Journal of Molecular Modeling最新文献

{"title":"The low-temperature dissolution characteristics of water in coal-based hydrocarbon fuels and its molecular dynamics simulation","authors":"Zengzhi He,&nbsp;Chongpeng Du,&nbsp;Jun Yu,&nbsp;Siyi Jing,&nbsp;Zonggang Du,&nbsp;Lichuan Gao,&nbsp;Chong Wang,&nbsp;Jiaxi Lei,&nbsp;Yonghong Zhu,&nbsp;Louwei Cui,&nbsp;Wei Han,&nbsp;Dong Li","doi":"10.1007/s00894-025-06302-1","DOIUrl":"10.1007/s00894-025-06302-1","url":null,"abstract":"<div><h3>Context</h3><p>As a substitute for traditional petroleum derived jet fuels, water in coal-based hydrocarbon fuels may precipitate into ice at low temperatures, leading to fuel system failures and endangering flight safety. This study employed Karl Fischer titration in conjunction with an optimized combination of an oil moisture detector to jointly measure the water solubility of coal-based hydrocarbon fuels at room temperature. The coefficient correction was performed on the oil moisture detector, and the water solubility curves of coal-based hydrocarbon fuels 233 to 313 K were finally measured and compared with other literature results. Due to the extremely low water content in actual fuel and the uneven distribution of water in the fuel, this study mainly considers the water enrichment zone in the fuel.</p><h3>Methods</h3><p>Materials Studio 2019 software was utilized to simulate a representative molecular model of coal-based hydrocarbon fuel and a molecular model of water. The positions and charges of the atoms were set and tested, with the COMPASS force field selected to describe interatomic interactions. This force field is the first de novo computing field capable of accurately predicting interactions between various molecules and polymers. Geometry optimization was performed in the Forcite module, and the Construction tool in the Amorphous Cell Tools module was used to construct a coal-based hydrocarbon fuel system. The two models consisted of 3674 and 3671 atoms, respectively, with initial dimensions of 33.2 × 33.2 × 33.2 Å, the boundary conditions are periodic boundary conditions, the energy of the two models is minimized, the conjugate gradient method is used as the optimization method, and then the NPT annealing and kinetic pre-equilibrium operations are carried out, and the molecular dynamics simulation is carried out after the system relaxes to steady state. Through the MD method, the macroscopic phenomenon of temperature decrease in coal-based hydrocarbon fuel systems was analyzed from a microscopic perspective using mean square displacement, diffusion coefficient, and radial distribution function. It was predicted that the crystallization process of coal-based hydrocarbon fuel systems was mainly around 248 to 258 K.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423177","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":"Molecular dynamics simulation shows enhanced stability in scaffold-based macromolecule, designed by protein engineering: a novel methodology adapted for converting Mtb Ag85A to a multi-epitope vaccine","authors":"Ditipriya Hazra,&nbsp;Shakilur Rahman,&nbsp;Manisha Ganguly,&nbsp;Amit Kumar Das,&nbsp;Amlan Roychowdhury","doi":"10.1007/s00894-025-06301-2","DOIUrl":"10.1007/s00894-025-06301-2","url":null,"abstract":"<div><h3>Context</h3><p>Multi-epitope vaccine (MEV) construction is a technique which combines multiple epitopes, both B cell epitopes and T cell epitopes which have the potential to elicit a much stronger immune response compared to a subunit vaccine. Therefore, recently, a lot of research has been focused on development and improvement of multiepitope vaccines. The strategy of designing a MEV in silico lies in a few basic steps, including procuring the amino acid sequence of the B cell and T cell epitopes from literature search, bioinformatics approach, to construct a potent immunogen capable of eliciting both humoral and cell-mediated response and finally joining these epitopes by linkers. However, a vaccine constructed by merely joining the epitopes may not always result in a stable globular structured protein. In this study, we have focused on developing a strategy where a potential vaccine candidate of <i>Mycobacterium tuberculosis</i> has been used as a scaffold and the low complexity regions of this scaffold have been replaced by the predicated epitopes. Essentially, instead of joining the epitopes by linkers, they have been carefully positioned on a scaffold of a protein that is itself a vaccine candidate to derive a MEV against <i>Mycobacterium tuberculosis.