Journal of Computational Chemistry最新文献

{"title":"Computing Accurate & Reliable Rovibrational Spectral Data for Aluminum-Bearing Molecules","authors":"C. Zachary Palmer,&nbsp;Rebecca A. Firth,&nbsp;Ryan C. Fortenberry","doi":"10.1002/jcc.27524","DOIUrl":"10.1002/jcc.27524","url":null,"abstract":"<div>\u0000 \u0000 <p>The difficulty of quantum chemically computing vibrational, rotational, and rovibrational reference data via quartic force fields (QFFs) for molecules containing aluminum appears to be alleviated herein using a hybrid approach based upon CCSD(T)-F12b/cc-pCVTZ further corrected for conventional CCSD(T) scalar relativity within the harmonic terms and simple CCSD(T)-F12b/cc-pVTZ for the cubic and quartic terms: the F12-TcCR+TZ QFF. Aluminum containing molecules are theorized to participate in significant chemical processes in both the Earth's upper atmosphere as well as within circumstellar and interstellar media. However, experimental data for the identification of these molecules are limited, showcasing the potential for quantum chemistry to contribute significant amounts of spectral reference data. Unfortunately, current methods for the computation of rovibrational spectral data have been shown previously to exhibit large errors for aluminum-containing molecules. In this work, ten different methods are benchmarked to determine a method to produce experimentally-accurate rovibrational data for theorized aluminum species. Of the benchmarked methods, the explicitly correlated, hybrid F12-TcCR+TZ QFF consistently produces the most accurate results compared to both gas-phase and Ar-matrix experimental data. This method combines the accuracy of the composite F12-TcCR energies along with the numerical stability of non-composite anharmonic terms where the non-rigid nature of aluminum bonding can be sufficiently treated.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874221","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":"Additive CHARMM Force Field for Pterins and Folates","authors":"Elsa Balduzzi,&nbsp;Wenlu Yin,&nbsp;Jean-Christophe Lambry,&nbsp;Hannu Myllykallio,&nbsp;Alexey Aleksandrov","doi":"10.1002/jcc.27548","DOIUrl":"10.1002/jcc.27548","url":null,"abstract":"<div>\u0000 \u0000 <p>Folates comprise a crucial class of biologically active compounds related to folic acid, playing a vital role in numerous enzymatic reactions. One-carbon metabolism, facilitated by the folate cofactor, supports numerous physiological processes, including biosynthesis, amino acid homeostasis, epigenetic maintenance, and redox defense. Folates share a common pterin heterocyclic ring structure capable of undergoing redox reactions and existing in various protonation states. This study aimed to derive molecular mechanics (MM) parameters compatible with the CHARMM36 all-atom additive force field for pterins and biologically important folates, including pterin, biopterin, and folic acid. Three redox forms were considered: oxidized, dihydrofolate, and tetrahydrofolate states. Across all protonation states, a total of 18 folates were parameterized. Partial charges were derived using the CHARMM force field parametrization protocol, based on targeting reference quantum mechanics monohydrate interactions, electrostatic potential, and dipole moment. Bonded terms were parameterized using one-dimensional adiabatic potential energy surface scans, and two-dimensional scans to parametrize in-ring torsions associated with the puckering states of dihydropterin and tetrahydropterin. The quality of the model was demonstrated through simulations of three protein complexes using optimized and initial parameters. These simulations underscored the significantly enhanced performance of the folate model developed in this study compared to the initial model without optimization in reproducing structural properties of folate–protein complexes. Overall, the presented MM model will be valuable for modeling folates in various redox states and serve as a starting point for parameterizing other folate derivatives.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874222","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":"Comprehensive Analysis of Deuterium Isotope Effects on Ionic H3O+…π Interactions Using Multi-Component Quantum Mechanics Methods","authors":"Taro Udagawa,&nbsp;Yusuke Kanematsu,&nbsp;Takayoshi Ishimoto,&nbsp;Masanori Tachikawa","doi":"10.1002/jcc.70000","DOIUrl":"10.1002/jcc.70000","url":null,"abstract":"<div>\u0000 \u0000 <p>Deuterium isotope effects on interaction energies and geometrical parameters in several H₃O⁺(D₃O⁺)^…ene and H₃O+(D₃O⁺)^…yne complexes, which involve O-H(D)^…π interactions, have been analyzed using the MP2 level of the multi-component molecular orbital method (MC_MP2), which can incorporate the nuclear quantum effects of light nuclei, such as protons and deuterons. The MC_MP2 calculations revealed that D₃O⁺ replacement reduced the interaction energies of the complexes and induced changes in geometrical parameters. In addition, natural energy decomposition analysis (NEDA) revealed a strong correlation between the H/D isotope effects on the H/D^…π distances and on each energy component.