Journal of Molecular Modeling最新文献

{"title":"Theoretical investigation of dual hydrogen-bonding interactions and ESIDPT mechanism associated with halogen substituted 2,5-bis(4,5-diphenyl-1H-imidazol-2-yl)benzene-1,4-diol derivatives","authors":"Jiaoni Pan,&nbsp;Jinfeng Zhao,&nbsp;Jiahe Chen","doi":"10.1007/s00894-025-06343-6","DOIUrl":"10.1007/s00894-025-06343-6","url":null,"abstract":"<div><h3>Context</h3><p>In this work, using the TDDFT method, we mainly focus on exploring the photo-induced excited state dual hydrogen-bonding interactions for halogen element substituted 2,5-bis(4,5-diphenyl-1H-imidazol-2-yl)benzene-1,4-diol (BDIBD) derivatives (i.e., BDIBD-FF, BDIBD-FCl and BDIBD-FBr). Analyses of chemical bond properties, bond lengths and bond angles, infrared (IR) spectral shifts, as well as the simulated core-valence bifurcation (CVB) parameters, we find upon excitation dual hydrogen bonds of BDIBD-FF, BDIBD-FCl, and BDIBD-FBr are strengthened in the S₁ state. Variations about photo-induced charge further reveal the excited state intramolecular double proton transfer (ESIDPT) tendency. By constructing potential energy surfaces (PESs), we not only clarify the stepwise ESIDPT mechanism for BDIBD derivatives, but also present the halogen element regulated ESIDPT behaviors.</p><h3>Methods</h3><p>Based on Gaussian 16 program, all BDIBD derivatives were optimized using DFT and TDDFT methods with D3-B3LYP and TZVP theoretical levels. By comparing geometries variations and exploring core-valence bifurcation indexes for predicting hydrogen-bonding strength using Multiwfn 3.8, dual hydrogen-bonding interactions were analyzed. Potential energy surfaces with transition state forms were explored to reveal the ESIDPT mechanism.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143632465","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":"Atomistic insights into the humidity response of nanocellulose: a molecular dynamics study","authors":"Bingjie Gao,&nbsp;Haojun Wang,&nbsp;Jing Wan,&nbsp;Hang Yin","doi":"10.1007/s00894-025-06340-9","DOIUrl":"10.1007/s00894-025-06340-9","url":null,"abstract":"<div><h3>Context</h3><p>TEMPO-oxidized cellulose nanofibers (TOCNFs) show significant potential for developing high-performance resistive humidity sensors due to their hydrophilicity and structural adaptability. However, the underlying atomic-scale mechanisms governing their humidity response remain poorly understood. Using molecular dynamics simulations, this study investigates how crystal facets, nanopore widths, and humidity levels influence the surface wettability, water permeability, and swelling of TOCNFs. Our findings reveal that the (1 <span>(stackrel{text{-}}{1})</span> 0) crystal facet exhibits the highest hydrophilicity, while the (100) facet is the least hydrophilic. Narrower nanopores and more hydrophilic facets enhance capillary adsorption, significantly influencing water penetration depth. Additionally, nanopore swelling is highly dependent on the crystal facet, with the (1 <span>(stackrel{text{-}}{1})</span> 0) facet showing the most pronounced expansion. These insights provide a foundation for designing high-performance TOCNF-based humidity sensors.</p><h3>Methods</h3><p>The humidity response of TOCNFs is simulated using the large-scale atomic molecular massively parallel simulator (LAMMPS) package with the OPLS-AA force field to describe interatomic interactions. The open-source visualization tool OVITO is employed to visualize the atomic configurations.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143594667","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 evidence of the CO(_{2}) reduction by a Mo-based complex: a DFT study based on the reaction force decomposed into four components","authors":"Jorge I. Martínez-Araya","doi":"10.1007/s00894-025-06335-6","DOIUrl":"10.1007/s00894-025-06335-6","url":null,"abstract":"<div><h3>Context</h3><p>The conversion of carbon dioxide into methanoic acid through direct hydrogenation with H<span>(_2)</span> in the gas phase implies overcoming a high activation energy (more than 60 kcal mol <span>(^{-1})</span>) that makes the process kinetically infeasible. In this study, the use of the [(PY<span>(_5)</span>Me<span>(_2)</span>)Mo(III)(H)(OH)]<span>(^{+})</span> complex instead of H<span>(_2)</span> lowered the activation energy of the hydrogenation by 98.5%. Reaction mechanism in the presence and absence of the Mo-based