Journal of Computational Chemistry最新文献

{"title":"Energetics and spectroscopic studies of \u0000 \u0000 \u0000 \u0000 CNO\u0000 \u0000 \u0000 (-)\u0000 \u0000 \u0000 \u0000 \u0000 (H\u0000 \u0000 \u0000 2\u0000 \u0000 \u0000 \u0000 \u0000 O)\u0000 \u0000 \u0000 n\u0000 \u0000 \u0000 clusters and the temperature dependencies of the isomers: An approach based on a combined recipe of parallel tempering and quantum chemical methods","authors":"Pulak Naskar,&nbsp;Srijeeta Talukder","doi":"10.1002/jcc.27480","DOIUrl":"10.1002/jcc.27480","url":null,"abstract":"<p>A system associated with several number of weak interactions supports numerous number of stable structures within a narrow range of energy. Often, a deterministic search method fails to locate the global minimum geometry as well as important local minimum isomers for such systems. Therefore, in this work, the stochastic search technique, namely parallel tempering, has been executed on the quantum chemical surface of the <span></span><math>\u0000 <mrow>\u0000 <msup>\u0000 <mrow>\u0000 <mtext>CNO</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mtext>(-)</mtext>\u0000 </mrow>\u0000 </msup>\u0000 <msub>\u0000 <mrow>\u0000 <mtext>(H</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mtext>2</mtext>\u0000 </mrow>\u0000 </msub>\u0000 <msub>\u0000 <mrow>\u0000 <mtext>O)</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mi>n</mi>\u0000 </mrow>\u0000 </msub>\u0000 </mrow></math> system for <span></span><math>\u0000 <mrow>\u0000 <mi>n</mi>\u0000 <mo>=</mo>\u0000 <mn>1</mn>\u0000 </mrow></math>–8 to generate global minimum as well as several number of local minimum isomers. IR spectrum can act as the fingerprint property for such system to be identified. Thus, IR spectroscopic features have also been included in this work. Vertical detachment energy has also been calculated to obtain clear information about number of water molecules in several spheres around the central anion. In addition, in a real experimental scenario, not only the global but also the local minimum isomers play an important role in determining the average value of a particular physically observable property. Therefore, the relative conformational populations have been determined for all the evaluated structures for the temperature range between 20K and 400K. Further to understand the phase change behavior, the configurational heat capacities have also been calculated for different sizes.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2749-2763"},"PeriodicalIF":3.4,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141992236","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":"Simulating the full spin manifold of triplet-pair states in a series of covalently linked TIPS-pentacenes","authors":"Timo Schulz,&nbsp;Christel M. Marian","doi":"10.1002/jcc.27475","DOIUrl":"10.1002/jcc.27475","url":null,"abstract":"&lt;p&gt;Combined density functional theory and multireference configuration interaction methods have been used to elucidate singlet fission (SF) pathways and mechanisms in three regioisomers of side-on linked pentacene dimers. In addition to the optically bright singlets (S&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mo&gt; &lt;/mo&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt; and S&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mo&gt; &lt;/mo&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt;) and singly excited triplets (T&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mo&gt; &lt;/mo&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt; and T&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mo&gt; &lt;/mo&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt;), the full spin manifold of multiexcitonic triplet-pair states (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msup&gt;\u0000 &lt;mo&gt; &lt;/mo&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msup&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt;ME, &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msup&gt;\u0000 &lt;mo&gt; &lt;/mo&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msup&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt;ME, &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msup&gt;\u0000 &lt;mo&gt; &lt;/mo&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;5&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msup&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt;ME) has been considered. In the &lt;i&gt;ortho&lt;/i&gt;- and &lt;i&gt;para&lt;/i&gt;-regioisomers, the &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msup&gt;\u0000 &lt;mo&gt; &lt;/mo&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msup&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt;ME and S&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mo&gt; &lt;/mo&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt; potentials intersect upon geometry relaxation of the