Tight-binding Research Articles

Periodic GFN1-xTB Tight Binding: A Generalized Ewald Partitioning Scheme for the Klopman–Ohno Function

Periodic GFN1-xTB Tight Binding: A Generalized Ewald Partitioning Scheme for the Klopman–Ohno Function

Impact of Fluctuations in the Peridinin-Chlorophyll a-Protein on the Energy Transfer: Insights from Classical and QM/MM Molecular Dynamics Simulations.

The peridinin-chlorophyll a-protein is a light-harvesting complex found in dinoflagellates, which has an unusually high fraction of carotenoids. The carotenoids are directly involved in the energy transfer to chlorophyll with high efficiency. The detailed mechanism of energy transfer and the roles of the protein in the process remain debated in the literature, in part because most calculations have focused on a limited number of chromophore structures. Here we investigate the magnitude of the fluctuations of the site energies of individual and coupled chromophores, as the results are essential to the understanding of experimental spectra and the energy transfer mechanism. To this end, we sampled conformations of the PCP complex by means of classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations. Subsequently we performed (supermolecular) excitation energy calculations on a statistically significant number of snapshots using TD-LC-DFT/CAM-B3LYP and the semiempirical time-dependent long-range corrected density functional tight binding (TD-LC-DFTB2) as the QM method. We observed that the magnitude of the site energy fluctuations is large compared to the differences of the site energies between the chromophores, and this also holds for the coupled chromophores. We also investigated the composition of the coupled states, the effect of coupling on the absorption spectra, as well as transition dipole moment orientations and the possibility of delocalized states with Chl a. Our study thus complements previous computational studies relying on a single structure and establishes the most prominent features of the coupled chromophores that are essential to the robustness of the energy transfer process.

Tight Binding Simulation of the MgO and Mg(OH)2 Hydration and Carbonation Processes.

Magnesium, the lightest engineering metal, has MgO and Mg(OH)2 as its common corrosion products, which can also be used for CO2 storage due to their chemical reactivity. In this study, we developed a DFTB model with monopole, dipole, and quadrupole electrostatics for magnesium compounds containing oxygen, hydrogen, and carbon and applied it in both static and molecular dynamics (DFTB-MD) calculations of the MgO and Mg(OH)2 hydration and carbonation processes. With our new model, the Electron Localization Function (ELF) and Charge Density Difference (CDD) were computed as part of the electronic structure analysis, providing insights into the electronic mechanism of MgO and Mg(OH)2 hydration and carbonation processes. The geometry for the brucite-water bulk system was analyzed, including the reconstruction of near-surface water molecules which may influence the dissolution, hydration, and carbonation processes. By comparing experimental, DFT, classical MD results and the results from other parameter set, the accuracy of the model was assessed. A strong covalent bond between CO2 and the (001) surface of MgO leads to the formation of a CO3 group, while no such CO3 group forms on the (101̅1) surface of Mg(OH)2. Defect sites, however, are more favorable for the formation of the CO3 group. In contrast, covalent bonds are not found for either surface when water interacted with them. This work provides new insights into the behavior of magnesium compounds interacting with water and carbon dioxide using our model, and it introduces a tool for effectively analyzing chemical electronic structures and bonding mechanisms.

Cleavage of structured RNAs is accelerated by high affinity DNAzyme agents.

DNAzymes (Dz) have been suggested as sequence-specific agents for cleaving RNA for therapeutic purposes. This concept paper discusses the challenges of Dz 10-23 in cleaving folded RNA substrates. Dz with traditionally designed RNA binding arms (Tm ~ 37oC) have low affinity to the folded RNA substrates, which limits the overall cleavage rate. The RNA cleavage can be facilitated using Dz with high-affinity arms. However, this strategy is efficient only for cleaving RNA into folded RNA products. The unfolded products inhibit multiple substrate turnover. In a more general approach, Dz should be equipped with additional RNA binding arms to achieve tight RNA binding. This can be accomplished by bivalent and multivalent Dz constructs that have multiple catalytic cores. In all cases, high selectivity toward single nucleotide variations can be achieved in addition to multiple turnovers. The presence of RNase H stabilizes the Dz:RNA complex and reduces its selectivity but significantly increases RNA cleavage efficiency. This work proposes changes in the algorithms of Dz design, which can help in constructing potent Dz agents for RNA inhibition both in cell cultures and in vivo. The concept article is supplemented with a quiz testing knowledge of the main concepts used in this work.

Valley-Contrasting Linear Dichroism and Excitonic Condensation in LaOBiS2.

