Journal of Computational Chemistry最新文献

{"title":"Optimized infrared spectrum of \u0000 \u0000 \u0000 \u0000 (\u0000 \u0000 \u0000 H\u0000 \u0000 \u0000 2\u0000 \u0000 \u0000 O\u0000 )\u0000 \u0000 \u0000 m\u0000 \u0000 \u0000 :\u0000 \u0000 \u0000 (\u0000 H\u0000 C\u0000 N\u0000 )\u0000 \u0000 \u0000 n\u0000 \u0000 \u0000 mixtures","authors":"D. P. Freitas,&nbsp;F. N. N. Pansini,&nbsp;A. J. C. Varandas","doi":"10.1002/jcc.27491","DOIUrl":"10.1002/jcc.27491","url":null,"abstract":"<p>Using density functional theory at D3-B3LYP/aug-cc-pVDZ level combined with the conductor-like polarizable continuum model (CPCM) solvent model, a study of the IR spectrum of <span></span><math>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mi>H</mi>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </msub>\u0000 <mi>O</mi>\u0000 </mrow></math>:HCN mixtures is reported. The CPCM solvent effect notably enhances the accuracy of the IR spectra compared to gas-phase calculations, while the dielectric constant value has minimum impact on the final spectrum. An optimized methodology is suggested that effectively minimizes the root mean square deviation between theoretical and experimental data. This novel approach not only enhances the quality of the final IR spectra but also captures relevant spectral features, highlighting its potential to decipher molecular interactions in such intricate mixtures.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2842-2847"},"PeriodicalIF":3.4,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142078633","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":"GNN-DDAS: Drug discovery for identifying anti-schistosome small molecules based on graph neural network","authors":"Xin Zeng,&nbsp;Peng-Kun Feng,&nbsp;Shu-Juan Li,&nbsp;Shuang-Qing Lv,&nbsp;Meng-Liang Wen,&nbsp;Yi Li","doi":"10.1002/jcc.27490","DOIUrl":"10.1002/jcc.27490","url":null,"abstract":"<p>Schistosomiasis is a tropical disease that poses a significant risk to hundreds of millions of people, yet often goes unnoticed. While praziquantel, a widely used anti-schistosome drug, has a low cost and a high cure rate, it has several drawbacks. These include ineffectiveness against schistosome larvae, reduced efficacy in young children, and emerging drug resistance. Discovering new and active anti-schistosome small molecules is therefore critical, but this process presents the challenge of low accuracy in computer-aided methods. To address this issue, we proposed GNN-DDAS, a novel deep learning framework based on graph neural networks (GNN), designed for drug discovery to identify active anti-schistosome (DDAS) small molecules. Initially, a multi-layer perceptron was used to derive sequence features from various representations of small molecule SMILES. Next, GNN was employed to extract structural features from molecular graphs. Finally, the extracted sequence and structural features were then concatenated and fed into a fully connected network to predict active anti-schistosome small molecules. Experimental results showed that GNN-DDAS exhibited superior performance compared to the benchmark methods on both benchmark and real-world application datasets. Additionally, the use of GNNExplainer model allowed us to analyze the key substructure features of small molecules, providing insight into the effectiveness of GNN-DDAS. Overall, GNN-DDAS provided a promising solution for discovering new and active anti-schistosome small molecules.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2825-2834"},"PeriodicalIF":3.4,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071599","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":"All-body concept and quantified limits of cooperativity and related effects in homodromic cyclic water clusters from a molecular-wide and electron density-based approach","authors":"Ignacy Cukrowski,&nbsp;Stéfan Zaaiman,&nbsp;Shahnawaz Hussain,&nbsp;Jurgens H. de Lange","doi":"10.1002/jcc.27489","DOIUrl":"10.1002/jcc.27489","url":null,"abstract":"<p>We strongly advocate distinguishing cooperativity from cooperativity-induced effects. From the MOW<i>e</i>D-based approach, the origin of <b>all-body</b> cooperativity is synonymous with physics- and quantum-based processes of electron (<i>e</i>) delocalization throughout water clusters. To this effect, over 10 atom-pairs contribute to the total <i>e</i>-density at a BCP(H,O) between water molecules in a tetramer. Intermolecular all-body <i>e</i>-delocalization, that is, cooperativity, is an energy-minimizing process that fully explains non-additive increase in stability of a water molecule in clusters with an increase in their size. A non-linear change in cooperativity and cooperativity-induced effects, such as (i) structural (e.g., a change in d(O,O)) or topological intra- and intermolecular properties in water clusters (e.g., electron density or potential energy density at bond critical points) is theoretically reproduced by the proposed expression. It predicted the limiting value of delocalized electrons by a H₂O molecule in homodromic cyclic clusters to be 1.58<i>e</i>. O-atoms provide the vast majority of electrons that “travel throughout a cluster predominantly on a <i>privileged</i> exchange quantum density highway” (⋅⋅⋅O–H⋅⋅⋅O–H⋅⋅⋅O–H⋅⋅⋅) using Bader's classical bond paths as density bridges linking water molecules. There are, however, <i>additional</i> electron exchange channels that are not seen on molecular graphs as bond paths. A 3D visual representation of the “privileged” and “additional” exchange channels as well as detailed intra- and inter-molecular patterns of <i>e</i>-sharing and (de)localizing is presented. The energy stabilizing contribution made by three O-atoms of neighboring water molecules was found to be large (−597 kcal/mol in cyclic hexamer) and 5 times more significant than that of a classical O–H⋅⋅⋅O intermolecular H-bond.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2812-2824"},"PeriodicalIF":3.4,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27489","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071598","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":"Sulfide release and rebinding in the mechanism for nitrogenase","authors":"Per E. M. Siegbahn","doi":"10.1002/jcc.27494","DOIUrl":"10.1002/jcc.27494","url":null,"abstract":"<p>Nitrogenases are the only enzymes that activate the strong triple bond in N₂. The mechanism for the activation has been very difficult to determine in spite of decades of work. In previous modeling studies it has been suggested that the mechanism for nitrogen activation starts out by four pre-activation steps (A₀–A₄) before catalysis. That suggestion led to excellent agreement with experimental Elecrtron Paramagnetic Resonance (EPR) observations in the step where N₂ becomes protonated (E₄). An important part of the pre-activation is that a sulfide is released. In the present paper, the details of the pre-activation are modeled, including the release of the sulfide. Several possible transition states for the release have been obtained. An A₄(E₀) state is reached which is very similar to the E₄ state. For completeness, the steps going back from A₄(E₀) to A₀ after catalysis are also modeled, including the insertion of a sulfide.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2835-2841"},"PeriodicalIF":3.4,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27494","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071600","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":"Molecular dynamics of liquid–electrode interface by integrating Coulomb interaction into universal neural network potential","authors":"Kaoru Hisama,&nbsp;Gerardo Valadez Huerta,&nbsp;Michihisa Koyama","doi":"10.1002/jcc.27487","DOIUrl":"10.1002/jcc.27487","url":null,"abstract":"<p>Computational understanding of the liquid–electrode interface faces challenges in efficiently incorporating reactive force fields and electrostatic potentials within reasonable computational costs. Although universal neural network potentials (UNNPs), representing pretrained machine learning interatomic potentials, are emerging, current UNNP models lack explicit treatment of Coulomb potentials, and methods for integrating additional charges on the electrode remain to be established. We propose a method to analyze liquid–electrode interfaces by integrating a UNNP, known as the preferred potential, with Coulomb potentials using the ONIOM method. This approach extends the applicability of UNNPs to electrode–liquid interface systems. Through molecular dynamics simulations of graphene–water and graphene oxide (GO)–water interfaces, we demonstrate the effectiveness of our method. Our findings emphasize the necessity of incorporating long-range Coulomb potentials into the water potential to accurately describe water polarization at the interface. Furthermore, we observe that functional groups on the GO electrode influence both polarization and capacitance.