First principles investigation of pressure dependent stability,phonon, Debye temperature,physical, mechanical and thermodynamic properties of Rh3Al intermetallic compound

ABSTRACT

Pressure dependence of stability, phonon, Debye temperature, physical, mechanical and thermodynamic properties of Rh₃Al intermetallic compound were investigated by first-principles The calculated cohesive energy (E_c), formation enthalpy (ΔH) show that Rh₃Al is a thermodynamically stable compound. Properties related to the phonons of Rh₃Al were also obtained. In addition, the transverse sound velocity (ν_s), longitudinal sound velocity (ν_l), average sound velocity (ν_m) and Debye temperature (Θ_D) of Rh₃Al were calculated by using the VRH method along with pressure range from 0 to 60?GPa. The values of lattice parameters, bulk modulus and its first-order pressure derivative are consistent well with other works. The band structure indicates that Rh₃Al compound exhibits a metallic character. Moreover, the total density of states, partial density of states, Mulliken charges and electron density difference have been analysed to explain the physical properties. Based on the stress–strain approach and the Born stability criteria, the mechanical properties were evaluated by elastic constants (C_ij), other modulus (B, E, G), (B/G) ratio, Poisson’s ratio (ν), the anisotropic index (A), hardness (H) and compressibility (K) for this intermetallic compound. Finally, the thermodynamic properties, including enthalpy, free energy, entropy and heat capacity are discussed range from 0 to 1000?K.     

Production,extraction, and thermodynamics protease partitioning from Aspergillus tamarii Kita UCP1279 using PEG/sodium citrate aqueous two-phase systems

Abstract

The protease from Aspergillus tamarii Kita UCP1279 extraction by aqueous two-phase PEG-Citrate (ATPS) systems, using a factorial design 2⁴, was investigated. Then, the variables studied were polyethylene glycol (PEG) molar mass (M_PEG), concentrations of PEG (C_PEG) and citrate (C_CIT), and pH. The responses analyzed were the partition coefficient (K), activity yield (Y) and purification factor (PF). The thermodynamic parameters of the ATPS partition were estimated as a function of temperature. ATPS was able to pre-purify the protease (PF = 1.6) and obtained 84% activity yield. The thermodynamic parameters ΔG°_m (?10.89?kJ mol^?1), ΔH_m (?5.0?kJ?mol^?1) and partition ΔS_m (19.74?J mol^?1 K^?1) showed that the preferential migration of almost all protein contaminants of the crude extract to the salt-rich phase, while the preferred protease was the PEG rich phase. The extracted enzyme presents optimum temperature and pH at range of 40–50?°C and 9.0–11.0, respectively. Moreover, the enzyme was identified as serine protease based on inhibition profile. ATPS showed the satisfactory performance as the first step for Aspergillus tamarii Kita UCP1279 protease pre-purification.     

Ab initio predictions of structural and elastic properties of struvite: contribution to urinary stone research

In the present work, we carried out density functional calculations of struvite – the main component of the so-called infectious urinary stones – to study its structural and elastic properties. Using a local density approximation and a generalised gradient approximation, we calculated the equilibrium structural parameters and elastic constants C _ijkl . At present, there is no experimental data for these elastic constants C _ijkl for comparison. Besides the elastic constants, we also present the calculated macroscopic mechanical parameters, namely the bulk modulus (K), the shear modulus (G) and Young's modulus (E). The values of these moduli are found to be in good agreement with available experimental data. Our results imply that the mechanical stability of struvite is limited by the shear modulus, G. The study also explores the energy-band structure to understand the obtained values of the elastic constants.     