In conjunction with the first-principles calculations, we confirm the fascinating valley-selective linear dichroism and the possibility of excitonic condensation in multiatomic-layer LaOBiS2 of a tetragonal lattice by the effective tight-binding model and many-body perturbation theory. In LaOBiS2, which indicates a spontaneous valley polarization due to crystalline symmetry reduction rather than conventional time-reversal symmetry breaking, we unravel that the excitons in X and X' valleys exclusively coupled to x- and y-linearly polarized lights, respectively. In sharp contrast to coupled quantum wells and van der Waals architectures, a new type of spatially indirect exciton is identified in single-crystal LaOBiS2, manifesting itself as an engaging platform for investigating the excitonic Bose-Einstein condensation (BEC) and superfluidity. In light of large binding energy, large radius, and small effective mass of the exciton, the transition temperature for BEC and superfluidity achieves record-high values of 325.1 and 81.3 K, respectively.

First-principles calculations of quartz–coesite interfaces

Atomistic interface structures compatible with periodic boundary conditions for the strain-induced subsolidus martensitic transition between quartz and coesite have been investigated. We identified layers of atoms that remained unchanged in terms of neighbor interactions throughout the transformation. Our analysis revealed that the orientation relationships between quartz and coesite, namely (1011)Qz||(010)Coe and (1321)Qz||(010)Coe, are consistent with experimental observations. Using density-functional-theory-based tight-binding model calculations, we determined an interface energy of approximately 660 mJ m−2 for these interfaces and strain energies of 196 (6) and 2760 (160) J mol−1 atom−1 for the (1321)Qz||(010)Coe and (1011)Qz||(010)Coe oriented interfaces, respectively. To visualize these interface structures and facilitate their identification in experiments, we simulated high-resolution transmission electron microscopy images and electron diffraction patterns.

Advancing band structure simulations of complex systems of C, Si and SiC: a machine learning driven density functional tight-binding approach.

We present a machine learning (ML) workflow for optimizing electronic band structures using density functional tight binding (DFTB) to replicate the results of costly hybrid functional calculations. The workflow is trained on carbon, silicon, and silicon carbide systems, encompassing bulk, slab, and defect geometries. Our method accurately reproduces hybrid functional results by applying a DFTB-ML scheme to train and predict the scaling parameters of two-center integrals and on-site energies, which is particularly accurate for electronic band structures near the Fermi energy. The DFTB-ML model demonstrates excellent scaling transferability, enabling training on smaller systems while maintaining hybrid functional-level accuracy when predicting larger systems. The high accuracy and adaptability of our model highlight its potential for precise band structure predictions across diverse chemical environments.

DYNAMICAL ANALYSIS OF ELECTRON-PHONON INTERACTIONS IN QUANTUM DOT MOLECULAR SYSTEMS

Theoretically, we analyze the effect of electron-phonon interaction in the dynamics of an electron trapped in a benzene-shaped quantum dot-molecule. The molecule consists of six small quantum dots coupled locally to a phonon bath. The tight-binding model is used to write the model Hamiltonian and to derive the set of equations of motion of different types of benzene quantum dot-molecules. The time-dependent model has a numerically exact solution, producing rich dynamics. The values of time-dependent occupations strongly depend on the electron-phonon coupling. A notable result of the present work is that one can tune the energy levels of quantum dots, the quantum contacts energy levels, and the benzene quantum dot-molecule configuration to enhance or diminish the heat flow between electrons and phonons in molecular junctions. This study contributes to the dynamic and expanding field of quantum dot molecular systems, providing insights for broader technological applications.

High-throughput virtual screening and empirical validation of probable inhibitors of Plasmodium falciparum and vivax glutathione transferase using bromosulfophthalein as the benchmark ligand.

Plasmodium falciparum Glutathione S-Transferase (PfGST) and Plasmodium vivax Glutathione S-Transferase (PvGST) play vital roles in detoxification and parasite survival, making them key targets for antimalarial drug development. These enzymes offer potential for creating therapies with improved efficacy, reduced resistance, and minimal toxicity. Natural compounds like flavonoids, known for their antiplasmodial properties, are promising scaffolds for new drug designs. This study computationally screened baicalin (BA) and 5,7,3'-Trihydroxy-6,4',5'-trimethoxyflavone (TTMF), synthesizable and affordable flavonoids from the MedChemExpress database, as potential inhibitors of PfGST and PvGST, outperforming BSP. Molecular dynamics simulations revealed that BA and TTMF stabilize enzyme interactions through hydrogen bonds and van der Waals forces, altering protein compactness and dynamics, suggesting non-competitive, allosteric inhibition. Empirical validation showed complete enzymatic inhibition by BA and TTMF with IC50 values of 1.69 and 1.71 μM, respectively, while minimizing human GST inhibition. Using 1-chloro-2,4-dinitrobenzene and reduced glutathione (GSH) as substrates, BA and TTMF demonstrated tight binding near the hydrophobic substrate-binding sites of PfGST and PvGST. Spectroscopic analysis using 8-anilino-1-naphthalenesulfonate (ANS) confirmed their ligandin effects and binding at the dimer interface. These findings highlight BA and TTMF as promising candidates for developing effective antimalarial therapies.