</i></p><h3>Method</h3><p>In this study, a methodology has been detailed to tackle this great challenge using a simple approach of protein engineering. A scaffold-based MEV has been designed against Mtb by converting a vaccine candidate protein, Ag85A, into a scaffold by truncating its low complexity non-immunogenic regions, and the gaps were supplemented by the highly immunogenic epitopes. Replicated 500 ns molecular dynamics simulation at different temperatures (300 K and 310 K) and principal component analysis proved that MEV built on the scaffold is more stable than the conventional one.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423255","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":"Rheological characterization of CuZr metallic glasses at the atomic scale","authors":"Nicolás Amigo","doi":"10.1007/s00894-025-06307-w","DOIUrl":"10.1007/s00894-025-06307-w","url":null,"abstract":"<div><h3>Context</h3><p>Understanding the shear response of metallic glasses is essential for predicting their mechanical performance and plasticity. Cu<span>(_{100-x})</span>Zr<span>(_x)</span> metallic glasses, in particular, exhibit complex shear-thinning behavior governed by atomic composition. Prior studies have highlighted the role of composition in influencing mechanical properties; however, the relationship between the structural characteristics of these alloys and their rheological behavior requires further investigation. This work focuses on the effects of Cu content on the plastic flow of CuZr metallic glasses, emphasizing how atomic-scale features influence yield stress, viscosity, and the onset of plasticity.</p><h3>Methods</h3><p>Molecular dynamics simulations using the embedded atom method potential in LAMMPS were conducted to study Cu<span>(_{100-x})</span>Zr<span>(_x)</span> metallic glasses. Samples were equilibrated at 2000 K and quenched to 300 K at 10<span>(^{11})</span> K/s. Shear tests at six rates (<span>(5 times 10^{7})</span> to <span>(1 times 10^{10})</span> s<span>(^{-1})</span>) were performed at 300 K, with the flow stress modeled using the Herschel-Bulkley equation. Structural features were analyzed via Voronoi polyhedra, focusing on local five-fold symmetry and liquid-like polyhedra populations. Visualization and data analysis were conducted using OVITO and Scikit-learn library for the Python programming language.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143396669","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":"Review on the DFT computation of bulk heterojunction and dye-sensitized organic solar cell properties","authors":"Nathália M. P. Rosa,&nbsp;Itamar Borges Jr.","doi":"10.1007/s00894-025-06304-z","DOIUrl":"10.1007/s00894-025-06304-z","url":null,"abstract":"<div><h3>Context</h3><p>Organic solar cells (OSCs) represent a promising renewable energy technology due to their flexibility, low production cost, and environmental sustainability. To advance OSC efficiency and stability, density functional theory (DFT) has emerged as a powerful computational tool, enabling the prediction and optimization of critical properties at the molecular and device levels. This review highlights the key properties of bulk heterojunction solar (BHJ) solar cells and dye-sensitized solar cells (DSSCs) that can be accurately computed using DFT, including <i>electronic structure properties</i> (HOMO–LUMO energy levels, bandgap energies, and exciton binding energies, which influence charge separation and transport); <i>optical properties</i> (absorption spectra and light-harvesting efficiency, essential for maximizing photon capture); <i>charge transport properties</i> (reorganization energies, electron, and hole mobilities, and charge transfer rates that govern carrier dynamics within devices); <i>interfacial properties</i> (energy alignment at donor–acceptor interfaces, contributing to efficient charge separation and minimizing recombination); and <i>chemical reactivity descriptors</i> (ionization potential, electron affinity, chemical hardness, and electrophilicity, which facilitate material screening for OSC applications). We also show how to compute OSCs’ power conversion efficiency (PCE) from DFT.</p><h3>Methods</h3><p>The review also discusses the importance of selecting appropriate exchange–correlation functionals and basis sets to ensure the accuracy of DFT predictions. By providing reliable computational insights, DFT accelerates the rational design of OSC materials, guides experimental efforts, and reduces resource demands. This work underscores DFT’s pivotal role in optimizing OSC performance and fostering the development of next-generation photovoltaic technologies.