Journal of Computational Chemistry最新文献

{"title":"VDAC Solvation Free Energy Calculation by a Nonuniform Size Modified Poisson–Boltzmann Ion Channel Model","authors":"Liam Jemison,&nbsp;Matthew Stahl,&nbsp;Ranjan K. Dash,&nbsp;Dexuan Xie","doi":"10.1002/jcc.70003","DOIUrl":"10.1002/jcc.70003","url":null,"abstract":"<div>\u0000 \u0000 <p>Voltage-dependent anion channel (VDAC) is the primary conduit for regulated passage of ions and metabolites into and out of a mitochondrion. Calculating the solvation free energy for VDAC is crucial for understanding its stability, function, and interactions within the cellular environment. In this article, numerical schemes for computing the total solvation free energy for VDAC—comprising electrostatic, ideal gas, and excess free energies plus the nonpolar energy—are developed based on a nonuniform size modified Poisson–Boltzmann ion channel (nuSMPBIC) finite element solver along with tetrahedral meshes for VDAC proteins. The current mesh generation package is also updated to improve mesh quality and accelerate mesh generation. A VDAC Solvation Free Energy Calculation (VSFEC) package is then created by integrating these schemes with the updated mesh package, the nuSMPBIC finite element package, the PDB2PQR package, and the OPM database, as well as one uniform SMPBIC finite element package and one Poisson–Boltzmann ion channel (PBIC) finite element package. With the VSFEC package, many numerical experiments are made using six VDAC proteins, eight ionic solutions containing up to four ionic species, including ATP⁴⁻ and Ca²⁺, two reference states, different boundary values, and different permittivity constants. The test results underscore the importance of considering nonuniform ionic size effects to explore the varying patterns of the total solvation free energy, and demonstrate the high performance of the VSFEC package for VDAC solvation free energy calculation.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886969","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":"Machine Learning Prediction of Physicochemical Properties in Lithium-Ion Battery Electrolytes With Active Learning Applied to Graph Neural Networks","authors":"Debojyoti Das,&nbsp;Debdutta Chakraborty","doi":"10.1002/jcc.70009","DOIUrl":"10.1002/jcc.70009","url":null,"abstract":"<div>\u0000 \u0000 <p>Accurate prediction of physicochemical properties, such as electronic energy, enthalpy, free energy, and average vibrational frequencies, is critical for optimizing lithium-ion battery (LIB) performance. Traditional methods like density functional theory (DFT) are computationally expensive and inefficient for large-scale screening. In this study, we apply active learning on top of graph neural networks (GNNs) to efficiently predict these properties. By focusing on uncertain data points, active learning reduces training data size while maintaining high accuracy. Applied to the LIBE and MPcules datasets, the model achieved an R-squared (<i>R</i>²) values of 0.9977 with a mean absolute error (MAE) of 9.66 Ha for electronic energy and an <i>R</i>² values of 0.957 with an MAE of 13.94 cm⁻¹ for average vibrational frequencies. SHapley Additive exPlanations (SHAP) provided insights into key features influencing predictions, such as atomic number and spin multiplicity. This approach enhances both predictive accuracy and model interpretability, offering a scalable solution for LIB electrolyte discovery.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887022","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":"Influence of Ligand Complexity on the Spectroscopic Properties of Type 1 Copper Sites: A Theoretical Study","authors":"Umut Ozuguzel,&nbsp;Serzat Safaltin,&nbsp;S. Pamir Alpay,&nbsp;Kenda Alkadry,&nbsp;Reed Nieman,&nbsp;Carol Korzeniewski,&nbsp;Adelia J. A. Aquino","doi":"10.1002/jcc.70013","DOIUrl":"10.1002/jcc.70013","url":null,"abstract":"<div>\u0000 \u0000 <p>Multi-copper oxidases (MCOs) are enzymes of significant interest in biotechnology due to their efficient catalysis of oxygen reduction to water, making them valuable in sustainable energy production and bio-electrochemical applications. This study employs time-dependent density functional theory (TDDFT) to investigate the electronic structure and spectroscopic properties of the Type 1 (T1) copper site in Azurin, which serves as a model for similar sites in MCOs. Four model complexes of varying complexity were derived from the T1 site, including 3 three-coordinate models and 1 four-coordinate model with axial methionine ligation, to explore the impact of molecular branches and axial coordination. Calculations using ωB97X-D3 functional, def2-TZVP basis set, and conductor-like polarizable continuum model (CPCM) solvation model reproduced key experimental spectral features, with increased model complexity improving agreement, particularly for the ~400 cm⁻¹ band splitting in resonance Raman spectra. This work enhances our understanding of T1 copper sites' electronic properties and spectra, bridging the gap between simplified models and complex proteins. The findings contribute to the interpretation of spectroscopic data in blue copper proteins and may inform future studies on similar biological systems.