Journal of Computational Chemistry最新文献

{"title":"AIMD-Based Protocols for Modeling Exciplex Fluorescence Spectra and Inter-System Crossing in Photocatalytic Chromophores","authors":"Goran Giudetti,&nbsp;Shaama Mallikarjun Sharada,&nbsp;Anna I. Krylov","doi":"10.1002/jcc.70049","DOIUrl":"10.1002/jcc.70049","url":null,"abstract":"<div>\u0000 \u0000 <p>This study introduces a computational protocol for modeling the emission spectra of exciplexes using excited-state ab initio molecular dynamics (AIMD) simulations. The protocol is applied to a model exciplex formed by oligo-p-phenylenes (OPPs) and triethylamine (TEA), which is of interest in the context of photocatalytic reduction of <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mtext>CO</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{CO}}_2 $$</annotation>\u0000 </semantics></math>. AIMD facilitates efficient sampling of the conformational space of OPP3 and OPP4 exciplexes with TEA, offering a dynamic alternative to previously employed static methods. The AIMD-based protocol successfully reproduces experimental emission spectra for OPP-TEA exciplexes, agreeing with previous computational and experimental findings. The results show that AIMD simulations provide an efficient means of sampling the conformational space of these exciplexes, requiring less user input and, in some instances, fewer computational resources than multiple excited-state optimizations initiated from user-specified initial structures. The study also evaluates the yield of intersystem crossing (ISC) using AIMD and Landau-Zener probability. The results suggest that ISC is a minor decay channel for OPP3 and OPP4. This work provides new insights into the structural flexibility and emission characteristics of OPP-TEA photoredox catalyst systems, potentially contributing to improved design strategies for organic chromophores in <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mtext>CO</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{CO}}_2 $$</annotation>\u0000 </semantics></math> reduction applications.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083727","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":"The Structural, Electronic and Vibrational Properties of LaCrO\u0000 \u0000 \u0000 \u0000 \u0000 3\u0000 \u0000 \u0000 $$ {}_3 $$\u0000 . A Quantum Mechanical Investigation by Using an All Electron Gaussian Type Basis Set and a Full Range Hybrid Functional","authors":"Khaled E. El-Kelany,&nbsp;Alexander Platonenko,&nbsp;Klaus Doll,&nbsp;Roberto Dovesi","doi":"10.1002/jcc.27523","DOIUrl":"10.1002/jcc.27523","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 &lt;p&gt;The geometrical, electronic and vibrational properties of LaCrO&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;&lt;/mrow&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {}_3 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; have been investigated by using an all electron Gaussian type basis set, the B3LYP functional and the CRYSTAL code, and compared with KVF&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;&lt;/mrow&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {}_3 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;: in the two compounds the transition metal is formally in d&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msup&gt;\u0000 &lt;mrow&gt;&lt;/mrow&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;/msup&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {}^3 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; configuration. The high spin t&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msubsup&gt;\u0000 &lt;mrow&gt;&lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;mi&gt;g&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;/msubsup&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {}_{2g}^3 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; ground state excludes the Jahn Teller deformation and the orbital ordering. The energy gain due to the rotation of the octahedra (from the cubic space group Pm&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mover&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;mo&gt;¯&lt;/mo&gt;\u0000 &lt;/mover&gt;\u0000 &lt;mtext&gt;m&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ overline{3}mathrm{m} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;, N. 221, to space group &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;P&lt;/mi&gt;\u0000 &lt;mfrac&gt;\u0000 &lt;mn&gt;4&lt;/mn&gt;\u0000 &lt;mi&gt;m&lt;/mi&gt;\u0000 &lt;/mfrac&gt;\u0000 &lt;mi&gt;bm&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ Pfrac{4}{m} bm $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;, N.127, and to &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;I&lt;/mi&gt;\u0000 &lt;mfrac&gt;\u0000 &lt;mn&gt;4&lt;/mn&gt;\u0000 &lt;mi&gt;m&lt;/mi&gt;\u0000 &lt;/mfrac&gt;\u0000 &lt;mi&gt;cm&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ Ifrac{4}{m} cm $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;, N. 140) in the