Thermo-mechanical properties of cubic titanium nitride

The equilibrium structure, elastic constants C_ij and thermodynamic functions of cubic titanium nitride (TiN) were calculated within the temperature range of 0–3100 K and under a pressure range 0–60 GPa. Properties were computed using the generalised gradient approximations (GGA) exchange-correlation functional. Calculated mechanical properties (Elastic constants, Young’s modulus and shear modulus) and phonon spectra of TiN obtained via robust DFT-QHA algorithm, were generally in a good agreement with available experimental and theoretical analogous values. In particular, a well-examined quasi-harmonic approximation method implemented in the Gibbs2 code is utilised herein to provide accurate estimation of thermal expansion coefficients, entropies, heat capacity values (at different combinations of temperature/volume/pressure) and Debye’s temperature. Parameters calculated herein shall be useful to elucidate the superior performance of TiN at harsh operational conditions encompassing elevated temperatures and pressures pertinent to cutting machineries and surface coatings.     

First-principles investigation of the novel structure,elastic and thermodynamic properties of IrAl3 coating

IrAl₃ coating is a promising advanced functional material. However, the crystal structure and relevant properties of IrAl₃ remain controversy. Here, we apply the first-principles calculations to investigate the crystal structure, elastic and thermodynamic properties of IrAl₃. The phonon dispersion curves and phonon density of states of IrAl₃ are calculated. We find that the reported hexagonal structure (P63/mmc) is dynamically instable. However, three new phases: tetragonal (P4/mbm) and cubic (Pm-3n and Pm-3?m) structures are predicted. In particular, IrTi₃-type structure is a derivative cubic structure because Al atom occurs migration from (0, 0.50, 0.50) site to (0, 0.25, 0.50) site. IrTi₃-type derivative cubic structure shows high shear deformation resistance and high elastic stiffness in comparison to other three structures. The strong shear deformation resistance and high elastic stiffness are attributed to the symmetrical Ir–Al bond. However, AuCu₃-type structure shows the high Debye temperature and low heat capacity in comparison to other structures.     

Vibrational and electronic optical activity of the chiral disulphide group: Implications for disulphide bridge conformation

Using dihydrogendisulphide (H₂S₂), dimethyl‐ ((CH₃)₂S₂), and diethyldisulphide ((CH₃CH₂)₂S₂)as model molecules, theoretical ECD, VCD, and ROA spectra of nonplanar disulphides were calculated by DFT methods. Most of the calculated electronic and vibrational chiroptical features suffer an equivocal relation between calculatedsigns of ECD, VCD, or ROA and the sense of disulphide nonplanarity as noted earlier for low‐lying ECD bands. This is a consequence of local C₂ symmetry of a disulphide group causing most electronic and vibrational transitions to occur as pairs falling to alternative A, B symmetry species, which become degenerate and switch their succession (and consequently the observed chiroptical sign pattern) at the energetically most favorable perpendicular conformation. According to present calculations, the key to resolving this ambiguity may involve the S? S stretching vibrational mode at ～500 cm^?1. The relation of signs of the relevant VCD and ROA features to sense of disulphide chirality seems simpler and less ambiguous. The right‐handed arrangement of the S? S group (0 < χ_{S? S} < 180°) results in mostly negative VCD signals. Although relation to ROA still suffers some ambiguity, it gets clearer along the series H₂S₂–(CH₃)₂S₂–(CH₃CH₂)₂S₂. ROA is also attractive for the analysis of disulphide‐containing peptides and proteins, because applying it to aqueous solutions is not problematic. Chirality, 2010. © 2009 Wiley‐Liss, Inc.     

Methyl 2-methoxy-7-(4-methylbenzoyl)-4-oxo-6-p-tolyl-4H-furo[3,2-c]pyran-3-carboxylate:A combined experimental and theoretical investigation

The title compound, methyl 2-methoxy-7-(4-methylbenzoyl)-4-oxo-6-p-tolyl-4H-furo[3,2-c]pyran-3-carboxylate (C₂₅H₂₀O₇), was prepared and characterized by IR and single-crystal X-ray diffraction (XRD). The compound crystallizes in the triclinic space group P ?1 with a?=?8.9554(9) Å, b?=?10.0018(10) Å, c?=?12.7454(13) Å, α?=?67.678(7)°, β?=?89.359(8)° and γ?=?88.961(8)°. In addition to the molecular geometry from X-ray experiment, the molecular geometry and vibrational frequencies of the title compound in the ground state have been calculated using semiempirical AM1 and PM3 methods, as well as Hartree-Fock (HF) and density functional (B3LYP) levels of theory with 6–31G(d) basis set. To determine conformational flexibility, molecular energy profile of the title compound was obtained by semi-empirical (AM1) calculations with respect to two selected degrees of torsional freedom, which were varied from ?180° to +180° in steps of 10°. Besides, frontier molecular orbitals (FMO) analysis and thermodynamic properties of the title compound were performed by the B3LYP/6–31G(d) method.     

