Journal of Molecular Modeling最新文献

{"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}

{"title":"Unveiling the properties of ascorbic acid against M. tb through in silico approach: A comparative drug-based study","authors":"Aviral Kaushik,&nbsp;Arti Peshrana,&nbsp;Rohit Barapatre,&nbsp;Shreya Pansheriya,&nbsp;Radhey Shyam Kaushal","doi":"10.1007/s00894-025-06322-x","DOIUrl":"10.1007/s00894-025-06322-x","url":null,"abstract":"<div><h3>Context</h3><p>Tuberculosis (TB) is a highly contagious and potentially life-threatening disease caused by <i>Mycobacterium tuberculosis</i> (<i>M. tb</i>). According to the World Health Organization (WHO), 7.5 million people were diagnosed with TB in 2022. Combating this disease requires ongoing efforts in TB drug discovery and the development of new treatment regimens. Identifying novel drug targets and inhibitory molecules is crucial in the fight against latent TB, particularly due to the rising issue of <i>M. tb</i> drug resistance. In modern drug discovery, the focus has shifted towards identifying new, safe natural compounds with enhanced biological activity against TB. One promising compound is ascorbic acid (Vitamin C), which possesses pro-oxidant properties that generate free radicals along with the first and second-line anti-TB drugs, aiding in the eradication of <i>M. tb</i> during latent infections.</p><h3>Methods</h3><p>In the current research, extensive in silico studies have been conducted to investigate the potential of ascorbic acid as an inhibitor of various <i>M. tb</i> pathways, especially those involving protein folding (chaperone-mediated) and detoxification pathways. The proteins were analysed by various physicochemical and pharmacological parameters. Molecular docking of the selected proteins with existing first-line, second-line drugs and ascorbic acid was performed. Furthermore, the top-scoring molecular docking of ascorbic acid was subjected to Molecular Dynamics Simulation. The 500 ns Molecular Dynamics Simulation studies were carried out by GROMACS v2024.1 using CHARMM27 force field, TIP3P water model and using triclinic box for solvation. The obtained trajectories were analysed through XMGRACE tool.</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":"143481183","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":"Computed libraries of avobenzone derivatives with sulfur groups as enhanced UVA filters","authors":"Deepak Kumar Sahoo,&nbsp;Smriti Moi,&nbsp;Konkallu Hanumae Gowd","doi":"10.1007/s00894-025-06315-w","DOIUrl":"10.1007/s00894-025-06315-w","url":null,"abstract":"<div><h3>Context</h3><p>Sunscreen formulations often contain avobenzone as a UVA filter to combat the deleterious effects of solar UV radiation. Avobenzone has notable drawbacks: (1) photounstability under UV radiation/sunlight and (2) tendency for skin penetration. The current report aims to improve both the intrinsic photostability and decrease the skin permeability of avobenzone through skeleton structure modification. The electron-donating -OMe group of avobenzone was replaced with diverse groups to compute molecular libraries of avobenzone derivatives. The studies were focused on the sulfur electron-withdrawing groups of avobenzone derivatives as the photostable UV filters contain –SO₃H groups. The UV spectra and bond dissociation energy of Norrish type I cleavages were computed using density functional theory (DFT). The tendency for skin permeability was evaluated by calculating transdermal transportation rate and membrane permeability.</p><h3>Methods</h3><p>A total of 2468 avobenzone derivatives were computed using the enumeration tool of the Schrödinger Material Suite platform. Searching for sulfur-containing derivatives yielded a total of 72 molecules, 23 of which exhibited electron-withdrawing properties. These molecules were evaluated for their UVA spectra using TDDFT with the B3LYP functional and a 6-311G + ** basis set. The bond dissociation energy for putative Norrish type I cleavages was calculated using the B3LYP functional in combination with the LACV3P** basis set. The membrane dG insert was calculated using the membrane permeability panel. The maximum transdermal transportation rate (<i>Jm</i>) was derived using the QikProp tool. These results indicate that avobenzone derivatives with sulfonic acid, sulfuric diamide, and sulfonamide functional groups demonstrated improved photochemical properties with a significant reduction in skin permeability compared to the native avobenzone.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143438680","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 adsorption behavior at the air/water interface of saturated cardanol nonionic surfactants through molecular dynamic simulations","authors":"Congying Lu,&nbsp;Xinyi Xu,&nbsp;Minjia Xia,&nbsp;Zhenyu Yuan,&nbsp;Haifeng Wang,&nbsp;Weiyang Liu,&nbsp;Qing Yang,&nbsp;Wei Ding","doi":"10.1007/s00894-025-06314-x","DOIUrl":"10.1007/s00894-025-06314-x","url":null,"abstract":"<div><h3>Context</h3><p>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.</p><h3>Method</h3><p>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.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143438723","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":"Exploring the dominant interactions: unveiling the stable structure of theobromine-water complexes through DFT and ab initio investigations","authors":"Tanvi,&nbsp;Mohd Tauheed Ilyas,&nbsp;G. S. S. Saini,&nbsp;Anamika Mukhopadhyay","doi":"10.1007/s00894-025-06309-8","DOIUrl":"10.1007/s00894-025-06309-8","url":null,"abstract":"<div><h3>Context</h3><p>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.</p><h3>Methods</h3><p>In this work, we have employed MP2/6-311++G(d,p) and <span>(omega )</span>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 <span>(omega )</span>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.</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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143430875","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}