Journal of Molecular Modeling最新文献

{"title":"Pharmacophore-based 3D-QSAR modeling, virtual screening, docking, molecular dynamics and biological evaluation studies for identification of potential inhibitors of alpha-glucosidase","authors":"Unnati Kushavah,&nbsp;Pinaki Prasad Mahapatra,&nbsp;Shakil Ahmed,&nbsp;Mohammad Imran Siddiqi","doi":"10.1007/s00894-024-06181-y","DOIUrl":"10.1007/s00894-024-06181-y","url":null,"abstract":"<div><h3>Context</h3><p>Alpha-glucosidase enzyme is considered an important therapeutic target for controlling hyperglycemia associated with type 2 diabetes. Novel scaffolds identified as potential alpha-glucosidase inhibitors from the Maybridge library utilizing pharmacophore modeling, molecular docking and biological evaluation are reported in this manuscript<i>.</i></p><h3>Method</h3><p>A total of 51 xanthone series scaffolds previously reported as alpha-glucosidase inhibitors were collected and used as training and test sets. These sets were employed to develop and validate a pharmacophore-based 3D-QSAR model with statistically meaningful results using Schrodinger software. The model showed a high <i>F</i> value (<i>F</i>, 80.1) at five component partial least square factors, a high cross-validation coefficient (<i>Q</i>², 0.66) and a good correlation coefficient (<i>R</i>², 0.95). Pearson correlation coefficient (<i>r</i>) of 0.8400 indicated a greater degree of confidence in the model. Subsequently, virtual screening was performed with PHASE module of Schrodinger software using the above model to identify novel alpha-glucosidase inhibitors, and mapped compounds were evaluated for their interactions with the protein. The X-ray co-crystallised structure of the alpha-glucosidase protein in complex with acarbose (PDB Code: 5NN8) was used for molecular docking analysis using GLIDE module and a total of eight compounds were further selected for biological evaluation. Molecular dynamics analysis using GROMACS software was performed in the active site of alpha-glucosidase protein to gain insights into binding mechanism of the four active compounds which were finally found to exhibit inhibitory activity in the biological assay.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142540683","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":"Understanding and simulating mechanochromism in dye-dispersed polymer blends: from atomistic insights to macroscopic properties","authors":"Qinfan Wang,&nbsp;Alistar Ottochian,&nbsp;Michele Turelli,&nbsp;Andrea Pucci,&nbsp;Ilaria Ciofini,&nbsp;Carlo Adamo","doi":"10.1007/s00894-024-06174-x","DOIUrl":"10.1007/s00894-024-06174-x","url":null,"abstract":"<div><h3>Context</h3><p>In this work, we propose a computational protocol enabling the simulation of mechanochromic responses in dye-dispersed polymer blends. The main objective is the modeling of the molecular-level structural changes responsible for the modulation of the photophysical properties that lead to the mechanochromic phenomenon. In this demonstrative study, we focus on predicting the changes in optical absorption displayed by a model system consisting of a dimer of a tetraphenylethylene derivative dispersed in a polyethylene matrix. The blend is subjected to an external stimulus that causes a modulation of the polymer matrix density that translates, in turn, into the emergence of specific mechanical constraints on the optically active dimers. The accurate description of this phenomenon requires the reliable sampling of the dimer configurations induced by the interaction with the matrix under stress. These molecular geometries are associated with modified electronic structures that confer novel absorption responses to the dispersed dyes.</p><h3>Methods</h3><p>In the present contribution, the sampling of these structures is achieved through classical molecular dynamics (MD) simulations including a model element to apply an anisotropic mechanical force. This element allows the microscopic modeling of the chains’ and dyes’ structural rearrangements under stress. After the sampling, we compare the results of two approaches for the prediction of the optical response: (i) the calculation of a mean response from a statistical average over quantum chemical calculations on the sampled MD structures and (ii) a prediction via a more expensive hybrid scheme allowing the relaxation of the sampled molecular geometries in the presence of the matrix constraints.