Dominant Electrostatic Interactions Research Articles

Elucidating capabilities of the ZIF-8-Zn metal organic framework as an adsorbent for COD removal of gas refinery wastewater under mild operating conditions

The chemical oxygen demand (COD) of gas refinery wastewater containing discharged ethanolamines and an extent of hydrocarbons was highly reduced utilizing ZIF-8-Zn metal organic framework adsorbent. The mesoporous adsorbent was initially synthesized through hydrothermal method and characterized via FT-IR, XRD, SEM, TEM, EDX, Zeta potential and BET analysis methods. The COD reduction of the wastewater was then followed with effects of pH (5.5–11.5), adsorbent concentration (0.2–2.5 g/L) and contact time (15–110 min). The response surface methodology (RSM) was employed for design of experiments, modelling and optimization of the process. Amazingly, 98.6 % COD reduction was achieved under mild operating conditions of pH 8.3, adsorbent concentration of 1.5 g/L and temperature of 293.2 K after 63 min contact time. A quadratic equation satisfactorily correlated the COD variations versus involved parameters. The data were also precisely correlated with the extended Langmuir isotherm and the mixed 1, 2-order kinetic model implying mono-layer adsorption of the multicomponent adsorbates through physisorption mechanism because of dominant electrostatic interactions. The results of thermodynamic analysis were also consistent with findings. The maximum adsorption capacity of 972.20 mg/g as well as nice reusability in five sequential cycles proved the promising capability of the adsorbent for decontaminating of the gas refinery wastewater.

Determination of Imprint Effects in Ferroelectrics from the Quantified Phase and Amplitude Response.

Piezoresponse force microscopy (PFM) is a robust characterization technique to explore ferroelectric properties at the nanoscale. However, the PFM signal can lead to misinterpretation of results due to the dominant electrostatic interaction between the tip and the sample. In this work, a detailed calibration process is presented and a procedure to identify the parasitic phase offset is demonstrated. To obtain artifact-free phase-amplitude loops, a methodology is developed by combining the outcomes from switching spectroscopy-PFM (SS-PFM) and Kelvin probe force microscopy (KPFM). It is demonstrated that the phase and amplitude loops obtained from SS-PFM at a specific read voltage, ascertained from the surface potential by KPFM, can convey accurate electromechanical information. These methodologies are applied to quantify the imprint voltage in BaTiO3 and BiFeO3, along with vertically aligned BaTiO3:Sm2O3 and BaTiO3:MgO nanocomposites. The variation of the imprint voltage measured under different tip voltages demonstrates the importance of selecting the correct read voltage in determining the local imprint voltage. Additionally, 2D imprint voltage maps in each domain of a BaTiO3 single crystal are obtained using the datacube-PFM technique, which allows pixel-by-pixel determination of artifact-free spatial variation of PFM phase-amplitude response.

Revisiting the Structure and Bonding in Li5H6- and the Exploration of Reactivity: Planar Pentacoordinate Hydrogen.

Recently, Guha and co-workers (Sarmah, K.; Kalita, A.; Purkayastha, S.; Guha, A. K. Pushing The Extreme of Multicentre Bonding: Planar Pentacoordinate Hydride. Angew. Chem. Int. Ed. 2024, e202318741) reported a highly intriguing bonding motif: planar pentacoordinate hydrogen (ppH) in Li5H6-, featuring C2v symmetry in the singlet state with two distinct H-Li (center-ring) bond distances. We herein revisited the potential energy surface of Li5H6- by using a target-oriented genetic algorithm. Our investigation revealed that the lowest-energy structure of Li5H6- exhibits a ppH configuration with very high D5h symmetry and a 1A1' electronic state. We did not find any electronic effect like Jahn-Teller distortion that could be responsible for lowering its symmetry. Moreover, our calculations demonstrated significant differences in the relative energies of other low-lying isomers. An energetically very competitive planar tetracoordinate hydrogen (ptH) isomer is also located, but it corresponds to a very shallow minimum on the potential energy surface depending on the used level of theory. Chemical bonding analyses, including AdNDP and EDA-NOCV, uncover that the optimal Lewis structure for Li5H6- involves H- ions stabilized by the Li5H5 crown. Surprisingly, despite the dominance of electrostatic interactions, the contribution from covalent bonding is also significant between ppH and the Li5H5 moiety, derived from H-(1s) → Li5H5 σ donation. Magnetically induced current density analysis revealed that due to minimal orbital overlap and the highly polar nature of the H-Li covalent interaction, the ppH exhibits local diatropic ring currents around the H centers, which fails to result in a global aromatic ring current. The coordination of Li5H6- with Lewis acids, BH3 and BMe3, instantly converts the ppH configuration to (quasi) ptH. These Lewis acid-bound ptH complexes show high electronic stability and high thermochemical stability against dissociation and, therefore, will be ideal candidates for the experimental realization.

