Journal of Molecular Modeling最新文献_第3页

The adsorption behavior at the air/water interface of saturated cardanol nonionic surfactants through molecular dynamic simulations

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-02-19 DOI: 10.1007/s00894-025-06314-x

Congying Lu, Xinyi Xu, Minjia Xia, Zhenyu Yuan, Haifeng Wang, Weiyang Liu, Qing Yang, Wei Ding

Context

Cardanol surfactants exhibit significant development potential owing to their advantages of abundant availability, low cost, and environmental sustainability. In this study, a series of saturated cardanol nonionic surfactants were designed. The structure–activity relationships of these surfactants with varying lengths and positions of PO and EO chains were investigated from three perspectives: surface activity, adsorption morphology, and molecular bonding forces. The results indicated that the chain length ratio and position of PO and EO significantly influenced the performance of cardanol nonionic surfactants at the air/water interface. The PO chains can significantly mitigate the solvation effect at the terminus of surfactants, thereby enhancing their aggregation at the air/water interface. Additionally, the ratio of PO to EO chains influences both the radius of gyration and tilt angle of hydrophilic and hydrophobic segments within surfactant molecules. Notably, when both PO and EO chain lengths are set to 8, optimal adsorption of surfactant molecules occurs at the interface. This phenomenon is primarily attributed to hydrogen bonding interactions that lead water molecules to exhibit varying degrees of aggregation around PO or EO chains; these effects, in conjunction with adsorption morphology, ultimately influence the interfacial properties of surfactants. This study provides a theoretical foundation and reference for the structural design, synthesis, and interfacial properties of cardanol surfactants.

Method

In this study, Packmol was employed for model construction, Gromacs for molecular dynamics simulations, and all simulations were conducted using the GAFF force field. The simulation process primarily involved the steepest descent method, followed by NPT ensemble simulations for 1 ns and 10 ns, respectively. The Berendsen and Parrinello-Rahman methods are employed to maintain system pressure. The LINCS algorithm and Lennard–Jones potential are utilized to effectively constrain molecular bond lengths and cutoff radius. The long-range electrostatic interactions are treated using the Particle-Mesh Ewald (PME) summation method.

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引用次数: 0

Exploring the dominant interactions: unveiling the stable structure of theobromine-water complexes through DFT and ab initio investigations

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-02-18 DOI: 10.1007/s00894-025-06309-8

Tanvi, Mohd Tauheed Ilyas, G. S. S. Saini, Anamika Mukhopadhyay

Context

Solute-solvent interactions are crucial for life processes, as biological reactions primarily take place in liquid environments. Water, owing to its remarkable capacity for hydrogen bonding, plays a pivotal role as a solvent in these biological systems. This study computationally investigates the hydration of theobromine, a molecule with significant therapeutic potential and a favorable safety profile. It focuses on the intermolecular interactions within 1:1 theobromine-water complexes in order to provide a comprehensive identification of the potential interaction sites for water when theobromine is dissolved in it. In addition, the research extends to investigate species with up to three water molecules to explore the potential for cooperative binding phenomena.

Methods

In this work, we have employed MP2/6-311++G(d,p) and (omega )B97XD/6-311++G(d,p) levels of theory within Gaussian09 to optimize geometries and calculate the energies of theobromine-water complexes. Eight stationary points have been identified on the 1:1 theobromine-water potential energy surface, with the majority exhibiting dual hydrogen bond motifs and deviations from linearity. The global minimum structure is characterized by the simultaneous presence of O-H—O and N-H—O hydrogen bonds, with interaction energies of 7.78 kcal/mol and 9.29 kcal/mol determined at the MP2/6-311++G(d,p) and (omega )B97XD/6-311++G(d,p) levels of theory, respectively. Natural bond orbital (NBO) analysis at the MP2/6-311++G(d,p) level has been used to quantify donor-acceptor charges and hyperconjugation energies. A linear correlation between interaction energy, charge density, and bond length elongation has been observed, highlighting the intricate interplay of these key parameters. To investigate cooperative hydrogen bonding, we have modeled complexes with up to three water molecules. Weak interactions have been further characterized using atoms in molecules (AIM) analysis and reduced density gradient (RDG) approach. We have found that increasing the hydration up to two water molecules significantly reduces the tautomerization barrier from 46.09 to 20.47 kcal/mol.

