scholarly journals Theory for weakly polydisperse cytoskeleton filaments

2022 ◽  
Author(s):  
Vadim Warshavsky ◽  
Marcelo Marucho
Keyword(s):  
Actin Filaments ◽  
Density Functional ◽  
Chemical Potential ◽  
Second Virial Coefficient ◽  
Number Density ◽  
Functional Theory ◽  
Cell Compartments ◽  
Pressure Chemical ◽  
Cellular Compartments ◽  
Equilibrium Polymerization

The ability of actins and tubulins to change dynamically from alterations in the number density of actins/tubulin, number density and type of binding agents, and electrolyte concentration is crucial for eukaryotic cells to regulate their cytoskeleton conformations in different cellular compartments. Conventional approaches on biopolymers solution break down for cytoskeleton filaments because they entail several approximations to treat their polyelectrolyte and mechanical properties. In this article, we introduce a novel density functional theory for polydisperse, semiflexible cytoskeleton filaments. The approach accounts for the equilibrium polymerization kinetics, length, and orientation filament distributions, as well as the electrostatic interaction between filaments and the electrolyte. This is essential for cytoskeleton polymerization in different cell compartments generating filaments of different lengths, sometimes long enough to become semiflexible. We characterized the thermodynamics properties of actin filaments in electrolyte aqueous solutions. We calculated the free energy, pressure, chemical potential, and second virial coefficient for each filament conformation. We also calculated the phase diagram of actin filaments solution and compared it with available experimental data.

Blue and black phosphorene on metal substrates: a density functional theory study

2021 ◽  
Author(s):  
Abhishek Kumar Adak ◽  
Devina Sharma ◽  
Shobhana Narasimhan
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Chemical Potential ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Atomic Size ◽  
Metal Substrates ◽  
Synthesis Conditions ◽  
Black Phosphorene ◽  
Blue Phosphorene

Abstract We have performed density functional theory calculations to study blue phosphorene and black phosphorene on metal substrates. The substrates considered are the (111) and (110) surfaces of Al, Cu, Ag, Ir, Pd, Pt and Au and the (0001) and (10$\bar{1}$0) surfaces of Zr and Sc. The formation energy $E_{\rm F}$ is negative (energetically favorable) for all 36 combinations of overlayer and substrate. By comparing values of $\Delta{\Omega}$, the change in free energy per unit area, as well as the overlayer-substrate binding energy $E_{\rm b}$, we identify that Ag(111), Al(110), Cu(111), Cu(110) and possibly Au(110) may be especially suitable substrates for the synthesis and subsequent exfoliation of blue phosphorene, and the Ag(110) and Al(111) substrates for the synthesis of black phosphorene. However, these conclusions are drawn assuming the source of P atoms is bulk phosphorus, and can alter upon changing synthesis conditions (chemical potential of phosphorus). Thus, when the source of phosphorus atoms is P$_4$, blue phosphorene is favored only over Pt(111). We find that for all combinations of overlayer and substrate, the charge transfer per bond can be captured by the universal descriptor $\mathcal{D} = \Delta \chi/\Delta \mathcal{R}$, where $\Delta \chi$ and $\Delta \mathcal{R}$ are, respectively, the differences in electronegativity and atomic size between phosphorus and the substrate metal.

Study of dynamic and thermodynamic properties of zinc-blend and wurtzite cadmium sulfide (CdS) using density functional theory

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Teshome Gerbaba Edossa ◽  
Menberu Mengasha Woldemariam
Keyword(s):  
Density Functional Theory ◽  
Thermodynamic Properties ◽  
Density Functional ◽  
Chemical Potential ◽  
Phonon Dispersion ◽  
Dynamic Properties ◽  
Dielectric Constants ◽  
High Symmetry ◽  
Functional Theory ◽  
Zinc Blend

