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Thermodynamic properties and hysteresis loops in a hexagonal core-shell nanoparticle. J Mol Graph Model 2021; 107:107967. [PMID: 34157438 DOI: 10.1016/j.jmgm.2021.107967] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 12/29/2022]
Abstract
We applied Monte Carlo simulation to investigate the thermodynamic properties and hysteresis loops of the hexagonal core-shell nanoparticle described by a ferrimagnetic mixed-spin (3/2, 5/2) Ising model. The results revealed the significance of the single-ion anisotropy, exchange coupling, external magnetic field in dominating various thermodynamic quantities and hysteresis loops. We obtained the variation of the critical temperature with various parameters. Under certain parameter conditions, the system may exhibit rich multiple-loop hysteresis behaviors, depending on the competition among the physical parameters.
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Barhoumi A, El Idrissi M, Zeroual A, Tounsi A, Bakkas S, El Hajbi A. Theoretical study of the chemical reactivity of a class of trivalent phosphorus derivatives towards polyhaloalkanes: DFT study. J Mol Model 2021; 27:197. [PMID: 34115227 DOI: 10.1007/s00894-021-04814-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/02/2021] [Indexed: 11/24/2022]
Abstract
In the current work, the chemical reactivity of some trivalent phosphorus derivatives R2PR' towards polyhaloalkanes CCl3POR ' '2 was studied by the quantum method DFT/B3LYP/6-311G(d,p). The introduction of substituents for the trivalent phosphorus derivative and polyhaloalkane allowed us to have more information on these reactions. On the one hand, the calculation of reactivity indices derived from the DFT/B3LYP/6-311G(d,p) method and the gapLUMO - HOMO show that trivalent organophosphorus derivatives behave as nucleophiles, while polyhaloalkanes act as electrophiles. On the other hand, the calculation of the activation barrier and the determination of the free enthalpy variation prove that the kinetic and thermodynamic products of these reactions result from the nucleophilic attack of the phosphorus atom on the chlorine halogen. All these theoretical predictions are in very good agreement with the experimental results.
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First-principles calculation of electronic, vibrational, and thermodynamic properties of triaminoguanidinium nitrate. J Mol Model 2021; 27:187. [PMID: 34037870 DOI: 10.1007/s00894-021-04803-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/17/2021] [Indexed: 10/21/2022]
Abstract
In recent years, the important energetic material triaminoguanidinium nitrate (TAGN) has been widely used, and the process of synthesizing TAGN has become more and more perfect. However, there are relatively few theoretical studies on TAGN. This paper uses first-principles calculations to more systematically study the crystal structure, and electronic, vibrational, and thermodynamic properties of TAGN. The calculation results show that the calculated unit cell parameters are relatively consistent with the values obtained through X-ray diffraction experiments. This article describes in detail the state density of the valence electrons of each atom. By analyzing the vibrational properties of TAGN crystal, the vibration mode corresponding to each optical wave is obtained. At the same time, the vibration mode of each peak in the Raman spectrum and the infrared spectrum is described in detail. Then, the calculated value is compared with the experimental value; it can be seen that the error is relatively small. According to the vibration characteristics, a series of thermodynamic functions such as enthalpy (H), Debye temperature (Θ), free energy (F), and entropy (S) are calculated. These thermodynamic functions can provide a certain reference for future research.
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Suparmi A, Permatahati LK, Faniandari S, Iriani Y, Marzuki A. Study of Bohr Mottelson Hamiltonian with minimal length effect for Woods-Saxon potential and its thermodynamic properties. Heliyon 2021; 7:e06861. [PMID: 34013074 PMCID: PMC8113724 DOI: 10.1016/j.heliyon.2021.e06861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/13/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022] Open
Abstract
The Bohr Mottelson Hamiltonian with the variable of β collective shape for the Woods-Saxon potential in the rigid deformed nucleus for γ=0 and the X(3) model was investigated in the presence of the minimal length formalism. The Bohr Mottelson Hamiltonian was solved approximately by proposing a new wave function. The q-deformed hyperbolic potential concept such that the rigid deformed nucleus of the Bohr Mottelson equation in the minimal length formalism for Woods-Saxon potential was used, so that the equation was reduced to the form of Schrodinger-like equation with cotangent hyperbolic potential. The hypergeometric method was used to obtain the energy spectra equation and the unnormalized wave function of the system. The results showed that the energy spectra were affected by the quantum number, the minimal length parameter, and the atomic mass. The larger mass of the atom affected the energy spectra to decrease, the increase of the values of the minimal length affected the increase of the energy spectra of all atoms. The energy spectra were used to determine the thermodynamic properties including the partition function, mean energy, specific heat, free energy, and entropy of the quantum system with the help of the imaginary error function.
