A study of the conformational stability and the vibrational spectra of 2,3-dichloro-1-propanol

The conformational stability and the three rotor internal rotations in 2,3-dichloro-1-propanol were investigated at DFT-B3LYP/6-311 + G**, MP2/6-311 + G** and MP4(SDQ) levels of theory. From the calculated potential energy surface, ten distinct minima were located all of which were predicted to have real frequencies at the B3LYP level of theory. The calculated lowest energy minima in the potential curves of the molecule were predicted to correspond to the Ggg and Gtg1 structures. The observed broad and very intense infrared band centered at about 3370 cm^?1 supports the existence of the strong intermolecular H-bonding in 2,3-dichloro-1-propanol. The equilibrium constants for the conformational interconversion in the molecule were estimated from the calculated Gibb's energies at the B3LYP/6-311 + G** level of calculation and found to correspond to an equilibrium mixture of about 49% Ggg, 27% Gtg1, 5% Ggt and 5% Tgg conformations at 298.15 K.     

Statistics of landscapes based on free energies,replication and degradation rate constants of RNA secondary structures

Summary RNA secondary structures are computed from primary sequences by means of a folding algorithm which uses a minimum free energy criterion. Free energies as well as replication and degradation rate constants are derived from secondary structures. These properties can be understood as highly sophisticated functions of the individual sequences whose values are mediated by the secondary structures. Such functions induce complex value landscapes on the space of sequences. The landscapes are analysed by random walk techniques, in particular autocorrelation functions and correlation lengths are computed. Free energy landscapes were found to be of AR(1) type. The rate constant landscapes, however, turned out to be more complex. In addition, gradient and adaptive walks are performed in order to get more insight into the complex structure of the landscapes.Dedicated to Prof. Dr. Dr. h.c. mult. Viktor Gutmann     

Densities and volume properties of (water + tert-butanol) over the temperature range of (274.15 to 348.15) K at pressure of 0.1 MPa

The densities of {water (1) + tert-butanol (2)} binary mixture were measured over the temperature range (274.15 to 348.15) K at atmospheric pressure using “Anton Paar” digital vibrating-tube densimeter. Density measurements were carried out over the whole concentration range at (308.15 to 348.15) K. The following volume parameters were calculated: excess molar volumes and thermal isobaric expansivities of the mixture, partial molar volumes and partial molar thermal isobaric expansivities of the components. Concentration dependences of excess molar volumes were fitted with Redlich–Kister equation. The results of partial molar volume calculations using four equations were compared. It was established that for low alcohol concentrations at T ? 208 K the inflection points at x₂ ≈ 0.02 were observed at concentration dependences of specific volume. The concentration dependences of partial molar volumes of both water and tert-butanol had extremes at low alcohol content. The temperature dependence of partial molar volumes of water had some inversion at х₂ ≈ 0.65. The temperature dependence of partial molar volumes of tert-butanol at infinite dilution had minimum at ≈288 K. It was discovered that concentration dependences of thermal isobaric expansivities of the mixture at small alcohol content and low temperatures passed through minimum.     

Cation−π interactions in high resolution protein−RNA complex crystal structures

In this work, we have analyzed the influence of cation–π interactions to the stability of 59 high resolution protein–RNA complex crystal structures. The total number of Lys and Arg are similar in the dataset as well as the number of their interactions. On the other hand, the aromatic chains of purines are exhibiting more cation–π interactions than pyrimidines. 35% of the total interactions in the dataset are involved in the formation of multiple cation–π interactions. The multiple cation–π interactions have been conserved more than the single interactions. The analysis of the geometry of the cation–π interactions has revealed that the average distance (d) value falls into distinct ranges corresponding to the multiple (4.28 Å) and single (5.50 Å) cation–π interactions. The G–Arg pair has the strongest interaction energy of −3.68 kcal mol⁻¹ among all the possible pairs of amino acids and bases. Further, we found that the cation–π interactions due to five-membered rings of A and G are stronger than that with the atoms in six-membered rings. 8.7% stabilizing residues are involved in building cation–π interactions with the nucleic bases. There are three types of structural motifs significantly over-represented in protein–RNA interfaces: beta-turn-ir, niche-4r and st-staple. Tetraloops and kink-turns are the most abundant RNA motifs in protein–RNA interfaces. Amino acids deployed in the protein–RNA interfaces are deposited in helices, sheets and coils. Arg and Lys, involved in cation–π interactions, prefer to be in the solvent exposed surface. The results from this study might be used for structure–based prediction and as scaffolds for future protein–RNA complex design.     

