Journal of Molecular Modeling最新文献

{"title":"Understanding the adsorption mechanism of geosmin, linalool, and o-cresol on Machilis hrabei olfactory receptor MhOR5 via statistical physics modeling and molecular docking simulation","authors":"Ismahene Ben Khemis,&nbsp;Salah Knani,&nbsp;Fatma Aouaini,&nbsp;Ghadeer Mohsen Albadrani,&nbsp;Amani Alruwaili,&nbsp;Abdelmottaleb Ben Lamine","doi":"10.1007/s00894-025-06327-6","DOIUrl":"10.1007/s00894-025-06327-6","url":null,"abstract":"<div><h3>Context</h3><p>This article suggests that the olfaction process can be simplified to an adsorption mechanism by utilizing the <i>Machilis hrabei</i> olfactory receptor MhOR5 as a biological adsorbent. The odorant molecules such as geosmin, linalool, and o-cresol were used as adsorbates. The aim of the present study is to provide new insights into the docking process of the tested odorants on MhOR5 using numerical simulation via an advanced statistical physics model to fit the corresponding response curves.</p><h3>Methods</h3><p>In the present work, an advanced theory based on statistical physics formalism is applied to understand and analyze the experimental dose-olfactory response curves of three odorant molecules on the <i>Machilis hrabei</i> olfactory receptor. Indeed, a monolayer model with four energy levels developed using the grand canonical ensemble was successfully applied to analyze the adsorption mechanism of geosmin, linalool, and o-cresol on MhOR5 through the interpretation of the different fitted parameters. Stereographically, it was found that geosmin, linalool, and o-cresol molecules were docked on MhOR5 binding pockets with nonparallel orientations (multi-molecular process) since all the numbers of the studied odorants adsorbed on one binding pocket were superior to 1. Energetically, the values of the molar adsorption energies <i>ΔE</i>_i (<i>i</i> = 1, 2, 3, and 4) related to the four types of binding pockets (varied between 6.18 and 18.43 kJ/mol) demonstrated that the three odorants were exothermically and physically docked on MhOR5 since all values of <i>ΔE</i>_i were positive and inferior to 40 kJ/mol. The proposed model may also be applied to calculate and interpret two thermodynamic potentials: the internal energy <i>E</i>_int and adsorption entropy <i>S</i>_a. Additionally, the physicochemical parameters may be used to stereographically and energetically characterize the heterogeneity of the insect MhOR5 surface. The docking simulation results demonstrated that the estimated binding affinities or energy score values (varied between 6.27 and 18.40 kJ/mol) were slightly similar to molar adsorption energy values and were included in the adsorption energy bands of the three adsorption energy distributions (AEDs).</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143521671","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":"Methyl formate synthesis via S(mathrm {_N})Acyl esterification on interstellar ice mantles","authors":"Giulia M. Bovolenta,&nbsp;Stefan Vogt-Geisse","doi":"10.1007/s00894-025-06310-1","DOIUrl":"10.1007/s00894-025-06310-1","url":null,"abstract":"<div><h3>Context</h3><p>Methyl formate (MF) has been detected in several interstellar environments, but whether or not the formation of this molecule takes place in the gas phase or on the ices of interstellar grains is still unclear. In this study, we explore the synthesis of methyl formate through the nucleophilic acyl substitution (S<span>(_{text {N}})</span>Acyl) reaction between methanol (CH<span>(_{3})</span>OH) and formic acid (HCOOH) on amorphous solid water, which is the main component of interstellar ice mantles.</p><h3>Methods</h3><p>Using density functional theory (DFT), we model MF formation by sampling HCOOH in different catalytic sites on the water clusters with CH<span>(_{3})</span>OH, and vice versa, for initial reactant configurations. We select the initial binding modes from the binding energy distributions of both reactant species. We assess the energy and synchronicity of the reaction by analyzing the reaction mechanisms through intrinsic reaction coordinate (IRC) energy, reaction force, and reaction electronic flux profiles. Using Wiberg bond order derivatives, we identify reaction events linked to hidden transition states that are encountered along the reaction coordinate.