Theoretical study on the structural,vibrational, and thermodynamic properties of the (Br<Subscript>2</Subscript>GaN<Subscript>3</Subscript>)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 1–4) clusters

The molecular geometries, vibrational properties, and thermodynamic properties of the clusters (Br₂GaN₃) _n (n = 1–4) were studied at the B3LYP/6-311+G* level. The optimized clusters (Br₂GaN₃) _n (n = 2–4) were all found to possess a cyclic structure consisting of Ga atoms bridged by the α-nitrogen of the azide groups. A discussion of the relationships between the geometrical parameters and the degree of oligomerization n is provided. Features in the IR spectra were assigned by vibrational analysis. Trends in thermodynamic properties with temperature and degree of oligomerization n are discussed. Thermodynamic analysis of the gas-phase reaction showed that the formation of the clusters (Br₂GaN₃) _n (n = 2–4) is thermodynamically favorable considering the enthalpies at 298.2 K. The calculated results for the Gibbs free energies were negative, which indicates that the oligomerizations can occur spontaneously at 298.2 K.     

Phosphoenolpyruvate Carboxylase Purified from Leaves of C3, C4, and C3-C4 intermediate species of Alternanthera: Properties at Limiting and Saturating Bicarbonate

Phosphoenolpyruvate carboxylase (PEPC) was purified from leaves of four species of Alternanthera differing in their photosynthetic carbon metabolism: Alternanthera sessilis (C₃), A. pungens (C₄), A. ficoides and A. tenella (C₃-C₄ intermediates or C₃-C₄). The activity and properties of PEPC were examined at limiting (0.05 mM) or saturating (10 mM) bicarbonate concentrations. The V_max as well as K_m values (for Mg²⁺ or PEP) of PEPC from A. ficoides and A. tenella (C₃-C₄ intermediates) were in between those of C₃ (A. sessilis) and C₄ species (A. pungens). Similarly, the sensitivity of PEPC to malate (an inhibitor) or G-6-P (an activator) of A. ficoides and A. tenella (C₃-C₄) was also of intermediate status between those of C₃ and C₄ species of A. sessilis and A. pungens, respectively. In all the four species, the maximal activity (V_max), affinity for PEP (K_m), and the sensitivity to malate (K_I) or G-6-P (K_A) of PEPC were higher at 10 mM bicarbonate than at 0.05 mM bicarbonate. Again, the sensitivity to bicarbonate of PEPC from C₃-C₄ intermediates was in between those of C₃- and C₄-species. Thus the characteristics of PEPC of C₃-C₄ intermediate species of Alternanthera are intermediate between C₃- and C₄-type, in both their kinetic and regulatory properties. Bicarbonate could be an important modulator of PEPC, particularly in C₄ plants. This revised version was published online in August 2006 with corrections to the Cover Date.     

Effect of Alcohols,Aldehydes and their Derivatives to Induce Nutritional Encephalomalacia in Starting Chicks

n-Decyl (C₁₀), undecyl (C₁₁), lauryl (C₁₂) and myristyl (C₁₄) alcohols induced nutritional encephalomalacia, when fed to one-day-old White Leghorn male chicks for 3 weeks, while n-heptyl (C₇), n-octyl (C₈), n-nonyl (C₉), cetyl (C₁₆) and stearyl (C₁₈) alcohols did not. Esters of the former group, i.e. n-decyl acetate, lauryl stearate and dilauryl succinate, and aldehydes corresponding to the former group, i.e. n-decyl aldehyde and lauraldehyde, also had the ability to induce encephalomalacia. The disease can be completely prevented by dietary supplementation of dl-β-tocopheryl acetate. Median lethal dietary level of n-decyl and lauryl alcohols and lauraldehyde was estimated to be 20, 18, and 12% respectively.     