Abstract The dynamic and thermodynamic properties of wurtzite (wz) and zinc-blend (zb) CdS are investigated within the density functional theory using different approximation methods such as LDA, PBE, and DFT+U. Hellmann–Feynman approach is implemented for the relaxation of atomic position for both phases. To guarantee the accuracy of calculation, the convergence test of total energy with respect to energy cutoff and k-point sampling is performed. The dynamic properties such as phonon dispersion, phonon density of state, frequency along with high symmetry points, static and dynamic polarizability, and dielectric constants are calculated. The obtained values are compared with previous theoretical results. DFT + U approximation gives a good result that is consistent with the available theory. Moreover, the vibrational energy, vibrational free energy, entropy, electron chemical potential, and constant-volume specific heat are obtained within LDA, PBE, and DFT + U approximations.

scholarly journals Anticancer Indole-Based Chalcones: A Structural and Theoretical Analysis

Molecules ◽  
2019 ◽  
Vol 24 (20) ◽  
pp. 3728 ◽  
Author(s):  
Farid A. Badria ◽  
Saied M. Soliman ◽  
Saleh Atef ◽  
Mohammad Shahidul Islam ◽  
Abdullah Mohammed Al-Majid ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Theoretical Analysis ◽  
Dft Calculations ◽  
Density Functional ◽  
Chemical Potential ◽  
Chemical Reactivity ◽  
Stacking Interactions ◽  
Functional Theory ◽  
Topology Analysis ◽  
Reactivity Indices

The crystal structures of five new chalcones derived from N-ethyl-3-acetylindole with different substituents were investigated: (E)-3-(4-bromophenyl)-1-(1-ethyl-1H-indol-3-yl)prop-2-en-1-one (3a); (E)-3-(3-bromophenyl)-1-(1-ethyl-1H-indol-3-yl)prop-2-en-1-one (3b); (E)-1-(1-ethyl-1H-indol-3-yl)-3-(4-methoxyphenyl)prop-2-en-1-one (3c); (E)-1-(1-ethyl-1H-indol-3-yl)-3-mesitylprop-2-en-1-one (3d); and (E)-1-(1-ethyl-1H-indol-3-yl)-3-(furan-2-yl)prop-2-en-1-one (3e). The molecular packing of the studied compounds is controlled mainly by C–H⋅⋅⋅O hydrogen bonds, C–H⋅⋅⋅π interactions, and π···π stacking interactions, which were quantitatively analyzed using Hirshfeld topology analysis. Using density functional theory (DFT) calculations, the order of polarity (3b ˂ 3d ˂ 3e ˂ 3a ˂ 3c) was determined. Several chemical reactivity indices such as the ionization potential (I), electron affinity (A), chemical potential (μ), hardness (η), electrophilicity (ω) and nucleophilicity (N) indices were calculated, and these properties are discussed and compared. In addition, the antiproliferative activity of the five new chalcones was studied.

scholarly journals Synthesis, Characterization, Catalytic Activity, and DFT Calculations of Zn(II) Hydrazone Complexes

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4043 ◽  
Author(s):  
Temiloluwa T. Adejumo ◽  
Nikolaos V. Tzouras ◽  
Leandros P. Zorba ◽  
Dušanka Radanović ◽  
Andrej Pevec ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Molecular Orbital ◽  
Density Functional ◽  
Chemical Potential ◽  
Chemical Reactivity ◽  
Geometry Optimization ◽  
Coupling Reaction ◽  
Functional Theory ◽  
Reactivity Descriptors

