Structural phase transition of SnSe under uniaxial stress and hydrostatic pressure: an ab initio study

We study the structural behavior of SnSe under the hydrostatic pressure using a constant pressure ab initio technique. We find SnSe undergoes a structural second order phase transition from the orthorhombic (Pnma) structure to orthorhombic (Cmcm) structure in the constant pressure simulation at 7 GPa which is in good agreement with the recent experimental study. The Cmcm structure is fivefold coordinated. This phase transition is also analyzed from the total energy calculations. Besides, we study the behavior of SnSe under uniaxial stress.     

Structural phase transition of CdTe: an ab initio study

A constant pressure ab initio MD technique and density functional theory with a generalized gradient approximation (GGA) was used to study the pressure-induced phase transition in zinc-blende CdTe. We found that CdTe undergoes a structural first-order phase transition to $ {\text{I}}\overline 4 {\text{m2}} $ (binary β-tin) tetragonal structure in the constant pressure molecular dynamics simulation at 20 GPa. When the pressure was increased to 50 GPa, the phase of tetragonal structure converted to a new Imm2 orthorhombic structure. These phase transformations were also calculated by using the enthalpy calculations. Transition phases, lattice parameters and bulk properties we attained are comparable with experimental and theoretical data.     

Homooligopeptides composed of hydrophobic amino acid residues interact in a specific manner by taking α-helix or β-structure toward lipid bilayers

In order to investigate the role of each amino acid residue in determining the secondary structure of the transmembrane segment of membrane proteins in a lipid bilayer, we made a conformational analysis by CD for lipid-soluble homooligopeptides, benzyloxycarbonyl-(Z-) Aaa_n-OEt (n = 5-7), composed of Ala, Leu, Val, and Phe, in three media of trifluoroethanol, sodium dodecyl sulfaie micelle, and phospholipid liposomes. The lipid-peptide interaction was also studied through the observation of bilayer phase transition by differential scanning cahrimetry (DSC). The CD studies showed that peptides except for Phe oligomers are present as a mainly random structure in trifluoroethanol, as a mixture of α-helix, β-sheet, β-turn, and /or random in micelles above the critical micellization concentration and preferably as an extended structure of α-helical or β-structure in dipalmitoyl-D,L -α-phosphatidylcholine (DPPC) liposomes of gel state. That the β-structure content of Val oligomers in lipid bilayers is much higher than that in micelles and the oligopeptides of Leu (n = 7) and Ala (n = 6) can take an α-helical structure with one to two turns in lipid bilayers despite their short chain lengths indicates that lipid bilayers can stabilize the extended structure of both α-helical and β-structures of the peptides. The DSC study for bilayer phase transition of DPPC / peptide mixtures showed that the Leu oligomer virtually affects neither the temperature nor the enthalpy of the transition, while Val and Ala oligomers slightly reduce the transition enthalpy without altering the transition temperature. In contrast, the Phe oligomer affects the phase transition in much more complicated manner. The decreasing tendency of the transition enthalpy was more pronounced for the Ala oligomer as compared with the Leu and Val oligomers, which means that the isopropyl group of the side chain has a less perturbing effect on the lipid acyl chain than the methyl group of Ala. © 1995 John Wiley & Sons, Inc.     

Computation of the bond dissociation enthalpies and free energies of hydroxylic antioxidants using the ab initio Hartree–Fock method

Abstract

Introduction

A new method for calculating theoretical bond dissociation enthalpy (BDE) and bond dissociation free energy (BDFE) of hydroxylic antioxidants is forwarded. BDE and BDFE may be understood as activation energies accompanying the formation of transition states, which may undergo downhill homolytic dissociation. The new method does not involve the complete fission of O–H bonds.

Method

Theoretical gas phase BDE values were calculated with the ab initio unrestricted Hartree–Fock (UHF) method, as changes in enthalpy between ground singlet states (GS) and triplet dissociative states (DS). Similarly, gas phase BDFEs were estimated from the corresponding changes in Gibbs free energy. The results were then compared with reliable experimental reports.

Results

The proposed theoretical approach of BDE and BDFE determination was tested using 10 simple phenols, 5 flavonoids, and l-ascorbic acid derivatives. The agreement between our calculated gas phase results and the adopted experimental values were generally within 0.5 kcal mol^?1, with a very few exceptions.

