Tyler Walker, Van-Quan Vuong, Stephan Irle, Jihong Ma
{"title":"Evaluation of Density-Functional Tight-Binding Methods for Simulation of Protic Molecular Ion Pairs","authors":"Tyler Walker, Van-Quan Vuong, Stephan Irle, Jihong Ma","doi":"10.1002/jcc.70064","DOIUrl":"https://doi.org/10.1002/jcc.70064","url":null,"abstract":"<p>In this work, we benchmark the accuracy of the density-functional tight-binding (DFTB) method, namely the long-range corrected second-order (LC-DFTB2) and third-order (DFTB3) models, for predicting energetics of imidazolium-based ionic liquid (IL) ion pairs. We compare the DFTB models against popular density functionals such as LC-ωPBE and B3LYP, using ab initio domain-based local pair-natural orbital coupled cluster (DLPNO-CC) energies as reference. Calculations were carried out in the gas phase, as well as in aqueous solution using implicit solvent methods. We find that the LC-DFTB2 model shows excellent performance in the gas phase and agrees well with reference energies in implicit solvent, often outperforming DFTB3 predictions for complexation energetics. Our study identifies a range of opportunities for use of the LC-DFTB method and quantifies its sensitivity to protonation states and the types of chemical interactions between ion pairs.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70064","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143396900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mechanistic Study of the Carbonylation of Aziridines to β-Lactams: Alkylation, Solvent and Molecular NaBr and MgO Clusters Catalysts Effects","authors":"Abir Jendoubi, Mohamed Oussama Zouaghi, Youssef Arfaoui, Frédéric Guégan, Muneerah Mogren Al-Mogren, Majdi Hochlaf","doi":"10.1002/jcc.70061","DOIUrl":"https://doi.org/10.1002/jcc.70061","url":null,"abstract":"<p>Using first principles methodology, we show that molecular NaBr and MgO nanoclusters are efficient ecofriendly and transition metal free catalysts for the carbonylation of aziridines to β-lactams. Multi-step mechanisms are proposed, where the activation energies of the rate-determining step are strongly lowered compared to gas phase reaction, exhibiting, however, a unique step. Also, these reactions are viewed to be favored thermodynamically in the presence of these catalysts and also in solvents, in particular in methanol. We suggest thus the use of NaBr and MgO nanoclusters for these reactions. Besides, the present findings allow to explain the experimentally observed regioselectivity of carbonylation of aziridines reactions, where CO is added on the more substituted C of aziridine three-membered ring. In sum, our work should motivate the use of such ecofriendly catalysts for carbonylation reactions without using transition metal catalysts.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70061","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143396895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Carsten Kutzner, Vedran Miletić, Karen Palacio Rodríguez, Markus Rampp, Gerhard Hummer, Bert L. de Groot, Helmut Grubmüller
{"title":"Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster","authors":"Carsten Kutzner, Vedran Miletić, Karen Palacio Rodríguez, Markus Rampp, Gerhard Hummer, Bert L. de Groot, Helmut Grubmüller","doi":"10.1002/jcc.70059","DOIUrl":"https://doi.org/10.1002/jcc.70059","url":null,"abstract":"<p>We benchmarked the performance of the GROMACS 2024 molecular dynamics (MD) code on a modern high-performance computing (HPC) cluster with AMD CPUs on up to 65,536 CPU cores. We used five different MD systems, ranging in size from about 82,000 to 204 million atoms, and evaluated their performance using two different Message Passing Interface (MPI) libraries, Intel-MPI and Open-MPI. The largest system showed near-perfect strong scaling up to 512 nodes or 65,536 cores, maintaining a parallel efficiency above 0.9 even at the highest level of parallelization. Energy efficiency for a given number of nodes was generally equal to or slightly better than parallel efficiency. We achieved peak performances of 687 ns/d for the 82k atom system, 116 ns/d for the 53M atom system, and about 35 ns/d for the largest 204M atom system. These results demonstrate that highly optimized software running on a state-of-the-art HPC cluster provides sufficient computing power to simulate biomolecular systems at the mesoscale of viruses and organelles, and potentially small cells in the near future.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70059","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143396894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Debojyoti Das, Erico S. Teixeira, Jorge A. Morales
