Journal of Computational Chemistry最新文献

{"title":"Appraisal of the Fragments-In-Fragments Method for the Energetics of Individual Hydrogen Bonds in Molecular Crystals","authors":"Bharti Dehariya,&nbsp;Mini Bharati Ahirwar,&nbsp;Ayush Shivhare,&nbsp;Milind M. Deshmukh","doi":"10.1002/jcc.70008","DOIUrl":"10.1002/jcc.70008","url":null,"abstract":"<div>\u0000 \u0000 <p>We report a direct application of the molecular tailoring approach-based (MTA-based) method to calculate the individual hydrogen bond (HB) energy in molecular crystal. For this purpose, molecular crystals of nitromalonamide (NMA) and salicylic acid (SA) were taken as test cases. Notably, doing a correlated computation using a large molecular crystal structure is difficult. Among 15 density functional theory functionals, the B3LYP provides accurate estimates of HB energies closed to the CCSD(T) ones using the 6–311 + G(d,p) basis set for all atoms. The direct application of the MTA-based method to these crystal structures is although straightforward. For instance, the calculated energy suggests that three intramolecular HBs in NMA crystal are of stronger strength (7.3–17.0 kcal/mol) than the intermolecular ones (2.7–4.0 kcal/mol). On the other hand, intermolecular HB in SA crystal is moderately stronger (9.9 kcal/mol) than intramolecular one (8.1 kcal/mol). However, these energy calculations by the MTA-based method are very expensive. For instance, the time needed to evaluate the energy of all seven HBs in NMA crystal (having molecules within maximum of 15 unit cells) is 122,681 min (~2.7 months). In view of this, we assessed our recently proposed linear-scaling Fragments-in-Fragments (<i>Frags-in-Frags</i>) method for estimating the single-point energies of parent molecular crystal and fragments of the MTA-based method. It has been found that the estimated HB energies by the <i>Frags-in-Frags</i> method are in excellent linear agreement with their MTA-based counterparts (R² = 0.9993). Furthermore, root mean square deviation is 0.12 kcal/mol. Mean and maximum absolute errors are 0.10 and 0.5 kcal/mol, respectively, and the standard deviation is 0.14 kcal/mol. Importantly, the <i>Frags-in-Frags</i> method is computationally efficient; it needs only 18,289 min (~12.7 days) for the estimation of energy of all HBs in NMA crystal and 3499 min (~2.4 days) for all HBs in SA crystal.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142925100","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 Closer Look at the FeS Heme Bonds in Azotobacter vinelandii Bacterioferritin: QM/MM and Local Mode Analysis","authors":"Marek Freindorf,&nbsp;Elfi Kraka","doi":"10.1002/jcc.70012","DOIUrl":"10.1002/jcc.70012","url":null,"abstract":"<p>Using the QM/MM methodology and a local mode analysis, we investigated a character and a strength of FeS bonds of heme groups in oxidized and reduced forms of Bacterioferritin from <i>Azotobacter vinelandii</i>. The strength of the FeS bonds was correlated with a bond length, an energy density at a bond critical point, and a charge difference of the F and S atoms. Changing the oxidation state from ferrous to ferric generally makes the FeS bonds weaker, longer, more covalent, and more polar. We also investigated the SFeS bond bending and found that the stronger FeS bond, generally makes the SFeS bond bending stiffer, which could play a key role in the balance between ferric and ferrous oxidation states and related biological activities.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917200","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":"Examining the Impact of Local Constraint Violations on Energy Computations in DFT","authors":"Vaibhav Khanna,&nbsp;Bikash Kanungo,&nbsp;Vikram Gavini,&nbsp;Ambuj Tewari,&nbsp;Paul M. Zimmerman","doi":"10.1002/jcc.70005","DOIUrl":"10.1002/jcc.70005","url":null,"abstract":"<p>This work examines the impact of locally imposed constraints in Density Functional Theory (DFT). Using a metric referred to as the extent of violation index (EVI), we quantify how well exchange-correlation functionals adhere to local constraints. Applying EVIs to a diverse set of molecules for GGA functionals reveals constraint violations, particularly for semi-empirical functionals. We leverage EVIs to explore potential connections between these violations and errors in chemical properties. While no correlation is observed for atomization energies, a significant statistical correlation emerges between EVIs and total energies. Similarly, the analysis of reaction energies suggests weak positive correlations for specific constraints. However, definitive conclusions about error cancellation mechanisms cannot be made at this time. These observations revealed by EVIs may be useful for consideration when designing future generations of semilocal functionals.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911933","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":"Machine Learning-Corrected Simplified Time-Dependent DFT for Systems With Inverted Single-t-o-Triplet Gaps of Interest for Photocatalytic Water Splitting","authors":"Kevin Curtis,&nbsp;Samuel O. Odoh","doi":"10.1002/jcc.70006","DOIUrl":"10.1002/jcc.70006","url":null,"abstract":"<div>\u0000 \u0000 <p>Hydrogen gas (H₂) can be produced via entirely solar-driven photocatalytic water splitting (PWS). A promising set of organic materials for facilitating PWS are the so-called inverted singlet-triplet, INVEST, materials. Inversion of the singlet (S₁) and triplet (T₁) energies reduces the population of triplet states, which are otherwise destructive under photocatalytic conditions. Moreover, when INVEST materials possess dark S₁ states, the excited state lifetimes are maximized, facilitating energy transfer to split water. In the context of solar-driven processes, it is also desirable that these INVEST materials absorb near the solar maximum. Many aza-triangulenes possess the desired INVEST property, making it beneficial to describe an approach for systematically and efficiently predicting the INVEST property as well as properties that make for efficient photocatalytic water splitting, while exploring the large chemical space of the aza-triangulenes. Here, we utilize machine learning to generate post hoc corrections to simplified Tamm–Dancoff approximation density functional theory (sTDA-DFT) for singlet and triplet excitation energies that are within 28–50 meV of second-order algebraic diagrammatic construction, ADC(2), as well as the singlet-to-triplet, ΔE_S1T1, gaps of PWS systems. Our Δ-ML model is able to recall 85% of the systems identified by ADC(2) as candidates for PWS. Further, with a modest database of ADC(2) excitation energies of 4025 aza-triangulenes, we identified 78 molecules suitable for entirely solar-driven PWS.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901926","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":"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}