oxide is about 70 times larger than in the fluoride (5.4 vs. 0.08 mE&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 ","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083917","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":"Rational Design for Antioxidant Diphenylamine Derivatives Using Quantitative Structure–Activity Relationships and Quantum Mechanics Calculations","authors":"Ayokanmi Joseph Aremu,&nbsp;Phiphob Naweephattana,&nbsp;Ismail Dwi Putra,&nbsp;Borwornlak Toopradab,&nbsp;Phornphimon Maitarad,&nbsp;Thanyada Rungrotmongkol","doi":"10.1002/jcc.70055","DOIUrl":"10.1002/jcc.70055","url":null,"abstract":"<div>\u0000 \u0000 <p>Diphenylamine (DPA) derivatives, used as antioxidants in rubber-based products, inhibit autoxidation by donating hydrogen atoms to peroxyl radicals. Octanol–water partition coefficient (LogK_ow), an antioxidant index, helps predict their distribution in hydrophobic polymer matrices. Therefore, this study aimed to investigate the relationship between the structure of DPA derivatives and their antioxidant activities, using machine learning with quantitative structure–activity relationships (QSAR) and quantum mechanics (QM). The structure of DPA derivatives was optimized using Density Functional Theory and analyzed for molecular properties. The QSAR models were trained using important descriptors identified through permutation importance. Among the models developed, the Gradient Boosting Regressor (GBR) showed the best performance, with <i>R</i>² of 0.983 and root mean square error (RMSE) of 0.642 for the test set. SHAP analysis revealed that molecular weight and electronic properties significantly influenced LogK_ow predictions. For instance, a higher molecular weight was associated with increased LogK_ow, and a higher positive charge of C2 correlated with higher LogK_ow predictions. Consequently, the two potent compounds (D1 and D2) were designed based on QSAR model guidance. The GBR model predicted LogK_ow values of 9.789 and 7.102 for D1 and D2, respectively, which are higher than the training compounds in the model. To gain molecular insight, the quantum chemical calculations with M062X/6–311++G(d,p)//M062X/6-31G(d,p) were performed to investigate the bond dissociation enthalpy (BDE). The results showed that D1 (79.50 kcal/mol) and D2 (72.43 kcal/mol) exhibited lower BDEs than the reference compounds, suggesting that the designed compounds have the potential for enhanced antioxidant activity. In addition, the antioxidant reaction mechanism was studied by using M062X/6–311++G(d,p)//M062X/6-31G(d,p) which found that the hydrogen atom transfer is the key step, where D1 and D2 showed activation energy barriers of 10.38 and 6.29 kcal/mol, respectively, compared to reference compounds of R3 (10.39 kcal/mol), R1 (10.40 kcal/mol), and R2 (18.26 kcal/mol). Therefore, our findings demonstrate that integrating QSAR with quantum chemical calculations can effectively guide the design of DPA derivatives with improved antioxidant properties.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083581","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":"Molecular and Electronic Structure and Properties of the Single Benzene-Based Fluorophores Containing Guanidine Subunit","authors":"Zoran Glasovac,&nbsp;Davor Margetić,&nbsp;Ivana Antol","doi":"10.1002/jcc.70054","DOIUrl":"10.1002/jcc.70054","url":null,"abstract":"<p>The Gibbs energies of protonation (Δ<i>G</i>_p) and the basic photophysical properties for single-benzene fluorophores (SBFs) containing guanidine and/or amino subunits and the changes that occur upon protonation were modeled by the TDDFT approach. The calculated Δ<i>G</i>_p energies for amino SBFs in the S₁ state range from 985 to 1100 kJ mol⁻¹ which are below the values for guanidines. The protonation of the guanidine-SBFs induces a hypsochromic shift of the absorption and the emission maxima with the Stokes shift of &gt; 100 nm in both cases. Isomerization through the ESIPT process is less probable than in amino-SBFs due to the unfavorable thermodynamics. Still, if it occurs, it leads to a strong red shift of the emission by &gt; 150 nm. Aromaticity indices point to strong antiaromatic character of the examined guanidino-SBFs in the FC region which decreases upon geometrical relaxation and ESIPT. The excited state proton transfer occurs in guanidine-SBF/phenol complexes in the S₁ state, stabilizing CT states and fluorescence quenching.