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143521634","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":"Plastic deformation mechanisms of ZnS and ZnTe under nanoindentation: molecular dynamics simulations","authors":"Chunmei Liu,&nbsp;Chao Xu,&nbsp;Huaping Liu","doi":"10.1007/s00894-025-06330-x","DOIUrl":"10.1007/s00894-025-06330-x","url":null,"abstract":"<div><h3>Context</h3><p>Zinc sulfide (ZnS) and (zinc telluride (ZnTe) are binary semiconductor compounds that exhibit excellent optical and electrical properties, and the mechanical behavior at the nanoscale level is crucial for their potential application. Nevertheless, experimental data are scarce regarding the mechanical characteristics of ZnS and ZnTe. For better applications of ZnS and ZnTe-based devices, it is crucial to understand, design, and control their mechanical properties. In this work, we have examined the indentation on (001), (110), and (111) planes of ZnS and ZnTe at the nanometric scale, along with an exploration of the associated plastic deformation utilizing molecular dynamics techniques. We compared and analyzed the loading curves, dislocation distribution evolutions, atomic displacement vectors, and stress distributions of the two materials under indentation.</p><h3>Method</h3><p>The indentation simulations were performed in molecular dynamics software LAMMPS, using the Stillinger–Weber potential model. Visual analysis is done using OVITO software. A spherical indenter with a diameter of 12.0 nm moves down to the substrates for a depth of 5.0 nm at a steady speed of 0.01 nm/ps. Distinct anisotropic characteristics can be detected from the loading forces, dislocation distributions, atomic displacement vectors, and stress distributions. The dislocation distributions exhibit fourfold, twofold, and threefold symmetries in the case of (001), (110), and (111) planes. Results indicate that stress underneath the indenter should prompt the atoms to move, subsequently leading to the formation, propagation, and distribution of the dislocations. Another notable characteristic is the emergence of prismatic loops in ZnS. The findings offering valuable data for future utilization considerations.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143521633","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":"Oleophobic nanopore in graphene membrane enhances CO2 capture and separation after spontaneous hydrocarbon adsorption","authors":"Zonglin Gu,&nbsp;Wenjing Gao,&nbsp;Jia Chen,&nbsp;Shuming Zeng","doi":"10.1007/s00894-025-06319-6","DOIUrl":"10.1007/s00894-025-06319-6","url":null,"abstract":"<div><h3>Context</h3><p>Membrane separation technology is a great candidate for capturing and separating CO₂ from air and flue gas, aiming at combating global warming. In particular, numerous experimental and theoretical investigations have revealed the outstanding performance of porous graphene membrane in sieving CO₂ due to its high-selectivity and energy-efficiency. Some experimental studies have confirmed that the graphene can be spontaneously contaminated by the hydrocarbons in ambient air, due to its large surface energy. However, how the covered hydrocarbons on porous graphene membrane affect the CO₂ capture and separation remains elusive. In this study, we employed molecular dynamics (MD) simulation approach to investigate CO₂/N₂ separation capacity of the oleophobic N24 nanopores and the oleophilic C24 nanopores in graphene membrane after covering the oleaginous hydrocarbon, C₈H₁₈, films. Interestingly, our MD simulations demonstrate that the oleophobic N24 nanopore shows higher CO₂ transport rate and CO₂/N₂ selectivity compared with the oleophilic C24 nanopore after the membrane adsorbed by C₈H₁₈ films, indicating that the oleophobic N24 graphene nanopore can ameliorate CO₂ capture and separation upon C₈H₁₈ films adsorption. Mechanically, on the one hand, C₈H₁₈ can more likely block the C24 nanopore, due to the stronger affinity of C₈H₁₈ to the C24 pore, which results in the reduced gas transport rate. On the other hand, the quadrupole interaction between CO₂ and N24 nanopore helps the favorable capture and separation of CO₂ by N24 nanopore. The combined effect thus determines the better CO₂ separation performance of hydrocarbon covered N24 nanopore. Therefore, our findings not only reveal the carbon capture and separation performance of porous graphene membrane upon spontaneously adsorbing hydrocarbon from the ambient air or the flue gas for the first time, but also exploit the oleophobic nanopore capable of ameliorating the membrane capacity, which is beneficial to future practical application of porous graphene membrane in CO₂ separation.