Discussion

Generally, steric interactions as well as intramolecular hydrogen bonding involving the dissociating OH group should be minimized in the GS. The DS are both electronically and vibrationally exited transition states. They have one unpaired electron on the carbon atom, which bears the homolytically dissociating OH group and are second order saddle points with a fixed <C–O–H bond angel of 180°.

Conclusion

It was concluded that ab initio UHF was well suited for the estimation of gas phase BDE and BDFE. The method presented has a good potential for application across a range of hydroxylic antioxidants. Currently, work is underway to extend its application in other class of antioxidants.     

TCNE-aniline charge transfer complex: ab initio and TDDFT investigations in gas phase

The geometric and electronic structure of tetracyanoethylene (TCNE)-aniline (donor-acceptor type) complex has been investigated in gas phase using ab initio and time dependent density functional theory calculations. Both the above calculations predict a composed structure for the complex, in which the interacting site is a C≡N and C=C bond center in the TCNE and, –NH₂ and π-electrons of aniline. The N atom of aniline is oriented toward the TCNE molecule. The charge transfer transition energy, estimated by calculating the ground-to-excited state transition electric dipole moments of the complex, agree well with the reported experimental value in chloroform medium. TCNE-aniline at ground state. TCNE-aniline at excited state     

Three‐Stage Inter‐Orthorhombic Evolution and High Thermoelectric Performance in Ag‐Doped Nanolaminar SnSe Polycrystals

The ultrahigh thermoelectric performance of SnSe‐based single crystals has attracted considerable interest in their polycrystalline counterparts. However, the temperature‐dependent structural transition in SnSe‐based thermoelectric materials and its relationship with their thermoelectric performance are not fully investigated and understood. In this work, nanolaminar SnSe polycrystals are prepared and characterized in situ using neutron and synchrotron powder diffraction measurements at various temperatures. Rietveld refinement results indicate that there is a complete inter‐orthorhombic evolution from Pnma to Cmcm by a series of layer slips and stretches along the a‐ and b‐axes over a 200 K temperature range. This phase transition leads to drastic enhancement of the carrier concentration and phonon scattering above 600 K. Moreover, the unique nanolaminar structure effectively enhances the carrier mobility of SnSe. Their grain and layer boundaries further improve the phonon scattering. These favorable factors result in a high ZT of 1.0 at 773 K for pristine SnSe polycrystals. The thermoelectric performances of polycrystalline SnSe are further improved by p‐type and n‐type dopants (i.e., doped with Ag and SnCl₂, respectively), and new records of ZT are achieved in Ag_0.015Sn_0.985Se (ZT of 1.3 at 773 K) and SnSe_0.985Cl_0.015 (ZT of 1.1 at 773 K) polycrystals.     

Thermodynamics of partitioning and efflux of phenothiazines from liposomes

Summary The partitioning of nine phenothiazines between dimyristoylphosphatidylcholine (DMPC) liposomes and 0.9% wt/vol saline at pH 6 has been studied both below and above the phase transition temperature (T _c ) of the phospholipid. Higher partitioning was observed aboveT _c . Both the entropy and enthalpy of partitioning were positive below and aboveT _c , and a linear relationship between the entropy and enthalpy has been derived. In general, the partitioning and transport of alkylaminophenothiazines in DMPC liposomes over the temperature range of 5 to 40°C is entropically controlled. The entropies and enthalpies of partitioning of various groups in the phenothiazine structure have been calculated.No relationship was found between particle size of the DMPC liposomes and the equilibrium partition coefficient at 25°C. However, the particle size of liposomes did increase with increasing acyl chain length of the phospholipid.Using differential scanning calorimetry, the enthalpy and entropy of transition of the DMPC liposomes in the absence and presence of phenothiazines has been calculated. The temperature dependence of the first-order rate constant of trimeprazine tartrate transport in DMPC liposomes was investigated and was found to be maximum at theT _c of the phospholipid.     