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886970","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":"A Polarizable CASSCF/MM Approach Using the Interface Between OpenMMPol Library and Cfour","authors":"Tommaso Nottoli,&nbsp;Mattia Bondanza,&nbsp;Filippo Lipparini,&nbsp;Benedetta Mennucci","doi":"10.1002/jcc.27550","DOIUrl":"10.1002/jcc.27550","url":null,"abstract":"<p>We present a polarizable embedding quantum mechanics/molecular mechanics (QM/MM) framework for ground- and excited-state Complete Active Space Self-Consistent Field (CASSCF) calculations on molecules within complex environments, such as biological systems. These environments are modeled using the AMOEBA polarizable force field. This approach is implemented by integrating the OpenMMPol library with the CFour quantum chemistry software suite. The implementation supports both single-point energy evaluations and geometry optimizations, facilitated by the availability of analytical gradients. We demonstrate the methodology by applying it to two distinct photoreceptors, exploring the impact of the protein environment on the structural and photophysical properties of their embedded chromophores.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27550","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879834","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":"Does Basis Set Superposition Error Significantly Affect Post-CCSD(T) Corrections?","authors":"Vladimir Fishman,&nbsp;Emmanouil Semidalas,&nbsp;Margarita Shepelenko,&nbsp;Jan M. L. Martin","doi":"10.1002/jcc.70007","DOIUrl":"10.1002/jcc.70007","url":null,"abstract":"<p>We have investigated the title question for both a subset of the W4-11 total atomization energies benchmark, and for the A24x8 noncovalent interactions benchmark. Overall, counterpoise corrections to post-CCSD(<i>T</i>) contributions are about two orders of magnitude less important than those to the CCSD(<i>T</i>) interaction energy. Counterpoise corrections for connected quadruple substitutions (<i>Q</i>) are negligible, and <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mfenced>\u0000 <mi>Q</mi>\u0000 </mfenced>\u0000 <mi>Λ</mi>\u0000 </msub>\u0000 <mo>−</mo>\u0000 <mfenced>\u0000 <mi>Q</mi>\u0000 </mfenced>\u0000 </mrow>\u0000 <annotation>$$ {(Q)}_{Lambda}-(Q) $$</annotation>\u0000 </semantics></math> or <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>T</mi>\u0000 <mn>4</mn>\u0000 </msub>\u0000 <mo>−</mo>\u0000 <mfenced>\u0000 <mi>Q</mi>\u0000 </mfenced>\u0000 </mrow>\u0000 <annotation>$$ {T}_4-(Q) $$</annotation>\u0000 </semantics></math> especially so. In contrast, for atomization energies, the <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>T</mi>\u0000 <mn>3</mn>\u0000 </msub>\u0000 <mo>−</mo>\u0000 <mfenced>\u0000 <mi>T</mi>\u0000 </mfenced>\u0000 </mrow>\u0000 <annotation>$$ {T}_3-(T) $$</annotation>\u0000 </semantics></math> counterpoise correction can reach about 0.05 kcal/mol for small basis sets like cc-pVDZ, thought it rapidly tapers off with cc-pVTZ and especially aug-cc-pVTZ basis sets. It is reduced to insignificance by the extrapolation of <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>T</mi>\u0000 <mn>3</mn>\u0000 </msub>\u0000 <mo>−</mo>\u0000 <mfenced>\u0000 <mi>T</mi>\u0000 </mfenced>\u0000 </mrow>\u0000 <annotation>$$ {T}_3-(T) $$</annotation>\u0000 </semantics></math> applied in both W4 and HEAT thermochemistry protocols. In noncovalent dimers, the differential BSSE on post-CCSD(<i>T</i>) correlation contributions is negligible even in basis sets as small as the unpolarized split-valence cc-pVDZ(no d).</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879923","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":"Advanced Computational Insights Into Cs₂NaScX₆ (X = Cl, Br) ₆ Double Perovskites: Structural Stability, Elastic Properties, and Optical Characteristics for Next-Generation Photovoltaics","authors":"Junaid Khan,&nbsp;Matiullah Khan,&nbsp;Tanvi Sharma,&nbsp;Imed Boukhris,&nbsp;M. S. Al-Buriahi","doi":"10.1002/jcc.70010","DOIUrl":"10.1002/jcc.70010","url":null,"abstract":"<div>\u0000 \u0000 <p>We investigate the comprehensive analysis's structural, electronic, optical, and elastic properties of Cs₂NaScX₆ (X = Cl, Br) double perovskites using density functional theory (DFT) implemented by the WIEN2k code. The results show that both compounds are in cubic phases. The calculated tolerance factors show both are stable compounds. The computed optimized lattice parameters are Cs₂NaScX₆ (X = Cl, Br) are 10.72 Å and 12.01 Å, respectively. Employing a modified Becke–Johnson (mBJ) potential electronic nature shows that both compounds are in semiconductor nature, that is, 3.138 eV and 3.977 eV. The calculated elastic constant and perimeters show the Cs₂NaScX₆ (X = Cl, Br) are mechanical stables and also ductile and anisotropic nature. The optical properties described the range of photon energies from 0 to 10 eV, revealing pronounced absorption within the visible spectrum, highlighting their considerable promise for transformative innovations in photovoltaic technology. These double perovskites exhibit superior absorption characteristics compared to their Cs₂NaScX₆ (X = Cl, Br) analogues, thus laying the groundwork for significant advancements in solar energy conversion and photovoltaic applications.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142880249","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":"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}