S&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mo&gt; &lt;/mo&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;&lt;/math&gt; excitation","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2727-2738"},"PeriodicalIF":3.4,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27475","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141974593","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":"Modeling adsorption reactions of ammonium perchlorate on rutile and anatase surfaces","authors":"Jerimiah A. Zamora,&nbsp;Armando de Rezende,&nbsp;Reed Nieman,&nbsp;Neil Vaz,&nbsp;Andrew R. Demko,&nbsp;Michelle L. Pantoya,&nbsp;Daniel Tunega,&nbsp;Adelia J. A. Aquino","doi":"10.1002/jcc.27476","DOIUrl":"10.1002/jcc.27476","url":null,"abstract":"<p>In this work, the effects of two TiO₂ polymorphs on the decomposition of ammonium perchlorate (NH₄ClO₄) were studied experimentally and theoretically. The interactions between AP and various surfaces of TiO₂ were modeled using density functional theory (DFT) calculations. Specifically, the adsorption of AP on three rutile surfaces (1 1 0), (1 0 0), and (0 0 1), as well as two anatase surfaces (1 0 1), and (0 0 1) were modeled using cluster models, along with the decomposition of adsorbed AP into small molecules. The optimized complexes of the AP molecule on TiO₂ surfaces were very stable, indicating strong covalent and hydrogen bonding interactions, leading to highly energetic adsorption reactions. The calculated energy of adsorption (Δ<i>E</i>_ads) ranged from −120.23 to −301.98 kJ/mol, with highly exergonic calculated Gibbs free energy (Δ<i>G</i>_ads) of reaction, and highly exothermic enthalpy of reaction (Δ<i>H</i>_ads). The decomposition of adsorbed AP was also found to have very negative Δ<i>E</i>_dec values between −199.08 and −380.73 kJ/mol. The values of Δ<i>G</i>_dec and Δ<i>H</i>_dec reveal exergonic and exothermic reactions. The adsorption of AP on TiO₂ surfaces anticipates the heat release of decomposition, in agreement with experimental results. The most common anatase surface, (1 0 1), was predicted to be more reactive for AP decomposition than the most stable rutile surface, (1 1 0), which was confirmed by experiments. DFT calculations show the mechanism for activation of the two TiO₂ polymorphs is entropy driven.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2739-2748"},"PeriodicalIF":3.4,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141981345","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":"Structure and intermolecular interactions in ionic liquid 1-ethyl-3-methylimidazolium bromide and its aqueous solutions investigated by vibrational spectroscopy and quantum chemical computations","authors":"Sergey A. Katsyuba,&nbsp;Stefan Grimme","doi":"10.1002/jcc.27472","DOIUrl":"10.1002/jcc.27472","url":null,"abstract":"<p>The recently developed efficient protocol to explicit quantum mechanical modeling of structure and IR spectra of liquids and solutions (S. A. Katsyuba, S. Spicher, T. P. Gerasimova, S. Grimme, <i>J. Phys. Chem. B</i> 2020, <i>124</i>, 6664) is applied to ionic liquid (IL) 1-ethyl-3-methylimidazolium bromide (EmimBr), its C2-deuterated analog [Emim-d]Br and its aqueous solutions. It is shown that the solvation strongly modifies frequencies and IR intensities of the CH/CD stretching vibrations (νCH/νCD) of the imidazolium ring. The main vibrational spectroscopic features of the neat IL are reproduced by the simulations for a cluster (EmimBr)₉, in which all three imidazolium CH moieties of the solvated cation form short contacts with three Br⁻ anions, and another two Br⁻ anions are located on top and bottom of imidazolium ring. Cluster models of aqueous solutions reproduce the experimental vibrational frequencies of actual solutions, provided that the Br⁻ anion of solvated contact ion pair (CIP) is situated on top of imidazolium ring, and CH/CD moieties of the latter participate in short contacts with surrounding water molecules. Both structural and spectroscopic analysis allow to interpret the short contacts CH/CD⋯Br⁻ and CH/CD⋯OH₂ as hydrogen bonds of approximately equal strength. Enthalpies of bonding of these liquid-state H-bonds, estimated with the use of empirical correlations, amount to ca. 1.4 kcal⋅mol⁻¹, while the analogous estimates obtained for the gas-phase charged species [Emim]₂Br⁺ increase to 5.6 kcal⋅mol⁻¹. It is shown that formation of solvent-shared ion pair (SIP) in aqueous solution, where the counterions of IL are separated by two water molecules H-bonded to a Br⁻ anion, produces frequency shifts ΔνCH/CD, strongly different from the case of CIP formation. This difference can be used for IR/Raman spectroscopic differentiation of the type of solvated ion pairs of EmimBr or other related ILs.