In this paper, we implement a GPU-accelerated molecular structure clustering module in FSATOOL (https://github.com/fsatool/fsatool.github.io). It supports K-medoids method, best-fit RMSD metric, multi-GPU platform and single or double precision data type. The clustering quality is indicated by Davies-Bouldin index (DBI) and Residue-Similarity index (RSI). Performance test shows that the program is able to complete the clustering calculation for one million snapshots of a 33-residue protein in a few seconds. This is hundreds of times faster than CPU. The program can be used as a high-throughput analysis tool for long molecular dynamics simulation trajectories.

DFT calculations of vibrational spectra of cluster models of ionic liquid (IL) and its aqueous solutions accurately reproduce the experimental spectra. This suggests a close correspondence of the cluster models to actual neat and aqueous IL, and allows to distinguish spectral signatures of contact and solvent-shared ion pairs.

Singlet fission (SF) is a promising pathway to generate multiple charge carriers from a single photon. Possible applications reach from photovolatic cells to quantum computing. A key intermediate in the process is the singlet-coupled triplet pair or multi-excitonic (ME) state. Despite many computational investigations emphasising the ME state, studies exploring the full spin manifold are scarce. This work investigates singlet, triplet and quintet ME species in a series of well-known covalently linked pentacene derivatives.

Adsorption and decomposition of ammonium perchlorate at several rutile and anatase surfaces were studied theoretically and experimentally.

Parallel tempering is used in elucidating energetics and spectroscopic aspects of cyanate-water clusters. For this type of clusters, a deterministic strategies are bound to face problems and hence the switch over to a stochastic route.

A strategy is described to inactivate ERRγ by competing with the native AF2 helical tail for its cognate binding site on the protein surface of ERRγ ligand-binding domain. A class of peptidic antagonists is derived from the ERRγ AF2 region characterized by a self-binding peptide, which can rebind potently to the AF2-cognate site by reducing its intrinsic disorder with hydrocarbon stapling.

Simulations of bifurcation dynamics, emanating from the ambimodal transition state, were conducted across a broad temperature range. The distribution of branching fractions displayed significant dependence on both temperature and potential energy landscapes. As temperature increases, trajectories tend to linger for longer periods in the intermediate region of the potential energy surface.

We demonstrate how the optimization of spin-polarization parameters strongly improves the accuracy of extended tight-binding methods. Further, we introduce an optimization strategy based on a sensitivity analysis for an efficient system- or property-dependent parameter optimization.

Based on the results of coupled-cluster methodologies, the cationic species of the C_nH₂ (n = 2 – 6) families, previously detected in the ion-induced desorption of solid methane, were identified. The calculated harmonic vibrational frequencies, vertical transition energies, and oscillator strengths allow for distinguishing between the neutral and cationic C_nH₂ species. Reliable computational data can facilitate the interpretation of interstellar observations.

Cooperativity, defined as intermolecular delocalization of electrons, increases nonlinearly with the size of a cyclic water clusters. O-atoms provide a vast majority of electrons that “travel mainly on a privileged density highway” (⋅⋅⋅O–H⋅⋅⋅O–H⋅⋅⋅O–H⋅⋅⋅) using H-bond density bridges linking water molecules.

The pre-activation steps in the mechanism of nitrogenase have been studied, including the release and rebinding of a sulphide.

1. Density functional theory including the solvent model has been used for studying the IR spectrum of H${\hspace{0.17em}}_2$O:HCN mixtures.

2. The solvent effect is found crucial to enhance accuracy compared to pure gas-phase modeling.

3. Interestingly, the employed dielectric constant value has shown no significant impact on the final spectrum.

4. A simple methodology is suggested to minimize the root mean square deviation between the calculated and experimental data. This novel approach not only enhances the quality of the final IR spectrum of H${\hspace{0.17em}}_2$O:HCN but suggests itself also for capturing relevant spectral features in the case of other mixtures.

The Wade's rules and Lipscomb's styx approach constitute a conceptual basis of chemical bonding in closo hydroborane clusters and similar compounds. Based on 3-center electron sharing indices obtained from DFT wavefunctions, the DR approach for analysis of multicenter bonding in clusters and intermetallic compounds is presented. By triangulation of multicenter bonding, it is capable characterizing the clusters' global mixed 2- and 3-center type of bonding and decompose it into local bond and triangle contributions.

Taking advantage of the Rust-based Electronic-Structure Toolkits (REST), we examine the XYG3-type doubly hybrid (xDH) methods. Our study ushers in a pivotal advance with a renormalized xDH method R-xDH7-SCC15, which not only outperforms other methods for main-group chemistry, but also achieves an unprecedented accuracy for transition-metal chemistry.

The solvated absorption spectra of p-nitroaniline (pNA), a prototypical push-molecule with electron-withdrawing and electron-donor groups, were investigated focusing on intermolecular charge transfer effects. Eight solvents of different polarities were examined. The ab initio wave function second-order algebraic diagrammatic construction (ADC(2)) combined with implicit and explicit solvation models were employed. For the first time, a second absorption band, not previously measured or computed theoretically, was found and characterized.

In this study, a graph neural network (GNN) and a convolutional neural network (CNN) are integrated sequentially to predict protein-ligand binding affinity. The incorporation of intermediate outputs from the GNN into input features of the CNN yields a substantial improvement in prediction accuracy.

A full-dimensional time-independent coupled channel capture method is proposed for atom-triatom systems, and applied to the H/D + O₃ reactions.

The accuracy of machine learning potentials (MLPs) depends on the quality of training data. MLPs constructed with insufficient data cause unphysical behavior. However, the indiscriminate expansion of the training data is an unwelcome approach from the standpoint of computational cost. This work proposed new training data sampling method, radial distribution function (RDF)-based data sampling, which improves the accuracy of MLPs. The incorporation of new training data via our sampling method led to a notable improvement in the RDFs and other physical properties. Our results demonstrate that this method is useful for constructing MLPs which are robust to extrapolation from molecular cluster system to periodic system.

Calculation of absorption spectra, excited state energies and charge transfer character (NTOs) of mitorubrins using TD-DFT and CC2 methods.

The computational cost of the DF-EOM-OCCD method for excitation energies is compared with that of the conventional EOM-OCCD method. Our results demonstrate that DF-EOM-OCCD excitation energies are dramatically accelerated compared to EOM-OCCD. There are almost 17-fold reductions for the C5H12 molecule in a aug-cc-pVTZ basis set with the RHF reference.

We herein report a DFT mechanistic study on the formation of aryl sulfonyl fluorides via Bi(III) redox-neutral catalysis. The significant role of base K₃PO₄, the origin of SO₂ insertion into the Bi(III)C(sp²) bond, and the competing pathways between S(IV)→S(VI) and Bi(III)→Bi(V) were discussed. Moreover, we rationally design new Bi(III)-catalyzed small molecule (NO₂, CO₂, etc.) insertion reactions and new Bi(III)/Sb(III)-catalysts for aryl sulfonyl fluoride formation reactions.

An influence of a battery of electronic structure/force field methods, gas-phase Gibbs free energy thermodynamic correction, and continuum solvation effect on organic carbonate molecular cluster (S)_n conformational and binding energies is examined. The results are relevant to molecular modeling of ion transfer in lithium- and sodium-ion batteries for which organic carbonates are primary solvents.