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The structural, electronic, and optical properties of hydrofluorinated germanene (GeH 1-xF x): a first-principles study. J Mol Model 2021; 27:123. [PMID: 33825096 DOI: 10.1007/s00894-021-04741-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/15/2021] [Indexed: 10/21/2022]
Abstract
The structural, electronic, and optical properties of hydrofluorinated germanene have been studied with different occupancy ratios of fluorine and hydrogen. The hybridization of H-1 s and Ge-4p orbitals in hydrogenated germanene and F-2p and Ge-4p orbitals in fluorinated germanene plays a significant role in creating an energy bandgap. The binding energy and phonon calculations confirm the stability of hydrofluorinated germanene decreases with the increase of the F to H ratio. The value of the energy bandgap decreased by increasing the ratio of F and H. The optical properties have been studied in the energy range of 0-25 eV. Six essential parameters such as energy bandgap (Eg), binding energy (Eb), dielectric constant ε(0), refractive index n(0), plasmon energy (ћωp), and heat capacity (Cp) have been calculated for different occupancies of H and F in hydrofluorinated germanene for the first time. The calculated values of structural parameters agree well with the reported values.
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Solutions of the Schrödinger equation and thermodynamic properties of a combined potential. Heliyon 2021; 7:e06425. [PMID: 33817363 PMCID: PMC8005774 DOI: 10.1016/j.heliyon.2021.e06425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/23/2021] [Accepted: 03/02/2021] [Indexed: 11/21/2022] Open
Abstract
The solution of the radial Schrödinger equation was obtained using the methodology of supersymmetric approach with a combination of modified generalized Pöschl-Teller potential and inversely quadratic Yukawa potential model. The non-relativistic ro-vibrational energy spectra and the corresponding wave functions were obtained and numerical results were generated for some states. The variation of energy of the combined potential and the subsets potentials with the screening parameter for various quantum number were graphically studied. The effect of the potential parameters on the energy for different states was also studied numerically. For more usefulness and applications of the work, the vibrational partition function and the various thermal properties like mean energy, Helmholtz energy, heat capacity and entropy were calculated. The behaviour of the thermodynamic properties with respect to temperature change for various quantum number and maximum quantum states were examined in detail. The temperature has positive effect on all the thermal properties except the free energy.
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The Change Mechanism of Structural Characterization and Thermodynamic Properties of Tannase from Aspergillus niger NL112 Under High Temperature. Appl Biochem Biotechnol 2021; 193:2225-2244. [PMID: 33686629 DOI: 10.1007/s12010-021-03488-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/07/2021] [Indexed: 10/22/2022]
Abstract
Tannase from Aspergillus niger NL112 was purified 5.1-fold with a yield of 50.44% via ultrafiltration, DEAE-Sepharose Fast Flow column chromatography, and Sephadex G-100 column chromatography. The molecular weight of the purified tannase was estimated as 45 kDa. The optimum temperature and pH for its activity were 45 °C and 5.0, respectively. The results of circular dichroism, FT-IR (Fourier transform infrared) spectroscopy, and fluorescence spectra indicated that high temperature could lead to the change of tannase secondary and tertiary structures. Tannase had a greater affinity for tannic acid at 40 °C with a Km value of 2.12 mM and the greatest efficiency hydrolysis (Kcat/Km) at 45 °C. The rate of inactivation (k) increased with the increase of temperature and the half-life (t1/2) gradually decreased. It was found to be 1.0 of the temperature quotient (Q10) value for tannic acid hydrolysis by tannase. The thermodynamic parameters of the interaction system were calculated at various temperatures. The positive enthalpy (ΔH) values and decreasing ΔH values with the increase of temperature indicated that the hydrolysis of tannase was an endothermic process. Our results indicated that elevated temperature could change the tertiary structure of tannase and reduce its thermostability, which caused a gradual decrease of tannase activity with an increase in temperature.