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2719-2726"},"PeriodicalIF":3.4,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141974594","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":"Clustering one million molecular structures on GPU within seconds","authors":"Junyong Gao,&nbsp;Mincong Wu,&nbsp;Jun Liao,&nbsp;Fanjun Meng,&nbsp;Changjun Chen","doi":"10.1002/jcc.27470","DOIUrl":"10.1002/jcc.27470","url":null,"abstract":"<p>Structure clustering is a general but time-consuming work in the study of life science. Up to now, most published tools do not support the clustering analysis on graphics processing unit (GPU) with root mean square deviation metric. In this work, we specially write codes to do the work. It supports multiple threads on multiple GPUs. To show the performance, we apply the program to a 33-residue fragment in protein Pin1 WW domain mutant. The dataset contains 1,400,000 snapshots, which are extracted from an enhanced sampling simulation and distribute widely in the conformational space. Various testing results present that our program is quite efficient. Particularly, with two NVIDIA RTX4090 GPUs and single precision data type, the clustering calculation on 1 million snapshots is completed in a few seconds (including the uploading time of data from memory to GPU and neglecting the reading time from hard disk). This is hundreds of times faster than central processing unit. Our program could be a powerful tool for fast extraction of representative states of a molecule among its thousands to millions of candidate structures.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2710-2718"},"PeriodicalIF":3.4,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141981344","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":"Extended benchmark set for lattice parameters of inorganic solids","authors":"Elodie Fernandes Lima,&nbsp;Thomas Bredow","doi":"10.1002/jcc.27479","DOIUrl":"10.1002/jcc.27479","url":null,"abstract":"<p>The development of novel methods in solid-state quantum chemistry necessitates reliable reference data sets for their assessment. The most fundamental solid-state property of interest is the crystal structure, quantified by the lattice parameters. In the last decade, several studies were conducted to assess theoretical approaches based on the agreement of calculated lattice parameters with respect to experiment as a measure. However, most of these studies used a limited number of reference systems with high symmetry. The present work offers a more comprehensive reference benchmark denoted as Sol337LC, which consists of 337 inorganic compounds with 553 symmetry-inequivalent lattice parameters, representing every element of the periodic table for atomic numbers between 1 and 86, except noble gases, the radioactive elements and lanthanoids. The reference values were taken from earlier benchmarks and from measurements at very low temperature or extrapolation to 0 K. The experimental low-temperature lattice parameters were then corrected for zero-point energy effects via the quasi-harmonic approximation for direct comparison with quantum-chemical optimized structures. A selection of standard density functional approximations was assessed for their deviations from the experimental reference data. The calculations were performed with the crystal orbital program CRYSTAL23, applying optimized atom-centered basis sets of triple-zeta plus polarization quality. The SCAN functional family and the global hybrid functional PW1PW, augmented with the D3 dispersion correction, were found to provide closest agreement with the Sol337LC reference data.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2702-2709"},"PeriodicalIF":3.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27479","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970174","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":"The high electron mobility for spin-down channel of two-dimensional spin-polarized half-metallic ferromagnetic EuSi2N4 monolayer","authors":"Bo Zhang,&nbsp;Huai-Qian Wang,&nbsp;Hui-Fang Li,&nbsp;Hao Zheng,&nbsp;Yong-Hang Zhang,&nbsp;Xun-Jie Mei,&nbsp;Jia-Ming Zhang,&nbsp;Kai-Le Jiang,&nbsp;Qing-Wei Jiang","doi":"10.1002/jcc.27474","DOIUrl":"10.1002/jcc.27474","url":null,"abstract":"<p>The two-dimensional (2D) monolayer material MoSi₂N₄ was successfully synthesized in 2020[Hong et al., Science 369, 670, (2020)], exhibiting a plethora of new phenomena and unusual properties, with good stability at room temperature. However, MA₂Z₄ family monolayer materials involve primarily transition metal substitutions for M atoms. In order to address the research gap on lanthanide and actinide MA₂Z₄ materials, this work conducts electronic structure calculations on novel 2D MSi₂N₄ (M = La, Eu) monolayer materials by employing first-principles methods and CASTEP. High carrier mobility is discovered in the indirect bandgap semiconductor 2D LaSi₂N₄ monolayer (~5400 cm² V⁻¹ s⁻¹) and in the spin (spin-down channel) carrier mobility of the half-metallic ferromagnetic EuSi₂N₄ monolayer (~2800 cm² V⁻¹ s⁻¹). EuSi₂N₄ monolayer supplements research on spin carrier mobility in half-metallic ferromagnetic monolayer materials at room temperature and possesses a magnetic moment of 5 <i>μ</i>_<i>B</i>, which should not be underestimated. Furthermore, due to the unique electronic band structure of EuSi₂N₄ monolayer (with the spin-up channel exhibiting metallic properties and the spin-down channel exhibiting semiconductor properties), it demonstrates a 100% spin polarization rate, presenting significant potential applications in fields such as magnetic storage, magnetic sensing, and spintronics.