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引用次数: 0

Local and non-local chemical potential and hardness: a grand canonical ensemble approach

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-02-18 DOI: 10.1007/s00894-025-06311-0

Paulino Zerón, Maurizio A. Pantoja-Hernández, Marco Franco-Pérez, José L. Gázquez

Context

The formulation of conceptual density functional theory in the grand canonical ensemble provides a theoretical framework that allows one to establish additional insights about the response functions that characterize this approach. In particular, through this procedure, one can establish the local counterpart of the chemical potential which, when integrated over all the space, leads to the global quantity and the local counterpart of the hardness that not only provides a function free of ambiguities, but also generates through its integration over all the space the well-defined value of the global quantity given by the difference of the vertical first ionization potential and electron affinity. In the present work, the non-local counterpart of these local reactivity descriptors is derived making use of the Fukui kernel descriptor previously developed by us. Then, the local and non-local chemical potential and hardness, thus obtained, are applied to study site and bond reactivities of several systems, to rationalize the behavior of kinetic and thermodynamic properties, through the chemical information that these indexes provide.

Methods

The electronic structure calculations required to evaluate the reactivity indexes analyzed in this work were done with the PBE0 exchange–correlation energy functional. The geometry optimization was done in all cases in a modified version of the NWChem program, while the Hirshfeld population analysis was done in a modified version of the demon2k program. For the electrophilic addition of hydrogen halides (HX) to several substituted ethenes and the hydration reaction of aldehydes and ketones, the 6-311G** basis set was used, while for the bond enthalpies of chemical reactions where there is a homolytic bond break and the trans influence in which the lability of the leaving ligand is modified by the ligand opposite to it, the Def2-TZVP was used.

{"title":"Local and non-local chemical potential and hardness: a grand canonical ensemble approach","authors":"Paulino Zerón, Maurizio A. Pantoja-Hernández, Marco Franco-Pérez, José L. Gázquez","doi":"10.1007/s00894-025-06311-0","DOIUrl":"10.1007/s00894-025-06311-0","url":null,"abstract":"<div><h3>Context</h3><p>The formulation of conceptual density functional theory in the grand canonical ensemble provides a theoretical framework that allows one to establish additional insights about the response functions that characterize this approach. In particular, through this procedure, one can establish the local counterpart of the chemical potential which, when integrated over all the space, leads to the global quantity and the local counterpart of the hardness that not only provides a function free of ambiguities, but also generates through its integration over all the space the well-defined value of the global quantity given by the difference of the vertical first ionization potential and electron affinity. In the present work, the non-local counterpart of these local reactivity descriptors is derived making use of the Fukui kernel descriptor previously developed by us. Then, the local and non-local chemical potential and hardness, thus obtained, are applied to study site and bond reactivities of several systems, to rationalize the behavior of kinetic and thermodynamic properties, through the chemical information that these indexes provide.</p><h3>Methods</h3><p>The electronic structure calculations required to evaluate the reactivity indexes analyzed in this work were done with the PBE0 exchange–correlation energy functional. The geometry optimization was done in all cases in a modified version of the NWChem program, while the Hirshfeld population analysis was done in a modified version of the demon2k program. For the electrophilic addition of hydrogen halides (HX) to several substituted ethenes and the hydration reaction of aldehydes and ketones, the 6-311G** basis set was used, while for the bond enthalpies of chemical reactions where there is a homolytic bond break and the trans influence in which the lability of the leaving ligand is modified by the ligand opposite to it, the Def2-TZVP was used.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06311-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143431085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mechanical enhancement of hydroxyapatite via carbon and boron nitride nanotubes: a molecular dynamics study

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-02-18 DOI: 10.1007/s00894-025-06317-8

Bugra Eyidogan, Mesut Kirca

Context

This study explores the mechanical limitations of hydroxyapatite (HAP), a critical bioceramic in bone tissue engineering and orthopedic implants, which is limited by its brittleness and low mechanical strength. By reinforcing HAP with carbon nanotubes (CNTs) and boron nitride nanotubes (BNNTs), the mechanical performance of HAP was significantly enhanced. The inclusion of CNTs led to a 25% increase in ultimate tensile strength (UTS), peaking at 9.18 GPa, while BNNTs improved ductility with a maximum UTS of 8.75 GPa. Toughness, representing the material’s energy absorption capacity, reached 15.8 kJ/m² in CNT-reinforced composites and 9.3 kJ/m² in BNNT-reinforced composites, emphasizing their distinct reinforcement contributions. The study highlights the potential of CNT-BNNT combinations, achieving a synergistic balance of strength, ductility, and toughness.

