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Energy Contributions (energy + contribution)
Selected AbstractsKaolin polytypes revisited ab initioACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2008Patrick H. J. Mercier The well known 36 distinguishable transformations between adjacent kaolin layers are split into 20 energetically distinguishable transformations (EDT) and 16 enantiomorphic transformations, hereafter denoted EDT*. For infinitesimal energy contribution of interactions between non-adjacent layers, the lowest-energy models must result from either (a) repeated application of an EDT or (b) alternate application of an EDT and its EDT*. All modeling, quantum input preparation and interpretation was performed with Materials Toolkit, and quantum optimizations with VASP. Kaolinite and dickite are the lowest-energy models at zero temperature and pressure, whereas nacrite and HP-dickite are the lowest-enthalpy models under moderate pressures based on a rough enthalpy/pressure graph built from numbers given in the supplementary tables. Minor temperature dependence of this calculated 0,K graph would explain the bulk of the current observations regarding synthesis, diagenesis and transformation of kaolin minerals. Other stackings that we list have energies so competitive that they might crystallize at ambient pressure. A homometric pair of energetically distinguishable ideal models, one of them for nacrite, is exposed. The printed experimental structure of nacrite correctly corresponds to the stable member of the pair. In our opinion, all recent literature measurements of the free energy of bulk kaolinite are too negative by ,,15,kJ,mol,1 for some unknown reason. [source] Magnetic Field-Induced Phase Transformation in NiMnCoIn Magnetic Shape-Memory Alloys,A New Actuation Mechanism with Large Work OutputADVANCED FUNCTIONAL MATERIALS, Issue 7 2009Haluk E. Karaca Abstract Magnetic shape memory alloys (MSMAs) have recently been developed into a new class of functional materials that are capable of magnetic-field-induced actuation, mechanical sensing, magnetic refrigeration, and energy harvesting. In the present work, the magnetic &!hyphen;field-induced martensitic phase transformation (FIPT) in Ni45Mn36.5Co5In13.5 MSMA single crystals is characterized as a new actuation mechanism with potential to result in ultra-high actuation work outputs. The effects of the applied magnetic field on the transformation temperatures, magnetization, and superelastic response are investigated. The magnetic work output of NiMnCoIn alloys is determined to be more than 1,MJ m,3 per Tesla, which is one order of magnitude higher than that of the most well-known MSMAs, i.e., NiMnGa alloys. In addition, the work output of NiMnCoIn alloys is orientation independent, potentially surpassing the need for single crystals, and not limited by a saturation magnetic field, as opposed to NiMnGa MSMAs. Experimental and theoretical transformation strains and magnetostress levels are determined as a function of crystal orientation. It is found that [111]-oriented crystals can demonstrate a magnetostress level of 140,MPa T,1 with 1.2% axial strain under compression. These field-induced stress and strain levels are significantly higher than those from existing piezoelectric and magnetostrictive actuators. A thermodynamical framework is introduced to comprehend the magnetic energy contributions during FIPT. The present work reveals that the magnetic FIPT mechanism is promising for magnetic actuation applications and provides new opportunities for applications requiring high actuation work-outputs with relatively large actuation frequencies. One potential issue is the requirement for relatively high critical magnetic fields and field intervals (1.5,3,T) for the onset of FIPT and for reversible FIPT, respectively. [source] The Role of Surface and Interface Energy on Phase Stability of Nanosized Insertion CompoundsADVANCED MATERIALS, Issue 25-26 2009Marnix Wagemaker Thermodynamic theory reveals the impact of surface and interface energies on the equilibrium properties and solubility limits of interstitial ions in nanosized crystallites. Applied to LixFePO4 especially interface energy contributions play important roles, and their effect explains observations of the narrowing of electrochemically measured miscibility gaps in nanostructured electrodes. [source] Modified regional self-interaction corrected time-dependent density functional theory for core excited-state calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2009Ayako Nakata Abstract A modified regional self-interaction correction (mRSIC) method is proposed for obtaining accurate core-excitation energies in time-dependent density functional theory (TDDFT) calculations. The mRSIC method is an improvement of the RSIC method (Tsuneda et al. J Comput Chem 2003, 24, 1592). It takes into account the energy contributions from 2s and higher atomic orbitals that the RSIC method neglects. Furthermore, mRSIC improves the poor description for the nuclear-electron cusp of Gaussian basis functions. The mRSIC method was combined with a long-range correction (LC) scheme, which has been proved to give accurate valence-, Rydberg-, and charge transfer (CT)-excitation energies. In so doing, it dramatically improved the accuracy of the calculated core-excitation energies and did not affect the already accurate values of valence-, Rydberg-, and CT-excitation energies produced by the LC functionals. These results mean that the combined scheme is accurate for all excitation energy forms. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2002Abstract QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169,176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (,16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 Å) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product,reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute ,40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1314,1322, 2002 [source] Molecular Modeling and Receptor-Dependent (RD) 3D-QSAR Approach to a Set of Antituberculosis DerivativesMOLECULAR INFORMATICS, Issue 11-12 2009Fernanda, Kerly, Mesquita Pasqualoto Abstract In this study, receptor-dependent (RD) 3D-QSAR models were built for a set of thirty-seven isoniazid derivatives bound to the enoyl-acp reductase from M. tuberculosis, called InhA (PDB entry code 1zid). Ligand-receptor (L-R) molecular dynamics (MD) simulations [500,000 steps; the step size was 0.001,ps (1,fs)] were carried out at 310,K (biological assay temperature). The hypothesized active conformations resulting from a previously reported receptor-independent (IR) 4D-QSAR analysis were used as the molecular geometries of each ligand in this structure-based L-R binding research. The dependent variable is the reported MIC values against M. tuberculosis var. bovis. The independent variables (descriptors) are energy terms of a modified first-generation AMBER force field combined with a hydration shell aqueous solvation model. Genetic function approximation (GFA) formalism and partial least squares (PLS) regression were employed as the fitting functions to develop 3D-QSAR models. The bound ligand solvation energy, the sum of electrostatic and hydrogen bonding energies of the unbound ligand, the bending energy of the unbound ligand, the electrostatic intermolecular L-R energy, and the change in hydrogen bonding energy upon binding were found as important energy contributions to the binding process. The 3D-QSAR model at 310,K has good internal and external predictability and may be regarded as representative of the binding process of ligands to InhA. [source] Magnetic anisotropy changes in ultrathin Co films grown on vicinal sapphire substratesPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 1 2006A. Stupakiewicz Abstract The aim of the work is to study the magnetic anisotropy changes in epitaxial ultrathin Co films grown on vicinal sapphire substrates with different miscut angles. Changes of the in-plane magnetic anisotropy symmetry were deduced from magnetooptical hysteresis loops shape and angular dependence analysis of the resonance field measured in the sample plane. Two-fold and four-fold symmetry of the in-plane anisotropy was observed for different miscut angles. The experimental data are discussed taking into account the following energy contributions: (i) demagnetization; (ii) perpendicular uniaxial anisotropy (iii) and step-induced uniaxial anisotropy. Magnetic anisotropy constants are fitted to the experimental results for different miscut angles. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Structural stability of clean GaAs nanowires grown along the [111] directionPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 2 2010Rita Magri Abstract Using a first-principles approach we have calculated the formation energies of small diameter GaAs nanowires (NWs) with both zinc-blende and wurtzite structure grown along the [111] direction. The section of the wires is hexagonal and the side facets are oriented either {11-20} and {10-10} in the case of the wurtzite structure, and {110} and {112} for the zinc-blende structure. The formation energy of the nanowires as a function of their radius is then interpreted in terms of a model in which the energy contributions from the bulks, the flat surfaces and the ridges are taken explicitly into account. We find that the nanowire stability is mainly explained by the competition between the bulk energy, favoring the zincblende structure and the surface energies favoring the wurtzite structure. We find also that the directly calculated formation energies of some small diameter wurtzite NWs can be reproduced by our model taking into account only the bulk and flat surface contributions. That is, the ridges do not contribute substantially to the nanowire formation energy. Inspection of the ridge structure and band structure reveals that this good agreement occurs when the NWs are semiconducting and the ridges do not add more dangling bonds to the surface