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142540753","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":"Computational chemistry facilitates the development of second near-infrared xanthene-based dyes","authors":"Qinlin Yuan,&nbsp;Mingyu Wang,&nbsp;Mingyue Ma,&nbsp;Pingping Sun,&nbsp;Chaoyuan Zeng,&nbsp;Weijie Chi","doi":"10.1007/s00894-024-06179-6","DOIUrl":"10.1007/s00894-024-06179-6","url":null,"abstract":"<div><h3>Context</h3><p>The dyes in the second near-infrared (NIR-II) region play a crucial role in advancing imaging technology. However, developing small-molecule dyes in NIR-II poses a significant bottleneck to meet the substantial demands in biological fields, which may be attributed to the lack of a rational design strategy. Herein, we designed a series of rhodamine analogs with more red-shifted emission by replacing the oxygen-bridge atom in xanthene-based dyes with –C(CH₃)₂, –Si(CH₃)₂, –SO₂, and –P(O)Ph. We investigated the frontier molecular orbital, electrostatic potential surfaces, the interaction region indicator, electron–hole distribution, and absorption and emission spectrum of xanthene-based dyes using (time-dependent) density functional theory. Our results demonstrated that these designed small molecular dyes exhibit long emission wavelengths covering 1377–1809 nm. We expected these findings to enable the targeted design of long-wavelength rhodamines.</p><h3>Method</h3><p>Geometry optimization of dyes in the ground and excited states was carried out at ω-B97XD/Def2SVP level using Gaussian 16 A03. The absorption and emission wavelengths were evaluated using 13 functional, including TPSSH, O3LYP, B3LYP*, B3LYP, PBE0, MPW1B95, PBE-1/3, PBE38, MPWB1K, MN15, BHandHLYP, ω-B97XD, and CAM-B3LYP.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520610","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":"A comparative study on the interaction of M3+(H2O)5–6 ions (M = Fe, Ru, and Os) with the hydroxy group","authors":"Dang T. Nguyen,&nbsp;Hai V. Mai,&nbsp;Han H. La,&nbsp;Anh D. Nguyen,&nbsp;Anh H. Nguyen","doi":"10.1007/s00894-024-06185-8","DOIUrl":"10.1007/s00894-024-06185-8","url":null,"abstract":"<div><h3>Context</h3><p>The heavy metal ions are the typical carcinogenic agents. Up to now, the interaction mechanism of toxic metal ions with the biomolecules such as carbohyrate have not been elucidated and reported in the detail. In this research work, the adjacent dissociation Gibbs energy (E_AB) of M³⁺(H₂O)₅(R-OH) complexes depended significantly on the molecular volume of primary alcohols and the inductive effects of substituent R in primary alcohols (R = CH₃, CH₃CH₂, CH₃CH₂CH₂, CH₃CH₂CH₂CH₂, Cl-CH₂, F-CH₂) as well as the length of linear cellulose. The affinity of M³⁺(H₂O)₅ ions with the sixth water molecule in gas phase reduced in the order as follows: Fe³⁺  &gt; Ru³⁺  &gt; Os³⁺, which were determined by the E_AB values and bond lengths of M–O. The water solvent made the E_AB values of Fe³⁺(H₂O)₆ ions and Fe³⁺(H₂O)₅(CH₃OH) ions changed completely in the case of the polarizable continuum model, while the Onsager model gave the good agreement with the gas phase model.</p><h3>Methods</h3><p>The nature of interaction between hydrated Fe³⁺(H₂O)₅ ion and the hydroxy groups of primary alcohols were investigated using density functional theory method at the B3LYP/6–311 + G** level, the PBEPBE/6–311 + G** level. The influence of water solvent was evaluated using the Onsager model and the polarizable continuum model. The two-layer ONIOM approach and the local softness analysis were employed for the hydroxy groups of linear cellulose at the B3LYP/6–311 + G**:HF/6-31G* level. The affinity of M³⁺(H₂O)₅ ions (M = Fe, Ru, and Os) with the sixth water molecule were probed at the B3LYP/QZVPP/6–311 + G** level (QZVPP basis set for the metal atoms).\u0000</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142524483","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 exploration of energetic molecular design strategy: functionalization of C or N and structural selection of imidazole or pyrazole","authors":"Qianxiong Chen,&nbsp;Jin Zhu,&nbsp;Suming Jing,&nbsp;Jiahao Deng,&nbsp;Yuanyuan Wang,&nbsp;Keyao Li,&nbsp;Zhineng Wang,&nbsp;Jia Liu,&nbsp;Shuai Bian","doi":"10.1007/s00894-024-06183-w","DOIUrl":"10.1007/s00894-024-06183-w","url":null,"abstract":"<div><h3>Context</h3><p>In researching energetic materials with high energy density, it is an effective method to introduce explosophoric groups. In this study, four series of