Methods

The study employed molecular dynamics simulations to model and analyze the mechanical behavior of nano-reinforced HAP. Simulations were performed using the LAMMPS software, with the CVFF-Interface Force Field for HAP and the AIREBO potential used to model carbon interactions in CNTs. BNNTs were simulated using the Tersoff potential to account for interactions between boron and nitrogen atoms. The effects of nano-reinforcements on the mechanical properties of HAP were evaluated through tensile stress–strain curves, which quantified improvements in Young's modulus, ultimate tensile strength (UTS), and strain at UTS. Additionally, combinations of CNTs and BNNTs in varying ratios were simulated to assess synergistic interactions, while different inclusion levels were investigated to understand their impact on the composite’s mechanical performance. Toughness values, representing the material's energy absorption capacity, were calculated by integrating the area under the stress–strain curves up to failure, providing deeper insights into the ductility and energy dissipation characteristics of the reinforced HAP composites.

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引用次数: 0

Reduction of hydrogen peroxide by amine-based diselenides: understanding the effect of substitutions on reactivity

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-02-18 DOI: 10.1007/s00894-025-06313-y

Vishnu Rama Chari, Raghu Nath Behera

Context

Many small organoselenium compounds, such as substituted diselenides, mimic the glutathione peroxidase (GPx) activity by catalysing the reduction of hydrogen peroxide. In this context, the effect of substitution in di-2(N-cyclohexyl,N-(methylamino)-methyl)phenyl diselenide (CMP) on its GPx-like activity (to reduce hydrogen peroxide) has been investigated using the density functional theory. It was observed that the presence of an electron donating group as well as secondary amino group (instead of tertiary one) favoured the peroxide reduction process, which is consistent with the experimental reports. This study revealed that the presence of electron donating group lowers the energy requirement for distortion in zwitterion of the selenol during the progress of the reaction, thereby enhancing its catalytic activity.

Methods

Geometry optimizations, Natural Bond Order (NBO) and the wavefunction calculations were carried out using Gaussian16 software at B3PW91/6–31+G(d,p) level of theory. Improved energy calculations were carried out at B3PW91/6–311++ G(3df,3pd)//B3PW91/6–31+G(d,p) level of theory. The solvent effect was modelled using the self-consistent reaction field (SCRF) method utilizing polarizable continuum model (PCM). Activation Strain Model was used to study the contributions of the steric and electronic effects due to substitutions. Wavefunction analysis was carried out using Multiwfn software.

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引用次数: 0

Monomer, cyclic dimer of dimethyl sulfoxide, and dimethyl sulfoxide-water hydrogen bonded complexes: FTIR studies and quantum chemical calculations

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-02-17 DOI: 10.1007/s00894-025-06300-3

R. Shanmugam, P. Dineshkumar, T. Sangeetha, P. Mounica, K. Ramya, A. Elangovan, G. Arivazhagan

Context

The dimethyl sulfoxide (DMSO), an excellent solvent, has many applications in biochemical and pharmacological technology and has self-associates. In the S = O stretching region of its infrared (IR) spectrum, it has been reported that two S = O stretching bands, each one for monomer and dimer, and two methyl stretching bands appear. The density functional theory (DFT) calculations reveal that one of the two methyl stretching bands is the dimer S = O stretching band. The analysis of IR spectrum of DMSO-water solution for the S = O stretching bands along with the theoretical bands shows that in the solution with water mole fraction less than 0.3, unlike the literature report that there are no DMSO-water interactions, DMSO-water H-bond complexation takes place. The second-order perturbation energy analysis indicates that the DMSO sulfur can act as H-bond acceptor and DMSO oxygen has three lone pair electrons when complexed with water. The (text{O}-text{H}cdots text{S}) interaction, represented by green region in the isosurfaces, is classified as weak by the topological parameters such as electron density and Laplacian of electron density. The results assume significance in view of understanding its self-association and H-bond interaction with water, of course any solute.

Method

The deconvolution of experimental envelop has been carried out using OriginPro 9.0 software. The DFT calculations were done with B3LYP/6–311 + + G(3df,3pd) basis set using Gaussian09W. The isosurface and topological parameters have been obtained using Multiwfn 3.8 package. The results have been visualized using GaussView 5.0 and visual molecular dynamics (VMD) softwares.