</p><h3>Methods</h3><p>We conducted all MD simulations with GROMACS software package. VMD software package was used to visualizing the simulation conformations and trajectories. Periodic boundary conditions were applied in all directions (x, y, and z). Temperature was constrained at 350 K using the v-rescale thermostat. Long-range electrostatic interactions were computed using the PME method, and van der Waals (vdW) interactions were calculated with a cutoff distance of 12 Å. Bonds involving hydrogen atoms were constrained to their equilibrium values using the LINCS algorithm. </p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496949","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 studies on the clusters of HONO•(H2O)n(n = 1–7): structures and enthalpy of formation","authors":"Jiadong Bai,&nbsp;Jia Cao","doi":"10.1007/s00894-025-06324-9","DOIUrl":"10.1007/s00894-025-06324-9","url":null,"abstract":"<div><h3>Context</h3><p>Nitrous acid (HONO) is often associated with many air pollution events, such as the ozone hole, acid rain, and human health. Herein, we performed the theoretical studies on the structures and enthalpy of formation for the hydrated clusters HONO∙(H₂O)_<i>n</i>(<i>n</i> = 1–7). Two different isomers of HONO including <i>cis</i>-HONO and <i>trans</i>-HONO were studied. Minima structures of <i>trans</i>-HONO∙(H₂O)_<i>n</i>(<i>n</i> = 1–7) and <i>cis</i>-HONO∙(H₂O)_<i>n</i>(<i>n</i> = 1–7) clusters containing forty-eight and twenty-one were found, respectively. The hydrogen-bonded interactions between HONO and water molecules in HONO∙(H₂O)_<i>n</i>(<i>n</i> = 1–7) clusters were analyzed. Enthalpies of the formation of the most stable isomers of <i>trans</i>-HONO∙(H₂O)_<i>n</i>(<i>n</i> = 1–7) and <i>cis</i>-HONO∙(H₂O)_<i>n</i>(<i>n</i> = 1–7) clusters are predicted theoretically. These results can provide a new understanding of the atmospheric circulation of HONO.</p><h3>Methods</h3><p>Geometric structures and vibrational frequencies of the HONO∙(H₂O)_<i>n</i>(<i>n</i> = 1–7) clusters were investigated by using the QCISD(T)/6–311 + G(3df,2p)//M06-2X/6–311 + G(3df,2p) method. Enthalpies of formation of the global minimal isomers of the HONO∙(H₂O)_<i>n</i>(<i>n</i> = 1–7) clusters were calculated at the CBS-QB3 level of theory. Atoms in molecules (AIM) theory was applied to the analysis of hydrogen-bonded interactions among the HONO∙(H₂O)_<i>n</i>(<i>n</i> = 1–7) clusters.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143489617","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":"DFT-calculations and RDG analysis (topology) of complexes between glutathione and nucleic bases of pyrymidine series","authors":"Marina S. Kurbatova,&nbsp;Vladimir P. Barannikov","doi":"10.1007/s00894-025-06323-w","DOIUrl":"10.1007/s00894-025-06323-w","url":null,"abstract":"<div><h3>Context</h3><p>Interactions between proteins and RNA, as well as between their structural fragments, are widespread in biological objects. We obtained the optimized structures of complexes of the glutathione anion with neutral molecules of uracil, thymine and cytosine. It was established that all complexes are stabilized by hydrogen bonds. The preference for various H-donors in nucleic base molecules (HN(1) or HN(3) in uracyl and thymine, N(1) or H2N in cytosine) for hydrogen bonding with the peptide has been analyzed. Chain elongation from dipeptide to tripeptide creates favorable conditions for increasing the number of hydrogen bonds in the complex. The strongest hydrogen bonds are formed with the carboxylate group of the peptide. Energy advantage of complexation with cytosine compared to other pyrimidine bases, and advantage of complexation with thymine compared to uracil have been established. The contributions of structural rearrangement of molecules, intermolecular interactions and H-bonding to the total values ​​of potential energy and Gibbs energy of the complexation process have been discussed.</p><h3>Methods</h3><p>The article combines the results of calculations by the DFT/ B97D/6–311 + + G(3d,3p) and QTAIM methods to model the structure of ion-molecular complexes between the tripolar anion of peptide (glutathione) and neutral nucleic bases (uracil, thymine, cytosine). The PCM was used for solvent (water). Conformational analysis of the glutathione molecule was performed by scanning the potential energy while varying the dihedral angles. Several initial structure of peptide – nucleic base complexes with different modes of coordination were created in accordance with the MEP results. Non-covalent specific interactions in the complex were highlighted by RDG analysis. The hydrogen bond energies in complexes were calculated based on the correlation with the electron density at bond critical points. Changes in the total energy and Gibbs energy during complex formation, as well as contributions ​​from intermolecular interactions and structural rearrangement of reagent molecules, were determined.