energetic compounds were designed by functionalizing with C- or N-, introducing energetic groups -CH(NO₂)₂, -CF(NO₂)₂, -C(NO₂)₂(NF₂), -C(NO₂)₃, and-CH(NF₂)₂ into imidazole and pyrazole structures. Density functional theory was employed to optimize the structure of the target compound and subsequently to predict and evaluate its performance based on this. Meanwhile, the sensitivity of the compounds was predicted based on their electrostatic potential analysis. Following analysis of the geometric structure, detonation performance, and sensitivity of the compounds, three factors were discussed: energetic groups, functionalization methods, and skeleton structure differences. The results indicate that C-functionalization has advantages only in density, but N-functionalization is better in thermal stability, heat of formation, and sensitivity. Meanwhile, the data shows that imidazole-based compounds exhibited greater density and detonation performance in the target compounds designed within this study, while pyrazoles have a higher heat of formation and chemical stability. By analyzing the design strategy of C- or N-functionalization of novel high-energy groups on energetic imidazole or pyrazole rings and selecting a more suitable molecular construction strategy, this study provides a theoretical approach for the development of new energetic materials with excellent performance.</p><h3>Method</h3><p>Gaussian 09 and Multiwfn 3.8 packages are the software used for calculation, and the electrostatic potentials were depicted using the VMD program. In this study, the imidazole and pyrazole derivatives were optimized at the B3PW91/6-311G (d, p) level to acquire the relevant data for the compounds.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492603","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":"Structural and dynamical insights revealed the anti-glioblastoma potential of withanolides from Withania coagulans against vascular endothelial growth factor receptor (VEGFR)","authors":"Khair Bux,&nbsp;Irsa Asim,&nbsp;Zainab Ismail,&nbsp;Samaha Hussain,&nbsp;Ralf Herwig","doi":"10.1007/s00894-024-06178-7","DOIUrl":"10.1007/s00894-024-06178-7","url":null,"abstract":"<div><h3>Context</h3><p>Glioblastoma (GBM), well known as grade 4 tumors due to its progressive malignant features such as vascular proliferation and necrosis, is the most aggressive form of primary brain tumor found in adults. Mutations and amplifications in the vascular endothelial growth factor receptor (VEGFR) contribute to almost 25% of GBM tumors. And thus, VEGFR has been declared the primary target in glioblastoma therapeutic strategies. However, many studies have been previously reported that include GBM as global therapeutics challenge, but they lack the molecular level insights that could help in understanding the biological function of a therapeutically important protein playing a major role in the disease and design the best strategies to develop the potential drugs.</p><h3>Methods</h3><p>Therefore, to the best of our knowledge, the present study is the first time of kind, which involves multi-in silico approaches to predict the inhibition potential of withanolides from <i>Withania coagulan</i> against VEGFR. The study is actually based on determining the mode of action of five isolates: withanolide J, withaperuvin, 27-hydroxywithanolide I, coagule E, and coagule E, along with their respective binding energies. Molecular docking simulations revealed primarily four ligands, withanolide J (− 7.33 kJ/mol), 27-withanolide (− 7.01 kJ/mol), ajugine, withaperuvin (− 6.89 kJ/mol), and ajugine E (− 6.39 kJ/mol), to have significant binding potencies against the protein. Ligand binding was found to enhance the confirmational stability of the protein revealed through RMSD analysis, and RMSF assessment revealed the protein residues especially from 900–1000 surrounding the binding of the protein. Structural and dynamics of the protein via dynamics cross-correlation movement (DCCM) and principal component analysis (PCA) in both the unbound form and complexed with most potent ligand, withanolide J, reveal the ligand binding affecting the entire conformational integrity of the protein stabilized by hydrogen bonds and electrostatic attractions. Free energy of binding estimations by means of molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method further revealed the withanolide J to have maximum binding potency of the all ligands. Withanolide J in final was also found to have suitable molecular characterizations to cross the blood–brain barrier (BBB +) and reasonable human intestinal absorption ability determined by ADMET profiling via admetSAR tools.