{"title":"Monomer, cyclic dimer of dimethyl sulfoxide, and dimethyl sulfoxide-water hydrogen bonded complexes: FTIR studies and quantum chemical calculations","authors":"R. Shanmugam, P. Dineshkumar, T. Sangeetha, P. Mounica, K. Ramya, A. Elangovan, G. Arivazhagan","doi":"10.1007/s00894-025-06300-3","DOIUrl":"10.1007/s00894-025-06300-3","url":null,"abstract":"<div><h3>Context</h3><p>The dimethyl sulfoxide (DMSO), an excellent solvent, has many applications in biochemical and pharmacological technology and has self-associates. In the S = O stretching region of its infrared (IR) spectrum, it has been reported that two S = O stretching bands, each one for monomer and dimer, and two methyl stretching bands appear. The density functional theory (DFT) calculations reveal that one of the two methyl stretching bands is the dimer S = O stretching band. The analysis of IR spectrum of DMSO-water solution for the S = O stretching bands along with the theoretical bands shows that in the solution with water mole fraction less than 0.3, unlike the literature report that there are no DMSO-water interactions, DMSO-water H-bond complexation takes place. The second-order perturbation energy analysis indicates that the DMSO sulfur can act as H-bond acceptor and DMSO oxygen has three lone pair electrons when complexed with water. The <span>(text{O}-text{H}cdots text{S})</span> interaction, represented by green region in the isosurfaces, is classified as weak by the topological parameters such as electron density and Laplacian of electron density. The results assume significance in view of understanding its self-association and H-bond interaction with water, of course any solute.</p><h3>Method</h3><p>The deconvolution of experimental envelop has been carried out using OriginPro 9.0 software. The DFT calculations were done with B3LYP/6–311 + + G(3df,3pd) basis set using Gaussian09W. The isosurface and topological parameters have been obtained using Multiwfn 3.8 package. The results have been visualized using GaussView 5.0 and visual molecular dynamics (VMD) softwares.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The low-temperature dissolution characteristics of water in coal-based hydrocarbon fuels and its molecular dynamics simulation

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-02-17 DOI: 10.1007/s00894-025-06302-1

Zengzhi He, Chongpeng Du, Jun Yu, Siyi Jing, Zonggang Du, Lichuan Gao, Chong Wang, Jiaxi Lei, Yonghong Zhu, Louwei Cui, Wei Han, Dong Li

Context

As a substitute for traditional petroleum derived jet fuels, water in coal-based hydrocarbon fuels may precipitate into ice at low temperatures, leading to fuel system failures and endangering flight safety. This study employed Karl Fischer titration in conjunction with an optimized combination of an oil moisture detector to jointly measure the water solubility of coal-based hydrocarbon fuels at room temperature. The coefficient correction was performed on the oil moisture detector, and the water solubility curves of coal-based hydrocarbon fuels 233 to 313 K were finally measured and compared with other literature results. Due to the extremely low water content in actual fuel and the uneven distribution of water in the fuel, this study mainly considers the water enrichment zone in the fuel.

Methods

Materials Studio 2019 software was utilized to simulate a representative molecular model of coal-based hydrocarbon fuel and a molecular model of water. The positions and charges of the atoms were set and tested, with the COMPASS force field selected to describe interatomic interactions. This force field is the first de novo computing field capable of accurately predicting interactions between various molecules and polymers. Geometry optimization was performed in the Forcite module, and the Construction tool in the Amorphous Cell Tools module was used to construct a coal-based hydrocarbon fuel system. The two models consisted of 3674 and 3671 atoms, respectively, with initial dimensions of 33.2 × 33.2 × 33.2 Å, the boundary conditions are periodic boundary conditions, the energy of the two models is minimized, the conjugate gradient method is used as the optimization method, and then the NPT annealing and kinetic pre-equilibrium operations are carried out, and the molecular dynamics simulation is carried out after the system relaxes to steady state. Through the MD method, the macroscopic phenomenon of temperature decrease in coal-based hydrocarbon fuel systems was analyzed from a microscopic perspective using mean square displacement, diffusion coefficient, and radial distribution function. It was predicted that the crystallization process of coal-based hydrocarbon fuel systems was mainly around 248 to 258 K.

