Journal of Molecular Modeling最新文献

{"title":"Hydrophenoxylation of alkynes by gold catalysts: a mini review","authors":"Miguel Ramos,&nbsp;Miquel Solà,&nbsp;Albert Poater","doi":"10.1007/s00894-024-06152-3","DOIUrl":"10.1007/s00894-024-06152-3","url":null,"abstract":"<div><h3>Context</h3><p>The field of chemistry has significantly evolved, with catalysis playing a crucial role in transforming chemical processes. From Valerius’ use of sulfuric acid in the sixteenth century to modern advancements, catalysis has driven innovations across various industries. The introduction of gold as a catalyst marked a pivotal shift, expanding its applications beyond ornamentation to homogeneous catalysis. Gold’s unique properties, such as its electrophilic nature and flexibility, have enabled its use in synthesizing complex molecules, including those in nanomedicine and sustainable chemical processes. The development of gold-based complexes, particularly in hydroalkoxylation and hydroamination reactions, showcases their efficiency in forming carbon–oxygen bonds under mild conditions. Recent studies on dual gold catalysis and heterobimetallic complexes further highlight gold’s versatility in achieving high turnover rates and selectivity. This evolution underscores the potential of gold catalysis in advancing environmentally sustainable methodologies and enhancing the scope of modern synthetic chemistry. The debate about the nature of monogold and dual-gold catalysis is open.</p><h3>Methods</h3><p>DFT calculations have played a key role in promoting the activation of alkynes, in particular the hydrophenoxylation of alkynes by metal-based catalysts. They not only help identify the most efficient and selective catalysts but also aid in screening for those capable of performing a dual metal catalytic mechanism. The most commonly used functionals are BP86 and B3LYP, with the SVP and 6-31G(d) basis sets employed for geometry optimizations, and M06 with TZVP or 6-311G(d,p) basis sets used for single-point energy calculations in a solvent. Grimme dispersion correction has been explicitly added either in the solvent single point energy calculations or in the gas phase geometry optimizations or in both. To point out that M06 implicitly includes part of this dispersion scheme.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338938","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}

{"title":"Investigation of structural, elastic, electronic, and optical properties of lead-free double perovskites Cs2XBeBr6 (X = Ge, Sn): a first-principles DFT study","authors":"Messaoud Caid,&nbsp;Habib Rached,&nbsp;Djamel Rached,&nbsp;Youcef Rached","doi":"10.1007/s00894-024-06158-x","DOIUrl":"10.1007/s00894-024-06158-x","url":null,"abstract":"<div><h3>Context</h3><p>In this study, the structural, elastic, electronic, and optical properties of Cs₂GeBeBr₆ and Cs₂SnBeBr₆ halide double perovskites (HDPs) were investigated using density functional theory (DFT) calculations. Notably, the Tran-Blaha modified Becke-Johnson (TB-mBJ) method was employed to predict indirect band gaps of 2.434 eV for Cs₂GeBeBr₆ and 2.855 eV for Cs₂SnBeBr₆. The stability of these compounds in a cubic (Fm-3m) structure was confirmed through formation energy, cohesive energy, tolerance factor, and elastic constants. Furthermore, the ductile nature of the materials was demonstrated through Poisson's and Pugh's ratios. Our optical property analysis, spanning the 0–13 eV energy range, revealed key insights into the dielectric functions, extinction coefficient, electron energy loss, refractive index, optical conductivity, reflectivity, and absorption coefficient. These results highlight the potential of Cs₂GeBeBr₆ and Cs₂SnBeBr₆ for future optoelectronic and photovoltaic applications.</p><h3>Methods</h3><p>In this investigation, we employed density functional theory (DFT), implemented using the Wien2k package. The exchange and correlation potentials were treated using the generalized gradient approximation (GGA) and the Tran-Blaha modified Becke-Johnson (TB-mBJ) method. To evaluate dynamic stability, we analyzed the phonon band structures using the CASTEP code.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338940","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}