Structure of binuclear Rh(II) carboxylato complexes with 2,2-bipyridine and an unprecedented rhodium wire with Rh4 core

Structures of rhodium(II) binuclear complexes [Rh₂(OOCCH₃)₂(bpy)₂(H₂O){(CH₃)₂CHOH}][B(C₆H₅)₄]₂ · H₂O (1), [Rh₂Cl₂(OOCCH₃)₂(bpy)₂] · 2H₂O (2), [Rh₂Br₂(OOCCH₃)₂(bpy)₂] · 3H₂O (3), and [Rh₂I₂(OOCCH₃)₂(bpy)₂] (4), as well as an unprecedented wire with infinite Rh-Rh chain, {[Rh₄(μ-OOCH)₄(bpy)₄](BF₄)}_n · 0.5nC₄H₈O₂ (5), have been determined and discussed. Mass spectra of complexes [Rh₂(OOCMe)₂(bpy)₂(H₂O)₂](MeCOO)₂ and [Rh₂(OOCMe)₂(phen)₂(H₂O)₂](MeCOO)₂ have showed stability of polynuclear cations with rhodium in oxidation states in the range +1.25 to +1.75.     

Stereochemistry of the reaction products of the oxidative addition reaction of methyl iodide to [Rh((C4H3S)COCHCOR)(CO)(PPh3)]: A NMR and computational study. R = CF3, C6H5, C4H3S

A NMR study of the reaction mixture of the square planar [Rh((C₄H₃S)COCHCOR)(CO)(PPh₃)] complex and CH₃I, where R = CF₃, C₆H₅ or C₄H₃S, revealed that two types of alkyl and one (R = CF₃) or two (R = C₆H₅ or C₄H₃S) types of acyl species exist in the system. Two isomers of each species with an unsymmetrical β-diketonato ligand were observed. ¹H-¹H NOESY NMR unambiguously showed that the PPh₃ group is in the apical position in the more stable Rh^III-alkyl product. Theoretical computations of the equilibrium geometry of the possible reaction products, consistent with experimental observations, revealed that the first alkyl product results from trans addition to Rh^I and that the second thermodynamic alkyl product adopts an octahedral geometry with the PPh₃ group and the iodide above and below the square planar plane. Theoretical computations also revealed that the thermodynamic acyl product adopts a square-pyramidal geometry with the COCH₃ group in the apical position.     

New polyacetylene glucosides from the florets of Carthamus tinctorius and their weak anti-inflammatory activities

Eight new linear polyacetylene glucosides (1–8), containing two C₁₀-, one C₁₃- and five C₁₄-acetylenes, together with three known polyacetylenes (9–11) were isolated from the florets of Carthamus tinctorius L. Their structures were elucidated by means of spectroscopic methods and chemical evidence. The absolute configurations of compounds 3–9 were confirmed by Snatzke and Gerards’s method, observing the induced circular dichroism after addition of dirhodium tetrakis (trifluoroacetate) [Rh₂(OCOCF₃)₄] in CHCl₃. All the isolated compounds (1–11) were also tested for inhibitory activities against LPS-induced NO production in murine macrophages and just showed weak activities at concentrations of 1 × 10⁻⁵ M.     

Synthesis, crystal and band structures, and optical and magnetic properties of a 1D copper coordination polymer with chelidamic acid ligand

A 1D coordination polymer, {[Cu₃(C₇H₂NO₅)₂(H₂O)₇]·2(H₂O)}_n (1), has been synthesized and characterized by X-ray single-crystal diffraction. The crystal structure of 1 features that distorted square-pyramidal coordination polyhedra composed of Cu atoms and chelidamic acid ligands are interlinked into a 1D polymer, further linked by hydrogen bonds into a 3D network. The optical properties were investigated in terms of diffuse reflectance and fluorescent spectra, which exhibit strong luminescence. The electronic band structure along with the density of states (DOSs) calculated by the DFT method indicate that compound 1 pose an energy band gap of 1.89 eV and that the origin of the emission band may be mainly ascribed to metal-to-ligand charge transfer (MLCT) where the electrons are transferred from the Cu-3d to O-2p and C-2p states.     