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143396668","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":"In silico insights into the membrane disruption induced by the protonation of ionizable lipids","authors":"Zhen Zhao,&nbsp;Hao Zhang,&nbsp;Xiaoyan Zhuang,&nbsp;Lijuan Yan,&nbsp;Guangyong Li,&nbsp;Jun Li,&nbsp;Hui Yan","doi":"10.1007/s00894-025-06308-9","DOIUrl":"10.1007/s00894-025-06308-9","url":null,"abstract":"<div><h3>Context</h3><p>Lipid nanoparticles (LNPs) are a novel type of drug delivery carrier, which play a protective role in nucleic acid drug delivery. LNPs are composed of various organic materials and these compositions assume corresponding tasks. Among these components, ionizable lipids undergo localized accumulation of lipids after exposure to the acidic pH environment of endosomes due to electrostatic interactions between lipid nanoparticles and phospholipids in endosomal membranes, which contributes to membrane fusion-disruption, endosomal escape, and cargo release. However, these extrapolations lack intuitive evidence at the molecular level, so we perform computational simulations to provide a microscopic view of molecular and cellular biological events. In this work, we performed molecular dynamics (MD) simulations to study the microscopic mechanism of membrane disruption induced by the protonation of ionizable lipids. Models containing different concentrations of ionizable lipids were obtained by simulating the uptake process of ionizable lipids by the endosomal membrane. The simulated results showed that the protonated ionizable lipids accumulated on one side of the endosomal membrane. Through the analysis of intermolecular interactions, it was found that the accumulation was due to the strong association of the head groups of the protonated ionizable lipids with the membrane lipids. Whereas the unprotonated ionizable lipids were dispersed on both sides of the bilayer, which served to stabilize the nanoparticles. The accumulation of ionizable lipids caused a sustained effect on lipid order parameters and the thickness of the simulated bilayer, which may be responsible for endosomal membrane rupture.</p><h3>Methods</h3><p>In this study, we employed MD simulations and used the GROMOS 54A7 united-atom force field to investigate the passive diffusion process of ionizable lipids. MD simulations were performed using the GROMACS 2019 software, focusing on the changes in the energy and molecular distribution of the system during the uptake process of ionizable lipids. Characteristics such as SDC, thickness, and energy of the system configuration at the end of the process are also analyzed. These configurations of the simulations were visualized using VMD. The GridMAT-MD package was adopted to analyze the thickness of the membrane. The other characters such as density distribution profiles and energies were analyzed using the tools within the GROMACS package.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143396653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural transformation in Pd nanoclusters induced by Cu doping: an ADFT study","authors":"L. Santiago-Silva,&nbsp;H. Cruz-Martínez,&nbsp;H. Rojas-Chávez,&nbsp;L. López-Sosa,&nbsp;P. Calaminici","doi":"10.1007/s00894-025-06305-y","DOIUrl":"10.1007/s00894-025-06305-y","url":null,"abstract":"<div><h3>Context</h3><p>Transition metal nanoparticles have gained great importance due to their promising applications in various fields such as energy, electronics, medicine, and agriculture. For these applications, materials with outstanding properties are currently required. Therefore, different strategies have been established to improve the properties of pure nanoparticles such as alloying, doping, and formation of composites. Among these strategies, doping is gaining great importance because it has been demonstrated that doped nanoparticles have better properties than pure nanoparticles. Therefore, it is essential to know the role of doping on the structures and properties of clusters with more than 16 atoms. Consequently, in this study, we propose a theoretical study of structures and properties focusing on pure Pd₁₉, Cu-doped Pd₁₈ (Pd₁₈Cu), and Cu₂-doped Pd₁₇ (Pd₁₇Cu₂) nanoclusters and thus elucidate the role of Cu atoms on the structures and properties of larger doped Pd nanoclusters than those already presented in the literature. We have selected a nanocluster with 19 atoms since the most stable structure of this system is characterized by defined shapes such as octahedron or double-icosahedron.</p><h3>Methods</h3><p>Ground state structures and properties of Pd₁₉, Pd₁₈Cu, and Pd₁₇Cu₂ nanoclusters were studied using the auxiliary density functional theory (ADFT), as implemented in the deMon2k code. For obtaining the ground state structures of Pd₁₉, Pd₁₈Cu, and Pd₁₇Cu₂ nanoclusters, several dozen initial structures were taken along Born–Oppenheimer molecular dynamics (BOMD) trajectories and subsequently optimized without symmetry restrictions. The optimizations were performed with the revised PBE functional in combination with TZVP-GGA for the Cu atoms and using an 18-electron QECP|SD basis set for the Pd atoms. Different energetic and electronic properties were calculated for the most stable structures of Pd₁₉, Pd₁₈Cu, and Pd₁₇Cu₂ nanoclusters. Interestingly, when the Pd nanocluster is doped with two Cu atoms (Pd₁₇Cu₂), there is a structural transition, because the most stable structures for Pd₁₉ and Pd₁₈Cu are icosahedral. While the Pd₁₇Cu nanocluster is characterized for a double-icosahedral-base structure. The binding energy per atom increases when the Cu concentration in the nanoclusters increases. According to the HOMO–LUMO gap, the chemical reactivity of the nanoclusters tends to increase as the Cu content in the nanoclusters increases.