Two new Zn(II) complexes with tridentate hydrazone-based ligands (condensation products of 2-acetylthiazole) were synthesized and characterized by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy and single crystal X-ray diffraction methods. The complexes 1, 2 and recently synthesized [ZnL3(NCS)2] (L3 = (E)-N,N,N-trimethyl-2-oxo-2-(2-(1-(pyridin-2-yl)ethylidene)hydrazinyl)ethan-1-aminium) complex 3 were tested as potential catalysts for the ketone-amine-alkyne (KA2) coupling reaction. The gas-phase geometry optimization of newly synthesized and characterized Zn(II) complexes has been computed at the density functional theory (DFT)/B3LYP/6–31G level of theory, while the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO and LUMO) energies were calculated within the time-dependent density functional theory (TD-DFT) at B3LYP/6-31G and B3LYP/6-311G(d,p) levels of theory. From the energies of frontier molecular orbitals (HOMO–LUMO), the reactivity descriptors, such as chemical potential (μ), hardness (η), softness (S), electronegativity (χ) and electrophilicity index (ω) have been calculated. The energetic behavior of the investigated compounds (1 and 2) has been examined in gas phase and solvent media using the polarizable continuum model. For comparison reasons, the same calculations have been performed for recently synthesized [ZnL3(NCS)2] complex 3. DFT results show that compound 1 has the smaller frontier orbital gap so, it is more polarizable and is associated with a higher chemical reactivity, low kinetic stability and is termed as soft molecule.

scholarly journals Analysis of the Gas Phase Acidity of Substituted Benzoic Acids Using Density Functional Concepts

Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1631
Author(s):  
Jorge A. Amador-Balderas ◽  
Michael-Adán Martínez-Sánchez ◽  
Ramsés E. Ramírez ◽  
Francisco Méndez ◽  
Francisco J. Meléndez
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Chemical Potential ◽  
Fukui Function ◽  
Ortho Position ◽  
Benzoic Acids ◽  
Functional Theory ◽  
Resonance Effects ◽  
Gas Phase Acidity ◽  
Substituted Benzoic Acids

A theoretical study of the effect of the substituent Z on the gas phase acidity of substituted benzoic acids ZC6H4COOH in terms of density functional theory descriptors (chemical potential, softness and Fukui function) is presented. The calculated gas phase ΔacidG° values obtained were close to the experimental ones reported in the literature. The good relationship between the ΔacidG° values and the electronegativity of ZC6H4COOH and its fragments, suggested a better importance of the inductive than polarizability contributions. The balance of inductive and resonance contributions of the substituent in the acidity of substituted benzoic acids showed that the highest inductive and resonance effects were for the -SO2CF3 and -NH2 substituents in the para- and ortho-position, respectively. The Fukui function confirmed that the electron-releasing substituent attached to the phenyl ring of benzoic acid decreased the acidity in the trend ortho > meta > para, and the electron-withdrawing substituent increased the acidity in the trend ortho < meta < para.

First-Principles Study of TiC(111) Surface

2012 ◽  
Vol 229-231 ◽  
pp. 82-86 ◽  
Author(s):  
Li Wang ◽  
Teng Fang ◽  
Jian Hong Gong
Keyword(s):  
First Principles ◽  
Density Functional ◽  
Chemical Potential ◽  
Charge Accumulation ◽  
Ab Initio Method ◽  
Functional Theory ◽  
Structural And Electronic Properties ◽  
Full Relaxation ◽  
Energy Plane ◽  
Large Charge

The structural and electronic properties of TiC(111) surfaces are calculated using the first-principles total-energy plane-wave pseudopotential method based on density functional theory. As a polar surface, (111) surface shows large charge depletion in the upper part of the atoms, while charge accumulation happens in the inferior part of the atoms, interlayer Ti-C chemical bonds are reinforced and the outermost interlayer distances are largely reduced. Meanwhile, the charge accumulation and depletion for Ti-terminated surface is more than that for C-terminated surface on the same position of the two slabs after full relaxation. The surface energy of C-terminated surface is in the range from 7.61 to 9.83 J/m2, much larger than that of Ti-terminated surface from 3.13 to 1.35 J/m2, and the Ti-terminated surface is thermodynamically more favorable over all of the range of (chemical potential of TiC slab). This present work makes a beneficial attempt at exploring TiC surface as an ab initio method for studying possible nucleation mechanism of Aluminum on it.

