A vibrational entropy term for DNA docking with autodock

2018 ◽  
Vol 74 ◽  
pp. 286-293 ◽  
Author(s):  
GW McElfresh ◽  
Christos Deligkaris
Keyword(s):  
Vibrational Entropy ◽  
Entropy Term ◽  
Dna Docking

scholarly journals The Impact of Vibrational Entropy on the Segregation of Cu to Antiphase Boundaries in Fe3Al

2021 ◽  
Vol 7 (8) ◽  
pp. 108
Author(s):  
Martin Friák ◽  
Miroslav Černý ◽  
Mojmír Šob
Keyword(s):  
Magnetic Moments ◽  
Energy Difference ◽  
Extended Defects ◽  
Vibrational Entropy ◽  
Phonon Modes ◽  
Antiphase Boundaries ◽  
Related Energy ◽  
Quantum Mechanical Study ◽  
Nonlinear Trends ◽  
The Impact

We performed a quantum mechanical study of segregation of Cu atoms toward antiphase boundaries (APBs) in Fe3Al. The computed concentration of Cu atoms was 3.125 at %. The APBs have been characterized by a shift of the lattice along the ⟨001⟩ crystallographic direction. The APB energy turns out to be lower for Cu atoms located directly at the APB interfaces and we found that it is equal to 84 mJ/m2. Both Cu atoms (as point defects) and APBs (as extended defects) have their specific impact on local magnetic moments of Fe atoms (mostly reduction of the magnitude). Their combined impact was found to be not just a simple sum of the effects of each of the defect types. The Cu atoms are predicted to segregate toward the studied APBs, but the related energy gain is very small and amounts to only 4 meV per Cu atom. We have also performed phonon calculations and found all studied states with different atomic configurations mechanically stable without any soft phonon modes. The band gap in phonon frequencies of Fe3Al is barely affected by Cu substituents but reduced by APBs. The phonon contributions to segregation-related energy changes are significant, ranging from a decrease by 16% at T = 0 K to an increase by 17% at T = 400 K (changes with respect to the segregation-related energy difference between static lattices). Importantly, we have also examined the differences in the phonon entropy and phonon energy induced by the Cu segregation and showed their strongly nonlinear trends.

scholarly journals First-Principles Study of Mechanical and Thermodynamic Properties of Binary and Ternary CoX (X = W and Mo) Intermetallic Compounds

Materials ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 1404
Author(s):  
Yunfei Yang ◽  
Changhao Wang ◽  
Junhao Sun ◽  
Shilei Li ◽  
Wei Liu ◽  
...  
Keyword(s):  
Free Energy ◽  
Thermodynamic Properties ◽  
Gibbs Free Energy ◽  
Density Functional ◽  
Vibrational Entropy ◽  
Functional Theory ◽  
Lattice Constants ◽  
The Density Functional Theory ◽  
Ductile Behavior ◽  
Pseudo Potential

In this study, the structural, elastic, and thermodynamic properties of DO19 and L12 structured Co3X (X = W, Mo or both W and Mo) and μ structured Co7X6 were investigated using the density functional theory implemented in the pseudo-potential plane wave. The obtained lattice constants were observed to be in good agreement with the available experimental data. With respect to the calculated mechanical properties and Poisson’s ratio, the DO19-Co3X, L12-Co3X, and μ-Co7X6 compounds were noted to be mechanically stable and possessed an optimal ductile behavior; however, L12-Co3X exhibited higher strength and brittleness than DO19-Co3X. Moreover, the quasi-harmonic Debye–Grüneisen approach was confirmed to be valid in describing the temperature-dependent thermodynamic properties of the Co3X and Co7X6 compounds, including heat capacity, vibrational entropy, and Gibbs free energy. Based on the calculated Gibbs free energy of DO19-Co3X and L12-Co7X6, the phase transformation temperatures for DO19-Co3X to L12-Co7X6 were determined and obtained values were noted to match well with the experiment results.