with respect to those provided by the sidewalls. Within our model we find the critical diameter for the wurtzite-zinc-blende transition at 6.3 nm. (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Bis[S -6-(2,2:6,,2,,-terpyridin-4,-yloxy)hexyl thioacetate]manganese(II) bis(hexafluorophosphate)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2009Kasper Moth-Poulsen The structure of a manganese(II) complex of terpyridine functionalized with acetylsulfanyl-terminated hexyloxy chains, [Mn(C23H25N3O2S)2](PF6)2, is described. This type of complex is of interest in the study of single-molecule transport properties in open-shell systems. The manganese coordination environment is distorted octahedral but, importantly, with no larger deviations from the idealized geometry than those observed for other metal,terpyridine complexes. The Mn,N bond lengths range from 2.192,(2) to 2.272,(3),Å. The title compound crystallizes with the cation and anions all on general positions, with the hexafluorophosphate anions exhibiting orientational disorder. When compared with other bis-terpyridine complexes, this structure demonstrates that manganese(II) is no more prone to undergo low-symmetry distortions than systems with ligand field stabilization energy contributions. [source] Partition of thermodynamic energies of drug,DNA complexationBIOPOLYMERS, Issue 9 2009V. V. Kostjukov Abstract We report a computation methodology, which leads to the ability to partition the Gibb's free energy for the complexation reaction of aromatic drug molecules with DNA. Using this approach, it is now possible to calculate the absolute values of the energy contributions of various physical factors to the DNA binding process, whose summation gives a value that is reasonably close to the experimentally measured Gibb's free energy of binding. Application of the methodology to binding of various aromatic drugs with DNA provides an answer to the question "What forces are the main contributors to the stabilization of aromatic ligand,DNA complexes?" © 2009 Wiley Periodicals, Inc. Biopolymers 91: 773,790, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Charge-Shift Bonding,A Class of Electron-Pair Bonds That Emerges from Valence Bond Theory and Is Supported by the Electron Localization Function ApproachCHEMISTRY - A EUROPEAN JOURNAL, Issue 21 2005Sason Shaik Prof. Abstract This paper deals with a central paradigm of chemistry, the electron-pair bond. Valence bond (VB) theory and electron-localization function (ELF) calculations of 21 single bonds demonstrate that along the two classical bond families of covalent and ionic bonds, there exists a class of charge-shift bonds (CS bonds) in which the fluctuation of the electron pair density plays a dominant role. In VB theory, CS bonding manifests by way of a large covalent-ionic resonance energy, RECS, and in ELF by a depleted basin population with large variances (fluctuations). CS bonding is shown to be a fundamental mechanism that is necessary to satisfy the equilibrium condition, namely the virial ratio of the kinetic and potential energy contributions to the bond energy. The paper defines the atomic propensity and territory for CS bonding: Atoms (fragments) that are prone to CS bonding are compact electronegative and/or lone-pair-rich species. As such, the territory of CS bonding transcends considerations of static charge distribution, and involves: a) homopolar bonds of heteroatoms with zero static ionicity, b) heteropolar , and , bonds of the electronegative and/or electron-pair-rich elements among themselves and to other atoms (e.g., the higher metalloids, Si, Ge, Sn, etc), c) all hypercoordinate molecules. Several experimental manifestations of charge-shift bonding are discussed, such as depleted bonding density, the rarity of ionic chemistry of silicon in condensed phases, and the high barriers of halogen-transfer reactions as compared to hydrogen-transfers. [source] Two Typical Examples of Scaling Ionic Partition Scheme for Estimating Correlation Energy of A2 Type MoleculesCHINESE JOURNAL OF CHEMISTRY, Issue 4 2004Shu-Ping Zhuo Abstract Based on the calculation results of pair correlation energy contributions of the various electron pairs in Naz and H2NNH2 systems and the application of the scaling ionic partition scheme for symmetrical A2 type systems, the total correlation energies of Na2 and H2NNH2 have been reproduced by using this simple scheme. The two results show that the absolute deviations are within an acceptable range of mr, however, in this way, more than 90% of computational work can be. saved. The most attractive result in present paper is that, in these two molecules the coefficients c1 and c2 in the estimation equation can be obtained by the proportion of correlation energy of A, to that of A+ singlet system. Therefore, it is believed that the proposed ionic partition scheme for symmetrical A2 molecules would be very useful to estimate the correlation energies of large symmetrical molecules. [source] | |||||||||||||||||||||||||