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 31","pages":"2678-2689"},"PeriodicalIF":3.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970208","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":"In silico study suggests potential drugs that target CD151 to treat breast cancer and glioblastoma","authors":"Gema Ramírez-Salinas,&nbsp;Martha Cecilia Rosales-Hernandéz,&nbsp;José Correa-Basurto,&nbsp;Issac Guerrero-González,&nbsp;Selene Saraí Hernández-Castro,&nbsp;Marlet Martinez-Archundia","doi":"10.1002/jcc.27439","DOIUrl":"10.1002/jcc.27439","url":null,"abstract":"<p>Recently tetraspanin CD151 has been identified as an important biological target involved in metastatic processes which include cell adhesion, tumor progression processes, and so forth in different types of cancers, such as breast cancer and glioblastoma. This in Silico study considered 1603 compounds from the Food and Drug Administration database, after performing an ADMET analysis; we selected 853 ligands, which were used for docking analysis. The most promising ligands were selected from docking studies, based on two criteria: (a) showed lowest affinity to the CD151 protein and (b) they interact with the QRD motif, located in the second extracellular loop. Furthermore, we investigate the stability of the protein-ligand complexes through MD simulations as well as free energy MM-PBSA calculations. From these results, loperamide and glipizide were identified as the best evaluated drugs. We suggest an in vitro analysis is needed to confirm our in silico prediction studies.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 31","pages":"2666-2677"},"PeriodicalIF":3.4,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854280","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":"Fault-tolerant quantum chemical calculations with improved machine-learning models","authors":"Kai Yuan,&nbsp;Shuai Zhou,&nbsp;Ning Li,&nbsp;Tianyan Li,&nbsp;Bowen Ding,&nbsp;Danhuai Guo,&nbsp;Yingjin Ma","doi":"10.1002/jcc.27459","DOIUrl":"10.1002/jcc.27459","url":null,"abstract":"<p>Easy and effective usage of computational resources is crucial for scientific calculations. Following our recent work of machine-learning (ML) assisted scheduling optimization [<i>J. Comput. Chem.</i> <b>2023</b>, 44, 1174], we further propose (1) the improved ML models for the better predictions of computational loads, and as such, more elaborate load-balancing calculations can be expected; (2) the idea of coded computation, that is, the integration of gradient coding, in order to introduce fault tolerance during the distributed calculations; and (3) their applications together with re-normalized exciton model with time-dependent density functional theory (REM-TDDFT) for calculating the excited states. Illustrated benchmark calculations include P38 protein, and solvent model with one or several excitable centers. The results show that the improved ML-assisted coded calculations can further improve the load-balancing and cluster utilization, owing primarily profit in fault tolerance that aims at the automated quantum chemical calculations for both ground and excited states.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 31","pages":"2640-2658"},"PeriodicalIF":3.4,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141786630","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":"Dr.Emb Appyter: A web platform for drug discovery using embedding vectors","authors":"Songhyeon Kim,&nbsp;Hyunsu Bong,&nbsp;Minji Jeon","doi":"10.1002/jcc.27469","DOIUrl":"10.1002/jcc.27469","url":null,"abstract":"<p>Using embedding methods, compounds with similar properties will be closely located in latent space, and these embedding vectors can be used to find other compounds with similar properties based on the distance between compounds. However, they often require computational resources and programming skills. Here we develop Dr.Emb Appyter, a user-friendly web-based chemical compound search platform for drug discovery without any technical barriers. It uses embedding vectors to identify compounds similar to a given query in the embedding space. Dr.Emb Appyter provides various types of embedding methods, such as fingerprinting, SMILES, and transcriptional response-based methods, and embeds numerous compounds using them. The Faiss-based search system efficiently finds the closest compounds of query in the library. Additionally, Dr.Emb Appyter offers information on the top compounds; visualizes the results with 3D scatter plots, heatmaps, and UpSet plots; and analyses the results using a drug-set enrichment analysis. Dr.Emb Appyter is freely available at https://dremb.korea.ac.kr.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 31","pages":"2659-2665"},"PeriodicalIF":3.4,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27469","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141786629","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}