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143489618","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":"First-principles study on energetic cocrystals of CL-20/4,5-MDNI with two different stoichiometric ratios under high pressure","authors":"Zikai Gao,&nbsp;Zhihui Gu,&nbsp;Mengjie Bao,&nbsp;Peng Zhang,&nbsp;Yuqin Chu,&nbsp;Yang Zhu,&nbsp;Peng Ma,&nbsp;Congming Ma","doi":"10.1007/s00894-025-06318-7","DOIUrl":"10.1007/s00894-025-06318-7","url":null,"abstract":"<div><h3>Context</h3><p>This research determined the crystal structure, molecular structure, electronic structure, optical properties, mechanical properties, and Hirshfeld analysis of the CL-20/4,5-MDNI cocrystal at two distinct stoichiometric ratios under hydrostatic pressures varying from 0 to 100 GPa. The findings revealed that the CL-20/4,5-MDNI cocrystal with a 1:1 ratio experienced two structural transitions at pressures of 80 GPa and 90 GPa. Notably, new covalent bonds, C10-O13 and C9-O14, were established, whereas the C10-H10C bond was disrupted. In contrast, the CL-20/4,5-MDNI cocrystal with a 1:3 ratio underwent three structural transformations at pressures of 55 GPa, 63 GPa, and 95 GPa, leading to the creation of new covalent bonds such as C17-N35, C25-N43, C14-O9, C21-O7, and N27-H9. These transitions were corroborated through the examination of lattice parameters, variations in covalent bond lengths, density of states, and optical coefficients. Additionally, the study explored the similarities and differences between the two cocrystals in terms of their crystal structure, molecular structure, electronic properties, optical properties, mechanical properties, and Hirshfeld analysis.</p><h3>Method</h3><p>In this investigation, the CASTEP module from the Materials Studio software package was utilized to perform first-principles calculations based on density functional theory (DFT). Specifically, the Broyden–Fletcher–Goldfarb–Shanno (BFGS) optimization technique was applied to refine the geometric structures of the CL-20/4,5-MDNI cocrystals, which were prepared in the stoichiometric ratios of 1:1 and 1:3. These calculations were conducted under a range of hydrostatic pressures, varying from 0 to 100 GPa. To achieve a fully relaxed state at atmospheric pressure, the Perdew–Zunger local density approximation (LDA/CA-PZ) functional was employed. The plane wave cutoff energy was meticulously set at 489 eV to ensure the convergence of the total energy within the unit cell system. Additionally, the <i>k</i>-point mesh was configured as 1 × 1 × 1 to facilitate accurate calculations. Before each simulation, different hydrostatic pressures were systematically applied to analyze the structural changes under varying conditions.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481212","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":"Dioscorea bulbifera seed peel chars as electrocatalysts for hydrogen evolution reactions—experimental and theoretical investigations","authors":"Edith C. Unoka,&nbsp;J. U. Iyasele,&nbsp;I. E. Uwidia,&nbsp;Precious C. Nnaji,&nbsp;Kevin Lobb,&nbsp;Nnaemeka Nnaji","doi":"10.1007/s00894-025-06312-z","DOIUrl":"10.1007/s00894-025-06312-z","url":null,"abstract":"<div><h3>Context</h3><p>This study presents hydrochars derived from <i>Dioscorea bulbifera</i> seed peel as electrocatalysts for hydrogen evolution reaction (HER). These hydrochars are produced at 150 °C and 200 °C and respectively designated DBP@H_150 and DBP@H_200. FTIR, BET surface area measurement, and Boehm titration were used to characterize these hydrochars. Evaluation metrics such as double layer capacity (Cdl) gave information on how well they performed electrocatalytically for hydrogen evolution reaction. Interestingly, hydrochar made at 150 °C showed a Cdl values of 2.0, 1.0, and 0.2 mF at neutral, alkaline and acidic pH, while hydrochar made at 200 °C showed values of 1.5 and 1.2 and 1.1 mF at neutral, alkaline, and acidic pH. Electrochemical impedance spectroscopy (EIS) gave charge transfer resistance (<i>R</i>_ct) values of 48.0 and 60.0 Ω and linear sweep voltammetry (LSV) gave Tafel slope values of 96.2 and 124.1 mV dec⁻¹ for DBP@H_150 and DBP@H_200 respectively, showing the hydrochar’s exceptional electrocatalytic activities. The computed energy gap values from density functional theoretical (DFT) calculations for DBP@H_200 have the highest HOMO–LUMO gap of 5.688 eV, suggesting that it is more chemically stable. A very strong correlation of more than 0.8 is found to exist between energy gaps of hydrochars under acidic, alkaline, and neutral environments and their corresponding double layer capacitance (Cdl).</p><h3>Method</h3><p>Here, the structural and electronic properties of molecular systems are ascertained using a quantum chemical method known as density functional theory (DFT), and molecular properties are calculated using the density functional, B3LYP. Using the GAUSSIAN 09 program, DFT calculations were carried out at the B3LYP/6 − 31 g(d) level of theory. Molecular characteristics were calculated for <i>Dioscorea bulbifera</i> seed peel–derived hydrochars (DBP@H), including energy of the lowest unoccupied molecular orbitals (<i>E</i>_LUMO), energy of the highest occupied molecular orbitals (<i>E</i>_HOMO), and energy gap.