{"title":"Temperature and pressure effects on the decomposition mechanisms of 2,6-diamino-3,5-dinitropyrazine-1-oxide crystal: ab initio molecular dynamics study","authors":"Jincheng Ji,&nbsp;Hui Li,&nbsp;Weihua Zhu","doi":"10.1007/s00894-024-06156-z","DOIUrl":"10.1007/s00894-024-06156-z","url":null,"abstract":"<div><h3>Context</h3><p>The decomposition process of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) crystal at high temperatures (2500 and 3390 K) and detonation pressure of 33.4 GPa coupled with temperatures were studied by ab initio molecular dynamics simulations. The results show that the initial decomposition mechanism of LLM-105 is the same under different conditions. The product analysis indicates that high temperature is conducive to the formation of N₂ and CO₂, but inhibited the formation of H₂O. It is found that the formation mechanism of H₂O is the same under different conditions, which involves the reaction between OH radical and H radical. Although the detailed processes of the formation of N₂ are different, they all involve the reaction between nitrogen-containing fragments, and its core is the formation of intermediates with R₁-NN-R₂ structure. The core of the formation of CO₂ under different conditions is to form the intermediate R₁-CO-R₂ with carbonyl structure, and then generate the fragment with -OCO- structure, and finally generate CO₂. This research may provide new insights into the initiation and subsequent decomposition mechanisms of energetic materials under extreme conditions.</p><h3>Methods</h3><p>The LLM-105 supercell was constructed using the Materials Studio 7.0 package. AIMD simulations were performed in the CASTEP package. AIMD simulations adopted NVT and NPT ensemble, and the temperature was controlled by Nosé thermostat, while the pressure was controlled by Andersen barostat. Besides, DFT calculations were carried out at the B3LYP/6–311 + G(d,p) level using the Gaussian 09 package.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338943","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}

{"title":"Rational analysis of hydrogen bonding interaction in phenazine, 2-hydroxynaphthalene (1:1) cocrystal: from molecular modeling to photophysical properties","authors":"T. Sundareswaran,&nbsp;R. Jagan,&nbsp;N. Karthikeyan,&nbsp;B. Milton Boaz","doi":"10.1007/s00894-024-06128-3","DOIUrl":"10.1007/s00894-024-06128-3","url":null,"abstract":"<div><h3>Context</h3><p>Organic cocrystals have a wide range of applications in the field of optics due to their photo responsive property. We present here a newly synthesized phenazine 2-hydroxynaphthalene (1:1) cocrystal, its structural and theoretical calculations which tend to the nonlinear optical property. In the crystal structure of the title cocrystal, the phenazine and 2-hydroxynaphthalene molecules from one- and two-dimensional supramolecular frameworks via O‒H…N hydrogen bonds and C‒H…N, C‒H…π interaction, respectively. The phenazine molecules from an infinite off-set stacking through π…π interaction in the three-dimensional molecular packing of the title cocrystal. The contribution of intermolecular interaction in the three-dimensional molecular packing and the interaction energy calculation is studied by the Hirshfeld surface analysis. The molecular geometry retrieved from the experimental X-ray diffraction analysis is in good agreement with the theoretically calculated parameters. Further, the molecular electrostatic potential (MEP) and frontier molecular orbital (FMO) analysis have been carried out to study the charge distribution and molecular reactive mechanism. Third-order nonlinear optical property of the cocrystals has been analyzed by Z-scan measurements. The determined nonlinear optical absorption coefficient value 6.442 × 10⁻⁰⁵ (m/W) and the nonlinear refractive index value − 5.535 × 10⁻² (m/W) suggest that the crystalline solid can be a good choice of potential nonlinear optical material.</p><h3>Method</h3><p>The crystal structures of phenazine 2-hydroxynaphthalene cocrystal was solved by direct methods procedure using SHELXS program and refined by full-matrix least square procedure on <i>F</i>² using SHELXL-2018 program on <i>Olex2</i> software. The computational calculation has been carried out using DFT/B3LYP quantum chemical function with triple zeta 6–311 +  + basis set in the ground state molecular stability using Gaussian 09W program suite. The Hirshfeld surface analysis mapping, associated 2D fingerprint plot, and intermolecular molecular interaction energy calculations were carried out using CrystalExplorer (version 21.5) software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338942","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}