Enhanced oxidation and removal of As(Ⅲ) from water using biomass-derived porous carbon-supported nZVI with high iron utilization and fast adsorption

Rapid and effective removal of As(III) from aqueous solutions is crucial and difficult due to its highly toxic and mobile properties. In this study, two kinds of carbonaceous supports, biomass-derived porous carbon (BPC) and biochar (BC), were fabricated for nZVI loading, and then served as adsorbent materials for As(III) removal from water. Characterization results indicated that BPC/nZVI showed more uniformly dispersed nZVI particles on the surface compared to BC/nZVI. Adsorption results showed that BPC/nZVI had highest adsorption capacity for As(III) with the fastest adsorption rate compared with BC/nZVI and pure nZVI. The porous structure and stronger electron accepting capacity for BPC enhanced the reactivity of loading nZVI compared to BC/nZVI. Batch experiments revealed that BPC/nZVI had the highest As(III) Langmuir adsorption capacity up to 177.8 mg/g at pH 7.0, and shorter adsorption equilibrium time within 90 min when compared to BC/nZVI and pure nZVI. The adsorption isotherm and adsorption kinetic of As(III) onto BPC/nZVI were described well by Langmuir model and the pesudo-second-order model, respectively. Additionally, BPC/nZVI exhibited excellent removal performance for As(III) in a broad pH and co-existing anions solution, and kept more than 80% As(III) removal rate after the fourth cycle. Our results indicate that oxidation and complexation are the dominant mechanisms and electrostatic interaction exists for As(III) removal by BPC/nZVI. This study indicates that BPC as supporting materials for nZVI loading is a promising strategy for efficient and fast remediation of As(III)-polluted wastewater.

The heteroaggregation and deposition behavior of nanoplastics on Al2O3 in aquatic environments

The ubiquitous Al2O3 is anticipated to interact with nanoplastics, affecting their fate and transport in aquatic environments. In this study, the heteroaggregation and deposition behaviors of polystyrene nanoplastics (PSNPs) on Al2O3 were systematically investigated under different conditions (ionic strength, pH, and natural organic matter). The results showed that significant heteroaggregation occurred between PSNPs and Al2O3 particles under acidic and neutral conditions. When the NaCl concentration was increased from 50 to 500 mM, the heteroaggregation ratio gradually increased. However, poly (acrylic acid) (PAA) inhibited the heteroaggregation of PSNPs-Al2O3 due to steric repulsion. The deposition of PSNPs on Al2O3 surfaces was inhibited as the NaCl concentration or pH values increased. Due to charge reversal and steric repulsion, humic acid (HA) and fulvic acid (FA) prevented the deposition of PSNPs onto Al2O3 surfaces, and the former was more effective in reducing the deposition rate. The interaction mechanism between PSNPs and Al2O3 was revealed by using various characterization techniques and density function theory (DFT) calculation. The results demonstrated that in addition to the dominant electrostatic interaction, there were also weak hydrogen bonds and van der Waals interactions. Our research is of great significance for predicting the migration and fate of PSNPs in aquatic environments.