Electronic Structure of Native Point Defects in Zngep2

2003 ◽  
Vol 799 ◽  
Author(s):  
Xiaoshu Jiang ◽  
M. S. Miao ◽  
Walter R. L. Lambrecht
Keyword(s):  
Point Defects ◽  
Density Functional ◽  
Chemical Potential ◽  
Local Density ◽  
High Energy ◽  
Orbital Method ◽  
Full Potential ◽  
Epr Spectrum ◽  
Functional Theory ◽  
Native Point Defects

ABSTRACTFirst-principles calculations are presented for various native point defects in ZnGeP2 us-ing a full-potential linearized muffin-tin orbital method in the local density approximation to density functional theory. Under Zn-poor conditions, the lowest Gibbs energy defects are found to be the Gezn antisite and Vzn. The Vae is found to have high energy of formation under any chemical potential conditions and is unstable towards formation of a Vzn and ZnGe pair. It is shown that the V−Zn cannot account for the ALI EPR spectrum commonly associated with this vacancy and an alternative model consisting of a Vzn – GeZn – Vzn is tentatively proposed.

scholarly journals Effect of Constituent Units, Type of Interflavan Bond, and Conformation on the Antioxidant Properties of Procyanidin Dimers: A Computational Outlook

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Ana María Mendoza-Wilson ◽  
René Renato Balandrán-Quintana
Keyword(s):  
Density Functional ◽  
Chemical Potential ◽  
Antioxidant Properties ◽  
Computational Method ◽  
Antioxidant Ability ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Fukui Indices ◽  
Homo Lumo

Procyanidin (PC) dimers are powerful antioxidants, abundant in plant tissues, and also bioavailable. However, the role of the molecular structure of PCs on their antioxidant properties is still a controversial and not fully understood issue that needs to be addressed in a more specific way. The objective of this study was to analyze the effect of the constituent units, type of interflavan bond, and conformation on the antioxidant properties of PC dimers including PB3, PB4, PB5, PB6, PB7, and PB8, using the density functional theory (DFT) computational method. The analysis was performed in function of parameters that allow determining the ability of the molecules to transfer or to capture electrons, among which the chemical potential, bond dissociation enthalpy (BDE), gap energy, Fukui indices, and charge distribution of HOMO-LUMO orbitals. The factors that showed the most notable effects on the antioxidant properties of the PC dimers were the type of interflavan bond and the conformation. The antioxidant ability of the dimers PB3 and PB4 containing the interflavan bond C4–C8, in their Compact conformation, was very similar to each other but greater than those of dimers PB5, PB6, PB7, and PB8 containing the C4–C6 interflavan bond. PB8 showed the lowest antioxidant ability.

scholarly journals Constant chemical potential approach for quantum chemical calculations in electrocatalysis

2014 ◽  
Vol 5 ◽  
pp. 668-676 ◽  
Author(s):  
Wolfgang B Schneider ◽  
Alexander A Auer
Keyword(s):  
Density Functional Theory ◽  
Quantum Chemical ◽  
Density Functional ◽  
Chemical Potential ◽  
Computational Effort ◽  
Electrochemical Potential ◽  
Implicit Solvent ◽  
Functional Theory ◽  
Solvent Models ◽  
Canonical Approach

In order to simulate electrochemical reactions in the framework of quantum chemical methods, density functional theory, methods can be devised that explicitly include the electrochemical potential. In this work we discuss a Grand Canonical approach in the framework of density functional theory in which fractional numbers of electrons are used to represent an open system in contact with an electrode at a given electrochemical potential. The computational shortcomings and the additional effort in such calculations are discussed. An ansatz for a SCF procedure is presented, which can be applied routinely and only marginally increases the computational effort of standard constant electron number approaches. In combination with the common implicit solvent models this scheme can become a powerful tool, especially for the investigation of omnipresent non-faradaic effects in electrochemistry.

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