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481213","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 study of the formation of inclusion complexes with some terpenes using different solvating models","authors":"Daniel Augusto Barra de Oliveira,&nbsp;Edenilson dos Santos Niculau","doi":"10.1007/s00894-025-06316-9","DOIUrl":"10.1007/s00894-025-06316-9","url":null,"abstract":"<div><h3>Context</h3><p>Essential oil molecules have various nutritional and medical uses. However, their applications are limited by their low polarity and high volatility. Inclusion complexes provide a way to overcome these limitations. Cyclodextrins are cyclic oligosaccharides composed of macrocyclic rings of glucose units linked by α-1,4 glycosidic bonds, which are used to prepare inclusion complexes with essential oils. Experiments on the formation of inclusion complexes show that essential oil molecules can bind to cyclodextrins in various ways. Electronic structure calculations help to understand why some essential oil molecules bind more effectively than others in the formation of inclusion complexes with cyclodextrins.</p><h3>Methods</h3><p>Our study employed theoretical calculations to investigate the interaction between beta-cyclodextrin and six essential oil molecules. The selected essential oil molecules were carvacrol, carvone, eugenol, limonene, p-cymene, and thymol. Molecular docking between the essential oil molecules and cyclodextrin resulted in both complexed structures and non-complexed structures, with some molecules positioned outside the cyclodextrin cavity. The interaction energies, calculated using the AutoDock Vina program, indicated that the complexed essential oil molecules exhibit the lowest energy. Electronic structure calculations were performed using the Gaussian16 program to analyze the structures obtained from the docking process. DFT calculations employing the ωB97XD functional to describe the inclusion complex and PM7 to describe the solvent model in the ONIOM approach revealed that molecules containing hydroxyl groups form hydrogen bonds with cyclodextrin, resulting in more stable structures compared to those lacking this functional group. Additionally, the use of explicit solvent facilitates the inclusion of essential oil molecules by altering the deformation energies of cyclodextrin. These theoretical results explain the advantage of using solvents in the preparation of experimental inclusion complexes.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481184","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":"Quantum mechanical and machine learning prediction of rotational energy barriers in halogenated aromatic alcohols","authors":"Steven T. Cerabona,&nbsp;Gordon G. Brown,&nbsp;Leah B. Casabianca","doi":"10.1007/s00894-025-06321-y","DOIUrl":"10.1007/s00894-025-06321-y","url":null,"abstract":"<div><h3>Context</h3><p>Rotation about a chemical bond is important in many chemical processes and can be influenced by neighboring substituents on a molecule. Rotational energy barriers can be predicted by density functional theory (DFT) calculations. Here, we specifically explore how substituents influence the barrier to rotation about the C-O bond in symmetrically halogenated aromatic alcohols. A machine learning model was trained on the DFT-calculated rotational energies and was found to do a good job predicting rotational energy barriers from the electronegativity, atomic radius, and Hammett constant for each substituent. The machine learning model was found to perform better when it was trained separately on pyrenols, anthranols, or phenols than when it was trained on all classes of compounds together. Even though the models were trained on compounds containing only one kind of substituent, they were found to perform similarly well on compounds containing mixed substituents. Machine learning was able to predict the rotational energy barrier heights better than correlations among parameters that would be expected to be relevant based on chemical intuition.</p><h3>Methods</h3><p>DFT calculations were done with Gaussian 16 software at the B3LYP/6–311 + G(d.p) level of theory. Machine learning was done using the classification and regression training (caret) package in R version 4.4.0.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06321-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481182","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}