Cooperative nonenzymic base recognition II. thermodynamics of the helix-coil transition of oligoadenylic + oligouridylic acids

The properties of oligonucleotide helices of adeuylic- and uridylic acid oligomers have been investigated by measurements of hypo-and hyperchromieity. High ionic strengths favor the formation of triple helices. Thus, the double helix-coil transition can be studied (without interference by triple helices) only at low ionic-strength. A “phase diagram” is given representing the T_m-values of the various transitions at different ionic strengths for the system A(pA)₁₇ + U(pU)₁₇. Oligonucleolides of chain lengths <8 always form both double and triple helices at the nucleotide concentrations required for base pairing. For this reason the double helix-coil transition without coupling of the triple helix equilibrium can only be measured for chain lengths higher than 7. Melting curves corresponding to this transition have been determined for chain lengths 8, 9, 10, 11, 14 and 18 at different concentrations. An increase in nucleotide concentration leads to an increase in melting temperature. The shorter the chain length the lower the T_m-value and the broader the helix-coil transition. The experimental transition curves have been analysed according to a staggering zipper model with consideration of the stacking of the adeuylic acid single strands and the electrostatic repulsion of tlip phosphate charges on opposite strands. The temperature dependence of the nucleation parameter has been accounted for by a slacking factor x. The stacking factor expresses the magnitude of the stacking enthalpy. By curve fitting xwas computed to be 0.7, corresponding to a stacking enthalpy of about S kcal/mole. The model described allows the reproduction of the experimental transition curves with relatively high accuracy. In an appendix the thermodynamic parameters of the stacking equilibrium of poly A and of the helix-coil equilibria of poly A + poly U at neutral pH are calculated (ΔH_A = ?7.9 kcal/mole for the poly A stacking and ΔH₁₂ = ?10.9 kcal/mole for the formation of the double helix from the randomly coiled single strands). A formula for the configurational entropy of polymers derived by Flory on the basis of a liquid lattice model is adapted to calculate the stacking entropies of adenylic oligomers.     

The effect of hashish compounds on phospholipid phase transition

The interaction of hashish compounds, Δ¹-tetrahydrocannabinol and cannabidiol, with dipalmitoyl phosphatidylcholine was investigated using differential scanning calorimetry. Both drugs affect the transition of dipalmitoyl phosphatidylcholine from the gel to liquid crystalline state, decreasing both the melting temperature and the enthalpy of melting. At a drug to dipalmitoyl phosphatidylcholine ratio of approx. 1:5, two peaks appear in the transition profile, suggesting a phase separation in the drug dipalmitoyl phosphatidylcholine mixture.     

Interactions between two sheets of a bilayer membrane and its internal lateral pressure

We have modelled a phospholipid bilayer as two monolayer sheets which interact with each other by a coupling which depends upon the states of the lipid hydrocarbon chains in each sheet. We make use of a model (Georgallas and Pink 1982a) and its parameters, already used to study monolayer phase changes at the LC-LE transition, in order to study the lipid main transition. Although the monolayer coexistence curve can be calculated exactly, we have made use of high-temperature series expansions to calculate the critical point of the bilayer. We also present the results of computer simulations on triangular lattices for the pressure-area isotherms. We find: (i) the interaction between the sheets of a DPPC bilayer is about 1.5–2% of the maximum interaction within the plane of each sheet; (ii) the internal lateral pressure of a DPPC bilayer is about 30.5 dyne/cm; (iii) the bilayer transition enthalpy depends sensitively upon the coupling between the sheets. Should this coupling vary from sample to sample (due, possibly, to its preparation) then very different values of transition enthalpy may be measured. (iv) We present a rough rule-of-thumb for estimating the internal lateral pressure of a bilayer from a knowledge of the corresponding monolayer pressure-area isotherms.Abbreviations LC-LE liquid condensed — liquid expanded - DPPC dipalmitoylphosphatidylcholine - Q transition enthalpy Work supported in part by the Natural Sciences and Engineering Research Council of Canada     

Structure and electronic absorption spectra of nematogenic alkoxycinnamic acids - a comparative study based on semiempirical and DFT methods

Structure of nematogenic p-n-Alkoxy cinnamic acids (nOCAC) with various alkyl chain carbon atoms (n = 2, 4, 6, 8) has been optimized using density functional B3LYP with 6-31+G (d) basis set using crystallographic geometry as input. Using the optimized geometry, electronic structure of the molecules has been evaluated using the semiempirical methods and DFT calculations. Molecular charge distribution and phase stability of these systems have been analyzed based on Mulliken and L?wdin population analysis. The electronic absorption spectra of nOCAC molecules have been simulated by employing DFT method, semiempirical CNDO/S and INDO/S parameterizations. Two types of calculations have been performed for model systems containing single and double molecules of nOCAC. UV-Visible spectra have been calculated for all single molecules. The UV stability of the molecules has been discussed in light of the electronic transition oscillator strength (f). The dimer complexes of higher homologues (n = 6, 8) have also been reported to enable the comparison between single and double molecules.     