The ENaC taste receptor’s perceived mechanism of mushroom salty peptides revealed by molecular interaction analysis

The ENaC receptor acts as a taste receptor to recognize and perceive salty substances. This study explored the mechanisms by which the ENaC taste receptor recognizes and binds mushroom-derived salty peptides using molecular interaction and molecular simulation. The three subunits α, β, and γ of the ENaC taste receptor (SCNN1α, SCNN1β, and SCNN1γ) showed different recognition characteristics for the salty peptide. The salty peptide binding to the SCNN1α receptor was an entropy-driven reaction, while to SCNN1β and SCNN1γ was an enthalpy-driven reaction. With the salty peptide spatial resistance increasing, salty peptides bind to the ENaC taste receptor shifted from receptor pockets binding to receptor surface binding, with salty octapeptide ESPERPFL preferentially binding to amino acid residues in the receptor pockets 2, 3, and 4, salty nonapeptide KSWDDFFTR and decapeptide RIEDNLVIIR binding to amino acid residues in the pockets 2, 4 and on the surface of the receptor, and salty undecapeptide GQEDYDRLRPL preferentially binding to the atoms on the surface of the receptor. Receptor extracellular arginine, glutamate, aspartate, and lysine residues were the critical amino acid residues recognized to bind salty peptides. The salty peptide-ENaC receptor binding complex was stable around 0.3 nm, and the tight and multisite binding was the main reason the ENaC receptor sensed the salty peptide, enabling it to exert its taste effect. This research can provide a theoretical basis for understanding the taste properties of salty peptides recognized and perceived by the ENaC taste receptor.

Strain dependent properties of the Bi2Sr2CaCu2O8 superconductor: an ab initio study.

Abstract Ab initio calculations were performed to investigate the effects of strain on the structural, electronic, and vibrational properties of the Bi2Sr2CaCu2O8 (Bi-2212) compound. To accurately represent the Bi-2212 ground state, a modulation correction was applied, generating a distorted structure with lower symmetry that better represents the incommensurate superstructure observed in this compound. Phonon spectra and electronic properties were calculated under various levels of c-axis strain, ranging from -2.0% to +2.0%. For the electronic properties, minor changes were observed in the electronic density of states and band structure. However, trends could be identified by analyzing the fine features of the band structure through a tight-binding model. The most significant changes were observed in the vibrational properties, where different trends emerged for the various Raman-active modes. The changes observed in the vibrational and electronic properties can be explained by examining the distances and overlap populations of the relevant bonds, as well as the reduced mass of certain modes. This work can serve as an input for analyzing experimental measurements, helping to distinguish structural effects from others.

MLTB: Enhancing Transferability and Extensibility of Density Functional Tight-Binding Theory with Many-body Interaction Corrections.

We present a hybrid semiempirical density functional tight-binding (DFTB) model with a machine learning neural network potential as a correction to the repulsive term. This hybrid model, termed machine learning tight-binding (MLTB), employs the standard self-consistent charge (SCC) DFTB formalism as a baseline, enhanced by the HIP-NN potential as an effective many-body correction for short-range pairwise repulsive interactions. The MLTB model demonstrates significantly improved transferability and extensibility compared to the SCC-DFTB and HIP-NN models. This work provides a practical computational framework for developing reliable SCC-DFTB models with additional many-body corrections that more closely approach the DFT level of accuracy. We illustrate this method with the development of an accurate model for the thorium-oxygen system, applied to the study of its nanocluster structures (ThO2)n.

RNA recognition by minimal ProQ from Neisseria meningitidis.