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2805-2811"},"PeriodicalIF":3.4,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27487","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142045806","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":"Energy and spectroscopic parameters of neutral and cations isomers of the CnH2 (n = 2–6) families using high-level ab-initio approaches","authors":"Lenin J. Díaz Soto,&nbsp;Ricardo R. Oliveira,&nbsp;Leonardo Baptista,&nbsp;Enio F. da Silveira,&nbsp;Marco Antonio Chaer Nascimento","doi":"10.1002/jcc.27485","DOIUrl":"10.1002/jcc.27485","url":null,"abstract":"<p>Cationic species, previously detected from ion-induced desorption of solid methane by plasma desorption mass spectrometry (PDMS), and neutral species, are investigated using high-level ab-initio approaches. From a set of 25 cationic and 26 neutral structures belonging to C_nH₂ (<i>n</i> = 2–6) families, it was obtained the energy, rotational constants, harmonic vibrational frequency, charge distribution and excitation energies. The ZPVE-corrected energies, at CCSD(T)-F12; CCSD(T)-F12/RI/(cc-pVTZ-F12, cc-pVTZ-F12-CABS, cc-pVQZ/C) (<i>n</i> = 2–5) and CCSD(T)/cc-pVTZ (<i>n</i> = 6) levels, reveal that the topology of the most stable isomer vary with <i>n</i> and the charge. Out of 674 harmonic frequencies, those with maximum intensity are generally in the 3000–3500 cm⁻¹ range. Analysis of 169 vertical transition energies calculated with the EOM-CCSD approach, suggest three C₆H₂ species as potential carriers of the diffuse interstellar bands (DIB). Systematic comparison of properties between neutral and cationic species can assist in the structural description of complex matrices.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2793-2804"},"PeriodicalIF":3.4,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142034710","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":"Spin parameter optimization for spin-polarized extended tight-binding methods","authors":"Siyavash Moradi,&nbsp;Rebecca Tomann,&nbsp;Josie Hendrix,&nbsp;Martin Head-Gordon,&nbsp;Christopher J. Stein","doi":"10.1002/jcc.27482","DOIUrl":"10.1002/jcc.27482","url":null,"abstract":"<p>We present an optimization strategy for atom-specific spin-polarization constants within the spin-polarized GFN2-xTB framework, aiming to enhance the accuracy of molecular simulations. We compare a sequential and global optimization of spin parameters for hydrogen, carbon, nitrogen, oxygen, and fluorine. Sensitivity analysis using Sobol indices guides the identification of the most influential parameters for a given reference dataset, allowing for a nuanced understanding of their impact on diverse molecular properties. In the case of the W4-11 dataset, substantial error reduction was achieved, demonstrating the potential of the optimization. Transferability of the optimized spin-polarization constants over different properties, however, is limited, as we demonstrate by applying the optimized parameters on a set of singlet-triplet gaps in carbenes. Further studies on ionization potentials and electron affinities highlight some inherent limitations of current extended tight-binding methods that can not be resolved by simple parameter optimization. We conclude that the significantly improved accuracy strongly encourages the present re-optimization of the spin-polarization constants, whereas the limited transferability motivates a property-specific optimization strategy.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2786-2792"},"PeriodicalIF":3.4,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27482","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142034711","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":"Temperature effects on the branching dynamics in the model ambimodal (6 + 4)/(4 + 2) intramolecular cycloaddition reaction","authors":"Tatsuhiro Murakami,&nbsp;Daiki Hayashi,&nbsp;Yuya Kikuma,&nbsp;Keita Yamaki,&nbsp;Toshiyuki Takayanagi","doi":"10.1002/jcc.27484","DOIUrl":"10.1002/jcc.27484","url":null,"abstract":"<p>C₁₄H₂₀ (tetradecapentaene) is a simple model system exhibiting post transition-state behavior, wherein both the (6 + 4) and (4 + 2) cycloaddition products are formed from one ambimocal transition state structure. We studied the bifurcation dynamics starting from the two ambimodal transition state structures, the chair-form and boat-form, using the quasi-classical trajectory, classical molecular dynamics, and ring-polymer molecular dynamics methods on the parameter-optimized semiempirical GFN2-xTB potential energy surface. It was found that the calculated branching fractions differ between the chair-form and boat-form due to the different nature in the IRC pathways. We also investigated the effects of temperature on bifurcation dynamics and found that, at higher temperatures, trajectories stay longer in the intermediate region of the potential energy surface.