Soft X-ray Emission Studies on Hydrate-Melt Electrolytes.

Highly salt-concentrated aqueous solutions are a new class of electrolytes, which provide a wide potential window exceeding 3 V and, hence, realize possibly inexpensive, safe, and high-energy-density storage devices. Herein, we investigate the evolution of the coordination structure and electronic state depending on the salt concentration through soft X-ray emission spectroscopy and first-principles molecular dynamics calculations. Close to the concentration limit, categorized as a "hydrate melt," a long-range hydrogen-bond network of water molecules disappears with emerging localized electronic states that resemble those in the gas phase. Such localized electronic states are attributed not only to their geometrically isolated nature but also to their dominant electrostatic interaction with Li+ cations. Therefore, the electrical properties of water in the hydrate melt can be more gaslike than liquidlike.

Insights on Alanine and Arginine Binding to Silica with Atomic Resolution.

Interactions of biomolecules with inorganic oxide surfaces such as silica in aqueous solutions are of profound interest in various research fields, including chemistry, biotechnology, and medicine. While there is a general understanding of the dominating electrostatic interactions, the binding mechanism is still not fully understood. Here, chromatographic zonal elution and flow microcalorimetry experiments were combined with molecular dynamic simulations to describe the interaction of different capped amino acids with the silica surface. We demonstrate that ion pairing is the dominant electrostatic interaction. Surprisingly, the interaction strength is more dependent on the repulsive carboxy group than on the attracting amino group. These findings are essential for conducting experimental and simulative studies on amino acids when transferring the results to biomolecule-surface interactions.

Cataloguing the Energetic Contributions to the Supramolecular Assembly of para-Substituted N,N′-Diphenylureas and Their Organometallic Derivatives in the Solid State: A Density Functional Theory Approach

Crystal engineering relies on the predictability of the elaborate interplay of cohesive and conformational energies driven by both intra- and intermolecular interactions of the constituent molecules. In an effort to better understand these influences on the crystal packing of para-substituted N,N′-diphenylureas (pDPUs) and organometallic derivatives, we present a detailed computational investigation of pDPU species utilizing solid-state density functional theory (DFT) and demonstrate the applicability of predictive supramolecular synthons applied toward the growth of related organometallic complexes. Dominant noncovalent interactions of pDPUs can be tuned by altering the electron-withdrawing character of the para substituents. The strength of this electron-withdrawing nature governs the inclination of the molecules to form either dominant electrostatic or π-stacking intermolecular interactions in the crystal structure due to potential molecular conformational stabilization through intramolecular C–H···O electrostatic interactions between ortho phenyl hydrogens and the urea oxygen atoms. This propensity is also influenced by the symmetry of para substitutions in mono- and disubstituted DPUs. The results of the holistic DFT investigation show a relationship between gas-phase and solid-state conformations and also present evidence of mechanisms leading to deviations in predicted crystallization behaviors on the basis of the balance of intra- and intermolecular interactions. The foundational computational study was expanded to build on previous experimental and theoretical work involving zerovalent transition-metal complexes in which p-isocyanophenyl DPUs were appended with group IV metal carbonyl fragments. In this study, we synthesized an asymmetric analogue of the latter in which N-(p-isocyanophenyl)-N′-phenylurea (pCNHDPU) was appended to a Mo(CO)5 metal carbonyl fragment, allowing us to associate the crystallization behaviors and interactions of organometallic DPU derivatives with those of simpler pDPUs. It was observed that the supramolecular assembly of the organometallic complexes display similar predictive patterns as well as additional complexities to molecular packing arising from the bulkier metal carbonyl substituents. An inclusive computational categorization of DPU-based systems in complement to experimental data will aid in the advancement of design rules for the patterned crystal growth of DPU and related systems for the development of innovative materials having unique solid-state properties.