Synthesis and biological evaluation of a new dysprosium(III) complex containing 2,9-dimethyl 1,10-phenanthroline

The binding of [Dy(dmp)₂Cl₃(OH₂)], where dmp is 2,9-dimethyl 1,10-phenanthroline, with Fish salmon DNA (FS-DNA) is investigated by absorption and emission spectroscopy, quenching studies, salt dependent, and gel electrophoresis. The binding constant (K_b) of the interaction is calculated as (1.27 ± .05) × 10⁵ M^?1 from absorption spectral titration data. The Stern–Volmer constant (K_SV), thermodynamic parameters involves ΔG°, ?H°, and ?S° are calculated by fluorescent data and Van’t Hoff equation. The thermodynamic studies show that the reaction for the binding of the complex with FS-DNA is endothermic and entropically driven (ΔS° > 0, ΔH° > 0). The effect of the complex concentration on FS-DNA cleavage reactions is also investigated by gel electrophoresis. Furthermore, the Dy(III) complex has been screened for its antibacterial activity. The experimental results suggest that the Dy(III) complex binds significantly to FS-DNA by hydrophobic groove binding mode and the complex has more efficient antibacterial activity compared to its metal salt.     

Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins

Short range side chain‐backbone hydrogen bonded motifs involving Asn and Gln residues have been identified from a data set of 1370 protein crystal structures (resolution ≤ 1.5 Å). Hydrogen bonds involving residues i ? 5 to i + 5 have been considered. Out of 12,901 Asn residues, 3403 residues (26.4%) participate in such interactions, while out of 10,934 Gln residues, 1780 Gln residues (16.3%) are involved in these motifs. Hydrogen bonded ring sizes (C_n, where n is the number of atoms involved), directionality and internal torsion angles are used to classify motifs. The occurrence of the various motifs in the contexts of protein structure is illustrated. Distinct differences are established between the nature of motifs formed by Asn and Gln residues. For Asn, the most highly populated motifs are the C₁₀ (CO^δ_i …NH_{i + 2}), C₁₃ (CO^δ_i …NH_{i + 3}) and C₁₇ (N^δH_i …CO_{i ? 4}) structures. In contrast, Gln predominantly forms C₁₆ (CO^ε_i …NH_{i ? 3}), C₁₂ (N^εH_i …CO_{i ? 2}), C₁₅ (N^εH_i …CO_{i ? 3}) and C₁₈ (N^εH_i …CO_{i ? 4}) motifs, with only the C₁₈motif being analogous to the Asn C₁₇structure. Specific conformational types are established for the Asn containing motifs, which mimic backbone β‐turns and α‐turns. Histidine residues are shown to serve as a mimic for Asn residues in side chain‐backbone hydrogen bonded ring motifs. Illustrative examples from protein structures are considered. Proteins 2012; © 2011 Wiley Periodicals, Inc.     

Linking vein properties to leaf biomechanics across 58 woody species from a subtropical forest

• Leaf venations have elements with relatively lower elasticity than other leaf tissue components, which are thought to contribute to leaf biomechanics. A better mechanistic understanding of relationships between vein traits and leaf mechanical properties is essential for ecologically relevant interpretation of leaf structural variations.
• We investigated 13 major (first to third order) and minor (>third order) vein traits, six leaf mechanical properties and other structural traits across 58 woody species from a subtropical forest to elucidate how vein traits contribute to leaf biomechanics.
• Across species, vein dry mass density (ρ_v), total vein dry mass per leaf area (VMA) and minor vein diameter (VD_min), but not the lower‐order vein density (VLA_1?2), were positively correlated with leaf force to punch (F_p) and force to tear (F_t). Structural equation models showed that ρ_v and VD_min not only contribute to leaf mechanical properties directly (direct pathway), but also had impacts on leaf biomechanics by influencing leaf thickness and leaf dry mass per area (indirect pathway).
• Our study demonstrated that vein dry mass density and minor vein diameter are the key vein properties for leaf biomechanics. We also suggest that the mechanical characteristics of venations are potential factors influencing leaf mechanical resistance, structure and leaf economics spectrum.