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Density functional theory for the thermodynamic gas-phase investigation of butanol biofuel and its isomers mixed with gasoline and ethanol. J Mol Model 2021; 27:80. [PMID: 33575832 DOI: 10.1007/s00894-021-04681-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/17/2021] [Indexed: 10/22/2022]
Abstract
Herein, we present the results of our study on the thermodynamic properties of the isomers of butanol (n-butanol, 2-butanol, i-butanol, and t-butanol) to evaluate their thermodynamic potential as a complementary biofuel and/or substitute for ethanol and gasoline. The Gaussian09W software was used to perform molecular geometry optimization calculations using density functional theory with the B3lyp hybrid function using the base set 6-311++g(d,p) and the compound methods G3, G4, and CBS-QB3. Calculations of the fundamental frequency of the molecules were performed to obtain the molecular vibration modes for the respective frequencies. These calculations provided thermodynamic parameters such as the entropy, enthalpy, and specific molar heat at constant pressure, all as a function of the temperature. The parameter values obtained by each method were compared to the experimental values available in the literature. The results showed good accuracy, especially those obtained at the B3lyp/6-311++g(d,p) level for n-butanol. The error between the theoretical and experimental values for the combustion enthalpy of n-butanol was less than 4% at 298.15 K; due to the good prediction of its thermodynamic properties, we used n-butanol as a model for the prediction of other thermodynamic properties. We started a molecular docking study of four ligands, namely, n-butanol, ethanol, propanol, heptane, isooctane, and methanol interacting with butanol isomers. The highest values of affinity energy found were for N-butanol. The possible formation of hydrogen bonds, associations by means of London forces, hydrogen, and alkyl interactions were analyzed. n-Butanol was added to ethanol-gasoline mixtures in the temperature range of 298.15 to 600 K and the results suggest that n-butanol has a higher calorific value than gasoline-ethanol mixtures in G30E, G40E, G50E, G60E, G70E, G80E, G90E, and E100 blends. As such, n-butanol releases greater amounts of heat during combustion and is thus a viable alternative to biofuels.
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Rietveld IB, Allouchi H, Barrio M, Ceolin R, Tamarit JL. Polymorphism of benzylthiouracil, an active pharmaceutical ingredient against hyperthyroidism. Int J Pharm 2021; 598:120378. [PMID: 33581273 DOI: 10.1016/j.ijpharm.2021.120378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/02/2021] [Accepted: 02/06/2021] [Indexed: 01/01/2023]
Abstract
The crystal structures of dimorphic benzylthiouracil, a drug against hyperthyroidism, have been redetermined and the atom coordinates of the two independent molecules of form I have been obtained for the first time. The dimorphism convincingly demonstrates the conformational versatility of the benzylthiouracil molecule. It has been established through calorimetric studies that the low-temperature form II transforms endothermically (ΔII→IH = 5.6(1.5) J g-1) into form I at 405.4(1.0) K. The high-temperature form I melts at 496.8(1.0) K (ΔI→LH = 152.6(4.0) J g-1). Crystallographic and thermal expansion studies show that form II is denser than form I, leading to the conclusion that the slope of the II-I equilibrium curve in the pressure-temperature phase diagram is positive. It follows that this dimorphism corresponds to a case of overall enantiotropic behaviour, which implies that both solid phases possess their own stable phase region irrespective of the pressure. Moreover, form II is clearly the stable polymorph under ambient conditions.
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Barbosa LS, Moreira E, Lopes AR, Fonseca ALA, Azevedo DL. Cubane and cubanoid: Structural, optoelectronic and thermodynamic properties from DFT and TD-DFT method. J Mol Graph Model 2021; 103:107820. [PMID: 33418467 DOI: 10.1016/j.jmgm.2020.107820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 11/28/2022]
Abstract
In this paper, we report structural, electronic and optical properties of cubane (C8H8) and cubanoids (cubane-like molecules) using Density Functional Theory (DFT). The cubanoids are cubanes for which Carbon atoms have been substituted by Nitrogen (N), Phosphorus (P), Boron (B), Silicon (Si), Arsenic (As), Antimony (Sb) or Bismuth (Bi) atoms. These molecules presented exceptional stability with several different symmetry point groups, being the majority Td. All calculated vibrational frequencies are positive for any studied molecules indicating that all these structures are in a stable state. The HOMO-LUMO gaps and DOS were calculated converged towards to values between 1.87 eV and 5.61 eV, actually showing promising electronic properties (Just for comparison, the cubane energy gap is 7.50 eV). The optical absorptions were also calculated for the cubanoid structure using the Time-Dependent Density Functional Theory (TD-DFT). Their dependence on the wavelength is analyzed, where five of theses structures absorb on the visible region. Finally, the extrapolation of thermodynamic properties indicates that these cubanoid could be potentially synthesized spontaneously, where four structures, the synthesis would occur for temperatures below 400 K, while for Si4Bi4H4 structure, the synthesis would occur at room temperature.
