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Energy Difference (energy + difference)
Kinds of Energy Difference Selected AbstractsEnergy-Modulated Heterostructures Made with Conjugated Polymers for Directional Energy Transfer and Carrier Confinement,ADVANCED FUNCTIONAL MATERIALS, Issue 15 2007R. Favarim Abstract In this paper we demonstrate that multilayer structures with modulated bandgaps can be used for efficient energy transfer and carrier confinement inside a nanostructured film of a light-emitting polymer. The films were produced with the layer-by-layer technique (LbL) with a poly(p -phenylene vinylene) (PPV) precursor and a long chain dodecylbenzenesulfonate ion (DBS). DBS is incorporated selectively into the precursor chain, and with a rapid, low temperature conversion process (100,°C) superstructures with variable HOMO,LUMO gap could be formed along the deposition direction by changing the DBS concentration. Structures with different stair-type energy modulations were produced, which are thermally stable and reproducible, as demonstrated by UV-VIS. absorption measurements. Energy differences of up to 0.5,eV between the lowest and highest conjugated layers inside the stair structure could be achieved, which was sufficient to guide the excitation over long distances to the lower bandgap layer. [source] A Rearrangement of Azobenzene upon Interaction with an Aluminum(I) Monomer LAl {L = HC[(CMe)(NAr)]2, Ar = 2,6- iPr2C6H3}EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 11 2005Hongping Zhu Abstract Reaction of LAl (1) or [LAl{,2 -C2(SiMe3)2}] (2) {L = HC[(CMe)(NAr)]2, Ar = 2,6- iPr2C6H3} with azobenzene affords a five-membered ring compound [LAl{N(H)- o -C6H4N(Ph)}] (3). In the formation of 3 a three-membered intermediate [LAl(,2 -N2Ph2)] (A) is suggested by a [1 + 2] cycloaddition reaction; A is not stable and further rearranges to 3. DFT calculations on similar compounds with modified L' {L' = HC[(CMe)(NPh)]2} show that the complexation energy of the reaction of L'Al with azobenzene to form [L'Al(,2 -N2Ph2)] is about,39 kcal,mol,1, and the best estimate of the energy difference between [L'Al(,2 -N2Ph2)] and [L'Al{N(H)- o -C6H4N(Ph)}] is,76 kcal,mol,1. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Nitrogen Trifluoride as a Bifunctional Lewis Base: Implications for the Adsorption of NF3 on Solid SurfacesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 5 2004Paola Antoniotti Abstract The structure, stability, and thermochemistry of isomeric adducts between NF3 and the Lewis acids BH3,nFn (n = 0,3) have been investigated at the coupled-cluster and at the Gaussian-3 (G3) level of theory. At the CCD/cc-pVDZ level both the nitrogen- and the fluorine-coordinated structures of all BH3,nFn,(NF3) (n = 0,3) adducts were characterized as true minima on the potential energy surface, thus providing the first theoretical evidence for the behavior of NF3 as a bifunctional Lewis base when interacting with neutral Lewis acids. At the G3 level, and 298.15 K, including the contribution of the entropy term, the H3B,NF3 adduct is predicted to be more stable than H3B,F,NF2 by 4.3 kcal mol,1; this free energy difference is 3.7 kcal mol,1 at the CCSD(T)/cc-pVTZ//CCD/cc-pVDZ level of theory. Conversely, at the latter computational level, the fluorine-coordinated isomers of the BH2F,(NF3), BHF2,(NF3), and BF3,(NF3) adducts are practically degenerate with the nitrogen-coordinated ones. BH3,nFn,(NF3) (n = 0,3) complexes feature typical bond dissociation energies of ca. 1,2 kcal mol,1, and are predicted to be thermodynamically stable only at low temperatures. However, the appreciable influence of the basis set superposition error (BSSE) prevents a quantitative assessment of these small computed dissociation energies. Finally, we briefly discuss the implications of our calculations for the adsorption of NF3 on solid surfaces. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] The Mechanism of the Stetter Reaction , A DFT StudyEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 33 2008Kirsty J. Hawkes Abstract On the basis of Breslow's mechanism for benzoin condensation, a model asymmetric Stetter reaction has been investigated using DFT methods. In contrast to the concerted benzoin condensation, after formation of the Breslow intermediate the Stetter reaction is found to be a two-step process in which the rate-determining C,C coupling of the Breslow intermediate and the Michael acceptor precedes final proton transfer. In addition, the enolamine is found to play a significant role in the stereochemistry of the product, with the energy difference between stereoisomers of this intermediate reflected throughout the remainder of the reaction sequence. Consequently, electronic and steric control of the stereochemistry of this intermediate should directly enhance the ee values of the product. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Radical Cation and Dication Derived from 4,8-Diethylbenzo[1,2- d:4,5- d,]bis[1,2,3]trithiole [DEBBT]: Change of Electronic State from Singlet-State Dication DEBBT(2+)- S to Triplet-State Dimer 2DEBBT(2+)- T in D2SO4 and CD3CN SolutionsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 24 2003Takeshi Kimura Abstract 4,8-Diethylbenzo[1,2- d:4,5- d,]bis[1,2,3]trithiole [DEBBT] was oxidized using concentrated D2SO4, leading to the generation of the radical cation DEBBT(·+) which was verified by ESR spectroscopy. DEBBT(·+) in the solution was further oxidized to produce the dication DEBBT(2+), as determined by 1H and 13C NMR spectroscopy. DEBBT(2+) was also prepared by treating DEBBT 1-oxide [DEBBT 1-O] with concentrated D2SO4, and was verified by 1H and 13C NMR spectroscopy. The 13C NMR chemical shifts of DEBBT(2+), calculated by the density functional theoretical (DFT) method at the B3LYP6-31G** level, correlated well with those obtained experimentally. The ESR signal of DEBBT(2+) generated from DEBBT 1-O was observed in solution, which implies that the singlet-state dication DEBBT(2+)- S isomerizes to the triplet-state dication DEBBT(2+)- T, and that two molecules of DEBBT(2+)- T further form a spin pair at one trithiole ring with significant distance between the two radical centers. The oxidation of DEBBT with one or two equivalents of single-electron oxidizing reagents produced DEBBT(·+) and DEBBT(2+), and the salts were isolated in a stable form. However, the DEBBT(2+) that was prepared by oxidation with NOPF6 proved silent for NMR in CD3CN, while ESR was active. The stability, electronic state, and NMR and ESR spectroscopy of the dication are affected by solvation with D2SO4 and CD3CN. The optimized structures and the total energy of the singlet- and triplet-state dication were calculated using the DFT method at the B3LYP6-31G** level, which shows that the structures of the singlet- and triplet-state dications have a completely planar form with 1.7 kcal/mol as the total energy difference between them. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Phase Diagrams and Glass Formation in Metallic Systems,ADVANCED ENGINEERING MATERIALS, Issue 6 2007M. Baricco Abstract The basic thermodynamic aspects of glass-formation in metallic systems are reviewed. In particular, the specific features of a phase diagram with respect to glass-formation are evidenced. On the basis of the regular solution model, the effect of various thermodynamic quantities on the free energy difference between undercooled liquid and crystal phases are outlined. In order to describe the amorphous phase, a specific heat difference between liquid and solid phases in the undercooling regime is introduced in the CALPHAD assessment of various binary systems. The glass-transition is described as a second order transition. Examples are given for different systems, including Fe-B and Cu-Mg. From the description of the free energy of various phases as a function of composition and temperature, the driving forces for nucleation of crystal phases and the T0 curves are estimated. [source] Vertical Phase Separation in Poly(3-hexylthiophene): Fullerene Derivative Blends and its Advantage for Inverted Structure Solar CellsADVANCED FUNCTIONAL MATERIALS, Issue 8 2009Zheng Xu Abstract A method which enables the investigation of the buried interfaces without altering the properties of the polymer films is used to study vertical phase separation of spin-coated poly(3-hexylthiophene) (P3HT):fullerene derivative blends. X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) analysis reveals the P3HT enrichment at the free (air) surfaces and abundance of fullerene derivatives at the organic/substrate interfaces. The vertical phase separation is attributed to the surface energy difference of the components and their interactions with the substrates. This inhomogeneous distribution of the donor and acceptor components significantly affects photovoltaic device performance and makes the inverted device structure a promising choice. [source] Formation of Nb2O5 Nanotube Arrays Through Phase Transformation**,ADVANCED MATERIALS, Issue 5 2008C. Yan The successful synthesis of monoclinic Nb2O5nanotube arrays (see figure) from pseudo-hexagonal Nb2O5 nanorod arrays is reported; the synthesis is based on phase transformation accompanied by void formation, where voids can be intriguingly generated during phase transformation. A key parameter for achieving nanotube growth is the energy difference between the pseudo-hexagonal and monoclinic Nb2O5 nanostructures, which determines the phase transformation. [source] Efficiency of nested Markov chain Monte Carlo for polarizable potentials and perturbed HamiltoniansINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2010Florent Calvo Abstract Nested Markov chain Monte Carlo is a rigorous way to enhance sampling of a given energy landscape using an auxiliary, approximate potential energy surface. Its practical efficiency mainly depends on how cheap and how different are the auxiliary potential with respect to the reference system. In this article, a combined efficiency index is proposed and assessed for two important families of energy surfaces. As illustrated for water clusters, many-body polarizable potentials can be approximated by simplifying the polarization contribution and keeping only the two-body terms. In small systems, neglecting polarization entirely is also acceptable. When the reference potential energy is obtained from diagonalization of a quantum mechanical Hamiltonian, a first-order perturbation scheme can be used to estimate the energy difference occuring on a Monte Carlo move. Our results indicate that this perturbation approximation performs well provided that the number of steps between successive diagonalization is adjusted beforehand. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2342,2346, 2010 [source] Ground states of BeC and MgC: A comparative multireference Brillouin,Wigner coupled cluster and configuration interaction study,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005Vasilios I. Teberekidis Abstract The competing X3,, and 5,, states of the experimentally unknown alkaline,earth metal carbides BeC and MgC are examined with the multireference Brillouin,Wigner coupled cluster method restricted to single and double excitations (MRBW-CCSD). The results are compared against the traditional single-reference CCSD approach, as well as with other single and multireference methods. In both molecules, the CCSD 5,, , X3,, energy difference is underestimated, leading to an "erroneous" ground-state prediction in BeC. The MRBW-CCSD method corrects this anomalous behavior, leading to fair agreement with multireference configuration interaction (MR-CI) predictions. Our results at the highest levels of theory are extrapolated to the basis set limit, and the core/valence correlation is taken into account, leading to very accurate energetics and spectroscopic constants in both carbides. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Mode-selective stereomutation tunneling as compared to parity violation in hydrogen diselenide isotopomers 1,2,3H280Se2ISRAEL JOURNAL OF CHEMISTRY, Issue 3-4 2003Michael Gottselig We present quantitative calculations of the mode-selective stereomutation tunneling in the chiral hydrogen diselenide isotopomers X2Se2 with X = H, D, and T. The torsional tunneling stereomutation dynamics were investigated with a quasi-adiabatic channel quasi-harmonic reaction path Hamiltonian approach, which treats the torsional motion anharmonically in detail and all remaining coordinates as harmonic (but anharmonically coupled to the reaction coordinate). We also investigated the influence of the excitation of fundamental modes on the stereomutation dynamics and predict which modes should be promoting or inhibiting. Our stereomutation dynamics results and the influence of parity violation on these are discussed in relation to our recent investigations for the analogous molecules H2O2, HSOH, H2S2, and Cl2S2. The electronic potential energy barrier heights for the torsional motion of hydrogen diselenide are similar to those of HSOH, whereas the torsional tunneling splittings are similar to the corresponding values of HSSH. The ground-state torsional tunneling splittings calculated here for D2Se2 are of the same order as the parity-violating energy difference reported by Laerdahl and Schwerdtfeger (Phys. Rev. A 1999, 60, 4439), whereas for T2Se2 the corresponding tunneling splitting is about three orders of magnitude smaller. [source] Lower critical solution temperature determination of smart, thermosensitive N -isopropylacrylamide- alt -2-hydroxyethyl methacrylate copolymers: Kinetics and physical propertiesJOURNAL OF APPLIED POLYMER SCIENCE, Issue 5 2008Mohammad M. Fares Abstract The lower critical solution temperatures (LCSTs) were verified and determined for different molar feed ratios of N -isopropylacrylamide (NIPAAm) and 2-hydroxyethyl methacrylate (HEMA) monomers with ultraviolet spectroscopy and differential scanning calorimetry techniques. Increases in the NIPAAm monomer content played a crucial role in the LCST, which increased up to 36.7°C at 50 mol %. However, a further increase in the NIPAAm monomer content steadily reduced the LCST, which decreased to 33°C at 100 mol % NIPAAm [i.e., pure poly(N -isopropylacrylamide)]. The rate of copolymerization, assessed by the conventional conversion (%),time method, and the apparent activation energies were determined. The reactivity ratios of the monomers, determined by the Kelen,Tudos and Fineman,Ross techniques, together with the results of an equation, showed that the copolymer which formed was an alternating copolymer. The Q,e values for the NIPAAm monomer were determined. The equation showed the linear Arrhenius behavior of ln(r1r2) versus the reciprocal of the temperature (where r1 and r2 are the reactivity ratios of NIPAAm and HEMA, respectively): the activation energy difference [i.e., (E12 + E21) , (E11 + E22), where E12, E21, E11, and E22 are various activation energies] was found to be ,109 kJ/mol. The copolymers were characterized with 1H-NMR, 13C-NMR, Fourier transform infrared, ultraviolet,visible, thermogravimetric analysis, differential scanning calorimetry, X-ray diffraction, and scanning electron microscopy techniques. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008 [source] Basic ingredients of free energy calculations: A reviewJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2010Clara D. Christ Abstract Methods to compute free energy differences between different states of a molecular system are reviewed with the aim of identifying their basic ingredients and their utility when applied in practice to biomolecular systems. A free energy calculation is comprised of three basic components: (i) a suitable model or Hamiltonian, (ii) a sampling protocol with which one can generate a representative ensemble of molecular configurations, and (iii) an estimator of the free energy difference itself. Alternative sampling protocols can be distinguished according to whether one or more states are to be sampled. In cases where only a single state is considered, six alternative techniques could be distinguished: (i) changing the dynamics, (ii) deforming the energy surface, (iii) extending the dimensionality, (iv) perturbing the forces, (v) reducing the number of degrees of freedom, and (vi) multi-copy approaches. In cases where multiple states are to be sampled, the three primary techniques are staging, importance sampling, and adiabatic decoupling. Estimators of the free energy can be classified as global methods that either count the number of times a given state is sampled or use energy differences. Or, they can be classified as local methods that either make use of the force or are based on transition probabilities. Finally, this overview of the available techniques and how they can be best used in a practical context is aimed at helping the reader choose the most appropriate combination of approaches for the biomolecular system, Hamiltonian and free energy difference of interest. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Predicting the tautomeric equilibrium of acetylacetone in solution.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2010Abstract This study investigates how the various components (method, basis set, and treatment of solvent effects) of a theoretical approach influence the relative energies between keto and enol forms of acetylacetone, which is an important model system to study the solvent effects on chemical equilibria from experiment and theory. The computations show that the most popular density functional theory (DFT) approaches, such as B3LYP overestimate the stability of the enol form with respect to the keto form by ,10 kJ mol,1, whereas the very promising SCS-MP2 approach is underestimating it. MP2 calculations indicate that in particular the basis set size is crucial. The Dunning Huzinaga double , basis (D95z(d,p)) used in previous studies overestimates the stability of the keto form considerably as does the popular split-valence plus polarization (SVP) basis. Bulk properties of the solvent included by continuum approaches strongly stabilize the keto form, but they are not sufficient to reproduce the reversal in stabilities measured by low-temperature nuclear magnetic resonance experiments in freonic solvents. Enthalpic and entropic effects further stabilize the keto form, however, the reversal is only obtained if also molecular effects are taken into account. Such molecular effects seem to influence only the energy difference between the keto and the enol forms. Trends arising due to variation in the dielectric constant of the solvent result from bulk properties of the solvent, i.e., are already nicely described by continuum approaches. As such this study delivers a deep insight into the abilities of various approaches to describe solvent effects on chemical equilibria. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interactionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2010Ling Wang Abstract Biomolecular association and dissociation reactions take place on complicated interaction free energy landscapes that are still very hard to characterize computationally. For large enough distances, though, it often suffices to consider the six relative translational and rotational degrees of freedom of the two particles treated as rigid bodies. Here, we computed the six-dimensional free energy surface of a dimer of water-soluble alpha-helices by scanning these six degrees of freedom in about one million grid points. In each point, the relative free energy difference was computed as the sum of the polar and nonpolar solvation free energies of the helix dimer and of the intermolecular coulombic interaction energy. The Dijkstra graph algorithm was then applied to search for the lowest cost dissociation pathways based on a weighted, directed graph, where the vertices represent the grid points, the edges connect the grid points and their neighbors, and the weights are the reaction costs between adjacent pairs of grid points. As an example, the configuration of the bound state was chosen as the source node, and the eight corners of the translational cube were chosen as the destination nodes. With the strong electrostatic interaction of the two helices giving rise to a clearly funnel-shaped energy landscape, the eight lowest-energy cost pathways coming from different orientations converge into a well-defined pathway for association. We believe that the methodology presented here will prove useful for identifying low-energy association and dissociation pathways in future studies of complicated free energy landscapes for biomolecular interaction. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Incorporating the effect of ionic strength in free energy calculations using explicit ionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2005Serena Donnini Abstract The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors calculated at five different ion concentrations is used as an example. We show that the free energy difference can be highly sensitive to the presence of explicit ions even in cases where the mutation itself does not involve a change in the overall charge. The effect is most significant if the molecule carries a net charge close to the site mutated. Furthermore, it is shown that the introduction of a small number of ions can lead to very severe sampling problems suggesting that in practical calculations convergence can best be achieved by incorporating either no counterions or by simulating at high ionic strength to ensure sufficient sampling of the ion distribution. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 115,122, 2005 [source] A computational study of conformational interconversions in 1,4-dithiacyclohexane (1,4-dithiane)JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2003Fillmore Freeman Abstract Ab initio molecular orbital theory with the 6-31G(d), 6-31G(d,p), 6-31+G(d), 6-31+G(d,p), 6-31+G(2d,p), 6-311G(d), 6-311G(d,p), and 6-311+G(2d,p) basis sets and density functional theory (BLYP, B3LYP, B3P86, B3PW91) have been used to locate transition states involved in the conformational interconversions of 1,4-dithiacyclohexane (1,4-dithiane) and to calculate the geometry optimized structures, relative energies, enthalpies, entropies, and free energies of the chair and twist conformers. In the chair and 1,4-twist conformers the CHax and CHeq bond lengths are equal at each carbon, which suggest an absence of stereoelectronic hyperconjugative interactions involving carbon,hydrogen bonds. The 1,4-boat transition state structure was 9.53 to 10.5 kcal/mol higher in energy than the chair conformer and 4.75 to 5.82 kcal/mol higher in energy than the 1,4-twist conformer. Intrinsic reaction coordinate (IRC) calculations showed that the 1,4-boat transition state structure was the energy maximum in the interconversion of the enantiomers of the 1,4-twist conformer. The energy difference between the chair conformer and the 1,4-twist conformer was 4.85 kcal/mol and the chair-1,4-twist free energy difference (,G°c-t) was 4.93 kcal/mol at 298.15 K. Intrinsic reaction coordinate (IRC) calculations connected the transition state between the chair conformer and the 1,4-twist conformer. This transition state is 11.7 kcal/mol higher in energy than the chair conformer. The effects of basis sets on the 1,4-dithiane calculations and the relative energies of saturated and unsaturated six-membered dithianes and dioxanes are also discussed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 909,919, 2003 [source] Application of the multiensemble sampling to the hydration free energyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2001Kyu-Kwang Han Abstract We demonstrate the feasibility of using multiensemble sampling method (MESM) to determine the free energy difference between two far states for which the configurational distributions do not overlap at all. The MESM is a recently developed non-Boltzmann sampling technique. The free energy of charging a sodium ion in water is accurately calculated in a single simulation, introducing nine intermediate ionic states. This is due to the ability of the method to explore the relevant parts of configuration space equally for every state, and this ability comes from the universality of weighting function W and the simplicity in adjusting its parameters. Detailed procedures of adjusting the parameters are presented. The comparison with a free energy perturbation method (FEPM) shows that the MESM is more reliable and efficient. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1004,1009, 2001 [source] Benzdiynes revisited: ab initio and density functional theoryJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2001Sundaram Arulmozhiraja Abstract Ab initio and density functional theory (DFT) studies were performed on three isomers of tetradehydrobenzene (benzdiynes). Four different density functionals (BPW91, BLYP, B3LYP, and B1LYP) and two higher levels of theory [QCISD and CCSD(T)] incorporating basis sets up to Dunning's correlation-consistent polarized valence triple-, (cc-pVTZ) were utilized for this purpose. Stability tests showed that more stable solutions were available for 1,4-benzdiyne with unrestricted than with restricted DFT, while solutions obtained with later descriptions of 1,3-benzdiyne and 1,2,3,5-tetradehydrobenzene were stable. UB3LYP provided better geometry for 1,4-benzdiyne. Unlike in an earlier study, the energy difference between 1,2,3,5-tetradehydrobenzene and 1,4-benzdiyne calculated with the B3LYP functional coincided well with that calculated at CCSD(T): 13.07 and 14.32 kcal/mol at the B3LYP/cc-pVTZ and CCSD(T)/cc-pVTZ levels, respectively. 1,2,3,5-Tetradehydrobenzene was 8 kcal/mol more stable than 1,3-benzdiyne at the CCSD(T)/cc-pVTZ level. The heats of formation of benzdiynes were obtained by using the G2, CBS-Q, and CBS-QB3 methodologies. The heats of formation calculated for 1,3-benzdiyne and 1,2,3,5-tetradehydrobenzene were 208.6 and 197.9 kcal/mol, respectively, at the CBS-QB3 level of theory. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 923,930, 2001 [source] Analyses of the partition coefficient, log P, using ab initio MO parameter and accessible surface area of solute moleculesJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2004Hiroshi Chuman Abstract To analyze the log Psol/w values (sol: n -octanol or chloroform, w: water) in the framework of the molecular orbital (MO) procedure, we selected solute descriptors such as the solvation energy difference between aqueous and organic solvent phases and the "surface" area of solute molecules to which water molecules are accessible. The solvation energy of solute molecules in their minimum free-energy conformation was calculated using the ab initio self-consistent reaction field-MO method with the conductor-like screening model. The experimentally measured log Psol/w value of various solutes except for those of amphiprotics was shown to be analyzable reasonably well by the MO model with additional descriptors for the hydrogen-bonding patterns in the solute,solvent interactions. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:2681,2697, 2004 [source] Computational study of the chair,chair interconversion and stereoelectronic interactions in 1,2,3-trithiacyclo-hexane (1,2,3-trithiane)JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 1 2004Fillmore Freeman Abstract Ab initio theory, density functional theory (DFT) and Møller,Plesset perturbation theory (MP2) with the 6,31G(d), 6,31++G(d), 6,31G(d,p), 6,31+G(d,p), 6,31++G(d,p), 6,311G(d,p) and 6,311+G(d,p) basis sets were used to study stereoelectronic hyperconjugative interactions and the mechanism of the chair,chair conformational interconversion in 1,2,3-trithiacyclohexane (1,2,3-trithiane). The relative energies, enthalpies, entropies, free energies and structural parameters of the chair, 1,4-twist and 2,5-twist conformers, a distorted 1,4-boat transition state and a 2,5-boat transition state were calculated. The HF calculated energy difference (,E) between the chair conformer of 1,2,3-trithiane and the distorted 1,4-boat transition state was 10.59,kcal,mol,1 (1 kcal=4.184,kJ). The 1,4-twist conformer and the 2,5-boat transition state are close in energy, as are the 2,5-twist conformer and the distorted 1,4-boat transition state. B3LYP/6,311+G(d,p) calculated the chair conformer of 1,2,3-trithiane to be 5.83, 10.09, and 5.96,kcal,mol,1, respectively, lower in energy than the 1,4-twist conformer, 2,5-twist conformer and 2,5-boat transition state. Intrinsic reaction coordinate (IRC) calculations were used to connect the transition state between the chair conformer and the 1,4-twist conformer. B3LYP/6,31+G(d,p) and B3LYP/6,311+G(d,p) calculated this transition state to be 14.25,kcal,mol,1 higher in energy than the chair conformer. In the chair conformer, the respective C4,H and C6,H bond lengths are equal, but the C5,Heq bond is longer than the C5,Hax bond. In the 1,4-twist conformer, the C4,Hiso bond lengths are equal, the C5,H,eq bond is longer than the C5,H,ax bond and the C6,H bond lengths are equal. In the 2,5-twist conformer, equal C,H bond lengths are found at C4 and at C5, but the C6,H,eq bond is longer than the C6,H,ax bond. Copyright © 2003 John Wiley & Sons, Ltd. Additional material for this paper is available in Wiley Intersciene [source] Changes in optical properties of MnAs thin films on GaAs(001) induced by ,- to ,-phase transitionPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 4 2008B. Gallas Abstract MnAs layers with 45 nm thickness were grown epitaxially on GaAs(001) substrates. Ellipsometry measurements were made in the spectral range 0.045 eV to 6 eV as a function of temperature (between ,10 °C and 50 °C) at 70° of incidence. In this way the transition from the hexagonal ,-phase to the orthorhombic ,-phase could be monitored. Non-zero off-diagonal elements of the Jones matrix for an azimuth of 38° off the [10] axis of the substrate indicate that the optical functions of MnAs are anisotropic in both phases. The optical conductivity exhibits low-energy interband transitions around 0.3 eV, more clearly seen in the ,-phase than in the ,-phase. Extrapolation of the optical conductivity to zero frequency confirms that the ,-phase is about two times more conducting than the ,-phase. A broad structure is observed in the visible range around 3 eV. The ,-phase is characterised by an anisotropy induced energy difference of this structure with a maximum at 2.8 eV for the extraordinary index and at 3.15 eV for the ordinary index. This difference vanishes in the ,-phase in which anisotropy mainly induces changes in amplitude of the 3 eV structure. The assignment of the structures will be discussed. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] The electronic structure and magnetism of a rocksalt FeN(001) surface: A density functional studyPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 12 2007J. I. Lee Abstract We investigated the electronic structure and magnetism of the rocksalt FeN(001) surface. We considered both the ferromagnetic and antiferromagnetic configurations. We calculated the electronic structure using the full-potential linearized augmented plane wave method within generalized gradient approximation. We found that the antiferromagnetic phase is more stable than the ferromagnetic one, as in bulk, with an energy difference of 0.14 eV per the considered slab. The magnetic moments of the Fe atoms in the antiferromagnetic phase slab are 2.90 ,B, ,2.26 ,B and 2.37 ,B for the surface, subsurface, and center layers, respectively, while the values for the ferromagnetic one are 2.85 ,B, 1.81 ,B, and 2.37 ,B, respectively. The detailed electronic structures for ferromagnetic and antiferromagnetic phases are compared and discussed with the calculated spin-densities and density of states. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Growth and characterization of isotopic natGa15N by molecular-beam epitaxyPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue S2 2009Yong-zhao Yao Abstract Isotopically enriched gallium nitride films, Ga14N and Ga15N, have been fabricated by molecular-beam epitaxy to study the effects of nitrogen atomic mass variation on structures and properties of GaN. The phonon frequency shift due to the isotopic substitution was clearly observed using Raman spectroscopy. The lattice constants of Ga15N differed from those of Ga14N; the unit cell volume of Ga15N was approximately 0.06% less than that of Ga14N. Temperature-dependent photoluminescence measurements revealed that the recombination mechanism in Ga14N and Ga15N was the same in the temperature range of 4-50 K, and the band gap energy difference was Eg15 -Eg14 = 6.0 ± 0.1 meV. This Eg difference is discussed in terms of volume shrinkage and change in phonon-electron interaction due to isotopic substitution. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Discrete luminescence bands in AlGaN-based quantum wellsPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue S2 2009Hideaki Murotani Abstract The excitation-power-density dependent photoluminescence (PL) spectra have been studied for AlGaN-based quantum wells (QWs) with a well-layer thickness of 2, 4, and 6 nm. With increasing excitation-power density, an additional luminescence line was observed at the higher energy side of an initial luminescence line for the QWs with the well-layer thickness of 4 and 6 nm. The additional line also shifted toward higher energy side with further increasing excitation-power density. It was found from a theoretical calculation of the transition energy under applied electric field that an energy difference between the additional and the initial lines agreed with an energy separation for a well-layer-thickness variation of 2 monolayer for each QW. Therefore, these observations indicated that in the QWs with the well-layer thickness of 4 and 6 nm, the screening of the internal electric field occurred effectively after the saturation of localized states caused by the interface disorder. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Free energy determinants of tertiary structure and the evaluation of protein modelsPROTEIN SCIENCE, Issue 11 2000Donald Petrey Abstract We develop a protocol for estimating the free energy difference between different conformations of the same polypeptide chain. The conformational free energy evaluation combines the CHARMM force field with a continuum treatment of the solvent. In almost all cases studied, experimentally determined structures are predicted to be more stable than misfolded "decoys." This is due in part to the fact that the Coulomb energy of the native protein is consistently lower than that of the decoys. The solvation free energy generally favors the decoys, although the total electrostatic free energy (sum of Coulomb and solvation terms) favors the native structure. The behavior of the solvation free energy is somewhat counterintuitive and, surprisingly, is not correlated with differences in the burial of polar area between native structures and decoys. Rather, the effect is due to a more favorable charge distribution in the native protein, which, as is discussed, will tend to decrease its interaction with the solvent. Our results thus suggest, in keeping with a number of recent studies, that electrostatic interactions may play an important role in determining the native topology of a folded protein. On this basis, a simplified scoring function is derived that combines a Coulomb term with a hydrophobic contact term. This function performs as well as the more complete free energy evaluation in distinguishing the native structure from misfolded decoys. Its computational efficiency suggests that it can be used in protein structure prediction applications, and that it provides a physically well-defined alternative to statistically derived scoring functions. [source] Pressure-induced polymorphism in phenolACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2002David R. Allan The high-pressure crystal structure of phenol (C6H5OH), including the positions of the H atoms, has been determined using a combination of single-crystal X-ray diffraction techniques and ab initio density-functional calculations. It is found that at a pressure of 