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2778-2785"},"PeriodicalIF":3.4,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27484","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142015779","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 C-terminal self-binding helical peptide of human estrogen-related receptor γ can be druggably targeted by a novel class of rationally designed peptidic antagonists","authors":"Zilong Li,&nbsp;Yue Peng,&nbsp;Haiyang Ye,&nbsp;Yunyi Zhang,&nbsp;Peng Zhou","doi":"10.1002/jcc.27473","DOIUrl":"10.1002/jcc.27473","url":null,"abstract":"<p>Orphan nuclear estrogen-related receptor γ (ERRγ) has been recognized as a potential therapeutic target for cancer, inflammation and metabolic disorder. The ERRγ contains a regulatory AF2 helical tail linked C-terminally to its ligand-binding domain (LBD), which is a self-binding peptide (SBP) and serves as molecular switch to dynamically regulate the receptor alternation between active and inactive states by binding to and unbinding from the AF2-binding site on ERRγ LBD surface, respectively. Traditional ERRγ modulators are all small-molecule chemical ligands that can be classified into agonists and inverse agonists in terms of their action mechanism; the agonists stabilize the AF2 in ABS site with an agonist conformation, while the inverse agonists lock the AF2 out of the site to largely abolish ERRγ transcriptional activity. Here, a class of ERRγ peptidic antagonists was described to compete with native AF2 for the ABS site, thus blocking the active state of AF2 binding to ERRγ LBD domain. Self-inhibitory peptide was derived from the SBP-covering AF2 region and we expected it can rebind potently to the ABS site by reducing its intrinsic disorder and entropy cost upon the rebinding. Hydrocarbon stapling was employed to do so, which employed an all-hydrocarbon bridge across the [<i>i</i>, <i>i</i> + 4]-anchor residue pair in the N-terminal, middle or C-terminal region of the self-inhibitory peptide. As might be expected, it is revealed that the stapled peptides are good binders of ERRγ LBD domain and can effectively compete with the native AF2 helical tail for ERRγ ABS site, which exhibit a basically similar binding mode with AF2 to the site and form diverse noncovalent interactions with the site, thus conferring stability and specificity to the domain–peptide complexes.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2771-2777"},"PeriodicalIF":3.4,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141999074","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":"PGA: A new particle swarm optimization algorithm based on genetic operators for the global optimization of clusters","authors":"Kai Wang","doi":"10.1002/jcc.27481","DOIUrl":"10.1002/jcc.27481","url":null,"abstract":"<p>We have developed a global optimization program named PGA based on particle swarm optimization algorithm coupled with genetic operators for the structures of atomic clusters. The effectiveness and efficiency of the PGA program can be demonstrated by efficiently obtaining the tetrahedral Au₂₀ and double-ring tubular B₂₀, and identifying the ground state <span></span><math>\u0000 <mrow>\u0000 <msubsup>\u0000 <mtext>ZrSi</mtext>\u0000 <mrow>\u0000 <mn>17</mn>\u0000 <mo>–</mo>\u0000 <mn>20</mn>\u0000 </mrow>\u0000 <mo>−</mo>\u0000 </msubsup>\u0000 </mrow></math> clusters through the comparison between the simulated and the experimental photoelectron spectra (PESs). Then, the PGA was applied to search for the global minimum structures of <span></span><math>\u0000 <mrow>\u0000 <msubsup>\u0000 <mi>Mg</mi>\u0000 <mi>n</mi>\u0000 <mo>−</mo>\u0000 </msubsup>\u0000 </mrow></math> (<i>n</i> = 3–30) clusters, new structures have been found for sizes <i>n</i> = 6, 7, 12, 14, and medium-sized 21–30 were first determined. The high consistency between the simulated spectra and the experimental ones once again demonstrates the efficiency of the PGA program. Based on the ground-state structures of these <span></span><math>\u0000 <mrow>\u0000 <msubsup>\u0000 <mi>Mg</mi>\u0000 <mi>n</mi>\u0000 <mo>−</mo>\u0000 </msubsup>\u0000 </mrow></math> (<i>n</i> = 3–30) clusters, their structural evolution and electronic properties were subsequently explored. The performance on Au₂₀, B₂₀, <span></span><math>\u0000 <mrow>\u0000 <msubsup>\u0000 <mtext>ZrSi</mtext>\u0000 <mrow>\u0000 <mn>17</mn>\u0000 <mo>–</mo>\u0000 <mn>20</mn>\u0000 </mrow>\u0000 <mo>−</mo>\u0000 </msubsup>\u0000 </mrow></math>, and <span></span><math>\u0000 <mrow>\u0000 <msubsup>\u0000 <mi>Mg</mi>\u0000 <mi>n</mi>\u0000 <mo>−</mo>\u0000 </msubsup>\u0000 </mrow></math> (<i>n</i> = 3–30) clusters indicates the promising potential of the PGA program for exploring the global minima of other clusters. The code is available for free upon request.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2764-2770"},"PeriodicalIF":3.4,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141994617","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}