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Kalita D, Jain S, Srivastava B, Goud VV. Sono-hydro priming process (ultrasound modulated hydration): Modelling hydration kinetic during paddy germination. ULTRASONICS SONOCHEMISTRY 2021; 70:105321. [PMID: 32906065 PMCID: PMC7786556 DOI: 10.1016/j.ultsonch.2020.105321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 05/09/2023]
Abstract
Application of ultrasound technology in modulating the hydration process during paddy germination was analyzed in this study. The effect of hydropriming (24 h) and sono-hydro priming (ultrasound priming, 12 h) on the hydration behaviour of paddies was determined at different temperatures (25-40 °C). Ultrasound pulse was applied for 10 min after every one hour for sono-hydro priming. Germination potential and microstructure analysis of treated paddies were also performed. Downward concave curve observed in hydration process of paddies indicates initial high-water absorptionthrough diffusion process. Sono-hydro priming process showed higher hydration rate compared to hydropriming. The changes in moisture content during hydration processes fitted to theoretical (Fick's model) and empirical model (Peleg model) exhibited high regression coefficient (R2 > 0.95) indicating suitability for predicting hydration behaviour in both paddies for germination. The Peleg model adequately predicted saturation moisture content and sono-hydro priming efficiently increased the water absorption rate. Effective moisture diffusivity determined from Fick's diffusion model increased for sono-hydro priming. Activation energy estimated from effective moisture diffusivity required in sono-hydro priming (Ea = 20.32 and 19.19 KJ/mol respectively) for pigmented rice and non-pigmented rice was lower than hydropriming (Ea = 27.11 and 32.15 KJ/mol respectively). Both hydration processes were endothermic and non-spontaneous inferred from thermodynamic properties. Sono-hydro priming exhibited < 95% germination potential with shorter soaking time (12 h) owing to the high mass transfer rate. SEM micrograph revealed water absorption through various micro-cavities during sono-hydro priming. Thus, sono-hydro priming potentially reduced the soaking process (approximately 50%) with higher germination rate in paddies beneficial for commercial malting of grains.
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Gaseous complex hydrides NaMH 4 and Na 2MH 5 (M = B, Al) as hydrogen storage materials: a quantum chemical study. J Mol Model 2020; 27:2. [PMID: 33331981 DOI: 10.1007/s00894-020-04601-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/08/2020] [Indexed: 10/22/2022]
Abstract
Metal hydrides are feasible for energy storage applications as they are able to decompose with hydrogen gas release. In this work, gaseous complex sodium hydrides, NaMH4 and Na2MH5 (M = B or Al), have been investigated using DFT/B3P86 and MP2 methods with 6-311++G(d,p) basis set; the optimized geometry, vibrational spectra and thermodynamic (TD) properties have been determined. Based on TD approach, a stability of the hydrides to different dissociation channels is analysed; the enthalpies of formation ∆fH°(0) of gaseous species have been obtained: - 1 ± 17 kJ mol-1 (NaBH4), 91 ± 14 kJ mol-1 (NaAlH4), - 13 ± 16 kJ mol-1 (Na2BH5), and 71 ± 16 kJ mol-1 (Na2AlH5). The complex hydrides are confirmed to produce gaseous products with hydrogen gas release at elevated temperature, whereas heterophase reactions, with NaH and B/Al products in condensed state, are predicted to occur spontaneously at lower temperature. Graphical abstract.
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Ait-Ramdane-Terbouche C, Abdeldjebar H, Terbouche A, Lakhdari H, Bachari K, Roisnel T, Hauchard D. Crystal structure, chemical reactivity, kinetic and thermodynamic studies of new ligand derived from 4-hydroxycoumarin: Interaction with SARS-CoV-2. J Mol Struct 2020; 1222:128918. [PMID: 32834114 PMCID: PMC7363612 DOI: 10.1016/j.molstruc.2020.128918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 11/20/2022]
Abstract
Currently, Covid-19 pandemic infects staggering number of people around the globe and causes a high rate of mortality. In order to fight this disease, a new coumarin derivative ligand (4-[(pyridin-3-ylmethyl) amino]-2H-chromen-2-one) (LTA) has been synthesized and characterized by single-crystal X-ray diffraction, NMR, ATR, UV-Visible and cyclic voltammetry. Chemical reactivity, kinetic and thermodynamic studies were investigated using DFT method. The possible binding mode between LTA and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that LTA crystallizes in a monoclinic system with P2 1 space group. The reactivity descriptors such as nucleophilic index confirm that LTA is more nucleophile, inducing complexation with binding species like biomolecules. The kinetic and thermodynamic parameters showed that the mechanism of crystal formation is moderately exothermic. The binding energy of the SARS-CoV-2/Mpro-LTA complex and the calculated inhibition constant using docking simulation showed that the active LTA molecule has the ability to inhibit SARS-CoV-2.