Ant colony optimization for predicting RNA folding pathways

RNA folding dynamics plays important roles in various functions of RNAs. To date, coarse-grained modeling has been successfully employed to simulate RNA folding dynamics on the energy landscape composed of secondary structures. In such a modeling, the energy barrier height between metastable structures is a key parameter that crucially affects the simulation results. Although a number of approaches ranging from the exact method to heuristic ones are available to predict the barrier heights, developing an efficient heuristic for this purpose is still an algorithmic challenge.We developed a novel RNA folding pathway prediction method, ACOfoldpath, based on Ant Colony Optimization (ACO). ACO is a widely used powerful combinatorial optimization algorithm inspired from the food-seeking behavior of ants. In ACOfoldpath, to accelerate the folding pathway prediction, we reduce the search space by utilizing originally devised structure generation rules. To evaluate the performance of the proposed method, we benchmarked ACOfoldpath on the known nineteen conformational RNA switches. As a result, ACOfoldpath successfully predicted folding pathways better than or comparable to the previous heuristics. The results of RNA folding dynamics simulations and pseudoknotted pathway predictions are also presented.     

The (water + acetonitrile) mixture revisited: A new approach for calculating partial molar volumes

Density and viscosity of (water + acetonitrile) mixtures were measured over the whole composition range at the temperatures: (298.15, 303.15, 308.15, 313.15, and 318.15) K. A new mathematical approach was developed which allows the calculation of the derivatives of density with respect to composition avoiding the appearance of local discontinuities. Thus, reliable partial molar volumes and thermal expansion coefficients were obtained.     

Nitrogen defect levels in InN: XANES study

The local and electronic structure of nitrogen-related defects in thin film of InN (0 0 0 1) has been studied using synchrotron-based X-ray absorption near edge structure (XANES) spectroscopy. Several defect levels within the band gap and the conduction band of InN were clearly resolved in XANES spectra around the nitrogen K-edge. Theoretical analysis of XANES data includes advanced “ab initio” simulations: self-consistent full multiple scattering calculations using muffin-tin approximation, non-muffin-tin finite difference approach to study the influence of non-muffin-tin effects on XANES shape as well as advanced local density approximation scheme for optimization of initial geometry around nitrogen defects. Theoretical analysis of XANES data allows to attribute the level observed at 1.7 eV above the conduction band mimimum to antisite nitrogen and a sharp resonance at 3.2 eV above the conduction band minimum to molecular nitrogen.     

Density functional study of small bimetallic Ag–Pd clusters

The geometric and electronic properties of small Ag_mPd_n clusters with m + n = 2–5 are studied within the framework of density functional theory in conjunction with two hybrid and one GGA exchange–correlation functional. For every composition, the global minimum is identified by using geometry optimization for a collection of initial structures. Results indicate that, for bimetallic tetramers and pentamers, the clusters shift from two-dimensional to three-dimensional structures with the addition of a second Pd atom. Ag₂Pd₂ is identified as the most stable tetramer by the calculation of the excess energy and second energy difference of bimetallic clusters. Concerning the fragmentation channels it is seen that the most favourable route in the majority of cases is via the evaporation of a single atom. Density of states calculations reveal that the increase of Pd content depletes the isolated s states close to the Fermi level, while at the same time shifts the d states to higher energies.     