{"title":"Analytical potential energy functions for CO(^+) in its ground and excited electronic states","authors":"Judith P. Araújo,&nbsp;Maikel Y. Ballester,&nbsp;Isadora G. Lugão,&nbsp;Rafael P. Silva,&nbsp;Mariana P. Martins","doi":"10.1007/s00894-024-06131-8","DOIUrl":"10.1007/s00894-024-06131-8","url":null,"abstract":"<div><h3>Context</h3><p>Accurate functions to analytically represent the potential energy interactions of CO<span>(^+)</span> diatomic system in <span>(mathrm {X^2Sigma ^+})</span>, <span>(mathrm {A^2Pi })</span>, and <span>(mathrm {B^2Sigma ^+})</span> electronic states are proposed. The new functions depend upon only four parameters directly obtained from experimental data, without any fitting procedure. These functions have been developed from the modified generalized potential proposed by Araújo and Ballester. The function for the <span>(mathrm {X^2Sigma ^+})</span> electronic state represents a significant improvement to the previously proposed model. To quantify the accuracy of the potential energy functions, the Lippincont test is used. The novel potential was also compared with the classical Morse potential and with the recently proposed Improved Generalized Pöschl-Teller potential. Furthermore, the main spectroscopic constants and vibrational energy levels are calculated and compared for all potentials. The present results agree excellently with the experiment Rydberg-Klein-Rees (RKR) potentials.</p><h3>Methods</h3><p>The rovibrational energy levels of the proposed diatomic potentials were asserted by solving radial the Schrödinger equation of the nuclear motion with the aid of the LEVEL program.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338936","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}

{"title":"Predicting biological activity and design of 5-HT6 antagonists through assessment of ANN-QSAR models in the context of Alzheimer’s disease","authors":"Daniel S. de Sousa,&nbsp;Aldineia P. da Silva,&nbsp;Laise P. A. Chiari,&nbsp;Rafaela M. de Angelo,&nbsp;Alexsandro G. de Sousa,&nbsp;Kathia M. Honorio,&nbsp;Albérico B. F. da Silva","doi":"10.1007/s00894-024-06134-5","DOIUrl":"10.1007/s00894-024-06134-5","url":null,"abstract":"<div><h3>Context</h3><p>Alzheimer’s disease (AD) is the leading cause of dementia around the world, totaling about 55 million cases, with an estimated growth to 74.7 million cases in 2030, which makes its treatment widely desired. Several studies and strategies are being developed considering the main theories regarding its origin since it is not yet fully understood. Among these strategies, the 5-HT₆ receptor antagonism emerges as an auspicious and viable symptomatic treatment approach for AD. The 5-HT₆ receptor belongs to the G protein-coupled receptor (GPCR) family and is closely implicated in memory loss processes. As a serotonin receptor, it plays an important role in cognitive function. Consequently, targeting this receptor presents a compelling therapeutic opportunity. By employing antagonists to block its activity, the 5-HT₆ receptor’s functions can be effectively modulated, leading to potential improvements in cognition and memory.</p><h3>Methods</h3><p>Addressing this challenge, our research explored a promising avenue in drug discovery for AD, employing Artificial Neural Networks–Quantitative Structure-Activity Relationship (ANN-QSAR) models. These models have demonstrated great potential in predicting the biological activity of compounds based on their molecular structures. By harnessing the capabilities of machine learning and computational chemistry, we aimed to create a systematic approach for analyzing and forecasting the activity of potential drug candidates, thus streamlining the drug discovery process. We assembled a diverse set of compounds targeting this receptor and utilized density functional theory (DFT) calculations to extract essential molecular descriptors, effectively representing the structural features of the compounds. Subsequently, these molecular descriptors served as input for training the ANN-QSAR models alongside corresponding biological activity data, enabling us to predict the potential efficacy of novel compounds as 5-hydroxytryptamine receptor 6 (5-HT₆) antagonists. Through extensive analysis and validation of ANN-QSAR models, we identified eight new promising compounds with therapeutic potential against AD.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338941","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}