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Sarwan M, M FS, Singh S. An analysis of structural phase transition and allied properties of cubic ReN and MoN compounds. J Mol Model 2020; 27:1. [PMID: 33294944 DOI: 10.1007/s00894-020-04615-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
The present work aims at the study of structural, elastic, electronic, and thermodynamic properties of transition metal nitrides: ReN and MoN in the zinc-blende (B3) phase. The plane wave pseudopotential and norm-conserving pseudopotential have been applied in Quantum-Espresso code based on density-functional theory (DFT). The results show a first-order phase transition from B3 to B1 (rock-salt) structure at 42 GPa and 2.5 GPa for ReN and MoN respectively. The elastic behaviors of these compounds are also unfolded in this work. The brittleness of the ReN and ductility of MoN is identified with the help of Pugh's index and Poisson's ratio. The strong anisotropic behaviors of both compounds are detected under the influence of pressure. The electronic and bonding features of proposed compounds are evaluated by means of band structures, the density of states (DOS), Fermi surface, and charge density plots. The obtained results forecast the metallic behavior and ionic bonding of ReN and MoN in both phases: B3 and B1. Additionally, various thermodynamic properties are also investigated under high pressures and temperatures (from 0 to 2000 K). Conceivably, these properties are reported for the first time in the B3 structure of these compounds and will be useful for many applications in modern technologies as well.
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Characterization of the ergometric properties of commercial bioactive dairy peptides. Curr Res Food Sci 2020; 3:296-303. [PMID: 33336191 PMCID: PMC7733010 DOI: 10.1016/j.crfs.2020.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The thermodynamic properties of bioactive peptides provide insights into their functional behavior and their biological efficacy. We conducted precise analyses of the density, the ultrasonic velocity and the relative attenuation of serial dilutions of three commercial dairy peptides prepared by enzymatic methods. From these we determined the partial specific volume and the partial specific adiabatic compressibility coefficient for the peptides. At concentrations greater than ~2.5 mg mL−1, the apparent values for specific volume and adiabatic compressibility were constant, differing between the three peptides at ±3% for specific volume and ±70% for compressibility. Both specific volume and adiabatic compressibility were highly dependent on concentration, indicating the importance of precise low concentration measurements to obtain correct values for these thermodynamic parameters. From these parameters it was apparent that restructuring of water molecules around the peptides (and their associated counterions) led to compact solutes that were also incompressible. These thermodynamic analyses are critical for understanding how the properties and the beneficial effects of bioactive peptides are influenced by their chemical environment. Dissolved dairy peptide properties distinguishable from ergometric analyses. Specific volume and adiabatic compressibility evaluate bioactive peptide hydration. Commercial bioactive dairy peptides are compact and incompressible. Compactness and incompressibility of peptide affected by hydrogen-bonding amino acids. Solution concentration affects values of measured thermodynamic parameters.
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Malekahmadi O, Zarei A, Botlani Esfahani MB, Hekmatifar M, Sabetvand R, Marjani A, Bach QV. Thermal and hydrodynamic properties of coronavirus at various temperature and pressure via molecular dynamics approach. JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY 2020; 143:2841-2850. [PMID: 33250660 PMCID: PMC7680216 DOI: 10.1007/s10973-020-10353-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/06/2020] [Indexed: 06/10/2023]
Abstract
COVID-19 is an epidemic virus arising from a freshly discovered coronavirus. Most people involved with the coronavirus will experience slight to moderate respiratory disease and recover without needing particular therapy. In this work, the atomic stability of the coronavirus at different thermodynamic properties such as temperature and pressure, was studied. For this purpose, the manner of this virus by atomic precession was described with a molecular dynamics approach. For the atomic stability of coronavirus description, physical properties such as temperature, total energy, volume variation, and atomic force of this structure were reported. In molecular dynamics approach, coronavirus is precisely simulated via S, O, N, and C atoms and performed Dreiding force field to describe these atoms interaction in the virus. Simulation results show that coronavirus stability has reciprocal relation with atomic temperature and pressure. Numerically, after 2.5 ns simulation, the potential energy varies from - 31,163 to - 26,041 eV by temperature changes from 300 to 400 K. Furthermore, this physical parameter decreases to - 28,045 eV rate at 300 K and 2 bar pressure. The volume of coronavirus is another crucial parameter to the stability description of this structure. The simulation shows that coronavirus volume 92% and 14% increases by 100 K and 2 bar variation of simulation temperature and pressure, respectively.