Surface composition of Pt-Rh alloys; The role of lattice vibrational entropy

1986 ◽  
Vol 178 (1-3) ◽  
pp. A678
Author(s):  
A.D. Van Langeveld ◽  
J.W. Niemantsverdriet
Keyword(s):  
Surface Composition ◽  
Vibrational Entropy

scholarly journals Моделирование твердых растворов NaGd(MoO-=SUB=-4-=/SUB=-)-=SUB=-2-=/SUB=-- NaEu(MoO-=SUB=-4-=/SUB=-)-=SUB=-2-=/SUB=- и Na-=SUB=-2-=/SUB=-Gd-=SUB=-4-=/SUB=-(MoO-=SUB=-4-=/SUB=-)-=SUB=-7-=/SUB=--Na-=SUB=-2-=/SUB=-Eu-=SUB=-4-=/SUB=-(MoO-=SUB=-4-=/SUB=-)-=SUB=-7-=/SUB=- методом межатомных потенциалов

2019 ◽  
Vol 61 (4) ◽  
pp. 678
Author(s):  
В.Б. Дудникова ◽  
Е.В. Жариков ◽  
Н.Н. Еремин
Keyword(s):  
Solid Solutions ◽  
Atomistic Simulation ◽  
Statistical Distribution ◽  
Partial Ordering ◽  
Interatomic Potentials ◽  
Vibrational Entropy ◽  
Solid State Lasers ◽  
General Utility ◽  
Gadolinium Molybdate

AbstractSimulation of the solid solutions in the system of double sodium–gadolinium and sodium–europium molybdates, which are promising matrices for solid state lasers and phosphors has been carried out by the method of interatomic potentials. Two types of solid solutions have been studied, one of which contains finite components corresponding to the stoichiometric NaGd(MoO_4)_2–NaEu(MoO_4)_2 compositions with statistical distribution of cations in the crystal lattice. Another object is a cation-deficient Na_2Gd_4(MoO_4)_7–Na_2Eu_4(MoO_4)_7 system, in which we have examined the variants of statistical distribution and partial ordering of cations over structural positions. Atomistic simulation has been performed using the GULP 4.0.1 software package (General Utility Lattice Program). It is shown that when we pass from sodium-gadolinium molybdate to sodium-europium molybdate, both of stoichiometric and cation-deficient compositions, an increase in the unit cell volume is observed, while the density of the crystal, the energy of interatomic interactions in the structure, the vibrational entropy and the heat capacity decrease along with increasing europium content. The energy of interatomic interactions in the structure for cation-deficient solid solutions is less than for stoichiometric ones. Other aforementioned characteristics for cation-deficient solid solutions have greater values than for stoichiometric ones. The role of cluster europium centers in concentration quenching in NaGd(MoO_4)_2–NaEu(MoO_4)_2 solid solutions has been examined.

scholarly journals Positive Selection on Two Mitochondrial Coding Genes and Adaptation Signals in Hares (Genus Lepus) from China

2020 ◽  
Author(s):  
Asma Awadi ◽  
Hichem Ben Slimen ◽  
Helmut Schaschl ◽  
Felix Knauer ◽  
Franz Suchentrunk
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Protein Function ◽  
Transmembrane Domain ◽  
Proton Translocation ◽  
Introgressive Hybridization ◽  
Vibrational Entropy ◽  
Mutant Type ◽  
Selection For ◽  
Protein Variants