     

An experimental and theoretical approach to the molecular structure of 2-{4-[3-(2,5-dimethylphenyl)-3-methylcyclobutyl]thiazol-2-yl}isoindoline-1,3-dione

The title compound, 2-{4-[3-(2,5-dimethylphenyl)-3-methylcyclobutyl]thiazol-2-yl}isoindoline-1,3-dione (C₂₄H₂₂N₂O₂S), was synthesized and characterized by IR-NMR spectroscopy and single-crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P2₁/c with a?=?19.7799(13) Å, b?=?6.7473(4) Å, c?=?15.7259(9) Å and β?=?103.416(5)°. In addition, the molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO) ¹H and ¹³C chemical shift values of the title compound in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (DFT/B3LYP) with 6–31G(d), 6–31 + G(d,p) and LANL2DZ basis sets, and compared with the experimental data. To determine conformational flexibility, molecular energy profile of the title compound was obtained by semi-empirical (AM1) calculations with respect to two selected degrees of torsional freedom, which were varied from ?180° to +180° in steps of 5°. Besides, molecular electrostatic potential, frontier molecular orbitals (FMO) analysis and thermodynamic properties of the title compound were investigated by theoretical calculations.     

Dinuclear Rh(II) complexes with one polypyridyl ligand, structure, properties and antitumor activity

Rhodium(II) complexes [Rh₂(μ-OAc)₂(OAc)(bpy)(H₂O)₂]PF₆ (1), [Rh₂(μ-OAc)₂(OAc)(phen)(H₂O)₂](PF₆)·H₂O (2), [Rh₂(μ-OOCCH₃)₃(OOCCH₃)(phen)] (3) and [Rh₂(μ-O₂CCH₃)₃(O₂CCH₃)(Ph₂phen)] (4) (Ph₂phen = 4,7-diphenyl-1,10-phenanthroline) have been synthesized and characterized by means of NMR, IR and UV-Vis spectroscopic methods. X-ray structure of complex 4·1.5(CH₃COCH₃) has been determined and its geometry and electronic structure has been elucidated using OPBE and B3LYP DFT methods. The compounds are active cytostatic agents against tumor cells.     

A spectroscopic and molecular dynamic approach on the interaction between ionic liquid type gemini surfactant and human serum albumin

The interactions of imidazolium bashed ionic liquid-type cationic gemini surfactant ([C₁₂-4-C₁₂im]Br₂) with HSA were studied by fluorescence, time-resolved fluorescence, UV-visible, circular dichroism, molecular docking and molecular dynamic simulation methods. The results showed that the [C₁₂-4-C₁₂im]Br₂ quenched the fluorescence of HSA through dynamic quenching mechanism as confirmed by time-resolved spectroscopy. The Stern–Volmer quenching constant (K_sv) and relevant thermodynamic parameters such as enthalpy change (ΔH), Gibbs free energy change (ΔG) and entropy change (ΔS) for interaction system were calculated at different temperatures. The results revealed that hydrophobic forces played a major role in the interactions process. The results of synchronous fluorescence, UV-visible and CD spectra demonstrated that the binding of [C₁₂-4-C₁₂im]Br₂ with HSA induces conformational changes in HSA. Inquisitively, the molecular dynamics study contribute towards understanding the effect of binding of [C₁₂-4-C₁₂im]Br₂ on HSA to interpret the conformational change in HSA upon binding in aqueous solution. Moreover, the molecular modelling results show the possible binding sites in the interaction system.