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Zhang Q, Jeganathan B, Dong H, Chen L, Vasanthan T. Effect of sodium chloride on the thermodynamic, rheological, and microstructural properties of field pea protein isolate/chitosan complex coacervates. Food Chem 2020; 344:128569. [PMID: 33280960 DOI: 10.1016/j.foodchem.2020.128569] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/11/2020] [Accepted: 11/02/2020] [Indexed: 01/18/2023]
Abstract
The effect of increasing sodium chloride concentration (cNaCl, 0-0.4 M) on the formation and rheological and microstructural properties of field pea protein isolate (FPPI)/chitosan (Ch) complex coacervates was investigated. The maximum turbidity and zeta potential of FPPI/Ch mixtures consistently decreased with the increasing cNaCl. The tertiary conformation of FPPI was altered to facilitate the aggregation of FPPI/Ch complexes via hydrophobic interactions. Changes in thermodynamic parameters during the titration of FPPI with Ch confirmed the addition of NaCl could cause the inhibition of electrostatic complexation and the induction of non-Coulombic interactions. FPPI/Ch complex coacervates exhibited first enhanced and then weakened viscoelastic properties and an initially tightened and then a loosened microstructure as the cNaCl increased. In summary, appropriate cNaCl favors the formation of FPPI/Ch complex coacervates with improved functionalities via the coordination of promoted hydrophobic interactions and inhibited electrostatic attractions, facilitating the application of this protein ingredient in food development.
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Ejuh GW, Ndjaka JMB, Tchangnwa Nya F, Ndukum PL, Fonkem C, Tadjouteu Assatse Y, Yossa Kamsi RA. Determination of the structural, electronic, optoelectronic and thermodynamic properties of the methylxanthine molecules theophylline and theobromine. OPTICAL AND QUANTUM ELECTRONICS 2020; 52:498. [PMID: 33162643 PMCID: PMC7603795 DOI: 10.1007/s11082-020-02617-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
RHF and DFT (wB97XD and B3LYP) methods with the 6-31++G** basis set have been used to study structural, optoelectronic and thermodynamic properties of Theophylline and Theobromine. Dipole moment, average polarizability, anisotropy, first-order molecular hyperpolarizability, second-order molecular polarizability, HOMO and LOMO energy gap, molar refractivity, chemical hardness, chemical softness, electronic chemical potential, electronegativity, electrophilicity index, dielectric constant, electric susceptibility, refractive index and their thermodynamic properties have equally been calculated. To understand the vibrational analysis of our system, IR and RAMAN frequencies were calculated and described. Results reveal that molecules can have applications in linear and nonlinear optical devices, photonic devices and in molecular electronics. Equally, from dipole moment, average polarizability, anisotropy, first-order molecular hyperpolarizability, second-order molecular polarizability, HOMO and LOMO energy gap, molar refractivity, chemical hardness, chemical softness, electronic chemical potential, electronegativity, electrophilicity index and literature we suggest that Theophylline and Theobromine be consider as candidates for the treatment of COVID-19 and other respiratory diseases.
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Gowdini E, Ahmad AA, Mabudi A, Hadipour NL, Kharazian B. A molecular dynamics study on the thermal properties of carbon-based gold nanoparticles. J Mol Model 2020; 26:307. [PMID: 33083893 DOI: 10.1007/s00894-020-04559-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/28/2020] [Indexed: 12/30/2022]
Abstract
Due to unique features in surface activity, thermal stability, electrical and thermal conductivity, and compatibility with biomolecules such as DNA and proteins, carbon-based nanoparticles are raised potential as a candidate for various applications such as catalytic processes, drug delivery, light, and electrical engineering. Based on this premise, thermodynamic features of pure, graphene, and carbon nanotube (CNT)-based gold nanoparticles (AuNPs) are investigated using molecular dynamics approach. Melting, heat capacity, thermal conductivity, contact angle of molten AuNPs, and phase transition are calculated as indicators of thermodynamic properties of pure and carbon-based AuNPs. Simulation results indicate that the presence of a carbon platform and its contact surface area has a significant role in the thermodynamic properties of AuNPs and leads the phononic heat capacity and thermal conductivity to decrease for AuNPs. The platform also causes the melting point temperature of AuNPs to increase. The melting of gold on the carbon base is of the first-order type. In addition, contact angle for molten AuNPs on the Graphene is significantly higher than the one on the CNT due to more contact area on the Graphene substrate.Graphical abstract .