</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":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492601","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":"The phosphodiester dissociative hydrolysis of a DNA model promoted by metal dications","authors":"Vinicius Lemes de Souza Santos,&nbsp;Felipe Augusto Ribeiro,&nbsp;Chang Dong Kim,&nbsp;Alejandro López-Castillo","doi":"10.1007/s00894-024-06184-9","DOIUrl":"10.1007/s00894-024-06184-9","url":null,"abstract":"<div><h3>Context</h3><p>Phosphodiester bonds, which form the backbone of DNA, are highly stable in the absence of catalysts. This stability is crucial for maintaining the integrity of genetic information. However, when exposed to catalytic agents, these bonds become susceptible to cleavage. In this study, we investigated the role of different metal dications (Ca²⁺, Mg²⁺, Zn²⁺, Mn²⁺, and Cu²⁺) in promoting the hydrolysis of phosphodiester bonds. A minimal DNA model was constructed using two pyrimidine nucleobases (cytosine and thymine), two deoxyribose units, one phosphate group, and one metallic dication coordinated by six water molecules. The results highlight that Cu²⁺ is the most efficient in lowering the energy barrier for bond cleavage, with an energy barrier of 183 kJ/mol, compared to higher barriers for metals like Zn²⁺ (202 kJ/mol), Mn²⁺ (202 kJ/mol), Mg²⁺ (210 kJ/mol), and Ca²⁺ (223 kJ/mol). Understanding the interaction between these metal ions and phosphodiester bonds offers insight into DNA stability and organic data storage systems.</p><h3>Methods</h3><p>DFT calculations were employed using Gaussian 16 software, applying the B3LYP hybrid functional with def2-SVP basis sets and GD3BJ dispersion corrections. Full geometry optimizations were performed for the initial and transition states, followed by identifying energy barriers associated with phosphodiester bond cleavage. The optimization criteria included maximum force, root-mean-square force, displacement, and energy convergence thresholds.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492602","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":"Towards a complete description of the reaction mechanisms between nitrenium ions and water","authors":"Sara Gómez,&nbsp;Natalia Rojas-Valencia,&nbsp;Chiara Cappelli,&nbsp;Frank Weinhold,&nbsp;Albeiro Restrepo","doi":"10.1007/s00894-024-06169-8","DOIUrl":"10.1007/s00894-024-06169-8","url":null,"abstract":"<div><h3>Context</h3><p>Nitrenium ions are intermediates in the metabolic routes producing the highly carcinogenic nitrosamines and binding to DNA molecules. The reaction mechanism of nitrenium molecules with explicit water molecules is sensibly dependent on the number of waters: when a second molecule is involved, it acts as a catalyst for the reaction, lowering intrinsic activation barriers regardless of the substituent. For all cases, the reaction force constants and reaction electron flux indicate highly synchronous reactions for <span>({n=1})</span>. Conversely, for <span>({n=2})</span> highly non-synchronous reactions are obtained, involving two separate proton transfers happening early and late in the reaction path. As a test case, for the simplest <span>([text {N}text {H}_{2}]^{+} + 2 text {H}_{2}text {O})</span> reactions, orbital interactions within the NBO paradigm, bond orders, and their derivatives indicate that each individual proton transfer is highly synchronous.</p><h3>Methods</h3><p>Molecular geometries were optimized and characterized at the B3LYP/6–311++G(<i>d, p</i>) level. Intrinsic reaction coordinates were calculated. CCSD(T) single point energies with the same basis were computed on all stationary points. The reaction force, reaction force constant, and reaction electron flux are used to study the evolution of the reacting systems. Natural bond orbitals are used to understand the primitive changes driving the reaction.