Abstract Background: Animal mitochondria play a central role in energy production in the cells through the oxidative phosphorylation (OXPHOS) pathway. Recent studies of selection on different mitochondrial OXPHOS genes have revealed the adaptive implications of amino acid changes in these subunits. In hares, climatic variation and/or introgression were suggested to be at the origin of such adaptation. Here we looked for evidence of positive selection in three mitochondrial OXPHOS genes, using tests of selection, protein structure modelling and effects of amino acid substitutions on the protein function and stability. We also used statistical models to test for climate and introgression effects on sites under positive selection. Results: Our results revealed seven sites under positive selection in ND4 and three sites in Cytb. However, no sites under positive selection were observed in the COX1 gene. All three subunits presented a high number of codons under negative selection. Sites under positive selection were mapped on the tridimensional structure of the predicted models for the respective mitochondrial subunit. Of the ten amino acid replacements inferred to have evolved under positive selection for both subunits, six were located in the transmembrane domain. On the other hand, three codons were identified as sites lining proton translocation channels. Furthermore, four codons were identified as destabilizing with a significant variation of Δ vibrational entropy energy between wild and mutant type. Moreover, the PROVEAN analysis suggested that among all positively selected sites two fixed amino acid replacements altered the protein functioning. The statistical model runs indicated significant effects of climate on the presence of ND4 and Cytb protein variants, but no effect by trans-specific mitochondrial DNA introgresson.Conclusions: Positive selection was observed in several codons in two OXPHOS genes. We found that substitutions in the positively selected codons have structural and functional impacts on the encoded proteins. Our results are concordantly suggesting that adaptations have strongly affected the evolution of mtDNA of hare species with potential effects on the protein function. Environmental/climatic changes appear to be a major trigger of this adaptation, whereas trans-specific introgressive hybridization seems to play no major role for the occurrence of protein variants.

scholarly journals Vibrational entropy of spinodal decomposition in FeCr

2005 ◽  
Vol 72 (2) ◽  
Author(s):  
T. L. Swan-Wood ◽  
O. Delaire ◽  
B. Fultz
Keyword(s):  
Spinodal Decomposition ◽  
Vibrational Entropy

scholarly journals Li-ion site disorder driven superionic conductivity in solid electrolytes: a first-principles investigation of β-Li3PS4

2017 ◽  
Vol 5 (3) ◽  
pp. 1153-1159 ◽  
Author(s):  
Gopi Krishna Phani Dathar ◽  
Janakiraman Balachandran ◽  
Paul R. C. Kent ◽  
Adam J. Rondinone ◽  
P. Ganesh
Keyword(s):  
First Principles ◽  
Solid Electrolytes ◽  
Energy Landscape ◽  
Ionic Transport ◽  
Vibrational Entropy ◽  
Schematic Representation ◽  
Configurational Energy ◽  
Superionic Conductivity ◽  
Site Disorder ◽  
Li Ion

A schematic representation of the configurational energy landscape linking configurational and vibrational entropy to ionic transport.

scholarly journals Unexpected Resistance to Base-Catalyzed Hydrolysis of Nitrogen Pyramidal Amides Based on the 7-Azabicyclic[2.2.1]heptane Scaffold

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2363 ◽  
Author(s):  
Diego Ocampo Gutiérrez de Velasco ◽  
Aoze Su ◽  
Luhan Zhai ◽  
Satowa Kinoshita ◽  
Yuko Otani ◽  
...  
Keyword(s):  
Nitrogen Atom ◽  
Amide Bond ◽  
Free Energies ◽  
Amide Nitrogen ◽  
Bond Rotation ◽  
Entropy Term ◽  
And Inversion ◽  
Kinetics Of ◽  
Hydrolysis Of ◽  
Amide Nitrogen Atom

Non-planar amides are usually transitional structures, that are involved in amide bond rotation and inversion of the nitrogen atom, but some ground-minimum non-planar amides have been reported. Non-planar amides are generally sensitive to water or other nucleophiles, so that the amide bond is readily cleaved. In this article, we examine the reactivity profile of the base-catalyzed hydrolysis of 7-azabicyclo[2.2.1]heptane amides, which show pyramidalization of the amide nitrogen atom, and we compare the kinetics of the base-catalyzed hydrolysis of the benzamides of 7-azabicyclo[2.2.1]heptane and related monocyclic compounds. Unexpectedly, non-planar amides based on the 7-azabicyclo[2.2.1]heptane scaffold were found to be resistant to base-catalyzed hydrolysis. The calculated Gibbs free energies were consistent with this experimental finding. The contribution of thermal corrections (entropy term, –TΔS‡) was large; the entropy term (ΔS‡) took a large negative value, indicating significant order in the transition structure, which includes solvating water molecules.

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