The Hydration Effect and Selectivity of Alkali Metal Ions on Poly(ethylene glycol) Models in Cyclic and Linear Topology

The effects of hydration and alkali metal ion (K⁺, Na⁺, Li⁺) bonding to two structural variants of poly­(ethylene glycol) (PEG), viz., a cyclic (18-crown-6) configuration and a linear chain model with two different lengths, are studied by ab initio density functional theory calculations. A total of 24 structural models are constructed, with different conformations of the PEG chain and its molecular environment. Detailed comparisons of the results enable us to obtain conclusive evidence on the effects of the different components of the solution environment on the PEG structural variants in terms of the binding energy, partial charge distribution, solvation effect, interfacial hydrogen bonding, and cohesion between different structural units in the system composed of PEG, alkali metal ions, and water. On the basis of these comprehensive and precise comparisons, we conclude that the ion–PEG interaction is strongly influenced by the presence of solvent and that the charge transfer in the PEG complex depends crucially on its topology, the type of alkali metal ion, and the solvent. The interaction between alkali metal ions in the two PEG models does not always scale with the ion size but depends on their local environment

Ab Initio Modeling of Structure and Properties of Single and Mixed Alkali Silicate Glasses

A density functional theory (DFT)-based <i>ab initio</i> molecular dynamics (AIMD) has been applied to simulate models of single and mixed alkali silicate glasses with two different molar concentrations of alkali oxides. The structural environments and spatial distributions of alkali ions in the 10 simulated models with 20% and 30% of Li, Na, K and equal proportions of Li–Na and Na–K are studied in detail for subtle variations among the models. Quantum mechanical calculations of electronic structures, interatomic bonding, and mechanical and optical properties are carried out for each of the models, and the results are compared with available experimental observation and other simulations. The calculated results are in good agreement with the experimental data. We have used the novel concept of using the total bond order density (TBOD), a quantum mechanical metric, to characterize internal cohesion in these glass models. The mixed alkali effect (MAE) is visible in the bulk mechanical properties but not obvious in other physical properties studied in this paper. We show that Li doping deviates from expected trend due to the much stronger Li–O bonding than those of Na and K doping. The approach used in this study is in contrast with current studies in alkali-doped silicate glasses based only on geometric characterizations

Atomic-Scale Quantification of Interfacial Binding between Peptides and Inorganic Crystals: The Case of Calcium Carbonate Binding Peptide on Aragonite

Using a specific explicitly solvated interface model between a calcium carbonate binding peptide and crystalline aragonite, we investigate the electronic structure, atomic bonding, solvation effect, and the role of hydrogen bonding on the cohesion, stability, and functionality of this complex hybrid system using density functional calculation. The large interface model is strategically constructed using a stepwise procedure followed by ab initio molecular dynamics to obtain the optimal conformation. The calculated data on the electronic structure and bonding are analyzed in terms of three structural parts: aragonite, peptide, and water. Next, we focus on the binding between aragonite (001) surface and the peptide mediated by water. Finally, specific interatomic bonding between the amino acids in peptide and the (001) surface of aragonite is quantified. A single quantum mechanical metric, the total bond order density (TBOD), infers the dynamic interplay of different competing interactions. Four amino acids HIS1, ARG6, MET7, and TRP11 in the peptide sequence have strong interfacial Ca–O bonding and O···H hydrogen bonding between aragonite and peptide. The calculated Young’s modulus 33.37 GPa is in line with the measured value for nacre. Our approach for interfacial study between aragonite and a calcium carbonate binding peptide offers a broad perspective for probing complex interactions between the biomimetic interfaces. TBOD can be used as an effective parameter in ranking the efficacy of peptide–surface interactions and in providing a programmable design for bio-inspired material interfaces based on computational means

Tables, Figures and structure data from Complex interplay of interatomic bonding in a multi-component pyrophosphate crystal: K₂Mg (H₂P₂O₇)₂·2H₂O

Structure comparison; bond order data; phonon figures, relaxed structure

Impact of Hydrogen Bonding in the Binding Site between Capsid Protein and MS2 Bacteriophage ssRNA

MS2 presents a well-studied example of a single-stranded RNA virus for which the genomic RNA plays a pivotal role in the virus assembly process based on the packaging signal-mediated mechanism. Packaging signals (PSs) are multiple dispersed RNA sequence/structure motifs varying around a central recognition motif that interact in a specific way with the capsid protein in the assembly process. Although the discovery and identification of these PSs was based on bioinformatics and geometric approaches, in tandem with sophisticated experimental protocols, we approach this problem using large-scale ab initio computation centered on critical aspects of the consensus protein–RNA interactions recognition motif. DFT calculations are carried out on two nucleoprotein complexes: wild-type and mutated (PDB IDs: 1ZDH and 5MSF). The calculated partial charge distribution of residues and the strength of hydrogen bonding (HB) between them enabled us to locate the exact binding sites with the strongest HBs, identified to be LYS43-A^–4, ARG49-C^–13, TYR85-C^–5, and LYS61-C^–5, due to the change in the sequence of the mutated RNA

First-principles calculation of lattice distortion, electronic structure and bonding properties of GeTe-based and PbSe-based high-entropy chalcogenides

This file consists of additional figures and tables supporting the manuscript

Designing the Interface of Carbon Nanotube/Biomaterials for High-Performance Ultra-Broadband Photodetection

Inorganic/biomolecule nanohybrids can combine superior electronic and optical properties of inorganic nanostructures and biomolecules for optoelectronics with performance far surpassing that achievable in conventional materials. The key toward a high-performance inorganic/biomolecule nanohybrid is to design their interface based on the electronic structures of the constituents. A major challenge is the lack of knowledge of most biomolecules due to their complex structures and composition. Here, we first calculated the electronic structure and optical properties of one of the cytochrome c (Cyt c) macromolecules (PDB ID: 1HRC) using ab initio OLCAO method, which was followed by experimental confirmation using ultraviolet photoemission spectroscopy. For the first time, the highest occupied molecular orbital and lowest unoccupied molecular orbital energy levels of Cyt c, a well-known electron transport chain in biological systems, were obtained. On the basis of the result, pairing the Cyt c with semiconductor single-wall carbon nanotubes (s-SWCNT) was predicted to have a favorable band alignment and built-in electrical field for exciton dissociation and charge transfer across the s-SWCNT/Cyt c heterojunction interface. Excitingly, photodetectors based on the s-SWCNT/Cyt c heterojunction nanohybrids demonstrated extraordinary ultra-broadband (visible light to infrared) responsivity (46–188 A W^–1) and figure-of-merit detectivity <i>D</i>* (1–6 × 10¹⁰ cm Hz^1/2 W^–1). Moreover, these devices can be fabricated on transparent flexible substrates by a low-lost nonvacuum method and are stable in air. These results suggest that the s-SWCNT/biomolecule nanohybrids may be promising for the development of CNT-based ultra-broadband photodetectors