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Abdel-Naby MA, El-Wafa WMA, Salem GEM. Molecular characterization, catalytic, kinetic and thermodynamic properties of protease produced by a mutant of Bacillus cereus-S6-3. Int J Biol Macromol 2020; 160:695-702. [PMID: 32485254 DOI: 10.1016/j.ijbiomac.2020.05.241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/19/2023]
Abstract
The proteolytic strain Bacillus cereus-S6-3 was subjected to mutagenic treatments viz. UV irradiations and methyl methane sulfonate (MMS). The obtained mutant strain, B. cereus-S6-3/UM90 showed 1.34 fold over the parent strain. Molecular characterization of proteases from the parent (PP/S6-3) and mutant (PM/UM90) strains indicated that they were consisted of two domains and binds a zinc ion and 4 calcium ions in the active site. Amino acid sequence alignment of PM/UM90 protease showed 19 amino acid residues were substituted compared to that of the wild-type enzyme. However, both proteases contained equal number of aromatic and hydrophobic amino acids. Protease from PM/UM90 showed an effective improvement in thermal properties in terms of reaction temperature, t1/2, the values of kd, activation energy (Ea), and decimal reduction time (D) within the temperature range from 60 to 80 °C. In addition, the kinetic and thermodynamic parameters for substrate hydrolysis (i.e., Km, Vmax, ΔH*, ΔG*, ΔS*, kcat, Vmax/Km, kcat/Km, ΔG*E-T and ΔG*E-S) showed a significant improvement of the catalytic efficiency for PM/UM90 protease. Furthermore, the correlation between thermodynamic properties and the patterns of amino acid substitution of wild-type enzyme to has been discussed.
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Rasouli S, Moghbeli MR, Nikkhah SJ. Molecular dynamics simulation of polystyrene copolymer with octyl short-chain branches in toluene. J Mol Model 2020; 26:80. [PMID: 32180007 DOI: 10.1007/s00894-020-4339-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/04/2020] [Indexed: 11/28/2022]
Abstract
In this study, dimensional, conformational and dynamic behaviors of a short-chain branched styrene/1-octene copolymer chain with different 1-octene percentages, i.e., 0, 2, 4 and 6%, in toluene are investigated at the temperature of 298.15 K via molecular dynamics simulation. The chain dimensions and flexibility in the solvent are evaluated by calculating the radius of gyration (Rg), end-to-end distance (<r0>), surface area (Ach), and volume (Vch) of the copolymer chain. The mean square displacement (MSD) and diffusivity coefficient for each copolymer chain are measured to determine its dynamic behavior and mobility in aromatic media. To consider the effect of increasing the 1-octene co-monomer percentage on the copolymer chain affinity to the solvent molecules, the interaction energy (Eint) and Flory-Huggins (FH) interaction parameter are calculated for each equilibrated solution model. The simulation results indicate that the co-monomer level increment in the copolymer structure reduces the chain Rg amount and its interaction with the solvent. The <r0> of the chain increases up to 4% co-monomer content, while further co-monomer content decreases the <r0> value. Additionally, the viscosity of the equilibrated dilute solutions is calculated via non-equilibrium molecular dynamics simulation (NEMD). Moreover, the steric hindrance of the copolymers and the solvent molecules capturing in the dilute solution is determined via radial distribution function (RDF) analysis. Helmholtz free energy and the system entropy changes are calculated to evaluate the tendency of the copolymer to the solvent molecules and its dilute solution irregularity, respectively. Graphical abstract The figure shows the variations trend of the poly(styrene-co-1-octene) chain dimensions in toluene aromatic solvent by increasing the 1-octene content (x), after the equilibration state. Red and blue colors represent the carbon atoms of the copolymer chain backbone and 1-octene side chains, respectively. The styrene rings and the hydrogen atoms of the chains were removed for better view.
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Hong D, Zeng W, Qin H, Jiang CL, Liu FS, Tang B, Liu QJ. Vibrational, thermodynamic, and dielectric properties of ε-CL-20: first-principles calculations. J Mol Model 2020; 26:47. [PMID: 32020344 DOI: 10.1007/s00894-020-4311-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/23/2020] [Indexed: 10/25/2022]
Abstract
The DFT theory is used to investigate the vibration forms of ε-CL-20 by discussing the phonon DOS and infrared and Raman spectra. By observing them, the detailed vibration forms can be obtained, and the vibrations are different in the different regions. Our calculated vibrational results are consistent with previous data. In order to deeply comprehend CL-20, we also investigate the thermodynamic properties, finding that entropy, enthalpy, Debye temperature, and heat capacity are increased with the rising temperature and the vibrational free energy decreases with the increasing temperature. The εxx, εyy, and εzz are similar, which reflects the small anisotropy among [100], [010], and [001]. Moreover, it can be noticed that the major contribution for static dielectric constants originates from the electronic contribution.