A strategy to find minimal energy nanocluster structures

An unbiased strategy to search for the global and local minimal energy structures of free standing nanoclusters is presented. Our objectives are twofold: to find a diverse set of low lying local minima, as well as the global minimum. To do so, we use massively the fast inertial relaxation engine algorithm as an efficient local minimizer. This procedure turns out to be quite efficient to reach the global minimum, and also most of the local minima. We test the method with the Lennard–Jones (LJ) potential, for which an abundant literature does exist, and obtain novel results, which include a new local minimum for LJ₁₃, 10 new local minima for LJ₁₄, and thousands of new local minima for . Insights on how to choose the initial configurations, analyzing the effectiveness of the method in reaching low‐energy structures, including the global minimum, are developed as a function of the number of atoms of the cluster. Also, a novel characterization of the potential energy surface, analyzing properties of the local minima basins, is provided. The procedure constitutes a promising tool to generate a diverse set of cluster conformations, both two‐ and three‐dimensional, that can be used as an input for refinement by means of ab initio methods. © 2013 Wiley Periodicals, Inc.     

Calculating all local minima on liquidus surfaces using the FactSage software and databases and the Mesh Adaptive Direct Search algorithm

It is often of interest, for a multicomponent system, to identify the low melting compositions at which local minima of the liquidus surface occur. The experimental determination of these minima can be very time-consuming. An alternative is to employ the CALPHAD approach using evaluated thermodynamic databases containing optimized model parameters giving the thermodynamic properties of all phases as functions of composition and temperature. Liquidus temperatures are then calculated by Gibbs free energy minimization algorithms which access the databases. Several such large databases for many multicomponent systems have been developed over the last 40 years, and calculated liquidus temperatures are generally quite accurate. In principle, one could then search for local liquidus minima by simply calculating liquidus temperatures over a compositional grid. In practice, such an approach is prohibitively time-consuming for all but the simplest systems since the required number of grid points is extremely large. In the present article, the FactSage database computing system is coupled with the powerful Mesh Adaptive Direct Search (MADS) algorithm in order to search for and calculate automatically all liquidus minima in a multicomponent system. Sample calculations for a 4-component oxide system, a 7-component chloride system, and a 9-component ferrous alloy system are presented. It is shown that the algorithm is robust and rapid.     

Calorimetric measurements and first principles to study the (Ag-Li) liquid system

Integral molar enthalpies of mixing were determined by drop calorimetry for (Ag-Li) liquid alloys at two temperatures (1253 and 873) K. The integral molar enthalpies of mixing are negative in the entire range of concentrations. For the mole fraction of lithium X_Li = 0.5664, minimum value of the integral enthalpy of mixing of at ΔH_m = −11.679 kJ/mol was observed. For (Ag-Li) liquid alloys, between T = (873 and 1253) K no temperature dependence was observed. Ab initio molecular dynamics was used to simulate liquid phase structures at T = 873 K (Li-rich side) and at T = 1250 K (Ag-rich phase) for subsequent calculation of the vibrational energy, respectively. Our measured and calculated data were compared with literature data.     

Properties of n-butylpyridinium nitrate ionic liquid and its binary mixtures with water

The density and surface tension of the pure ionic liquid n-butylpyridinium nitrate ([BuPy]NO₃) were determined at temperature range from T = (293.15 to 338.15) K. The coefficient of thermal expansion, molecular volume and lattice energy of [BuPy]NO₃ were calculated from the experimental values of density. The surface entropy and enthalpy of [BuPy]NO₃ were investigated. The IL studied show much lower surface enthalpy and lattice energy in comparison with fused salts. The densities and surface tensions of binary mixtures of [BuPy]NO₃ with water have been measured within the whole composition range at T = 298.15 K and atmospheric pressure. Excess molar volumes V^E and surface tension deviations δγ were then deduced from the experimental results as well as partial molar volumes and excess partial molar volumes. Excess molar volumes have a negative deviation from ideal behavior and the surface tension deviations are negative over the whole compositions range. V^E and δγ were correlated with suitable equation respectively.     

High-temperature transport and stability of SrFe1−xNbxO3 − δ

The conductivity is measured in the series of solid solutions SrFe_1 ? xNb_xO_3 ? δ, where x = 0.05, 0.1, 0.2, 0.3, 0.4, within the oxygen partial pressure limits 10^?18–0.5 atm and temperature range 650–950 °C. The contributions to the total conductivity from oxygen ions, electrons and electron holes are obtained based on their different pressure dependences. The doped derivative with x = 0.1 is found to be a singular composition where ion conductivity attains a maximal value while activation energy for ion transport is minimal. This peculiar behavior is attributed to formation of favorable microstructure in the oxide. The deeper doping results in deterioration of ion transport, which is explained by oxygen vacancy filling. It is shown that replacement of iron for niobium favors enhanced thermodynamic stability towards reduction. The oxygen permeability is evaluated from the conductivity data, and it achieves rather high values in the doped derivatives. These oxides can, therefore, be recommended for further evaluation as oxygen separating membrane materials for partial oxidation of natural gas.     

