Journal of Computational Chemistry最新文献

In this work, the effects of two TiO₂ polymorphs on the decomposition of ammonium perchlorate (NH₄ClO₄) were studied experimentally and theoretically. The interactions between AP and various surfaces of TiO₂ were modeled using density functional theory (DFT) calculations. Specifically, the adsorption of AP on three rutile surfaces (1 1 0), (1 0 0), and (0 0 1), as well as two anatase surfaces (1 0 1), and (0 0 1) were modeled using cluster models, along with the decomposition of adsorbed AP into small molecules. The optimized complexes of the AP molecule on TiO₂ surfaces were very stable, indicating strong covalent and hydrogen bonding interactions, leading to highly energetic adsorption reactions. The calculated energy of adsorption (ΔE_ads) ranged from -120.23 to -301.98 kJ/mol, with highly exergonic calculated Gibbs free energy (ΔG_ads) of reaction, and highly exothermic enthalpy of reaction (ΔH_ads). The decomposition of adsorbed AP was also found to have very negative ΔE_dec values between -199.08 and -380.73 kJ/mol. The values of ΔG_dec and ΔH_dec reveal exergonic and exothermic reactions. The adsorption of AP on TiO₂ surfaces anticipates the heat release of decomposition, in agreement with experimental results. The most common anatase surface, (1 0 1), was predicted to be more reactive for AP decomposition than the most stable rutile surface, (1 1 0), which was confirmed by experiments. DFT calculations show the mechanism for activation of the two TiO₂ polymorphs is entropy driven.

Combined density functional theory and multireference configuration interaction methods have been used to elucidate singlet fission (SF) pathways and mechanisms in three regioisomers of side-on linked pentacene dimers. In addition to the optically bright singlets (S ${}_1$ and S ${}_2$ ) and singly excited triplets (T ${}_1$ and T ${}_2$ ), the full spin manifold of multiexcitonic triplet-pair states ( ${}^1$ ME, ${}^3$ ME, ${}^5$ ME) has been considered. In the ortho- and para-regioisomers, the ${}^1$ ME and S ${}_1$ potentials intersect upon geometry relaxation of the S ${}_1$ excitation. In the meta-regioisomer, the crossing occurs upon delocalization of the optically bright excitation. The energetic accessibility of these conical intersections and the absence of low-lying charge-transfer states suggests a direct SF mechanism, assisted by charge-resonance effects in the ${}^1$ ME state. While the ${}^5$ ME state does not appear to play a role in the SF mechanism of the ortho- and para-regioisomers, its participation in the disentanglement of the triplet pair is conceivable in the meta-regioisomer.

The recently developed efficient protocol to explicit quantum mechanical modeling of structure and IR spectra of liquids and solutions (S. A. Katsyuba, S. Spicher, T. P. Gerasimova, S. Grimme, J. Phys. Chem. B 2020, 124, 6664) is applied to ionic liquid (IL) 1-ethyl-3-methylimidazolium bromide (EmimBr), its C2-deuterated analog [Emim-d]Br and its aqueous solutions. It is shown that the solvation strongly modifies frequencies and IR intensities of the CH/CD stretching vibrations (νCH/νCD) of the imidazolium ring. The main vibrational spectroscopic features of the neat IL are reproduced by the simulations for a cluster (EmimBr)₉, in which all three imidazolium CH moieties of the solvated cation form short contacts with three Br^- anions, and another two Br^- anions are located on top and bottom of imidazolium ring. Cluster models of aqueous solutions reproduce the experimental vibrational frequencies of actual solutions, provided that the Br^- anion of solvated contact ion pair (CIP) is situated on top of imidazolium ring, and CH/CD moieties of the latter participate in short contacts with surrounding water molecules. Both structural and spectroscopic analysis allow to interpret the short contacts CH/CD⋯Br^- and CH/CD⋯OH₂ as hydrogen bonds of approximately equal strength. Enthalpies of bonding of these liquid-state H-bonds, estimated with the use of empirical correlations, amount to ca. 1.4 kcal⋅mol^-1, while the analogous estimates obtained for the gas-phase charged species [Emim]₂Br⁺ increase to 5.6 kcal⋅mol^-1. It is shown that formation of solvent-shared ion pair (SIP) in aqueous solution, where the counterions of IL are separated by two water molecules H-bonded to a Br^- anion, produces frequency shifts ΔνCH/CD, strongly different from the case of CIP formation. This difference can be used for IR/Raman spectroscopic differentiation of the type of solvated ion pairs of EmimBr or other related ILs.

