Journal of Computational Chemistry最新文献

Recently tetraspanin CD151 has been identified as an important biological target involved in metastatic processes which include cell adhesion, tumor progression processes, and so forth in different types of cancers, such as breast cancer and glioblastoma. This in Silico study considered 1603 compounds from the Food and Drug Administration database, after performing an ADMET analysis; we selected 853 ligands, which were used for docking analysis. The most promising ligands were selected from docking studies, based on two criteria: (a) showed lowest affinity to the CD151 protein and (b) they interact with the QRD motif, located in the second extracellular loop. Furthermore, we investigate the stability of the protein-ligand complexes through MD simulations as well as free energy MM-PBSA calculations. From these results, loperamide and glipizide were identified as the best evaluated drugs. We suggest an in vitro analysis is needed to confirm our in silico prediction studies.

Easy and effective usage of computational resources is crucial for scientific calculations. Following our recent work of machine-learning (ML) assisted scheduling optimization [J. Comput. Chem. 2023, 44, 1174], we further propose (1) the improved ML models for the better predictions of computational loads, and as such, more elaborate load-balancing calculations can be expected; (2) the idea of coded computation, that is, the integration of gradient coding, in order to introduce fault tolerance during the distributed calculations; and (3) their applications together with re-normalized exciton model with time-dependent density functional theory (REM-TDDFT) for calculating the excited states. Illustrated benchmark calculations include P38 protein, and solvent model with one or several excitable centers. The results show that the improved ML-assisted coded calculations can further improve the load-balancing and cluster utilization, owing primarily profit in fault tolerance that aims at the automated quantum chemical calculations for both ground and excited states.

Using embedding methods, compounds with similar properties will be closely located in latent space, and these embedding vectors can be used to find other compounds with similar properties based on the distance between compounds. However, they often require computational resources and programming skills. Here we develop Dr.Emb Appyter, a user-friendly web-based chemical compound search platform for drug discovery without any technical barriers. It uses embedding vectors to identify compounds similar to a given query in the embedding space. Dr.Emb Appyter provides various types of embedding methods, such as fingerprinting, SMILES, and transcriptional response-based methods, and embeds numerous compounds using them. The Faiss-based search system efficiently finds the closest compounds of query in the library. Additionally, Dr.Emb Appyter offers information on the top compounds; visualizes the results with 3D scatter plots, heatmaps, and UpSet plots; and analyses the results using a drug-set enrichment analysis. Dr.Emb Appyter is freely available at https://dremb.korea.ac.kr.

The present computational study provides a benchmark of density functional theory (DFT) methods in describing hydrogen evolution processes catalyzed by [Cp*Rh]-containing organometallic complexes. A test set was composed of 26 elementary reactions featuring chemical transformations and bonding situations essential for the field, including the emerging concept of non-innocent Cp* behavior. Reference values were obtained from a highly accurate 3/4 complete basis set and 6/7 complete PNO space extrapolated DLPNO-CCSD(T) energies. The performance of lower-level extrapolation procedures was also assessed. We considered 84 density functionals (DF) (including 13 generalized gradient approximations (GGA), nine meta-GGAs, 33 hybrids, and 29 double-hybrids) and three composite methods (HF-3c, PBEh-3c, and r²SCAN-3c), combined with different types of dispersion corrections (D3(0), D3BJ, D4, and VV10). The most accurate approach is the PBE0-DH-D3BJ (MAD of 1.36 kcal mol⁻¹) followed by TPSS0-D3BJ (MAD of 1.60 kcal mol⁻¹). Low-cost r²SCAN-3c composite provides a less accurate but much faster alternative (MAD of 2.39 kcal mol⁻¹). The widely used Minnesota-family M06-L, M06, and M06-2X DFs should be avoided (MADs of 3.70, 3.94, and 4.01 kcal mol⁻¹, respectively).

Development of organic nonlinear optical materials has become progressively more important due to their emerging applications in new-generation photonic devices. A novel series of chromophores based on innovative thiophene and furan-fused cyclopentadienyl bridge with various powerful donor and acceptor moieties were designed and theoretically investigated for applications in nonlinear optics. To unravel the structure–property relationship between this new push-pull conjugated systems and their nonlinear optical property, multiple methods, including density of states analysis, coupled perturbed Kohn–Sham (CPKS) method, sum-over-states (SOS) model, the two-level model (TSM), hyperpolarizability density analysis, and the (hyper)polarizability contribution decomposition, were performed to comprehensively investigated the nonlinear optical and electronic properties of this new π-system. Due to excellent charge transfer ability of new bridge and distinctive structure of donor and acceptor, the designed chromophores exhibit deep HOMO levels, low excitation energy, high dipole moment difference and large hyperpolarizability, indicating the appealing air-stable property and remarkable electrooptic performance of them. Importantly, THQ-CS-A3 and PA-CS-A3 shows outstanding NLO response properties with β_tot value of 6953.9 × 10⁻³⁰ and 5066.0 × 10⁻³⁰ esu in AN, respectively. The influence of the push-pull strength, the heterocycle and the π-conjugation of new bridge on the nonlinear optical properties of this novel powerful systems are clarified. This new series of chromophores exhibit remarkable electro-optical Pockels and optical rectification effect. More interestingly, PA-CS-A3 and THQ-CS-A2 also show appealing SHG effect. This study will help people understand the nature of nonlinear optical properties of innovative heteroarene-fused based cyclopentadienyl chromophores and offer guidance for the rational design of chromophores with outstanding electrooptic (EO) performance in the future.