0.16,GPa, which is just sufficient to cause crystallization of a sample held at a temperature just above its ambient-pressure melting point (313,K), a previously unobserved monoclinic structure with P21 symmetry is formed. The structure is characterized by the formation of hydrogen-bonded molecular chains, and the molecules within each chain adopt a coplanar arrangement so that they are ordered in an alternating 1-1-1 sequence. Although the crystal structure of the ambient-pressure P1121 phase is also characterized by the formation of molecular chains, the molecules adopt an approximate threefold arrangement. A series of ab initio calculations indicates that the rearrangement of the molecules from helical to coplanar results in an energy difference of only 0.162,eV,molecule,1 (15.6,kJ,mole,1) at 0.16,GPa. The calculations also indicate that there is a slight increase in the dipole moment of the molecules, but, as the high-pressure phase has longer hydrogen-bond distances, it is found that, on average, the hydrogen bonds in the ambient-pressure phase are stronger. [source] Interaction of an echinomycin,DNA complex with manganese ionsACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2009Roland Pfoh The crystal structure of an echinomycin,d(ACGTACGT) duplex interacting with manganese(II) was solved by Mn-SAD using in-house data and refined to 1.1,Å resolution against synchrotron data. This complex crystallizes in a different space group compared with related complexes and shows a different mode of base pairing next to the bis-intercalation site, suggesting that the energy difference between Hoogsteen and Watson,Crick pairing is rather small. The binding of manganese to N7 of guanine is only possible because of DNA unwinding induced by the echinomycin, which might help to explain the mode of action of the drug. [source] Electronic Structure and Bonding in Neutral and Dianionic Boradiphospholes: R,BC2P2R2 (R=H, tBu, R,=H, Ph)CHEMISTRY - A EUROPEAN JOURNAL, Issue 34 2009Dandamudi Usharani Abstract Classical and non-classical isomers of both neutral and dianionic BC2P2H3 species, which are isolobal to Cp+ and Cp,, are studied at both B3LYP/6-311++G(d,p) and G3B3 levels of theory. The global minimum structure given by B3LYP/6-311++G(d,p) for BC2P2H3 is based on a vinylcyclopropenyl-type structure, whereas BC2P2H32, has a planar aromatic cyclopentadienyl-ion-like structure. However, at the G3B3 level, there are three low-energy isomers for BC2P2H3: 1),tricyclopentane, 2),nido and 3),vinylcyclopropenyl-type structures, all within 1.7,kcal,mol,1 of each other. On the contrary, for the dianionic species the cyclic planar structure is still the minimum. In comparison to the isolobal Cp+ and HnCnP5,n+ isomers, BC2P2H3 shows a competition between ,-delocalised vinylcyclopropenyl- and cluster-type structures (nido and tricyclopentane). Substitution of H on C by tBu, and H on B by Ph, in BC2P2H3 increases the energy difference between the low-lying isomers, giving the lowest energy structure as a tricyclopentane type. Similar substitution in BC2P2H32, merely favours different positional isomers of the cyclic planar geometry, as observed in 1),isoelectronic neutral heterodiphospholes EtBu2C2P2 (E=S, Se, Te), 2),monoanionic heterophospholyl rings EtBu2C2P2 (E=P,, As,, Sb,) and 3),polyphospholyl rings anions tBu5,nCnP5,n (n=0,5). The principal factors that affect the stability of three-, four-, and five-membered ring and acyclic geometrical and positional isomers of neutral and dianionic BC2P2H3 isomers appear to be: 1),relative bond strengths, 2),availability of electrons for the empty 2p boron orbital and 3),steric effects of the tBu groups in the HBC2P2tBu2 systems. [source] Structures and Vibrational Spectra of the Sulfur-Rich Oxides SnO (n = 4,9): The Importance of ,*,,* InteractionsCHEMISTRY - A EUROPEAN JOURNAL, Issue 2 2007Wah Wong Prof. Abstract The structures of a large number of isomers of the sulfur oxides SnO with n = 4,9 have been calculated at the G3X(MP2) level of theory. In most cases, homocyclic molecules with exocyclic oxygen atoms in an axial position are the global minimum structures. Perfect agreement is obtained with experimentally determined structures of S7O and S8O. The most stable S4O isomer as well as some less stable isomers of S5O and S6O are characterized by a strong ,*,,* interaction between SO and SS groups, which results in relatively long SS bonds with internuclear distances of 244,262,pm. Heterocyclic isomers are less stable than the global minimum structures, and this energy difference approximately increases with the ring size: 17 (S4O), 40 (S5O), 32 (S6O), 28 (S7O), 45 (S8O), and 54,kJ,mol,1 (S9O). Owing to a favorable ,*,,* interaction, preference for an axial (or endo) conformation is calculated for the global energy minima of S7O, S8O, and S9O. Vapor-phase decomposition of SnO molecules to SO2 and S8 is strongly exothermic, whereas the formation of S2O and S8 is exothermic if n<7, but slightly endothermic for S7O, S8O, and S9O. The calculated vibrational spectra of the most stable isomers of S6O, S7O, and S8O are in excellent agreement with the observed data. [source] | |||||||||||||||||||||||||||||||||||||