Neisseria meningitidis minimal ProQ is a global RNA binding protein belonging to the family of FinO-domain proteins. The N. meningitidis ProQ consists only of the FinO domain accompanied by short N- and C-terminal extensions. To better understand how this minimal FinO-domain protein recognizes RNAs, we compared its binding to seven different natural RNA ligands of this protein. Next, two of these RNAs, rpmG-3' and AniS, were subject to further mutational studies. The data showed that N. meningitidis ProQ binds the lower part of the intrinsic transcription terminator hairpin, and that the single-stranded sequences on the 5' and 3' side of terminator stem are required for tight binding. However, the specific lengths of 5' and 3' RNA sequences required for optimal binding differed between the two RNAs. Additionally, our data show that the 2'-OH and 3'-OH groups of the 3' terminal ribose contribute to RNA binding by N. meningitidis ProQ. In summary, the minimal ProQ protein from N. meningitidis has generally similar requirements for RNA binding as the isolated FinO domains of other proteins of this family, but differs from them in detailed RNA features that are optimal for specific RNA recognition.

Biochemical evidence for the diversity of LHCI proteins in PSI-LHCI from the red alga Galdieria sulphuraria NIES-3638.

Red algae are photosynthetic eukaryotes whose light-harvesting complexes (LHCs) associate with photosystem I (PSI). In this study, we examined characteristics of PSI-LHCI, PSI, and LHCI isolated from the red alga Galdieria sulphuraria NIES-3638. The PSI-LHCI supercomplexes were purified using anion-exchange chromatography followed by hydrophobic-interaction chromatography, and finally by trehalose density gradient centrifugation. PSI and LHCI were similarly prepared following the dissociation of PSI-LHCI with Anzergent 3-16. Polypeptide analysis of PSI-LHCI revealed the presence of PSI and LHC proteins, along with red-lineage chlorophyll a/b-binding-like protein (RedCAP), which is distinct from LHC proteins within the LHC protein superfamily. RedCAP, rather than LHC proteins, exhibited tight binding to PSI. Carotenoid analysis of LHCI identified zeaxanthin, β-cryptoxanthin, and β-carotene, with zeaxanthin particularly enriched, which is consistent with other red algal LHCIs. A Qy peak of chlorophyll a in the LHCI absorption spectrum was blue-shifted compared with those of PSI-LHCI and PSI, and a fluorescence emission peak was similarly shifted to shorter wavelengths. Based on these results, we discuss the diversity of LHC proteins and RedCAP in red algal PSI-LHCI supercomplexes.

Quantum anomalous Hall effect in a nonmagnetic bismuth monolayer with a high Chern number.

The quantum anomalous Hall effect (QAHE) with a high Chern number hosts multiple dissipationless chiral edge channels, which is of fundamental interest and promising for applications in spintronics. However, QAHE is currently limited in two-dimensional (2D) ferromagnets with Chern number . Using a tight-binding model, we put forward that Floquet engineering offers a strategy to achieve QAHE in 2D nonmagnets, and, in contrast to generally reported QAHE in 2D ferromagnets, a high-Chern-number is obtained accompanied by the emergence of two chiral edge states. Moreover, based on the first-principles calculations, we identify tetragonal bismuth as an experimentally feasible candidate of the proposed light-induced QAHE, where remarkably a topological phase transition from the 2D 2 topological insulator to QAHE occurs. Our results open new opportunities to realize exotic QAH physics that increases the feasibility of experimental realization and applications in spintronics devices.

Probing structural requirements for thiazole-based mimetics of sunitinib as potent VEGFR-2 inhibitors.

Novel thiazole analogs 3a, 3b, 4, 5, 6a-g, 8a, 8b, 9a-c, 10a-d and 11 were designed and synthesized as molecular mimetics of sunitinib. In vitro antitumor activity of the obtained compounds was investigated against HepG2, HCT-116, MCF-7, HeP-2 and HeLa cancer cell lines. The obtained data showed that compounds 3b and 10c are the most potent members toward HepG2, HCT-116, MCF-7 and HeLa cells. Moreover, compounds 3a, 3b, 6g, 8a and 10c were assessed for their in vitro VEGFR-2 inhibitory activity. Results proved that compound 10c exhibited outstanding VEGFR-2 inhibition (IC50 = 0.104 μM) compared to sunitinib. Compound 10c paused the G0-G1 phase of the cell cycle in HCT-116 and MCF-7 cells and the S phase in HeLa cells. Additionally, compound 10c elevated caspase-3/9 levels in HCT-116 and HeLa cells, leading to cancer cell death via apoptosis. Furthermore, compound 10c showed a significant reduction in tumor volume in Swiss albino female mice as an in vivo breast cancer model. Docking results confirmed the tight binding interactions of compound 10c with the VEGFR-2 binding site, with its binding energy surpassing that of sunitinib. In silico PK studies predicted compound 10c to have good oral bioavailability and a good drug score with low human toxicity risks.

Macrocyclic Peptide-Based Dual-Sensor Platform for Linkage-Specific Visualization of Ubiquitin Chain Assembling in Live Cells.