complex is analyzed through the reaction force, its components, and their respective reaction works. It was found that the high activation energy for the direct hydrogenation of CO<span>(_2)</span> with H<span>(_2)</span> is a consequence of a predominance of three types of reaction force components acting as retarding forces while a fourth type of reaction force component is acting as a driving force from the reactant state until the transition state. On the contrary, the low activation energy for the hydrogenation of CO<span>(_2)</span> assisted by the Molybdenum-based complex is a consequence of opposing types of force components balancing each other, where two act as retarding forces against two reaction force components acting as driving forces.</p><h3>Method</h3><p>Quantum chemistry calculations were performed through DFT methods with the BP86 density functional along with MWB28 pseudopotentials including a proper basis set for Mo and 6-31+G(d,p) basis set for the remaining atoms implemented in Gaussian 16. AOMix post-SCF software was employed to determine bond orders on stationary points. The reaction force analysis focused on the reaction mechanisms of both chemical reactions using numerical differentiation of energy profiles with OriginPro 2020.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06335-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143594668","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":"Computable properties of selected monomeric acylphloroglucinols with anticancer and/or antimalarial activities and first-approximation docking study","authors":"Neani Tshilande,&nbsp;Liliana Mammino","doi":"10.1007/s00894-025-06299-7","DOIUrl":"10.1007/s00894-025-06299-7","url":null,"abstract":"<div><h3>Context</h3><p>Malaria and cancer tend to become drug-resistant a few years after a drug is introduced into clinical use. This prompts the search for new molecular structures that are sufficiently different from the drugs for which resistance has developed. The present work considers eight selected acylphloroglucinols (ACPLs) with proven antimalarial and/or anticancer activities. ACPLs are compounds of natural origin structurally derivative from 1,3,5-trihydroxybenzene and characterized by the presence of an acyl group R–C = O. The selected ACPLs contain only one acylphloroglucinol moiety and are, therefore, monomeric ACPLs (also occasionally called “simple” ACPLs). They were studied computationally <i>in vacuo</i> and in-three-solvents with different polarities, using different levels of theory. The findings on molecular properties relevant to the understanding of biological activities align with previous studies, enhancing the reliability of predictions for molecules of the same class and providing insights into their behaviour in different environments. Structure-based virtual screening was used to study the interactions between these molecules and selected proteins known as relevant drug targets for antimalarial and anticancer activities; the screening showed that most of these ACPLs bind well with the selected proteins, thus being interesting for further studies. The results also suggest that most of these ACPLs have the potential for dual therapeutic applications (antimalarial and anticancer), offering a cost-effective drug development option. Furthermore, the ADME-T predictions indicated favourable pharmacokinetic properties for these ACPLs.</p><h3>Methods</h3><p>Computational studies of the selected ACPLs were performed using Gaussian-09, <i>in vacuo</i> and in-three-solvents with different polarities. Three different levels of theory were used – Hartree Fock (HF), Density Functional Theory (DFT) with the B3LYP functional, and second order Møller-Plesset Perturbation Theory (MP2). HF and MP2 used a 6-31G(d,p) basis set, while DFT used a 6-31G + (d,p), for consistency with previous studies on ACPLs. The investigated molecular properties include conformational preferences, intramolecular hydrogen bonding patterns, HOMO–LUMO energy gap, dipole moments, as well as the solvent effect for the three considered solvents. Virtual screening was conducted using the Schrödinger suite, including Maestro 9.3 with GLIDE for docking and GlideScore for evaluating binding affinities. In addition, the QikProp tool provided ADME-T predictions for pharmacokinetic properties.