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857880","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":"MARVEL Analysis of High-Resolution Rovibrational Spectra of 16O13C18O","authors":"Ala'a A. A. Azzam,&nbsp;Jonathan Tennyson,&nbsp;Sergei N. Yurchenko,&nbsp;Tibor Furtenbacher,&nbsp;Attila G. Császár","doi":"10.1002/jcc.27541","DOIUrl":"10.1002/jcc.27541","url":null,"abstract":"<p>A large set of validated experimental transitions and empirical rovibrational energy levels are reported for the fifth most abundant carbon dioxide isotopologue, ¹⁶O¹³C¹⁸O (in a shorthand notation, 638). Validation of the transitions and determination of the empirical energy levels are based on a compiled and carefully checked dataset, collected from 35 literature sources, containing 12 348/7432 measured/unique lines in the wavenumber range of 578–9318 cm⁻¹. The MARVEL (Measured Active Rotational-Vibrational Energy Levels) protocol, built upon the theory of spectroscopic networks, not only validates the vast majority of the measured transitions, but also yields 3975 empirical rovibrational energy levels, with uncertainty estimates compliant with the experimental uncertainties of the transitions.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27541","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849301","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":"CoTCNQ as a Catalyst for CO2 Electroreduction: A First Principles r2SCAN Meta-GGA Investigation","authors":"Oliver J. Conquest,&nbsp;Yijiao Jiang,&nbsp;Catherine Stampfl","doi":"10.1002/jcc.27528","DOIUrl":"10.1002/jcc.27528","url":null,"abstract":"<div>\u0000 \u0000 <p>Using first principles calculations we investigate cobalt-coordinated tetracyanoquinodimethane (R-CoTCNQ) as a potential catalyst for the CO₂ electroreduction reaction (CO₂ERR). We determine that exchange–correlation functionals beyond the generalized gradient approximation (GGA) are required to accurately describe the spin properties of R-CoTCNQ, therefore, the meta-GGA r²SCAN functional is used in this study. The free energy CO₂ERR reaction pathways are calculated for the reduced catalyst ([R-CoTCNQ]^−1<i>e</i>) with reaction products HCOOH and HCHO predicted depending on our choice of electrode potential. Calculations are also performed for [R-CoTCNQ]^−1<i>e</i> supported on a H-terminated diamond (1 1 0) surface with reaction pathways being qualitatively similar to the [R-CoTCNQ]^−1<i>e</i> monolayer. The inclusion of boron-doping in the diamond support shows a slightly improved CO₂ERR reaction pathway. Furthermore, structurally, supported R-CoTCNQ provide a high specific area of active Co active sites and could be promising catalysts for future experimental consideration.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142825024","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":"Groupy: An Open-Source Toolkit for Molecular Simulation and Property Calculation","authors":"Ruichen Liu,&nbsp;Li Wang,&nbsp;Xiangwen Zhang,&nbsp;Guozhu Li","doi":"10.1002/jcc.27527","DOIUrl":"10.1002/jcc.27527","url":null,"abstract":"<div>\u0000 \u0000 <p>In this work, an open-source, versatile, and flexible code named Groupy is present for calculating various molecular properties and preparing input files of molecular simulation software such as Gaussian. This code requires only SMILES as input, but can output many new useful data and files in multiple formats. The output information is clear and easy to read. The tips to the users are very detailed and easy to follow when using. Message passing interface (MPI) parallelization is supported to reduce computing time when the properties of a large number of molecules are calculated. Groupy not only supports the calculation of molecular properties using the traditional group contribution method, but also directly outputs the group-contribution-style molecular fingerprints for machine learning. The code has strong extensibility, which can be used as an external library to build other programs. We hope that Groupy brings great convenience to both computational and experimental chemists in their daily research. The code of Groupy can be freely obtained at https://github.com/47-5/Groupy</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142825025","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":"Tuning Electronic Relaxation of Nanorings Through Their Interlocking","authors":"Laura Alfonso-Hernandez,&nbsp;Victor M. Freixas,&nbsp;Tammie Gibson,&nbsp;Sergei Tretiak,&nbsp;Sebastian Fernandez-Alberti","doi":"10.1002/jcc.27533","DOIUrl":"10.1002/jcc.27533","url":null,"abstract":"<div>\u0000 \u0000 <p>Electronic and vibrational relaxation processes can be optimized and tuned by introducing alternative pathways that channel excess energy more efficiently. An ensemble of interacting molecular systems can help overcome the bottlenecks caused by large energy gaps between intermediate excited states involved in the relaxation process. By employing this strategy, catenanes composed of mechanically interlocked carbon nanostructures show great promise as new materials for achieving higher efficiencies in electronic devices. Herein, we perform nonadiabatic excited state molecular dynamics on different all-benzene catenanes. We observe that catenanes experience faster relaxations than individual units. Coupled catenanes present overlapping energy manifolds that include several electronic excited states spatially localized on the different moieties, increasing the density of states that ultimately improve the efficiency in the energy relaxation. This result suggests the use of catenanes as a viable strategy for tuning the internal conversion rates in a quest for their utilization for new optoelectronic applications.