Chlorine is an important chemical which has long been produced in chlor-alkali process using dimensionally stable anodes (DSA). However, some serious drawbacks of DSA inspire the development of alternative anodes for chlorine evolution reaction (CER). In this study, we focused on the graphene- and carbon nanotube-supported platinum tetra-phenyl porphyrins as electrocatalysts for CER, which have been theoretically investigated based on density functional theory. Our results reveal that the supported substrates possess potential CER electrocatalytic activity with very low thermodynamic overpotentials (0.012–0.028 V) via Cl* pathway instead of ClO*. The electronic structures analyses showed that electron transfer from the support to the adsorbed chlorine via the Pt center leads to strong Pt–Cl interactions. Furthermore, the supported electrocatalysts exhibited excellent selectivity toward CER because of high overpotentials and reaction barriers of oxygen evolution process. Therefore, our results may pave the way for designing CER electrocatalyst utilizing emerging carbon nanomaterials.

The electronic structure of the strongly correlated electron system plutonium hexaboride is studied by using single-particle approximations and a many-body approach. Imaginary components of impurity Green's functions show that 5f_j=5/2 and 5f_j=7/2 manifolds are in conducting and insulating regimes, respectively. Quasi-particle weights and their ratio suggest that the intermediate coupling mechanism is applicable for Pu 5f electrons, and PuB₆ might be in the orbital-selective localized state. The weighted summation of occupation probabilities yields the interconfiguration fluctuation and average occupation number of 5f electrons n_5f ~ 5.101. The interplay of 5f–5f correlation, spin-orbit coupling, Hund's exchange interaction, many-body transition of 5f configurations, and final state effects might be responsible for the quasiparticle multiplets in electronic spectrum functions. Prominent characters in the density of state, such as the coexistence of atomic multiplet peaks in the vicinity of the Fermi level and broad Hubbard bands in the high-lying regime, suggest that PuB₆ could be identified as a Racah material. Finally, the quasiparticle band structure is also presented.

Metal halide perovskites are crystalline materials with a sharp increase in popularity and rapidly becoming a major contender for optoelectronic device applications. In this work, we provide the optoelectronic features of a possible novel candidate, ZSnCl₃ (Z = Na/K) Sn-based on a detailed numerical simulation. The output of the current computations is compared to the results that are currently available, and a respectable agreement is noted. The studied compounds were cubic in nature and structurally stabe. The mechanical properties reflect the mechanical stability and ductility of the proposed materials. The Sn-based single perovskite compounds proposed in this study are mechanically stable and ductile. The narrow direct band gap for NaSnCl₃ and KSnCl₃ are 1.36 eV and 1.47 eV, respectively, using the HSE06 hybrid function with the Boltztrp2 integrated in Quantum ESPRESSO (QE) software. The effective use of these compounds in perovskite solar cells and other optoelectronic applications was confirmed by optical absorption spectral measurements conducted in the photon energy range of 0–20 eV.

Empirical rovibrational energy levels are presented for the third most abundant, asymmetric carbon dioxide isotopologue, ¹⁶O¹²C¹⁸O, based on a compiled dataset of experimental rovibrational transitions collected from the literature. The 52 literature sources utilized provide 19,438 measured lines with unique assignments in the wavenumber range of 2–12,676 cm⁻¹. The MARVEL (Measured Active Rotational-Vibrational Energy Levels) protocol, which is built upon the theory of spectroscopic networks, validates the great majority of these transitions and outputs 8786 empirical rovibrational energy levels with an uncertainty estimation based on the experimental uncertainties of the transitions. Issues found in the literature data, such as misassignment of quantum numbers, typographical errors, and misidentifications, are fixed before including them in the final MARVEL dataset and analysis. Comparison of the empirical energy-level data of this study with those in the line lists CDSD-2019 and Ames-2021 shows good overall agreement, significantly better for CDSD-2019; some issues raised by these comparisons are discussed.