Interactions of lamotrigine with single- and double-stranded DNA under physiological conditions

This study presents evaluation of the possible mechanisms of interaction between the antiepileptic drug lamotrigine (LMT) and single- and double-stranded DNA (ssDNA and dsDNA, respectively). These interactions were studied in phosphate-buffered saline (PBS) at physiological pH 7.4 by cyclic voltammetry (CV) and square wave voltammetry (SWV) using a glassy carbon electrode (GCE) in a bulk incubated solution. The addition of both types of DNA to LMT solution decreased peak currents and led to a negative shift in peak potentials, thus indicating the dominance of electrostatic interactions. UV–Vis absorption spectroscopy was also used to assess the interaction between ds/ssDNA and LMT. The data obtained from spectroscopic analysis confirmed that electrostatic interaction is the predominant interaction between LMT and both types of DNA. The calculated binding constants for LMT-dsDNA and LMT-ssDNA complexes as determined by SWV were 6.46 × 105 and 1.81 × 106, respectively, while the values obtained from UV–Vis spectroscopy were 6.93 × 105 and 1.19 × 106, respectively. The obtained results indicated a higher affinity of LMT for ssDNA than for dsDNA.

Reconciling Electrostatic and n→π* Orbital Contributions in Carbonyl Interactions.

Interactions between carbonyl groups are prevalent in protein structures. Earlier investigations identified dominant electrostatic dipolar interactions, while others implicated lone pair n→π* orbital delocalisation. Here these observations are reconciled. A combined experimental and computational approach confirmed the dominance of electrostatic interactions in a new series of synthetic molecular balances, while also highlighting the distance‐dependent observation of inductive polarisation manifested by n→π* orbital delocalisation. Computational fiSAPT energy decomposition and natural bonding orbital analyses correlated with experimental data to reveal the contexts in which short‐range inductive polarisation augment electrostatic dipolar interactions. Thus, we provide a framework for reconciling the context dependency of the dominance of electrostatic interactions and the occurrence of n→π* orbital delocalisation in C=O⋅⋅⋅C=O interactions.

Reconciling Electrostatic and n→π* Orbital Contributions in Carbonyl Interactions

AbstractInteractions between carbonyl groups are prevalent in protein structures. Earlier investigations identified dominant electrostatic dipolar interactions, while others implicated lone pair n→π* orbital delocalisation. Here these observations are reconciled. A combined experimental and computational approach confirmed the dominance of electrostatic interactions in a new series of synthetic molecular balances, while also highlighting the distance‐dependent observation of inductive polarisation manifested by n→π* orbital delocalisation. Computational fiSAPT energy decomposition and natural bonding orbital analyses correlated with experimental data to reveal the contexts in which short‐range inductive polarisation augment electrostatic dipolar interactions. Thus, we provide a framework for reconciling the context dependency of the dominance of electrostatic interactions and the occurrence of n→π* orbital delocalisation in C=O⋅⋅⋅C=O interactions.

Microsolvation of lithium–phosphorus double helix: a DFT study

The chemistry of complexes becomes interesting due to their structural diversity in different environments like in aqueous phase, in gas-phase or in the interior of a host. In the last few decades, powerful tools for the determination of gas-phase have been developed. In this context, the microsolvation approach of Li7P7 helix, where the passage from the bare double-strand helix to the hydrated denatured helix, has been addressed through successive attachment of water molecules using density functional theory. The stability of helical structure of the small clusters has been analyzed on the basis of polar bonding interaction between oxygen end of water molecule and Li centers of the Li7P7 helix. The Li7P7 helix is favored when associated with zero to eight water molecules, but the binding of the ninth water molecule brings a drastic change in the structure. Our results suggest that the natural charges on some sites in Li7P7 are large enough to induce partial and eventually total dissociation of water molecules. We shed light on the bonding situation through natural bond orbital, quantum theory of atoms in molecules and energy decomposition analyses which suggest dominant electrostatic interaction between Li centers of Li7P7 and O centers of water molecules (accounting for 60–64% of total bonding attraction). Nevertheless, 31–36% of total attraction is also originated from the orbital interaction. Variation in reactivity on microhydration is also analyzed. In order to check the site selectivity, we have computed conceptual density functional theory-based local reactivity descriptors such as dual descriptor based on the Fukui function, Δf(r), and multiphilic descriptor based on the philicity, Δω(r).

