involving the quinoline fragment is present in all the molecules.

Climate change induced risk in water quality control problems

A modeling framework is presented in this paper, integrating hydrologic scenarios projected from a General Circulation Model (GCM) with a water quality simulation model to quantify the future expected risk. Statistical downscaling with a Canonical Correlation Analysis (CCA) is carried out to develop the future scenarios of hydro-climate variables starting with simulations provided by a GCM. A Multiple Logistic Regression (MLR) is used to quantify the risk of Low Water Quality (LWQ) corresponding to a threshold quality level, by considering the streamflow and water temperature as explanatory variables. An Imprecise Fuzzy Waste Load Allocation Model (IFWLAM) presented in an earlier study is then used to develop adaptive policies to address the projected water quality risks. Application of the proposed methodology is demonstrated with the case study of Tunga-Bhadra river in India. The results showed that the projected changes in the hydro-climate variables tend to diminish DO levels, thus increasing the future risk levels of LWQ. (C) 2012 Elsevier B.V. All rights reserved.

Effect of selenium addition on the GeTe phase change memory alloys

Compositional dependent investigations of the bulk GeTe chalcogenides alloys added with different selenium concentrations are carried out by X-ray diffraction (XRD), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), electron probe micro-analyzer (EPMA) and differential scanning calorimetry (DSC). The measurements reveal that GeTe crystals are predominant in alloys up to 0.20 at.% of Se content indicating interstitial occupancy of Se in the Ge vacancies. Raman modes in the GeTe alloys changes to GeSe modes with the addition of Se. Amorphousness in the alloy increases with increase of Se and 0.50 at.% Se alloy forms a homogeneous amorphous phase with a mixture of Ge-Se and Te-Se bonds. Structural changes are explained with the help of bond theory of solids. Crystallization temperature is found to be increasing with increase of Se, which will enable the amorphous stability. For the optimum 0.50 at.% Se alloy, the melting temperature has reduced which will reduce the RESET current requirement for the phase change memory applications. (C) 2012 Elsevier B.V. All rights reserved.