{"title":"Intermolecular interactions in water and ethanol solution of ethyl acetate: Raman, DFT, MEP, FMO, AIM, NCI-RDG, ELF, and LOL analyses","authors":"Abduvakhid Jumabaev,&nbsp;Stève-Jonathan Koyambo-Konzapa,&nbsp;Hakim Hushvaktov,&nbsp;Ahmad Absanov,&nbsp;Bekzod Khudaykulov,&nbsp;Utkirjon Holikulov,&nbsp;Zokhid Ernazarov,&nbsp;Noureddine Issaoui,&nbsp;Omar M. Al-Dossary,&nbsp;Mama Nsangou","doi":"10.1007/s00894-024-06147-0","DOIUrl":"10.1007/s00894-024-06147-0","url":null,"abstract":"<div><h3>Context</h3><p>The intermolecular interactions of ethyl acetate (EtOAc)-water (H₂O)/ethanol (EtOH) mixtures were investigated using a combination of Raman spectroscopy and quantum chemical calculations. The computational approach was used to analyze the structure of hydrogen-bonded complexes of ethyl acetate with water/ethanol molecules, based on density functional theory (DFT). The calculated frequencies closely matched the experimental Raman values, with differences being under 4%. Experimental data show that when the concentrations of ethyl acetate in the ethyl acetate/water/ethanol solutions were reduced, almost all Raman spectral bands are blue-shifted. The AIM analysis reveals that all the given complexes possess a positive energy density, indicating that the molecules interact electrostatically. The energy and bond length indicate that the methyl group forms relatively weak hydrogen bonds. Analysis indicates that EtOAc forms weak H-bonding C = O∙∙∙H and C-H∙∙∙O, which are recognized as van der Waals interactions. As the amount of ethyl acetate decreases in the complex, the interaction forces also decrease. This could also explain why the bands are blue-shifted. It was discovered that the title complexes’ hydrogen bond energy decreased exponentially as bond length increased.</p><h3>Methods</h3><p>The geometries of the molecular complexes were optimized using the Gaussian 09W program and the B3LYP/6–311 +  + G(d,p) set of functions. The potential energy distribution (PED) analysis was performed using VEDA 4.0 software. Raman spectra were drawn using the Origin 8.5 software. The Multiwfn 3.8 software was used to calculate topological parameters of electron density in molecular systems. GaussView 6.0 and Visual Molecular Dynamics (VMD) 1.9.3 tools were used to visualize all computational results.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338939","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}

{"title":"Characterization of 1,1- and 1,2-ethenedithiol, elusive compounds of potential astrochemical interest","authors":"Al Mokhtar Lamsabhi,&nbsp;Otilia Mó,&nbsp;Jean-Claude Guillemin,&nbsp;Manuel Yáñez","doi":"10.1007/s00894-024-06149-y","DOIUrl":"10.1007/s00894-024-06149-y","url":null,"abstract":"<div><h3>Context</h3><p>1,1- and 1,2-ethenedithiol are elusive systems that could potentially exist in interstellar space, similar to analogous diols. In this paper, we investigate the structure, stability, and bonding characteristics of these compounds as well as the ions produced by protonation, deprotonation, or simple ionization processes. 1,2-ethenedithiol has two isomers, <i>Z</i> and <i>E</i>, with the most stable conformer being <i>syn-anti</i> for the <i>Z</i> isomer and <i>anti-anti</i> for the <i>E</i> isomer. However, the energy gaps between the different conformers are never larger than 6 kJ·mol⁻¹. For 1,1-ethenedithiol, the global minimum is the <i>syn-anti</i> conformer. The vertical and adiabatic ionization processes as well as the intrinsic basicities and acidities of these families of compounds were analyzed and compared with those of the corresponding diols previously reported in the literature. This comparison revealed not only the numerical differences in these thermodynamic properties but also distinct trends between the two families of compounds.</p><h3>Methods</h3><p>State-of-the-art G4 ab initio calculations were employed to calculate the structures and total energies of the systems under investigation. The QTAIM, ELF, and NBO approaches were used to analyze the electron density of all the neutral and charged systems included in our study. Van der Waals contributions, when relevant, were analyzed by locating regions of low reduced density gradient(s) using the NCIPLOT approach.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306921","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}