Antioxidant activity of phenolic and related compounds: a density functional theory study on the O–H bond dissociation enthalpy

Abstract

We report here on calculations at the hybrid DFT/HF (B3-LYP/6-31G(d, p)) level of the O–H bond dissociation enthalpy (O–H BDE) of phenylpropenoic acids (caffeic, ferulic, p-coumaric and cinnamic) and phenolic acids and related compounds (gallic, methylgallate, vanillic and gentisic) in order to gain insight into the understanding of structure–antioxidant activity relationships. The results were correlated and discussed mainly on the basis of experimental data in a companion work (Galato D, Giacomelli C, Ckless K, Susin MF, Vale RMR, Spinelli A. Antioxidant capacity of phenolic and related compounds: correlation among electrochemical, visible spectroscopy methods and structure-antioxidant activity. Redox Report 2001; 6: 243–250). The O–H BDE values showed remarkable dependence on the hydroxyl position in the benzene ring and the existence of additional interaction due to hydrogen bonding. For parent molecules, the experimental antioxidant activity (AA) order was properly obeyed only when intramolecular hydrogen bonding was present in the radicalized structures of o-dihydroxyl moieties. In structurally related compounds, excellent correlation with experimental data was in general observed (0.64 < ρ < 0.99). However, it is shown that excellent correlation can also be obtained for this series of compounds considering p-radicalized structures which were not stabilized by intramolecular hydrogen bonding, but this had no physical meaning. These findings suggested that the antioxidant activity evaluation of phenolic and related compounds must take into consideration the characteristics of each particular compound.     

Conformational changes in transfer RNA. I. Equilibrium theory

We report the results of semi-empirical calculations describing thermodynamic properties of transfer RNA conformations. The most important new features of the procedure are: (1) the use of parameters obtained from model oligoribonucleotides to evaluate the free energy of helical regions and small hairpin loops, and (2) the use of a model which is somewhat more realistic than the freely jointed chain for evaluating internal loops and intermediate size hairpin loops. The new parameters lead to important quantitative and qualitative differences from predictions which would have been made in the past and lead to a priori predictions of tRNA melting temperatures which are within about 6°C of the experimental values. The results suggest the following conclusions: (1) The early melting transition observed in several tRNA's is partly the result of tertiary unfolding, and partly the result of the loss of some secondary structure. (2) The part of the secondary structure which melts during the early transition is different for different tRNA's. For fMet and Tyr from E. coli, the calculations predict that the dihydrouradiene arm melts out early. For yeast Phe the acceptor stem and anticodon helix melt first. (3) The results also suggest the possibility that tertiary unfolding and early secondary structural melting do not occur independently but are coupled, so that the two types of structure are probably mutually stabilizing.     

Ceramide acyl chain length markedly influences miscibility with palmitoyl sphingomyelin in bilayer membranes