BINDING STUDIES OF VALGANCICLOVIR TO HUMAN SERUM ALBUMIN BY MULTISPECTROSCOPIC TECHNIQUES

Objective: The aim of the present study was to investigate the mode and mechanism of interactions involved towards binding of valganciclovir (VGC) with Human Serum Albumin (HSA) by spectroscopic and molecular modeling studies which can be extrapolated for the ten folds increase of bioavailability over its prodrug galanciclovir.Methods: Herein we employed fluorescence spectroscopy for evaluating the binding constant value, site of interaction and changes in the microenvironment of HSA fluorophores. Circular dichroism (CD) and UV-Visible spectroscopy is used for conformational changes of HSA in the event of binding of valaganciclovir. These experimental studies were further corroborated with molecular modeling studies.Results: Considerable quenching of fluorescence intensities of fluorophores in the presence of VGC showed that VGC interacts with HSA strongly with a binding constant of 4.11x104 M-1 with a free energy change of-6.26 Kcal/mol. Synchronous fluorescence and CD studies show that the microenvironment and confirmation of HSA are slightly altered in the presence of VGC. Though site marker experiments does not give any clue for identification of site, molecular docking studies showed that VGC binds to site IB of HSA.Conclusion: The weaker dominant electrostatic interactions with minor contributions of hydrophobic interactions of VGC with HSA at site IB (catalytic domain) might be the probable reason for the relative increase of hydrolysis of VGC to galanciclovir. And moderate binding constant value with HSA implies that HSA can be able to transport VGC under physiological conditions.

Biologically active meta-substituted ferrocenyl nitro and amino complexes: Synthesis, structural elucidation, and DFT calculations

In our search for new anticancer and DNA interacting drugs, ferrocene-incorporated nitro 1a-1b and aniline compounds 2a-2b were successfully synthesized and characterized by various physicochemical and spectroscopic methods. The proposed nitrophenylferrocenes were prepared by the coupling reaction between ferrocene and the diazonium salts of different nitroanilines using a phase transfer catalyst. In the subsequent reactions, these nitro compounds were reduced to the corresponding anilines using zinc dust/ammonium formate. Charge distribution and the HOMO/LUMO energies of the optimized structures that were calculated using the DFT/B3LYP method correlate well with the experimentally determined redox potential values. The nature and extent of binding of these complexes with the biomolecule, SS-DNA was examined by cyclic voltammetry, UV–Vis spectroscopy, and viscometry; the complexes exhibited good binding strengths to DNA. The diffusion coefficients of the compound-DNA adducts for all the complexes are lower than that of the free compound and the small values of the binding site sizes also indicate the dominance of electrostatic interactions. These compounds have also been demonstrated to be decent candidates in terms of free radical scavenging, protein kinase inhibition, and cytotoxicity.

Regulation of Nucleosome Stacking and Chromatin Compaction by the Histone H4 N-Terminal Tail–H2A Acidic Patch Interaction

Chromatin folding and dynamics are critically dependent on nucleosome–nucleosome interactions with important contributions from internucleosome binding of the histone H4 N-terminal tail K16-R23 domain to the surface of the H2A/H2B dimer. The H4 Lys16 plays a pivotal role in this regard. Using in vitro reconstituted 12-mer nucleosome arrays, we have investigated the mechanism of the H4 N-terminal tail in maintaining nucleosome–nucleosome stacking and mediating intra- and inter-array chromatin compaction, with emphasis on the role of K16 and the positive charge region, R17-R23. Analytical ultracentrifugation sedimentation velocity experiments and precipitation assays were employed to analyze effects on chromatin folding and self-association, respectively. Effects on chromatin folding caused by various mutations and modifications at position K16 in the H4 histone were studied. Additionally, using charge-quenching mutations, we characterized the importance of the interaction of the residues within the H4 positive charge region R17-R23 with the H2A acidic patch of the adjacent nucleosome. Furthermore, crosslinking experiments were conducted to establish the proximity of the basic tail region to the acidic patch. Our data indicate that the positive charge and length of the side chain of H4 K16 are important for its access to the adjacent nucleosome in the process of nucleosome–nucleosome stacking and array folding. The location and orientation of the H4 R17-R23 domain on the H2A/H2B dimer surface of the neighboring nucleosome core particle (NCP) in the compacted chromatin fiber were established. The dominance of electrostatic interactions in maintaining intra-array interaction was demonstrated.