{"title":"The low-temperature dissolution characteristics of water in coal-based hydrocarbon fuels and its molecular dynamics simulation","authors":"Zengzhi He, Chongpeng Du, Jun Yu, Siyi Jing, Zonggang Du, Lichuan Gao, Chong Wang, Jiaxi Lei, Yonghong Zhu, Louwei Cui, Wei Han, Dong Li","doi":"10.1007/s00894-025-06302-1","DOIUrl":"10.1007/s00894-025-06302-1","url":null,"abstract":"<div><h3>Context</h3><p>As a substitute for traditional petroleum derived jet fuels, water in coal-based hydrocarbon fuels may precipitate into ice at low temperatures, leading to fuel system failures and endangering flight safety. This study employed Karl Fischer titration in conjunction with an optimized combination of an oil moisture detector to jointly measure the water solubility of coal-based hydrocarbon fuels at room temperature. The coefficient correction was performed on the oil moisture detector, and the water solubility curves of coal-based hydrocarbon fuels 233 to 313 K were finally measured and compared with other literature results. Due to the extremely low water content in actual fuel and the uneven distribution of water in the fuel, this study mainly considers the water enrichment zone in the fuel.</p><h3>Methods</h3><p>Materials Studio 2019 software was utilized to simulate a representative molecular model of coal-based hydrocarbon fuel and a molecular model of water. The positions and charges of the atoms were set and tested, with the COMPASS force field selected to describe interatomic interactions. This force field is the first de novo computing field capable of accurately predicting interactions between various molecules and polymers. Geometry optimization was performed in the Forcite module, and the Construction tool in the Amorphous Cell Tools module was used to construct a coal-based hydrocarbon fuel system. The two models consisted of 3674 and 3671 atoms, respectively, with initial dimensions of 33.2 × 33.2 × 33.2 Å, the boundary conditions are periodic boundary conditions, the energy of the two models is minimized, the conjugate gradient method is used as the optimization method, and then the NPT annealing and kinetic pre-equilibrium operations are carried out, and the molecular dynamics simulation is carried out after the system relaxes to steady state. Through the MD method, the macroscopic phenomenon of temperature decrease in coal-based hydrocarbon fuel systems was analyzed from a microscopic perspective using mean square displacement, diffusion coefficient, and radial distribution function. It was predicted that the crystallization process of coal-based hydrocarbon fuel systems was mainly around 248 to 258 K.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular dynamics simulation shows enhanced stability in scaffold-based macromolecule, designed by protein engineering: a novel methodology adapted for converting Mtb Ag85A to a multi-epitope vaccine

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-02-15 DOI: 10.1007/s00894-025-06301-2

Ditipriya Hazra, Shakilur Rahman, Manisha Ganguly, Amit Kumar Das, Amlan Roychowdhury

Context

Multi-epitope vaccine (MEV) construction is a technique which combines multiple epitopes, both B cell epitopes and T cell epitopes which have the potential to elicit a much stronger immune response compared to a subunit vaccine. Therefore, recently, a lot of research has been focused on development and improvement of multiepitope vaccines. The strategy of designing a MEV in silico lies in a few basic steps, including procuring the amino acid sequence of the B cell and T cell epitopes from literature search, bioinformatics approach, to construct a potent immunogen capable of eliciting both humoral and cell-mediated response and finally joining these epitopes by linkers. However, a vaccine constructed by merely joining the epitopes may not always result in a stable globular structured protein. In this study, we have focused on developing a strategy where a potential vaccine candidate of Mycobacterium tuberculosis has been used as a scaffold and the low complexity regions of this scaffold have been replaced by the predicated epitopes. Essentially, instead of joining the epitopes by linkers, they have been carefully positioned on a scaffold of a protein that is itself a vaccine candidate to derive a MEV against Mycobacterium tuberculosis.

Method

In this study, a methodology has been detailed to tackle this great challenge using a simple approach of protein engineering. A scaffold-based MEV has been designed against Mtb by converting a vaccine candidate protein, Ag85A, into a scaffold by truncating its low complexity non-immunogenic regions, and the gaps were supplemented by the highly immunogenic epitopes. Replicated 500 ns molecular dynamics simulation at different temperatures (300 K and 310 K) and principal component analysis proved that MEV built on the scaffold is more stable than the conventional one.

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引用次数: 0

Rheological characterization of CuZr metallic glasses at the atomic scale

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-02-13 DOI: 10.1007/s00894-025-06307-w

Nicolás Amigo

Context

Understanding the shear response of metallic glasses is essential for predicting their mechanical performance and plasticity. Cu(_{100-x})Zr(_x) metallic glasses, in particular, exhibit complex shear-thinning behavior governed by atomic composition. Prior studies have highlighted the role of composition in influencing mechanical properties; however, the relationship between the structural characteristics of these alloys and their rheological behavior requires further investigation. This work focuses on the effects of Cu content on the plastic flow of CuZr metallic glasses, emphasizing how atomic-scale features influence yield stress, viscosity, and the onset of plasticity.