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06299-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143594695","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":"First-principles studies of the SCl2 adsorption on the doped boron phosphide monolayer","authors":"Akari Narayama Sosa,&nbsp;Sandra Esteban Gómez,&nbsp;Juan Carlos Moreno Hernández,&nbsp;Dolores García Toral,&nbsp;Gregorio Hernández Cocoletzi","doi":"10.1007/s00894-025-06333-8","DOIUrl":"10.1007/s00894-025-06333-8","url":null,"abstract":"<div><h3>Context</h3><p>Sulfur dichloride (SCl₂) molecules form a harmful substance; however, it is widely used in the industry as insecticide and in organic synthesis. In contact with water, these molecules produce other toxic and corrosive gases. Therefore, it is important to remove them from the environment. In this work, we have studied the boron phosphide (BP) monolayer (ML) doped with metal atoms to be considered as a sensor material for the detection of sulfur dichloride (SCl₂) molecules. Studies are done by applying the density functional theory (DFT) according to the PWscf code of the Quantum ESPRESSO, using the projector-augmented-wave (PAW) method within the framework of the generalized gradient approximation (GGA) with the PBE parameterization. The results obtained indicate weak interactions between the SCl₂ molecule and the pristine BP monolayer. However, after metal-doping (with atoms of: Ga, In, N and As) the interactions between the SCl₂ molecule and the ML was increased, as expected. Parameters such as the adsorption energy (E_ad), work function (Ф), Bandgaps (E_g), recovery time (τ), electronegativity (χ) and chemical potential (μ) have been analyzed. The results suggest that the metal-doped BP monolayer may be a promising sensing material for gas sensor devices to detect SCl₂ molecules.</p><h3>Methods</h3><p>The SCl₂-metal-doped BP ML has been investigated using DFT calculations as implemented in the PWscf code of the Quantum ESPRESSO, and using PAW pseudopotential within the framework of the GGA-PBE and energy cutoff of 40Ry. The force components were smaller than 0.05 eV/Å and the Grimme-D2 scheme was considered. The Brillouin zone was sampled using a Monkhorst–Pack grid of 5 × 5 × 1 and 17 × 17 × 1 k-points for structural relaxations and electronic-properties calculations.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06333-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143570946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of product formation in the H + H2C = C = CH reaction: a comparison of experimental and theoretical kinetics","authors":"Hoang T. T. Trang,&nbsp;Nghiem T. Thuong,&nbsp;Tien V. Pham","doi":"10.1007/s00894-025-06325-8","DOIUrl":"10.1007/s00894-025-06325-8","url":null,"abstract":"<div><h3>Context</h3><p>The H₂CCCH radical plays a crucial role in combustion chemistry, astrophysical processes, and the formation of complex organic molecules, serving as a key intermediate in the synthesis of polycyclic aromatic hydrocarbons and soot precursors. The reactions of H₂CCCH with small species are significant for understanding the mechanisms of hydrocarbon transformation in combustion, atmospheric chemistry, and interstellar environments. In the present study, the mechanism and kinetics of the H + H₂CCCH have been thoroughly characterized. The calculated results indicate that the reaction can proceed via H-addition to the H₂CCCH carbon chain without an energy barrier, forming the adducts (C₃H₄). These intermediates can then undergo H₂-abstraction or carbon-chain cleavage to create various products, in which PR₁ (¹HCCCH + H₂) and PR₄ (H₂CCC + H₂) are the main products of the reaction system. Furthermore, the triplet potential surface shows the dominant channel forming the product PR₁₁ (³HCCCH + H₂). In the low-temperature region, PR₄ is dominant, exhibiting a 70% branching ratio at 400 K; at higher temperatures, the PR₁₁ product prevails, with a 65.7% branching ratio at 2000 K. The bimolecular rate constants of the reaction are positively dependent on temperatures but negatively dependent on pressures. The calculated rate constants in this study agree well with the available literature data. The computational results of the H + H₂CCCH reaction provide profound insights into the theoretical aspects and offer valuable applications for modeling reaction systems involving the propargyl radicals.