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Hossain MT, Rahman MA. A first principle study of the structural, electronic, and temperature-dependent thermodynamic properties of graphene/MoS 2 heterostructure. J Mol Model 2020; 26:40. [PMID: 32008139 DOI: 10.1007/s00894-020-4306-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/20/2020] [Indexed: 11/30/2022]
Abstract
After an initial assessment of the structural and electronic properties of graphene, monolayer MoS2, and graphene/MoS2 bilayer hetero-structure, the temperature-dependent thermodynamic properties of graphene/MoS2 bilayer hetero-structure are examined by using density functional theory calculations. The structure, bandgap, partial density of states, and thermodynamic properties of graphene, monolayer MoS2 and graphene/MoS2 system are investigated and analyzed. Findings from the present study are in good agreement with the previously reported theoretical and experimental studies. Monolayer MoS2 and graphene form a stable Van der Waals heterostructure owing to their negative binding energy, and the system acts as a zero-bandgap semiconductor. Debye temperature and the heat capacity of graphene, MoS2 monolayer, and graphene/MoS2 system are calculated from phonon dispersion relations to be 2100 K, 600 K, and 1400 K, and 0.7 J/g.K, 0.218 J/g.K, and 0.46 J/g.K, respectively. Introduction of graphene into the MoS2 semiconductor is, therefore, found to improve the overall thermodynamic properties of the composite as graphene preserved its superior thermal properties. The findings will be beneficial to calculate thermal conductivity of the graphene/MoS2 heterostructure for minimizing the temperature effect in electronic or optoelectronic devices.
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Mangold F, Pilz S, Bjelić S, Vogel F. Equation of state and thermodynamic properties for mixtures of H 2 O , O 2 , N 2 , and CO 2 from ambient up to 1000 K and 280 MPa. J Supercrit Fluids 2019; 153:104476. [PMID: 31885417 PMCID: PMC6919335 DOI: 10.1016/j.supflu.2019.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Supercritical water oxidation (SCWO) is an effective technique to treat wet organic wastes. Its modeling requires an accurate calculation of thermodynamic properties. In this work an equation of state (EOS) is proposed which accurately predicts the thermodynamic state of mixtures of water, oxygen, nitrogen, and carbon dioxide for a wide range of compositions, temperatures, and pressures including supercritical conditions. The EOS includes a volume translation, an evolved α -function and non-quadratic mixing rules. The introduced parameters are regressed to experimental data. From the pressure-explicit EOS, enthalpy, specific heats at constant volume and constant pressure, and fugacity coefficients are derived and calculated. The binary mixtures H 2 O / O 2 , H 2 O / N 2 , H 2 O / CO 2 , N 2 / CO 2 as well as the ternary mixture H 2 O / O 2 / N 2 are well predicted by the proposed EOS with relative errors below 10% and 15%, respectively. The region of low temperature and high pressure is most difficult to predict with relative errors up to 20%.
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Mushtaq M, Dar SA, Sattar MA, Kouser R. First-principles study of structural, electronic, magnetic, thermodynamic and mechanical properties of ferromagnetic Mn 2MoAl Heuslar alloy. J Mol Graph Model 2019; 95:107507. [PMID: 31837479 DOI: 10.1016/j.jmgm.2019.107507] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 11/16/2019] [Accepted: 12/02/2019] [Indexed: 11/18/2022]
Abstract
The Mn-based Mn2MoAl type ternary Heusler alloy is of particular interest due to its potential ferromagnetic properties and high spin-polarization. The present paper aims to explore the physical properties of this new alloy for its possible technological applications and also provide theoretical basis to the future experiments. The electronic structure, magnetism, and elastic properties of the alloy are studied by using first-principles calculations based on density functional theory (DFT), along with calculation of thermodynamic properties within quasi-harmonic approximation. The structural analysis predicts the optimized lattice constant of 5.90 Å and the ferromagnetic stable state. The electronic band structure calculations at GGA-level reveal that present alloy is nearly half-metal with spin-polarization up to 94% at the Fermi level, whereas, GGA + U calculations reveal Mn2MoAl alloy to be a quite spin polarized metal. The calculated total magnetic moment Mt of the unit-cell is found to be 1.04 μB, which nearly obeys Mt = │Zt-24│formula. The individual Mn, Mo and Al atoms carry magnetic moment of 0.70 μB, -0.28 μB, -0.01μB, respectively. Employing quasi-harmonic approximation, interesting thermodynamic properties of the alloy have been investigated. Furthermore, the elastic and mechanical properties have been investigated. The results confirm that Mn2MoAl alloy is mechanically stable, ductile, anisotropic, with metallic inter-atomic bonding and is expected to be beneficial for the spintronic technology.
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