{"title":"Recurrent Neural Network/Machine Learning Predictions of Reactive Channels in H+ + C2H4 at ELab = 30 eV: A Prototype of Ion Cancer Therapy Reactions","authors":"Debojyoti Das, Erico S. Teixeira, Jorge A. Morales","doi":"10.1002/jcc.70033","DOIUrl":"https://doi.org/10.1002/jcc.70033","url":null,"abstract":"<div>\u0000 \u0000 <p>We present a simplest-level electron nuclear dynamics/machine learning (SLEND/ML) approach to predict chemical properties in ion cancer therapy (ICT) reactions. SLEND is a time-dependent, variational, on-the-fly, and nonadiabatic method. In SLEND, nuclear and electronic parameters determine reactants-to-products trajectories in a quantum phase space; this establishes a mapping between reactants' initial conditions and products' properties. To accelerate simulations, SLEND/ML utilizes a modicum of SLEND trajectories to train ML methods on the aforesaid mapping and employs them to predict chemical properties. We employ SLEND/ML to predict reaction types and products' charges in H<sup>+</sup> + C<sub>2</sub>H<sub>4</sub> at <i>E</i><sub>Lab</sub> = 30 eV, a prototype of ICT reactions involving double-bonded compounds. For reaction predictions, a recurrent neural network (RNN) and <i>k</i>-nearest neighbor method are the best models with 98.23% and 95.13% accuracy. RNN correctly predicts frequent and infrequent reaction types and generalizes over data sets. For charge predictions, the RNN exhibits low mean absolute errors of 0.02–0.07.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Richard M. Venable, Anthony J. Pane, Amy Rice, Richard W. Pastor
{"title":"Effects of a Polarizable Force Field on Membrane Dynamics: Surface Viscosity, Lipid Diffusion, and Peptide Induced Pore Formation","authors":"Richard M. Venable, Anthony J. Pane, Amy Rice, Richard W. Pastor","doi":"10.1002/jcc.70001","DOIUrl":"https://doi.org/10.1002/jcc.70001","url":null,"abstract":"<div>\u0000 \u0000 <p>The effects of the newly developed CHARMM polarizable lipid force field (FF), Drude2023, on selected lipid dynamical properties are compared with the additive CHARMM36 (C36), and an extension of C36, termed C36/LJ-PME, which includes long-range Lennard–Jones (LJ) interactions. Polarizability and long-range LJ interactions increase the membrane surface viscosity, which decreases the translational diffusion constants. Simulated diffusion constants for dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC) extrapolated to infinite system size agree well with experiment for Drude2023, but overestimate experiment by 60% (on average) and a factor of 2.5 for C36/LJ-PME and C36, respectively. The relaxation time of lipid wobble is described about equally well by C36/LJ-PME and Drude2023, as consistent with the hexadecane viscosity for the FF, and both are more accurate than C36. Hence, physical improvements in the FF, which slowed down these dynamic processes led to better agreement with experiment. Lastly, bilayers containing 10 influenza fusion peptides and high fractions of lysolipids (which are known to accelerate pore formation) were simulated with C36 and Drude2023. Pore formation rates were comparable for the two FF for the bilayers with 80% and 90% lysolipid. However, while no pores formed in 24 μs (including a single 20 μs trajectory) in the 70% lysolipid with C36, 4 of 15 replicates formed pores in less than 1 μs with Drude. While the pathway to poration is qualitatively similar for the additive and polarizable FF for the systems studied, Drude2023 should be considered for quantitative studies of pore formation, and, in some cases, will accelerate the process.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Highly Efficient Numerical Method for Modeling Mofs Containing Transition Metal Ions","authors":"D. D. Raenko, A. L. Tchougreeff","doi":"10.1002/jcc.27546","DOIUrl":"https://doi.org/10.1002/jcc.27546","url":null,"abstract":"<div>\u0000 \u0000 <p>Employing a group-function based semiempirical approach, a new program package <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>ΣHΘΩ</mi>\u0000 </mrow>\u0000 <annotation>$$ varSigma HvarTheta varOmega $$</annotation>\u0000 </semantics></math> (<i>seethoo</i>), targeted to modeling of metal-organic frameworks (MOFs) containing transition metal ions (TMIs) with open <i>d</i>-shells is developed. In this proof of concept study it is shown that the <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>ΣHΘΩ</mi>\u0000 </mrow>\u0000 <annotation>$$ varSigma HvarTheta varOmega $$</annotation>\u0000 </semantics></math> package has potential to accurately compute <i>d</i>-shell low-spin (LS) —high-spin (HS) gaps and charge distributions in MOFs in <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>O</mi>\u0000 <mfenced>\u0000 <mrow>\u0000 <msup>\u0000 <mrow>\u0000 <mi>N</mi>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>1</mn>\u0000 <mo>.</mo>\u0000 <mn>33</mn>\u0000 </mrow>\u0000 </msup>\u0000 </mrow>\u0000 </mfenced>\u0000 </mrow>\u0000 <annotation>$$ Oleft({N}^{1.33}right) $$</annotation>\u0000 </semantics></math> time with reasonable accuracy. The calculations were carried out for a variety of MOFs and MOF-like systems containing doubly and triply charged Mn, Fe, Co and Ni ions. For Fe-containing systems, parameters of <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msup>\u0000 <mrow></mrow>\u0000 <mrow>\u0000 <mn>57</mn>\u0000 </mrow>\u0000 </msup>\u0000 <mtext>Fe</mtext>\u0000 </mrow>\u0000 <annotation>$$ {}^{57}mathrm{Fe} $$</annotation>\u0000 </semantics></math> Mössbauer spectra were also computed. For the test runs, the results reasonably agree with available experimental data up to errors introduced by use of the CNDO parametrization in the test manner.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
H. Cruz-Martínez, H. Rojas-Chávez, L. Santiago-Silva, L. López-Sosa, P. Calaminici