</p><h3>Methods</h3><p>The B3LYP and CCSD(T) methods, combined with the aug-cc-pVnZ (<i>n</i> = T, Q, 5) basis sets, were employed to optimize structures and calculate single-point energies for all species involved in the reaction. The temperature range (200 – 2000 K) and pressure range (0 – 7600 Torr) were used to calculate the bimolecular rate constants for the dominant reaction pathways. The TST, VRC-TST, and RRKM models, with the small curvature tunneling correction, were employed for the kinetic calculations.\u0000</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143570947","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 effect of pressure on the mechanical properties of hydroxyl-terminated polybutadiene-based propellants","authors":"Tao Guo,&nbsp;Zhong-e Chen,&nbsp;Tieshan He,&nbsp;Cheng Li,&nbsp;Shejuan Xie,&nbsp;Ning Wang","doi":"10.1007/s00894-025-06329-4","DOIUrl":"10.1007/s00894-025-06329-4","url":null,"abstract":"<div><h3>Context</h3><p>In order to estimate the mechanical behavior of the propellant under working pressures, the effect of pressure on the mechanical properties of hydroxyl-terminated polybutadiene (HTPB) propellants was studied by analyzing the uniaxial tensile strength and maximum strain master curves under the test conditions of – 20 ~ 70 °C, 0.5 mm/min ~ 500 mm/min with different pressures from 0 to 10 MPa. The results show that the master curves for tensile strength are obviously affected by the pressure in the range of 0.15 ~ 3 MPa, while the master curves for tensile strength are insensitive to pressures below 0.15 MPa or above 3 MPa. The master curves for maximum strain are unaffected in the whole concerned pressure range. A power function can be used to study the relationship between tensile strength and temperature or strain rate and to predict the change trend of the temperature and strain rate sensitive indexes with the pressure, which may be useful in the formulation designing of HTPB solid propellants.</p><h3>Methods</h3><p>The uniaxial tensile propellant test was used to obtain the tensile strength and maximum strain master curves under different pressures, which were plotted at a reference temperature of 20 °C under different pressures by means of the overlap joints method. A power function method was developed to study the relationship between tensile strength and temperature or strain rate.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564306","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 explosive potential of 2,3-dihydrofuran derivatives as novel insensitive high-energy density materials","authors":"Fasila P. M.,&nbsp;Rahana Ameen,&nbsp;Biju A. R.","doi":"10.1007/s00894-025-06334-7","DOIUrl":"10.1007/s00894-025-06334-7","url":null,"abstract":"<div><h3>Context</h3><p>In this study, a series of carefully designed oxygen-rich bicyclic ozonides, derived from 2,3-dihydrofuran (2,6,7,8-tetraoxabicyclo[3.2.1]octane), have been studied with meticulous attention to the incorporation of nitro and/or trinitromethyl (TNM) substituents. These compounds exhibit significant promise as high-energy–density materials (HEDMs), thus representing a pioneering avenue in the realm of advanced energetic materials. Evaluating the energetic performances and impact sensitivity is the focus of our theoretical calculations. The majority of the designed compounds exhibit elevated density, complemented by outstanding detonation properties. Each of these compounds demonstrates a high positive heat of formation, with many of them displaying impact sensitivities well suited for applications in high-energy density materials (HEDMs). Due to their significant oxygen content, all 45 designed compounds maintain a high positive oxygen balance. This unique combination of high-performance characteristics and low sensitivities positions them as promising candidates for high-energy explosives. Notably, among the compounds, FOZ23 (3-nitro-5-(trinitromethyl)-2,6,7,8-tetraoxabicyclo[3.2.1]octane), FOZ19 (3-nitro-4-(trinitromethyl)-2,6,7,8-tetraoxabicyclo[3.2.1]octane), and FOZ24 (1-nitro-5-(trinitromethyl)-2,6,7,8-tetraoxabicyclo[3.2.1]octane) exhibit exceptional performance and sensitivities, warranting further investigation and consideration. From the analysis of BDE of C-NO₂ and O–O linkages, it was found that the peroxide bond is stronger than C-NO₂ bond. Therefore, peroxides can be used for various applications in the nearby future by incorporating proper substitutions.