{"title":"Theoretical investigation of potential energetic material CL-20/TNBP co-crystal explosive based on molecular dynamics method","authors":"Jihang Du,&nbsp;Baoguo Wang,&nbsp;Yafang Chen,&nbsp;Xinyi Li,&nbsp;Chunguang Wang","doi":"10.1007/s00894-024-06154-1","DOIUrl":"10.1007/s00894-024-06154-1","url":null,"abstract":"<div><h3>Context</h3><p>The exploration of CL-20 eutectic has been a subject of fervent interest within the realm of high-energy material modification. Through the utilization of density functional and molecular dynamics methods, an investigation into the characteristics of hexanitrohexaazaisowurtzitane (CL-20)/4,4′,5,5′-tetranitro-2H,2′H-3,3′-bipyrazole (TNBP)within the molar ratio range of 4:1–1:4 was conducted. This inquiry encompassed the scrutiny of molecular interaction pathways, attachment force, initiating molecular distance, unified energy concentration, and physical characteristics. Furthermore, the EXPLO-5 was harnessed to prognosticate the explosion features and byproducts of unadulterated CL-20, TNBP, and CL-20/TNBP frameworks. The findings delineate a substantial differentiation in the electrostatic charge distribution on the surface between CL-20 and TNBP particles, signifying the preeminence of intermolecular interactions between disparate entities over those within similar entities, thus intimating the plausibility of the eutectic constitution. Remarkably, the identification of maximal attachment force at a molar ratio of 1:1 suggests the heightened likelihood of eutectic formation, propelled primarily by electrostatic and van der Waals forces. The resultant eutectic explosive evinces intermediate reactivity and exemplary mechanical attributes. Moreover, the detonation achievement of the eutectic with a molar proportion of 1:1 straddles that of CL-20 and TNBP, representing a new type of insensitive high-energy material.</p><h3>Methods</h3><p>The testing method employs the Materials Studio software and utilizes the molecular dynamics (MD) method to predict the properties of CL-20/TNBP cocrystals with different ratios and crystal faces. The MD simulation time step is set to 1 fs, and the total MD simulation time is 2 ns. An isothermal-isobaric (NPT) ensemble is used for the 2 ns MD simulation. The COMPASS force field is employed, with the temperature set to 295 K. The prediction of detonation characteristics and products is conducted using the EXPLO-5 software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306924","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}

{"title":"Effect of confinement on water properties in super-hydrophilic pores using MD simulations with the mW model","authors":"Vikas Kumar Sinha,&nbsp;Chandan Kumar Das","doi":"10.1007/s00894-024-06145-2","DOIUrl":"10.1007/s00894-024-06145-2","url":null,"abstract":"<div><h3>Context</h3><p>We explore the influence of strongly hydrophilic confinement on various properties of water, such as density, enthalpy, potential energy, radial distribution function, entropy, specific heat capacity, structural dynamics, and transition temperatures (freezing and melting temperatures), using monatomic water (mW) model. The properties of water are found to be dependent on confinement and the wall-fluid surface interaction. Hysteresis loops are observed for density, enthalpy, potential energy, and entropy around the transition temperatures, while the size of hysteresis loops varies with confinement and surface interaction. In smaller pore sizes (<i>H</i> ≤ 20), the solid phase displays a higher density compared to the liquid phase, which is unconventional behavior compared to bulk water systems due to the pronounced hydrophilic properties of the confinement surface. Specific heat capacity exhibits more oscillations in the confined system compared to bulk water, stemming from uneven enthalpy differences across equal temperature intervals. During phase transformation in both heating and quenching processes, there is an abrupt change observed in specific heat capacity. Confinement exerts a notable impact on entropy in the solid phase, but its influence is negligible in the liquid phase. At lower pore sizes (<i>H</i> &lt; 25 Å), there is more fluctuation in freezing temperature for all wall-fluid interactions, which diminishes beyond pore sizes of <i>H</i> &gt; 25 Å. Similarly, more oscillatory behavior is observed in melting temperatures at lower pore sizes (<i>H</i> &lt; 40 Å), which diminishes at higher pore sizes (<i>H</i> &gt; 40 Å). During the quenching process, a sudden jump in the in-plane orientational and tetrahedral order parameters indicates the formation of an ordered phase, specifically a diamond crystalline structure. The percentages of different crystalline structures (cubic diamond, hexagonal diamond, and 2D hexagonal) vary with both the confinement size and the wall-fluid interaction strength.</p><h3>Methods</h3><p>Cooling and heating simulations are conducted with the mW water model using LAMMPS for different nanoscale confinement separation sizes ranging from 8.5 to 70 Å within the temperature range of 100–350 K. The water is modeled using two-body and three-body interaction potential (Stillinger–Weber potential) and the confinement is introduced using LJ 9–3 water-wall interaction potential. Entropy is calculated using RDF data obtained from the simulation experiments for each temperature point with increments or decrements of 2.5 K. The transition temperatures are estimated using the specific heat capacity analysis.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306922","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}