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142825027","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":"Ultrafast Dynamics of Diketopyrrolopyrrole Dimers","authors":"Ali Al-Jaaidi,&nbsp;Josene M. Toldo,&nbsp;Mario Barbatti","doi":"10.1002/jcc.27547","DOIUrl":"10.1002/jcc.27547","url":null,"abstract":"<p>Diketopyrrolopyrroles (DPPs) have attracted attention for their potential applications in organic photovoltaics due to their tunable optical properties and charge-carrier mobilities. In this study, we investigate the excited-state dynamics of a DPP dimer using time-dependent density functional theory (TDDFT) and nonadiabatic molecular dynamics simulations. Our results reveal a near-barrierless hydrogen migration state intersection that facilitates ultrafast internal conversion with a lifetime of about 400 fs, leading to fluorescence quenching. Electronic density analysis along the relaxation pathway confirms a hydrogen atom transfer mechanism. These findings highlight the critical role of state intersections in the photophysical properties of DPP dimers, providing new insights for the design of functionalized DPP systems aimed at suppressing nonradiative decay for enhanced performance in photovoltaic applications.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27547","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820960","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 Influence of the Solvation on the Bonding of Molecular Complexes of Diatomic Halogens With Nitrogen-Containing Donors and Their Stability With Respect to the Heterolytic Halogen-Halogen Bond Splitting","authors":"Anna V. Pomogaeva,&nbsp;Anna S. Lisovenko,&nbsp;Alexey Y. Timoshkin","doi":"10.1002/jcc.27549","DOIUrl":"10.1002/jcc.27549","url":null,"abstract":"<div>\u0000 \u0000 <p>In the framework of SMD approach a systematic computational study of structural, electronic and thermodynamic properties of molecular complexes of Cl₂, ICl and I₂ with series of N-containing Lewis bases in solvents of different polarity was carried out. Results indicate that molecular complexes of Cl₂ with strong and medium-strong LB undergo spontaneous ionization in the acetonitrile solution. The increase of the solvent polarity can change the nature of interaction in X'X<span></span>LB systems from molecular X'X ← LB donor-acceptor complexes to 3-center 4-electron bound X'<span></span>→X⁺ ← LB in solvents of medium polarity and to the contact ion pairs X'<span></span>→[X<span></span>LB]⁺ in polar solvents. Thus, the controlled generation of cationic [LB∙X]⁺ species is possible by varying the nature of LB, varying the nature of the solvent, and varying the nature of the halogen X. Molecular Cl₂ has the greatest tendency to form ionic species in polar solvents. Spontaneous ionization of molecular nσ complexes of chlorine with strong LB in medium-polar solvents (starting from OEt₂, <i>ε</i> = 4.24) should not be neglected and single point solvation energy computations on gas phase optimized geometries are not reliable for such systems.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816170","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":"pKa prediction in non-aqueous solvents","authors":"Jonathan W. Zheng,&nbsp;Emad Al Ibrahim,&nbsp;Ivari Kaljurand,&nbsp;Ivo Leito,&nbsp;William H. Green","doi":"10.1002/jcc.27517","DOIUrl":"10.1002/jcc.27517","url":null,"abstract":"&lt;p&gt;Acid dissociation constants (&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;msub&gt;\u0000 &lt;mi&gt;K&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{p}{K}_{mathrm{a}} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;) are widely measured and studied, most typically in water. Comparatively few datasets and models for non-aqueous &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;msub&gt;\u0000 &lt;mi&gt;K&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{p}{K}_{mathrm{a}} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; values exist. In this work, we demonstrate how the &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;msub&gt;\u0000 &lt;mi&gt;K&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{p}{K}_{mathrm{a}} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; in one solvent can be accurately determined using reference data in another solvent, corrected by solvation energy calculations from the COSMO-RS method. We benchmark this approach in 10 different solvents, and find that &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;msub&gt;\u0000 &lt;mi&gt;K&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{p}{K}_{mathrm{a}} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; values calculated in six solvents deviate from experimental data on average by less than 1 &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;msub&gt;\u0000 &lt;mi&gt;K&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{p}{K}_{mathrm{a}} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; unit. We observe comparable performance on a more diverse test set including amino acids and drug molecules, with higher error for large molecules. The model performance in four other solvents is worse, with one MAE exceeding 3 &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;msub&gt;\u0000 &lt;mi&gt;K&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathrm{p}{K}_{mathrm{a}} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; units; we discuss how such errors arise due to both model error and ","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27517","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805037","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}