Isothermal phase equilibria for the (xenon + cyclopropane) mixed-gas hydrate system

Isothermal three-phase equilibria of gas, aqueous, and hydrate phases for the {xenon (Xe) + cyclopropane (c-C₃H₆)} mixed-gas hydrate system were measured at two different temperatures (279.15 and 289.15) K. The structural phase transitions from structure-I to structure-II and back to structure-I, depending on the mole fraction of guest mixtures, occur in the (Xe + c-C₃H₆) mixed-gas hydrate system. The isothermal pressure–composition relations have two local pressure minima. The most important characteristic in the (Xe + c-C₃H₆) mixed-gas hydrate system is that the equilibrium pressure–composition relations exhibit the complex phase behavior involving two structural phase transitions and two homogeneous negative azeotropes. One of two structural phase transitions exhibits the heterogeneous azeotropic-like behavior.     

Observation of possible quantum interference effects in SrRuO3 epitaxial thin films grown by high-oxygen pressure dc sputtering

A careful study of the electronic transport and magnetotransport properties of metallic ferromagnetic SrRuO₃ (SRO) thin films is reported. Epitaxial (～150 nm) SRO films were grown on (001)-oriented SrTiO₃ (STO) substrates by dc sputtering technique at high oxygen pressure. Resistivity measurements were performed up to temperatures as low as 2 K in magnetic fields strengths of up to 9 T, applied perpendicular to the film plane. The films featured excellent metallic behavior at room temperature, with a resistivity, ρ(300 K) < 600 μΩ cm. The presence of minima in the ρ–T plots at ～4 K was clearly detected from these measurements. The 9 T magnetic field did not remove the minima signaling its nonmagnetic origin In addition, the ρ(μ₀H = 9 T,T) minima was slightly shifted to higher temperature and the ρ(μ₀H = 9 T,T ≤ 4 K) was larger when it was compared with ρ(μ₀H = 0 T,T ≤ 4 K). Increasing relevance of quantum corrections to the conductivity as the temperature is lowered has been invocated as possible cause of this anomalous electrical behavior. In this case, effects arising from quantum interference of the electronic wavelength are expected. Weak localization and renormalized electron–electron interaction have been considered as possible sources giving rise to quantum correction to the conductivity.     

The energy spectrum of 662 keV photons in a water equivalent phantom

Investigation is made on the energy spectrum of photons originating from interactions of 662 keV primary gamma-ray photons emitted by a point source positioned at the centre of a water equivalent solid phantom of dimensions 19 cm×19 cm×24 cm. Peaks resulting from total energy loss (photopeak) and multiple and back scattering have been observed using a 51 mm×51 mm NaI(Tl) detector; good agreement being found between the measured and simulated response functions. The energy spectrum of the gamma photons obtained through the Monte Carlo simulation reveals local maxima at about 100 keV and 210 keV, being also observed in the experimental response function. Such spectra can be used as a method of testing the water equivalence of solid phantom media before their use for dosimetry measurements.     

Modelling the interaction of several bisphosphonates with hydroxyapatite using the generalised AMBER force field