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-025-06305-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143379827","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":"Theoretical prediction of disulfide defects (S22−) in molybdenum disulfide monolayers","authors":"Maxim R. Ryzhikov,&nbsp;Svetlana G. Kozlova","doi":"10.1007/s00894-025-06306-x","DOIUrl":"10.1007/s00894-025-06306-x","url":null,"abstract":"<div><h3>Context</h3><p>Defects have a noticeable influence on many properties of two-dimensional materials. The controlled formation of defects can be used for fine-tuning the electronic and chemical properties of transition metal dichalcogenide monolayers. The formation of a new type of displacement defect on the molybdenum disulfide (MoS₂) monolayer surface has been studied using density functional theory. In the defect structure, two sulfur atoms form a disulfide bridge between the Mo atoms. The sulfur-sulfur bond is confirmed by interatomic distances, atomic charges, and Electron Localization Function analysis.</p><h3>Methods</h3><p>The PBEsol density functional in the BAND2017 and VASP software packages was used for structural relaxation and NEB pathway calculations for the MoS₂ monolayers. The Slater-type orbital basis set TZP and PAW pseudopotential were used in the BAND2017 and VASP 6.2.0 codes, respectively. Additionally, single-point calculations with SCAN and HSE06 density functionals were performed. QTAIM charges and ELF distributions were calculated using the BAND2017 package.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143379828","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":"In silico pentapeptide design for the inhibition between S100 calcium-binding A9 (S100A9) proteins","authors":"Jintao Pan,&nbsp;Chong Lee Ng,&nbsp;Theam Soon Lim,&nbsp;Yee Siew Choong","doi":"10.1007/s00894-025-06298-8","DOIUrl":"10.1007/s00894-025-06298-8","url":null,"abstract":"<div><h3>Context</h3><p>S100 calcium-binding protein A9 (S100A9) is easily assembled into amyloid aggregates in solution. These amyloid aggregates cause retinal toxicity and act as an attachment core for Aβ fibrillar plaques that contribute to Alzheimer’s disease progression. The overexpression of S100A9 is also noticed in various malignancies. Therefore, the S100A9 amyloid formation inhibition is of significant interest. In comparison with small-molecule drugs, short peptides demonstrate higher specificity, potency, and biosafety. Hence, it could be beneficial to identify potential peptides to inhibit or disrupt S100A9 amyloid aggregation. Typical peptide design and identification via experimental means requires extensive preparation procedures and is limited to random selection of peptides. Virtual screening therefore offers an unbiased, higher throughput, and economically efficient approach in peptide drug development. Here, we reported <i>in silico</i> pentapeptide design against S100A9 and studied the interaction of pentapeptide with S100A9 that leads to the binding of the peptide with S100A9.</p><h3>Method</h3><p>Docking simulation resulted in three top binding free energy tripeptides (WWF, WPW, and YWF) with comparable affinity towards a known S100A9 inhibitor (polyphenol oleuropein aglycone; OleA). Subsequently, pentapeptides that consist of the three core tripeptides were selected from a pre-constructed pentapeptide library for further evaluation with docking simulation. Based on best docked binding free energy, two pentapeptides (WWPWH and WPWYW) were selected and subjected to 500 ns molecular dynamics (MD) simulation to study the important features that lead to the binding with S100A9. MMGBSA binding free energy calculation estimated − 30.38, − 24.58, and − 30.31 kcal/mol for WWPWH, WPWYW, and OleA, respectively. The main driving force for pentapeptide-S100A9 recognition was contributed by the electrostatic interaction. The results demonstrate that at <i>in silico</i> level, this workflow is able to design potential pentapeptides that are comparable with OleA and might be the lead molecule for future use to disaggregate S100A9 fibrils.