Methods

Molecular dynamics simulations using the embedded atom method potential in LAMMPS were conducted to study Cu(_{100-x})Zr(_x) metallic glasses. Samples were equilibrated at 2000 K and quenched to 300 K at 10(^{11}) K/s. Shear tests at six rates ((5 times 10^{7}) to (1 times 10^{10}) s(^{-1})) were performed at 300 K, with the flow stress modeled using the Herschel-Bulkley equation. Structural features were analyzed via Voronoi polyhedra, focusing on local five-fold symmetry and liquid-like polyhedra populations. Visualization and data analysis were conducted using OVITO and Scikit-learn library for the Python programming language.

{"title":"Rheological characterization of CuZr metallic glasses at the atomic scale","authors":"Nicolás Amigo","doi":"10.1007/s00894-025-06307-w","DOIUrl":"10.1007/s00894-025-06307-w","url":null,"abstract":"<div><h3>Context</h3><p>Understanding the shear response of metallic glasses is essential for predicting their mechanical performance and plasticity. Cu<span>(_{100-x})</span>Zr<span>(_x)</span> metallic glasses, in particular, exhibit complex shear-thinning behavior governed by atomic composition. Prior studies have highlighted the role of composition in influencing mechanical properties; however, the relationship between the structural characteristics of these alloys and their rheological behavior requires further investigation. This work focuses on the effects of Cu content on the plastic flow of CuZr metallic glasses, emphasizing how atomic-scale features influence yield stress, viscosity, and the onset of plasticity.</p><h3>Methods</h3><p>Molecular dynamics simulations using the embedded atom method potential in LAMMPS were conducted to study Cu<span>(_{100-x})</span>Zr<span>(_x)</span> metallic glasses. Samples were equilibrated at 2000 K and quenched to 300 K at 10<span>(^{11})</span> K/s. Shear tests at six rates (<span>(5 times 10^{7})</span> to <span>(1 times 10^{10})</span> s<span>(^{-1})</span>) were performed at 300 K, with the flow stress modeled using the Herschel-Bulkley equation. Structural features were analyzed via Voronoi polyhedra, focusing on local five-fold symmetry and liquid-like polyhedra populations. Visualization and data analysis were conducted using OVITO and Scikit-learn library for the Python programming language.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143396669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Review on the DFT computation of bulk heterojunction and dye-sensitized organic solar cell properties 块状异质结和染料敏化有机太阳能电池特性的 DFT 计算综述

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-02-13 DOI: 10.1007/s00894-025-06304-z

Nathália M. P. Rosa, Itamar Borges Jr.

Context

Organic solar cells (OSCs) represent a promising renewable energy technology due to their flexibility, low production cost, and environmental sustainability. To advance OSC efficiency and stability, density functional theory (DFT) has emerged as a powerful computational tool, enabling the prediction and optimization of critical properties at the molecular and device levels. This review highlights the key properties of bulk heterojunction solar (BHJ) solar cells and dye-sensitized solar cells (DSSCs) that can be accurately computed using DFT, including electronic structure properties (HOMO–LUMO energy levels, bandgap energies, and exciton binding energies, which influence charge separation and transport); optical properties (absorption spectra and light-harvesting efficiency, essential for maximizing photon capture); charge transport properties (reorganization energies, electron, and hole mobilities, and charge transfer rates that govern carrier dynamics within devices); interfacial properties (energy alignment at donor–acceptor interfaces, contributing to efficient charge separation and minimizing recombination); and chemical reactivity descriptors (ionization potential, electron affinity, chemical hardness, and electrophilicity, which facilitate material screening for OSC applications). We also show how to compute OSCs’ power conversion efficiency (PCE) from DFT.

Methods

The review also discusses the importance of selecting appropriate exchange–correlation functionals and basis sets to ensure the accuracy of DFT predictions. By providing reliable computational insights, DFT accelerates the rational design of OSC materials, guides experimental efforts, and reduces resource demands. This work underscores DFT’s pivotal role in optimizing OSC performance and fostering the development of next-generation photovoltaic technologies.

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引用次数: 0