The ability of the Generalised AMBER Force Field (GAFF) of Kollman and co-workers to model the structures of bisphosphonate ligands, C(R₁)(R₂)(PO₃²⁻)₂, important compounds in the treatment of bone cancer, by molecular mechanics methods is evaluated. The structure of 50 bisphosphonates and nine bisphosphonate esters were predicted and compared to their crystal structures. Partial charges were assigned from a RHF/6-31G¹ single point calculation at the geometry of the crystal structure. Additional parameters required for GAFF were determined using the methods of the force field’s developers. The structures were found to be well replicated with virtually all bond lengths reproduced to within 0.015 Å, or within 1.2σ of the crystallographic mean. Bond angles were reproduced to within 1.9° (0.8σ). The observed gauche or anti conformation of the molecules was reproduced, although in several instances gauche conformations observed in the solid state energy-minimised into anti conformations, and vice versa. The interaction of MDP (R₁ = R₂ = H), HEDP (R₁ = OH, R₂ = CH₃), APD (R₁ = OH, R₂ =  (CH₂)₂NH₃⁺), alendronate (R₁ = OH, R₂ = (CH₂)₃NH₃⁺) and neridronate (R₁ = OH, R₂ = (CH₂)₅NH₃⁺) with the (001), (010) and (100) faces of hydroxyapaptite was examined by energy-minimising 20 random orientations of each ligand 20 Å from the mineral (where there is no interaction), and then at about 8 Å from the surface whereupon the ligand relaxes onto the surface. The difference in energy between the two systems is the interaction energy. In all cases interaction with hydroxyapatite caused a decrease in energy. When modelled with a dielectric constant of 78ε_o, non-bonded interactions dominate; electrostatic interactions become important when the dielectric constant is <10ε_o. Irrespective of the value of the dielectric constant used, the structure of the ligands on the hydroxyapatite surface is very similar. On the (001) face, both phosphonate groups interact near a surface Ca²⁺ ion. The magnitude of the exothermic interaction energy varies with molecular volume (MDP<HEDP<APD<alendronate) except for neridronate which interacts less effectively than alendronate because the long amino side chain folds in on itself and does not align with the surface of the mineral. The bisphosphonates adopt two conformations on the (010) face. In the first of these, found for MDP and 40% of the alendronate structures, both phosphonates interact with the surface and the side chain points away from the surface. Hence, the interaction energy is similar for both species. In the second conformation, adopted by the majority of ligands, one phosphonate and the Cα side chain interact with the surface. The interaction energy, the magnitude of which is very similar to that on the (001) face, increases with the molecular volume of the ligand, again with the exception of neridronate. Two conformations also occur on the (100) face. In the first conformation, only one of the phosphonate groups points towards the surface and the Cα side chain interacts with the surface; in the second conformation the Cα side chain interacts strongly with the surface and both phosphonate groups point away from the surface towards the solution. The first conformation, which is the more common, is energetically more favourable. Its magnitude is virtually insensitive to the nature of the side chain and is similar to the magnitude of the interaction energy on the other two faces. The magnitude of the second conformation increases with the size of the Cα side chain.     

Electron momentum density in ZnSe: Theory and experiment

We present experimental Compton profiles of ZnSe along [1 0 0] and [1 1 0] directions using our 740 GBq ¹³⁷Cs Compton spectrometer. We have also computed the momentum densities, energy bands, density of states (DOS) and band gaps using density functional theory (local density and generalized gradient approximations) and pseudopotential (PP) approach. The anisotropy in the momentum density is well reproduced by the density functional calculations. The energy bands and bond length are interpreted in terms of the anisotropies.     

Guided macro-mutation in a graded energy based genetic algorithm for protein structure prediction

Protein structure prediction is considered as one of the most challenging and computationally intractable combinatorial problem. Thus, the efficient modeling of convoluted search space, the clever use of energy functions, and more importantly, the use of effective sampling algorithms become crucial to address this problem. For protein structure modeling, an off-lattice model provides limited scopes to exercise and evaluate the algorithmic developments due to its astronomically large set of data-points. In contrast, an on-lattice model widens the scopes and permits studying the relatively larger proteins because of its finite set of data-points. In this work, we took the full advantage of an on-lattice model by using a face-centered-cube lattice that has the highest packing density with the maximum degree of freedom. We proposed a graded energy—strategically mixes the Miyazawa–Jernigan (MJ) energy with the hydrophobic-polar (HP) energy—based genetic algorithm (GA) for conformational search. In our application, we introduced a 2 × 2 HP energy guided macro-mutation operator within the GA to explore the best possible local changes exhaustively. Conversely, the 20 × 20 MJ energy model—the ultimate objective function of our GA that needs to be minimized—considers the impacts amongst the 20 different amino acids and allow searching the globally acceptable conformations. On a set of benchmark proteins, our proposed approach outperformed state-of-the-art approaches in terms of the free energy levels and the root-mean-square deviations.