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70054","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143084175","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":"Probability Density Analysis Reveals Substantial Differences Between the Dinitrogen and Acetylene Triple Bonds","authors":"Michel V. Heinz,&nbsp;Emma Gorgas,&nbsp;Nicole Maser,&nbsp;Arne Lüchow","doi":"10.1002/jcc.70037","DOIUrl":"10.1002/jcc.70037","url":null,"abstract":"<p>In earlier publications, it was shown that the electron positions maximizing the probability density <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msup>\u0000 <mfenced>\u0000 <mi>Ψ</mi>\u0000 </mfenced>\u0000 <mn>2</mn>\u0000 </msup>\u0000 </mrow>\u0000 <annotation>$$ {left|Psi right|}^2 $$</annotation>\u0000 </semantics></math> resemble the Lewis structures for most small molecules. While this holds for the triple bond in acetylene, this is not the case for the triple bond in dinitrogen. Because of recent advances in studying the topology of wave functions, this peculiar case is revisited. In this work, the dinitrogen wave function is analyzed and compared to that of acetylene. Significant differences of the electron positions maximizing <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msup>\u0000 <mfenced>\u0000 <mi>Ψ</mi>\u0000 </mfenced>\u0000 <mn>2</mn>\u0000 </msup>\u0000 </mrow>\u0000 <annotation>$$ {left|Psi right|}^2 $$</annotation>\u0000 </semantics></math> are uncovered and explained by the presence of hydrogen atoms in acetylene and by electron arrangements resulting from calculations of the nitrogen and carbon atoms. Moreover, insights into the electron delocalization of both molecules are gained by investigating electron exchange paths. Considering the different chemical behaviors of dinitrogen and acetylene, these differences should be expected.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143084148","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":"Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model","authors":"Hideo Doi,&nbsp;Tatsuya Nakano,&nbsp;Kota Sakakura,&nbsp;Kazuki Akisawa,&nbsp;Koji Okuwaki,&nbsp;Yoshinori Hirano,&nbsp;Eiji Yamamoto,&nbsp;Kenji Yasuoka,&nbsp;Satoshi Ohshima,&nbsp;Takahiro Katagiri,&nbsp;Yuji Mochizuki","doi":"10.1002/jcc.70052","DOIUrl":"10.1002/jcc.70052","url":null,"abstract":"<p>The spike protein of SARS-CoV-2 is a challenging target for theoretical approaches. Here we report a benchmark calculation of the spike protein droplet model by the fragment molecular orbital (FMO) at the second-order Møller-Plesset perturbation (MP2) level on the supercomputer Fugaku. One hundred structure samples from molecular dynamics (MD) simulations were used for both the closed and open forms of this protein (PDB IDs 6XLU and 6XM0 respectively). The number of total fragments is about 20,000, and the job time per structure was about 2 h on 8 racks of Fugaku.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 4","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70052","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077132","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":"Projector-Based Quantum Embedding Study of Iron Complexes","authors":"Jonathan M. Waldrop,&nbsp;Ajay Panyala,&nbsp;Daniel Mejia-Rodriguez,&nbsp;Theresa L. Windus,&nbsp;Niranjan Govind","doi":"10.1002/jcc.70043","DOIUrl":"10.1002/jcc.70043","url":null,"abstract":"<div>\u0000 \u0000 <p>Projection-based embedding theory (PBET) is used to calculate and assess the challenging spin-crossover energies for a selection of small Fe-containing systems by embedding the metal center into the frozen potential of the ligands. MP2, CCSD, and CCSD(T) are embedded in potentials from the SCAN and r²SCAN functionals and compared with the canonical values for the constituent methods and previously reported reference values. Considering the PBET calculations as a correction for the underlying DFT, the embedding calculations are able to provided improvement for most cases. In some cases, the PBET methods are able to compensate for limitations in the wave function methods and produce results similar to more rigorous calculations from the literature. For the systems with spin-crossover energies near zero, the current methodology fails to provide consistent improvement. The isolated recalculation of the electronic structure around the metal center when embedded into a DFT treatment of the ligand field shows promise as a pragmatic and lower cost treatment compared to the canonical treatment of the whole system of the difficult class of spin-crossover complexes.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143056387","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":"PSSKB: A Web Application to Study Protein Structures","authors":"Denis V. Petrovskiy,&nbsp;Kirill S. Nikolsky,&nbsp;Liudmila I. Kulikova,&nbsp;Vladimir R. Rudnev,&nbsp;Tatiana V. Butkova,&nbsp;Kristina A. Malsagova,&nbsp;Valeriya I. Nakhod,&nbsp;Arthur T. Kopylov,&nbsp;Anna L. Kaysheva","doi":"10.1002/jcc.70046","DOIUrl":"10.1002/jcc.70046","url":null,"abstract":"<div>\u0000 \u0000 <p>The proteins expressed during the cell cycle determine cell function and ensure signaling pathway activation in response to environmental influences. Developments in structural biology, biophysics, and bioinformatics provide information on the structure and function of particular proteins including that on the structural changes in proteins due to post-translational modification (PTM) and amino acid substitutions (AAS), which is essential for understanding protein function and life cycle. These are PTMs