Ceramides are precursors of major sphingolipids and can be important cellular effectors. The biological effects of ceramides have been suggested to stem from their biophysical effects on membrane structure affecting the lateral and transbilayer organization of other membrane components. In this study we investigated the effect of acyl chain composition in ceramides (C4-C24:1) on their miscibility with N-palmitoyl-sphingomyelin (PSM) using differential scanning calorimetry. We found that short-chain (C4 and C8) ceramides induced phase separation and lowered the T _m and enthalpy of the PSM endotherm. We conclude that short-chain ceramides were more miscible in the fluid-phase than in the gel-phase PSM bilayers. Long-chain ceramides induced apparent heterogeneity in the bilayers. The main PSM endotherm decreased in cooperativity and enthalpy with increasing ceramide concentration. New ceramide-enriched components could be seen in the thermograms at all ceramide concentrations above X _Cer = 0.05. These broad components had higher T _m values than pure PSM. C24:1 ceramide exhibited complex behavior in the PSM bilayers. The miscibility of C24:1 ceramide with PSM at low (X _Cer = 0.05–0.10) concentrations was exceptionally good according to the cooperativity of the transition. At higher concentrations, multiple components were detected, which might have arisen from interdigitated gel-phases formed by this very asymmetric ceramide. The results of this study indicate that short-chain and long-chain ceramides have very different effects on the sphingomyelin bilayers. There also seems to be a correlation between their miscibility in binary systems and the effect of ceramides of different hydrophobic length on sphingomyelin-rich domains in multicomponent membranes.     

Sterol chemical configuration influences the thermotropic phase behaviour of dipalmitoylphosphatidylcholine bilayers containing 5α-cholestan-3β- and 3α-ol

It is commonly believed that all membrane sterols are rigid all-trans ring systems with a fully extended alkyl side-chain and that they similarly influence phospholipid bilayer physical properties. Here, we report the sterol concentration-dependent, thermotropic phase behaviour of binary dipalmitoylphosphatidylcholine (DPPC)/sterol mixtures containing two similar 5α-H sterols with different functional group orientations (3α-OH or 3β-OH), which adopt an ideal all-trans planar ring conformation but lack the deformed ring B conformation of cholesterol (Chol) and epicholesterol (Echol), using differential scanning calorimetry (DSC). Our deconvolution of the DSC main phase transition endotherms show differences in the proportions of sterol-poor (sharp) and sterol-rich (broad) domains in the DPPC bilayer with increasing sterol concentration, which delineate gel/liquid-crystalline (P_β′/L_α) and disordered gel (L_β)/liquid-ordered (l_o) phase regions. There are similarities in the DPPC main phase transition temperature, cooperativity and enthalpy for each 3β-ol and 3α-ol pair with increasing sterol concentration and differences in the parameters obtained for both the sterol-poor and sterol-rich regions. The sterol-poor domain persists over a greater concentration range in both 3α-ol/DPPC mixtures, suggesting that either those domains are more stable in the 3α-ols or that those sterols are less miscible in the sterol-rich domain. Corresponding parameters for the sterol-rich domain show that at sterol concentrations up to 20 mol%, the 5α-H,3β-ol is more effective at reducing the phase transition enthalpy of the broad component () than Chol, but is less effective at higher concentrations. Although mixtures containing Echol and 5α-cholestan-3α-ol have similar positive slopes below 7 mol% sterol, suggesting that they abolish the L_β/l_o phase transition equally effectively at low concentrations, Echol is more effective than the saturated 3α-ol at higher sterol concentrations. A comparison of obtained for the saturated and unsaturated pairs suggests that the latter sterols stabilize the l_o phase and broaden and abolish the DPPC main phase transition more effectively than the saturated sterols at physiologically relevant concentrations, supporting the idea that the double bond of Chol and Echol promotes greater sterol miscibility and the formation of l_o phase lipid bilayers relative to corresponding saturated sterols in biological membranes.     

A pH titration study on the ionic bridging within lipopolysaccharide aggregates

The packing of lipopolysaccharide aggregates from rough strains of Escherichia coli was examined at different pH values. Lipopolysaccharide head-group motion, measured with an electron spin resonance probe, was found to be dependent on pH, and indicated the existence of multiple ionizable groups. Lipopolysaccharide from a rough (Ra) and a heptose-less (Re) mutant were more rigid at pH 5 than at pH 10.5. In addition, head-group mobility of the magnesium salt of Ra lipopolysaccharide was substantially less than that of the sodium salt at pH 7.0, whereas at high pH (pH 12) the two salts were equally fluid. Changes in head-group packing were also reflected in pH-dependent changes in the phase transition measured with differential scanning calorimetry. The enthalpy of the transition, ΔH_t, for the sodium salt of Re lipopolysaccharide was greatest at pH 7.5 and approached zero in both the acidic and the basic pH ranges. We propose that fixed charges in the core and lipid A regions significantly influence lipopolysaccharide head-group motion and the lipopolysaccharide aggregation state. Furthermore, ionic bridging among phosphate groups dramatically rigidifies head group interactions in the neutral to acidic pH ranges.     