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492604","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":"Structural and energetic properties of cluster models of anatase-supported single late transition metal atoms: a density functional theory benchmark study","authors":"Xavier Deraet,&nbsp;Umut Çilesiz,&nbsp;Viktorya Aviyente,&nbsp;Frank De Proft","doi":"10.1007/s00894-024-06173-y","DOIUrl":"10.1007/s00894-024-06173-y","url":null,"abstract":"<div><h3>Context</h3><p>Single-atom catalytic systems constitute an intriguing research topic due to their inherently different chemical behavior as compared to classic heterogeneous catalysts. In this study, cluster systems representing single late transition metal atoms adsorbed on anatase were constructed starting from previously generated periodic models and subjected to a density functional theory (DFT) benchmark study. The ability of different density functional approximations representing all rungs of the Jacob’s Ladder classification to accurately describe bond lengths and adsorption energies was assessed for these clusters with the aim of revealing the functional that allows to retain the structural characteristics of the initial periodic system, while also delivering reliable energetics. In this regard, our results indicate that optimisation of the clusters with the meta-GGA functionals TPSS or RevTPSS provides the lowest mean unsigned error and root-mean-square deviations with respect to the periodic models. Moreover, these functionals and, to a slightly lesser degree, PW91 were also found to provide adsorption energies that are statistically the least deviating from the CCSD(T) reference data. More complex hybrid functionals appear to be performing less well.</p><h3>Methods</h3><p>Cluster geometries were determined at the Kohn–Sham DFT level using the LANL2DZ basis set for the transition metals and the Pople 6-31G(d) basis set for O and H. The density functional approximations considered were SVWN, PBE, BP86, BLYP, PW91, TPSS, RevTPSS, M06L, M11L, B3LYP, PBE0, M06, M06-2X, MN15, ωB97X-D, CAM-B3LYP, M11, and MN12-SX. Reference adsorption energies of the metals on the support cluster were obtained at the CCSD(T)/LANL2TZ (transition metals)/6–311 +  + G(d,p)//RevTPSS/LANLD2DZ (transition metals)/6-31G*. Besides the above-mentioned functionals, energy calculations using the double-hybrid functionals, DSDPBEP86, PBE0-DH, and B2PLYP, were also performed. All adsorption energy calculations were carried out on the RevTPSS geometries.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453068","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":"Adsorption grand potential of OH on metal oxide surfaces","authors":"Claudia Islas-Vargas,&nbsp;Alfredo Guevara-García,&nbsp;Marcelo Galván","doi":"10.1007/s00894-024-06170-1","DOIUrl":"10.1007/s00894-024-06170-1","url":null,"abstract":"<div><h3>Context</h3><p>Describing chemical processes at solid–liquid interfaces as a function of a fixed electron chemical potential presents a challenge for electronic structure calculations and is essential for understanding electrochemical phenomena. Grand Canonical Density Functional Theory (GCDFT) allows treating solid–liquid interfaces in such a way that studying the influence of a fixed electron potential arises naturally. In this work, GCDFT is used to compute the adsorption grand potential (AGP), a key parameter for understanding and predicting the behavior of adsorbates on surfaces. We focused on the adsorption of an OH molecule on three metallic surfaces commonly used in electrochemical processes, such as the oxygen evolution reaction (OER). Our study aims to offer insights into how AGP can be used to compare adsorption strengths under different fixed electron chemical potentials, which is crucial for designing efficient electrode materials. By determining the average number of electrons self-consistently under varying chemical potentials, we showed how one can distinguish between electron acquisition and depletion during the adsorption process, offering a deeper understanding of the adsorbate–surface interactions.</p><h3>Methods</h3><p>The approach used in this work employs the Kohn–Sham-Mermin formulation of the Grand Canonical Density Functional Theory. The computations were performed using the periodic open-source density functional theory software, JDFTx, with the Garrity-Bennett-Rabe-Vanderbilt library of ultrasoft pseudopotentials. Calculations were made using truncated Coulomb potentials and the auxiliary Hamiltonian method with the PBE exchange–correlation functional, along with DFT-D2 long-range dispersion corrections. The implicit solvation model CANDLE was used to describe the electrolyte with a 1 M concentration.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142443216","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}