and AASs that often modulate the function and alter the stability and localization of a protein in a cell. PSSKB is a platform that integrates all necessary tools for modeling the five common natural modifications and all canonical AASs in proteins. The available tools are not limited to the local database, so the user can select a protein from Uniprot ID or PDB ID. The result will be a three-dimensional (3D) representation of the modified structure, as well as an analysis of the changes in the performance of the intact and modified structures after energy minimization compared with the original structure, which not only makes it possible to evaluate AAS/PTM influence of on a protein's characteristics but also to use the 3D model for further studies. Additionally, PSSKB enables the user to search, align, overlay, and determine the exact coordinates of protein structure fragments. The search results are a set of structural motifs similar to the query and ranked by statistical significance. The platform is fully functional and publicly available at https://psskb.org/. No registration is required to access the platform. A tutorial video can be found at https://psskb.org/page/about. Services provided on the platform are based on previously developed and published software. SCPacker applied for PTM Modeling and AAS services available at GitHub (https://github.com/protdb/SCPacker). SaFoldNet applied for a Similar Search service is also available at GitHub (https://github.com/protdb/ABBNet).</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055437","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":"Mechanism of the Non-Kasha Fluorescence in Pyrene","authors":"Sourav Majumdar,&nbsp;Robin Grotjahn,&nbsp;Ahmadreza Rajabi,&nbsp;Bibo Feng,&nbsp;Luke Nambi Mohanam,&nbsp;Gabriel S. Phun,&nbsp;Nicolas Lutfi,&nbsp;Mohammad Khan,&nbsp;Dmitrij Rappoport,&nbsp;Filipp Furche","doi":"10.1002/jcc.70040","DOIUrl":"10.1002/jcc.70040","url":null,"abstract":"<div>\u0000 \u0000 <p>The high-energy shoulder in the gas-phase fluorescence emission spectrum of pyrene is a well-known example of non-Kasha emission. We comparatively assess two approaches, vibronic perturbation theory and nonadiabatic dynamics, in their ability to predict and explain the gas-phase fluorescence spectrum of pyrene. While both methods qualitatively capture the non-Kasha emission, they differ in their computational requirements, accuracy, and physical interpretation. Vibronic perturbation theory and nonadiabatic dynamics are complementary and can be combined in a two-step approach to non-Kasha fluorescence.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055011","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":"Theoretical Study on Adsorption of Halogenated Benzenes on Montmorillonites Modified With M(I)/M(II) Cations","authors":"Daniel Tunega,&nbsp;Martin H. Gerzabek,&nbsp;Leonard Böhm","doi":"10.1002/jcc.70042","DOIUrl":"10.1002/jcc.70042","url":null,"abstract":"<p>Halogenated benzenes (HBs) are hydrophobic organic chemicals belonging to persistent organic pollutants. Owing to their persistence, they represent a serious problem in environmental contamination, specifically of soils and sediments. One of the most important physical processes determining the fate of HBs in soils is adsorption to main soil components such as soil organic matter and soil minerals. Smectites, layered clay minerals of the 2:1 type, are common minerals in clay-rich soils, of which montmorillonite (Mt) is a typical representative. This work focuses on a systematic modeling study of the adsorption mechanism of selected HBs interacting with the basal (001) surface, which is the dominant surface of Mt particles. The HB···Mt interactions were studied by means of a quantum chemical approach based on the density functional theory method. HBs were represented by five molecules, particularly C₆F₆, C₆Cl₃F₃, C₆Cl₆, C₆Br₃Cl₃, and C₆Br₆. In mixed HBs (C₆Cl₃F₃ and C₆Br₃Cl₃) Cl atoms are in 1,3,5 or rather 2,4,6 positions. The effect of a different cation type on adsorption was investigated for M⁺/M²⁺-Mt models with cations from alkali group (M⁺: Li, K, Na, Rb, Cs) and alkaline earth metal group (M²⁺: Mg, Ca, Sr., Ba). The calculations were also performed on the gas phase HB···M⁺/M²⁺ complexes for comparison. Adsorption energies and distances of the main HB molecular plane from the Mt surface were calculated as a measure of the adsorption strength. The results showed that the strongest HB adsorption is for the Na⁺-Mt and Ca²⁺-Mt surfaces. The strongest affinity was observed for hexabromobenzene, while the weakest adsorption was found for hexafluorobenzene. The decomposition of the adsorption energy showed that its dominant component is dispersion energy and less important is the cation-π interaction. The calculated adsorption energies showed a good correlation with experimentally determined log <i>K</i>_d values.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055012","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}