</p><h3>Methods</h3><p>Gaussian 09 program was used for geometry optimization and vibrational frequency analysis of the selected compounds. The method employed for the study was density functional theory at the B3LYP level of approximation using aug-cc-pVDZ as the basis set. Multiwfn program was employed for Electrostatic potential analysis.</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":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143553993","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":"Structure and dynamics of anacardic acid in hexane, ethanol, and carbon tetrachloride: a molecular dynamics investigation","authors":"Ritesh K. Patil,&nbsp;Rontu Das,&nbsp;Debashis Kundu","doi":"10.1007/s00894-025-06320-z","DOIUrl":"10.1007/s00894-025-06320-z","url":null,"abstract":"<div><h3>Context</h3><p>Anacardic acid (AA), a key compound in cashew nut shell liquid, is used in medicines and food preservation because of its antimicrobial and antioxidant properties. AA has four forms: saturated, monoene, diene, and triene. Extracting these forms using different solvents is difficult through experiments. To solve this, molecular dynamics (MD) simulations are used to study how AA behaves in three solvents: hexane, ethanol, and carbon tetrachloride. The results show that ethanol forms stronger hydrogen bonds with AA and allows higher movement of AA molecules, making it a better solvent for extraction. These findings help in selecting efficient and sustainable solvents for AA extraction.</p><h3>Methods</h3><p>MD simulations utilize the Optimized Potential for Liquid Simulations force field to describe the interactions of AA with hexane, ethanol, and carbon tetrachloride. MD simulations are performed using GROMACS open-source package. Structural properties, such as radial distribution functions and hydrogen bonding, and transport properties, like mean square displacement (MSD), are studied to understand how AA behaves in each solvent. These simulations reveal detailed interactions between AA and the solvents, showing why ethanol works better for extraction.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143553941","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":"LeScore: a scoring function incorporating hydrogen bonding penalty for protein–ligand docking","authors":"Aowei Xie,&nbsp;Guangjian Zhao,&nbsp;Huicong Liang,&nbsp;Ting Gao,&nbsp;Xinru Gao,&nbsp;Ning Hou,&nbsp;Fengjiao Wei,&nbsp;Jiajie Li,&nbsp;Hongtao Zhao,&nbsp;Ximing Xu","doi":"10.1007/s00894-025-06328-5","DOIUrl":"10.1007/s00894-025-06328-5","url":null,"abstract":"<div><h3>Context</h3><p>Molecular docking is vital for structure-based virtual screening and heavily depends on accurate and robust scoring functions. Scoring functions often inadequately account for the breakage of solvent hydrogen bonds, hindering the accuracy of predicting binding energy. Here, we introduce LeScore, a novel scoring function that specifically incorporates the hydrogen bonding penalty (HBP) in an aqueous environment, aiming to penalize unfavorable polar interactions when hydrogen bonds with water are broken but the energy loss is not fully compensated by newly formed protein–ligand interactions. LeScore was optimized for descriptor combinations and subsequently validated using a testing data set, achieving a Pearson correlation coefficient (rp) of 0.53 in the training set and 0.52 in the testing set. To evaluate its screening capability, a subset of the Directory of Useful Decoys: Enhanced (DUD-E) was used. And LeScore achieved an AUC of 0.71 for specific targets, outperforming models without HBP and enhancing the ranking and classification of active compounds. Overall, LeScore provides a robust tool for improving virtual screening, especially in cases where hydrogen bonding is crucial for ligand binding.</p><h3>Method</h3><p>LeScore is formulated as a linear combination of descriptors, including van der Waals interactions, hydrogen bond energy, ligand strain energy, and newly integrated HBP. The function was optimized using multiple linear regression (MLR) on the PDBbind 2019 dataset. Evaluation metrics, such as Pearson and Spearman correlation coefficients were utilized to assess the performance of 12 descriptor combinations. Additionally, the study employed datasets from the DUD-E to evaluate LeScore’s ability to distinguish active ligands from decoys across multiple target proteins.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143529983","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}