Intracellular monitoring of protein ubiquitination and differentiating polyubiquitin chain topology are crucial for understanding life processes and drug discovery, which is challenged by the high complexity of the ubiquitination process and a lack of molecular tools. Herein, a synthetic dual-sensor platform specific for K48-linked ubiquitin oligomers was tailored for in situ visualization of polyubiquitin chain assembling in live biosystems. This is achieved using macrocyclic peptides as recognition motifs and a tetraphenylethylene derivative as an activatable reporter. The efficient cell penetration, tight binding, and protection of polyubiquitin delivered a "freeze-and-image" approach, allowing fluorescent readout of polyubiquitin linkage type and chain elongation without perturbing the physiological environment. Motivated by these unique features, mapping of K48-ubiquitination dynamics during protein degradation was facilely achieved. Rapid, sensitive, and intracellular assessment of the mechanism of action and potency dependence for proteolysis-targeting chimeras (PROTACs) was demonstrated, presenting the sensors as promising molecular tools for PROTAC drug development.

Second-order topological insulators in Kekulé-patterned hexagonal biphenylene networks

Biphenylene network, a two-dimensional material, has recently been extensively studied, owing to its potential applications. Here, we introduce an experimentally synthesized configuration of hexagonal biphenylene network (h-BPN) as a second-order topological insulator (SOTI). We begin by discussing the higher-order topological origin of h-BPN, which is an extended model of the Kekulé lattice characterized by a multi-node π-conjugation. Through first-principles calculations and tight-binding model, we reveal SOTI in h-BPN, characterized by non-zero fractional corner charges. Furthermore, we show that by varying the number of biphenylene units, h-BPN exhibits adjustable second-order topological phases with alternating parity. Specifically, odd biphenylene indices in the h-BPN system correspond to a SOTI, while even indices result in a trivial insulator. We propose that the h-BPN evolves from the Kekulé lattice. These materials will have important applications in two-dimension devices as higher-order topological materials.

Electronic band evolution between Lieb and kagome nanoribbons

We investigate the electronic properties of nanoribbons made out of monolayer Lieb, transition, and kagome lattices using the tight-binding model with a generic Hamiltonian. It allows us to map the evolutionary stages of the interconvertibility process between Lieb and kagome nanoribbons by means of only one control parameter. Results for the energy spectra, the density of states, and spatial probability density distributions are discussed for nanoribbons with three types of edges: straight, bearded, and asymmetric. We explore for different nanoribbon terminations: (i) the semiconductor-metallic transition due to the interconvertibility of the Lieb and kagome lattices, (ii) the effect of both nanoribbon width and inclusion of the next-nearest-neighbor hopping term on the degeneracy of the quasi-flat states, (iii) the behavior of the energy gap versus the nanoribbon width, (iv) the existence and evolution of edge states, and (v) the nodal spatial distributions of the total probability densities of the non-dispersive states.

Quick Freezing-Induced Au Nanoparticle Aggregates (QFIAAs) for Near-IR (NIR) Surface-Enhanced Raman Scattering (SERS) Substrates.

Here, we report a simple method to prepare near-IR (NIR) surface-enhanced Raman scattering (SERS) substrates by quickly freezing a citrate-capped Au nanoparticle (AuNP) solution in liquid nitrogen, followed by thawing it at room temperature. This process aggregates AuNPs in a controlled manner by forming ice crystals with smaller grain sizes when compared to a slow freezing process. The resulting smaller AuNP aggregates remain suspended in solution long enough to conduct high-throughput chemical analysis in a microwell plate using the NIR SERS spectroscopy. We named these aggregates quick freezing-induced AuNP aggregates (QFIAAs). The aggregation state of QFIAAs in solution is stable for at least three months when stored at 4 °C. Several QFIAAs were prepared using monodisperse citrate-capped AuNPs of various sizes. QFIAAs prepared from AuNPs with an average diameter of 70 nm (70 nm QFIAAs) showed the best performance, considering both NIR SERS activity and the repeatability of the results. The NIR SERS enhancement factor of the 70 nm QFIAAs measured using 57 nM Rhodamine 6G (R6G) was 5 × 104. The R6G molecules could not displace the citrates present in the hotspots of QFIAAs, indicating that the long-term stability of QFIAAs originates from the tight interparticle binding through the citrates. The limit of detection (LOD) of R6G was 2 × 101 nM using the 70 nm QFIAAs. We anticipate that the QFIAA system can be used not only to screen reporter molecules for the NIR SERS bioimaging but also to detect analytes with background fluorescence that can be suppressed with NIR excitation wavelengths.