A theoretical model of the temperature- and pressure-induced phase transition of phospholipid bilayers

A statistical thermodynamic model of phospholipid bilayers is developed. In the model, a new concept of a closely packed system is applied, i.e., a system of hard cylinders of equal radii, the radius being a function of the average number of gauche rotations in a hydrocarbon chain. Using this concept of a closely packed system, reasonable values are obtained for the change in specific volume at the order-disorder transition of lecithin bilayers. In addition to interactions between the lipid matrix and water molecules, between the head groups themselves and between hydrocarbon chains, as well as the intramolecular energy associated with chain conformation, the Hamiltonian of the membrane also includes the energy of the pressure field. Thus, the phase transition of phospholipid membranes induced not only by temperature hut also by hydrostatic pressure is described by this model simultaneously. In accordance with the experimental results, a linear relationship is obtained between the phase transition temperature and phase transition pressure. The other calculated phase transition properties of lecithin homologues. e.g., changes in enthalpy, surface area. thickness and gauche number per chain are in agreement with the available experimental data. The ratio of kink to interstitial conduction of bilayers is also estimated.     

The helix-coil transitions of poly (dA)-poly (dT) and poly (dA-dT)-poly (dA-dT)

Helix–coil transition curves are calculated for poly (dA) poly(dT) and poly (dA-dT) poly (dA-dT) using the integral equation approach of Goel and Montroll.⁵ The transitions are described by the loop entropy model with the exponent of the loop entropy factor, k, remaining an arbitrary constant. The theoretical calculations are compared with experimental transition curves of the two polymers. Results indicate that the stacking energies for these two polymers differ by about 1 kcal/mole of base pairs. Also, a fit between theory and experiment was not possible for k > 1.70.     

Structural phase transition of BeTe: an ab initio molecular dynamics study

Beryllium telluride (BeTe) with cubic zinc-blende (ZB) structure was studied using ab initio constant pressure method under high pressure. The ab initio molecular dynamics (MD) approach for constant pressure was studied and it was found that the first order phase transition occurs from the ZB structure to the nickel arsenide (NiAs) structure. It has been shown that the MD simulation predicts the transition pressure P _T more than the value obtained by the static enthalpy and experimental data. The structural pathway reveals MD simulation such as cubic → tetragonal → orthorhombic → monoclinic → orthorhombic → hexagonal, leading the ZB to NiAs phase. The phase transformation is accompanied by a 10% volume drop and at 80 GPa is likely to be around 35 GPa in the experiment. In the present study, our obtained values can be compared with the experimental and theoretical results.

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Graphical abstract The energy-volume relation and ZB phase for the BeTe

     

High sensitivity differential scanning calorimetry of the bilayer to hexagonal phase transitions of diacylphosphatidylethanolamines

The bilayer to hexagonal phase transition of dioleoylphosphatidylethanolamine has been detected for the first time by differential scanning calorimetry. The observed transition is dependent on scan rate. This dependence can be explained by assuming that at rapid scan rates, the rate of conversion of bilayer to hexagonal phase is too slow at low temperatures for equilibration to take place. At higher temperatures the rate of interconversion becomes more rapid. The transition is observed to occur at 14°C using a scan rate of 0.74 K/min while it is centered at 8°C using a scan rate of 0.19 K/min. The enthalpy of the transition is 290 ± 40 cal/mol lipid and the transition is characterized by a ΔCp of −9 ± 1 mcal K⁻¹ (g lipid)⁻¹. The bilayer to hexagonal phase transition of dielaidoylphosphatidylethanolamine and of 1-palmitoy1-2-oleoylphosphatidylethanolamine occurs at 65.6°C and 71.4°C, respecitvely, with a corresponding transition enthalpy of 450 ± 20 and 400 ± 30 cal/mol lipid. The transitions of these phosphatidylethanolamines, occuring at higher temperatures, are independent of scan rate and show a higher degree of cooperativity than that of dioleoylphosphatidylethanolamine. Compared with the gel to liquid-crystalline transition of bilayer phospholipids the transition to hexagonal phase has a much lower enthalpy.