Structure clustering is a general but time-consuming work in the study of life science. Up to now, most published tools do not support the clustering analysis on graphics processing unit (GPU) with root mean square deviation metric. In this work, we specially write codes to do the work. It supports multiple threads on multiple GPUs. To show the performance, we apply the program to a 33-residue fragment in protein Pin1 WW domain mutant. The dataset contains 1,400,000 snapshots, which are extracted from an enhanced sampling simulation and distribute widely in the conformational space. Various testing results present that our program is quite efficient. Particularly, with two NVIDIA RTX4090 GPUs and single precision data type, the clustering calculation on 1 million snapshots is completed in a few seconds (including the uploading time of data from memory to GPU and neglecting the reading time from hard disk). This is hundreds of times faster than central processing unit. Our program could be a powerful tool for fast extraction of representative states of a molecule among its thousands to millions of candidate structures.

The development of novel methods in solid-state quantum chemistry necessitates reliable reference data sets for their assessment. The most fundamental solid-state property of interest is the crystal structure, quantified by the lattice parameters. In the last decade, several studies were conducted to assess theoretical approaches based on the agreement of calculated lattice parameters with respect to experiment as a measure. However, most of these studies used a limited number of reference systems with high symmetry. The present work offers a more comprehensive reference benchmark denoted as Sol337LC, which consists of 337 inorganic compounds with 553 symmetry-inequivalent lattice parameters, representing every element of the periodic table for atomic numbers between 1 and 86, except noble gases, the radioactive elements and lanthanoids. The reference values were taken from earlier benchmarks and from measurements at very low temperature or extrapolation to 0 K. The experimental low-temperature lattice parameters were then corrected for zero-point energy effects via the quasi-harmonic approximation for direct comparison with quantum-chemical optimized structures. A selection of standard density functional approximations was assessed for their deviations from the experimental reference data. The calculations were performed with the crystal orbital program CRYSTAL23, applying optimized atom-centered basis sets of triple-zeta plus polarization quality. The SCAN functional family and the global hybrid functional PW1PW, augmented with the D3 dispersion correction, were found to provide closest agreement with the Sol337LC reference data.

The two-dimensional (2D) monolayer material MoSi₂N₄ was successfully synthesized in 2020[Hong et al., Science 369, 670, (2020)], exhibiting a plethora of new phenomena and unusual properties, with good stability at room temperature. However, MA₂Z₄ family monolayer materials involve primarily transition metal substitutions for M atoms. In order to address the research gap on lanthanide and actinide MA₂Z₄ materials, this work conducts electronic structure calculations on novel 2D MSi₂N₄ (M = La, Eu) monolayer materials by employing first-principles methods and CASTEP. High carrier mobility is discovered in the indirect bandgap semiconductor 2D LaSi₂N₄ monolayer (~5400 cm² V^-1 s^-1) and in the spin (spin-down channel) carrier mobility of the half-metallic ferromagnetic EuSi₂N₄ monolayer (~2800 cm² V^-1 s^-1). EuSi₂N₄ monolayer supplements research on spin carrier mobility in half-metallic ferromagnetic monolayer materials at room temperature and possesses a magnetic moment of 5 μ_B, which should not be underestimated. Furthermore, due to the unique electronic band structure of EuSi₂N₄ monolayer (with the spin-up channel exhibiting metallic properties and the spin-down channel exhibiting semiconductor properties), it demonstrates a 100% spin polarization rate, presenting significant potential applications in fields such as magnetic storage, magnetic sensing, and spintronics.

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.