{"title":"Metal Dimers-Doped h-BN Structures as Novel Toxic Gases Sensors With Enhanced Sensitivity Properties: An ADFT Study","authors":"H. Cruz-Martínez, H. Rojas-Chávez, L. Santiago-Silva, L. López-Sosa, P. Calaminici","doi":"10.1002/jcc.70062","DOIUrl":"https://doi.org/10.1002/jcc.70062","url":null,"abstract":"<div>\u0000 \u0000 <p>Toxic gases monitoring and detection are fundamental to lessening public health problems. Therefore, in this work, to explore emergent sensor materials, 3<i>d</i>-metal dimers-doped hexagonal boron nitride (h-BN) structures were investigated employing auxiliary density functional theory (ADFT) as novel CO and NO gas sensors. Firstly, the stabilities of Co<sub>2</sub>, Ni<sub>2</sub>, and Cu<sub>2</sub> dimers deposited on defective h-BN were determined. Then, sensitivities of 3<i>d</i>-metal dimers-doped h-BN structures towards the NO and CO gases were investigated. It was found that the interaction energies of these 3<i>d</i>-metal dimers embedded on defective h-BN are higher than those deposited on pristine h-BN structure, which indicates that the 3<i>d</i>-metal dimers exhibit good stability on defective h-BN. Moreover, this work demonstrated that the CO and NO adsorption energies on 3<i>d</i>-metal dimers-doped h-BN structures are higher than those computed in the literature for pristine h-BN structure. Consequently, the here considered 3<i>d</i>-metal dimers-doped h-BN structures can be good candidates for toxic CO and NO gas detection.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143380649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Book Review: “Electron Localization-Delocalization Matrices” by Chérif F. Matta, Paul W. Ayers, and Ronald Cook","authors":"Lou Massa","doi":"10.1002/jcc.70048","DOIUrl":"10.1002/jcc.70048","url":null,"abstract":"<p>\u0000 \u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Elongation Method-Based Alternating Multi-Directional Automated Property Optimization Process and Its Application","authors":"Shichen Lin, Yuuichi Orimoto, Yuriko Aoki","doi":"10.1002/jcc.70058","DOIUrl":"https://doi.org/10.1002/jcc.70058","url":null,"abstract":"<div>\u0000 \u0000 <p>Elongation (ELG) method-based property optimization (POPT) is an effective approach for designing large systems from one terminal to the other. An alternating multi-directional ELG method is introduced to enable alternating POPT for complex systems with multiple growth directions, improving efficiency. (Hyper)polarizabilities of donor-acceptor-substituted polydiacetylenes (PDAs) aligned along the <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>z</mi>\u0000 </mrow>\u0000 <annotation>$$ z $$</annotation>\u0000 </semantics></math>-axis are optimized by alternating POPT, where donor- and acceptor-substituted diacetylene monomers are alternately selected and attached to two PDA terminals. Alternating POPT's capability in designing systems with expected properties, efficiency, and accuracy has been validated. For <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>n</mi>\u0000 </mrow>\u0000 <annotation>$$ n $$</annotation>\u0000 </semantics></math> types of donor and acceptor groups, the existing simultaneous ELG-based POPT requires calculating <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msup>\u0000 <mrow>\u0000 <mi>n</mi>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </msup>\u0000 </mrow>\u0000 <annotation>$$ {n}^2 $$</annotation>\u0000 </semantics></math> combinations, as monomers are simultaneously attached in both elongation directions. In contrast, the alternating ELG-based POPT only requires <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 <mi>n</mi>\u0000 </mrow>\u0000 <annotation>$$ 2n $$</annotation>\u0000 </semantics></math> combinations, halving the number of basis functions involved in calculations and significantly enhancing efficiency.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Peter Poliak, Patrick Bleiziffer, Felix Pultar, Sereina Riniker, Chris Oostenbrink
{"title":"A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS","authors":"Peter Poliak, Patrick Bleiziffer, Felix Pultar, Sereina Riniker, Chris Oostenbrink","doi":"10.1002/jcc.70053","DOIUrl":"10.1002/jcc.70053","url":null,"abstract":"<p>The integration of quantum mechanics and molecular mechanics (QM/MM) within molecular dynamics simulations is crucial to accurately model complex biochemical systems. Here, we present an enhanced implementation of the QM/MM interface in the GROMOS simulation package, introducing significant improvements in functionality and user control. We present new features, including the link atom scheme, which allows the modeling of QM regions as a part of bigger molecules. Benchmark tests on various systems, including QM water in water, amino acids in water, and tripeptides validate the reliability of the new functionalities. Performance evaluations demonstrate that the updated implementation is efficient, with the primary computational burden attributed to the QM program rather than the QM/MM interface or the MD program itself. The improved QM/MM interface enables more advanced investigations into biomolecular reactivity, enzyme catalysis, and other phenomena requiring detailed quantum mechanical treatment within classical simulations. This work represents a significant advancement in the capabilities of GROMOS, providing enhanced tools to explore complex molecular systems.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}