Journal of Molecular Modeling最新文献

{"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}

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

{"title":"Mechanical enhancement of hydroxyapatite via carbon and boron nitride nanotubes: a molecular dynamics study","authors":"Bugra Eyidogan,&nbsp;Mesut Kirca","doi":"10.1007/s00894-025-06317-8","DOIUrl":"10.1007/s00894-025-06317-8","url":null,"abstract":"<div><h3>Context</h3><p>This study explores the mechanical limitations of hydroxyapatite (HAP), a critical bioceramic in bone tissue engineering and orthopedic implants, which is limited by its brittleness and low mechanical strength. By reinforcing HAP with carbon nanotubes (CNTs) and boron nitride nanotubes (BNNTs), the mechanical performance of HAP was significantly enhanced. The inclusion of CNTs led to a 25% increase in ultimate tensile strength (UTS), peaking at 9.18 GPa, while BNNTs improved ductility with a maximum UTS of 8.75 GPa. Toughness, representing the material’s energy absorption capacity, reached 15.8 kJ/m² in CNT-reinforced composites and 9.3 kJ/m² in BNNT-reinforced composites, emphasizing their distinct reinforcement contributions. The study highlights the potential of CNT-BNNT combinations, achieving a synergistic balance of strength, ductility, and toughness.</p><h3>Methods</h3><p>The study employed molecular dynamics simulations to model and analyze the mechanical behavior of nano-reinforced HAP. Simulations were performed using the LAMMPS software, with the CVFF-Interface Force Field for HAP and the AIREBO potential used to model carbon interactions in CNTs. BNNTs were simulated using the Tersoff potential to account for interactions between boron and nitrogen atoms. The effects of nano-reinforcements on the mechanical properties of HAP were evaluated through tensile stress–strain curves, which quantified improvements in Young's modulus, ultimate tensile strength (UTS), and strain at UTS. Additionally, combinations of CNTs and BNNTs in varying ratios were simulated to assess synergistic interactions, while different inclusion levels were investigated to understand their impact on the composite’s mechanical performance. Toughness values, representing the material's energy absorption capacity, were calculated by integrating the area under the stress–strain curves up to failure, providing deeper insights into the ductility and energy dissipation characteristics of the reinforced HAP composites.</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":"143430825","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":"Reduction of hydrogen peroxide by amine-based diselenides: understanding the effect of substitutions on reactivity","authors":"Vishnu Rama Chari,&nbsp;Raghu Nath Behera","doi":"10.1007/s00894-025-06313-y","DOIUrl":"10.1007/s00894-025-06313-y","url":null,"abstract":"<div><h3>Context</h3><p>Many small organoselenium compounds, such as substituted diselenides, mimic the glutathione peroxidase (GPx) activity by catalysing the reduction of hydrogen peroxide. In this context, the effect of substitution in di-2(N-cyclohexyl,N-(methylamino)-methyl)phenyl diselenide (CMP) on its GPx-like activity (to reduce hydrogen peroxide) has been investigated using the density functional theory. It was observed that the presence of an electron donating group as well as secondary amino group (instead of tertiary one) favoured the peroxide reduction process, which is consistent with the experimental reports. This study revealed that the presence of electron donating group lowers the energy requirement for distortion in zwitterion of the selenol during the progress of the reaction, thereby enhancing its catalytic activity.</p><h3>Methods</h3><p>Geometry optimizations, Natural Bond Order (NBO) and the wavefunction calculations were carried out using Gaussian16 software at B3PW91/6–31+G(d,p) level of theory. Improved energy calculations were carried out at B3PW91/6–311++ G(3df,3pd)//B3PW91/6–31+G(d,p) level of theory. The solvent effect was modelled using the self-consistent reaction field (SCRF) method utilizing polarizable continuum model (PCM). Activation Strain Model was used to study the contributions of the steric and electronic effects due to substitutions. Wavefunction analysis was carried out using <i>Multiwfn</i> software.</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":"143430874","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}