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143361785","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":"Malaria parasite cysteine and aspartic proteases as key drug targets for antimalarial therapy","authors":"Akinwunmi O. Adeoye,&nbsp;Kevin A. Lobb","doi":"10.1007/s00894-025-06303-0","DOIUrl":"10.1007/s00894-025-06303-0","url":null,"abstract":"<div><h3>Context</h3><p>Cysteine and aspartic proteases are enzyme families that play crucial roles in the life cycle of <i>Plasmodium</i>, the parasite responsible for malaria. These proteases are involved in vital biological processes, such as hemoglobin degradation within the host’s red blood cells, protein turnover, and regulation of parasite development. Inhibiting these proteases with small molecule drugs can block the parasite’s growth and survival. Chemically, these enzymes have specific active sites where inhibitors can bind, preventing the breakdown of key proteins, making them attractive targets for the design of novel antimalarial compounds. Understanding the structure and catalytic mechanisms of these proteases is critical for developing selective and potent inhibitors. The degradation of hemoglobin occurs in the parasite’s digestive vacuole, and disruption of this process by targeting these proteases can inhibit parasite development, leading to the death of the parasite. Hence, these proteases are critical for maintaining the parasite’s metabolic functions, and inhibiting them can disrupt the parasite’s life cycle. Malaria remains a major global health problem, particularly in tropical and subtropical regions, where resistance to existing antimalarial drugs, such as chloroquine and artemisinin-based therapies, is an escalating issue. The emergence of drug-resistant <i>Plasmodium</i> strains highlights the urgent need for new therapeutic strategies. Targeting cysteine and aspartic proteases offers a novel approach to antimalarial drug development, as these enzymes are crucial for parasite survival and have not been widely exploited in current therapies. By inhibiting these proteases, researchers aim to develop new antimalarial treatments that could overcome resistance mechanisms and provide more effective options for malaria control and eradication.</p><h3>Methods</h3><p>The application of computational methods such as molecular docking, dynamics simulations, and quantum mechanical calculations, combined with powerful molecular modeling tools, provides a comprehensive framework for discovering and optimizing inhibitors targeting <i>Plasmodium</i> cysteine and aspartic proteases. These methods facilitate the rational design of novel antimalarial drugs, offering a pathway to overcome drug resistance and improve therapeutic outcomes.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143361784","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 total energy from X-ray electron density?","authors":"Lou Massa,&nbsp;Chérif F. Matta","doi":"10.1007/s00894-024-06224-4","DOIUrl":"10.1007/s00894-024-06224-4","url":null,"abstract":"<div><h3>Context</h3><p>This approach to quantum crystallography ensures the satisfaction of three quantum conditions, namely, idempotency, hermiticity, and normalization of the one-body density matrix, simultaneously as the X-ray diffraction problem is solved to reproduce the observed structure factors. The variational theorem used to optimize energy will only hold true if the density matrices used for such purpose are <i>N</i>-representable. The point of <i>N</i>-representability is to ensure the mapping of a density matrix to an <i>N</i>-body antisymmetric wavefunction. The antisymmetry is consistent with the experimental indistinguishability of fermions. This article develops a procedure for the fast and accurate application of quantum crystallography to large systems while guaranteeing that the results are <i>N</i>-representable.</p><h3>Methods</h3><p>For large molecules, it is advantageous to have the one-body density matrix assembled from sub-matrices of fragments within a scheme known as the kernel energy method (KEM). KEM accounts for up to two-body interactions between all fragments and ignores higher order interactions, an approximation that proved accurate through extensive past numerical testing. Since this approach to quantum crystallography rests on a single-determinant description, an explicit form of the corresponding <i>N</i>-representable two-body density matrix, which is determined by its one-body counterpart, is also given along with its use to calculate the total energy. This approach can be applied to extract conceptual density functional theory properties, quantum theory of atoms in molecules (QTAIM) properties, etc. from experimental structure factors.</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 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254417","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}