PH-Dependent Selective Protein Adsorption into Mesoporous Silica

The adsorption of lysozyme, cytochrome c and myoglobin, similar-sized globular proteins of approximately 1.5 nm radius, into the mesoporous silica material Santa Barbara Amorphous-15 (SBA-15) with 3.3 nm mean pore radius has been studied photometrically for aqueous solutions containing a single protein type and for binary protein mixtures. Distinct variations in the absolute and relative adsorption behavior are observed as a function of the solution's pH-value, and thus pore wall and protein charge. The proteins exhibit the strongest binding below their isoelectric points pI, which indicates the dominance of electrostatic interactions between charged amino acid residues and the -OH groups of the silica surface in the mesopore adsorption process. Moreover, we find for competitive adsorption in the restricted, tubular pore geometry that the protein type which shows the favoured binding to the pore wall can entirely suppress the adsorption of the species with lower binding affinity, even though the latter would adsorb quite well from a single component mixture devoid of the strongly binding protein. We suggest that this different physicochemical behavior along with the large specific surface and thus adsorption capability of mesoporous glasses can be exploited for separation of binary mixtures of proteins with distinct pI by adjusting the aqueous solution's pH.

The structural requirements of organophosphorus insecticides (OPI) for reducing chicken embryo NAD+ content in OPI-induced teratogenesis in chickens

The objective of this study was to determine the structural requirements of organophosphorus insecticides (OPI) for reducing chicken embryo nicotinamide adenine dinucleotide (NAD+) content in OPI-induced teratogenesis and compare them with those needed for OPI inhibition of yolk sac membrane kynurenine formamidase (KFase), the proposed primary target for OPI teratogens in chicken embryos. The comparative molecular field analysis (COMFA) of three-dimensional quantitative structure–activity relationship (3D QSAR) revealed the electrostatic and steric fields as good predictors of OPI structural requirements to reduce NAD+ content in chicken embryos. The dominant electrostatic interactions were localized at nitrogen-1, nitrogen-3, nitrogen of 2-amino substituent of the pyrimidinyl of pyrimidinyl phosphorothioates, and at the oxygen of crotonamide carbonyl in crotonamide phosphates. Bulkiness of the substituents at carbon-6 of the pyrimidinyls and/or N-substituents of crotonamides was the steric structural component that contributed to superiority of those OPI for reducing embryonic NAD+ levels. Both electrostatic and steric requirements are similar to those defined in our previous study for OPI inhibition of chicken embryo yolk sac membrane KFase. The findings of this study provide another piece of evidence for the cause-and-effect relationship between yolk sac membrane KFase inhibition and reduced embryo NAD+ content in NAD-associated OPI-induced teratogenesis in chickens.

Interaction with Deoxyribonucleic Acid and Determination of Orientin in Lophatherum gracile Brongn by High-Performance Liquid Chromatography with Amperometric Detection

The mechanisms of the electrochemical oxidation of orientin and its interaction with deoxyribonucleic acid have been investigated using glassy carbon electrode. The electrochemical response of orientin is due to oxidation of phenolic hydroxyl groups on orientin. The whole process is controlled by the adsorption step and concerned 4 electrons and 4 protons. Negative shift of potential and decrease of peak current for electrochemical oxidation of orientin can be observed at bare glassy carbon electrode and deoxyribonucleic acid modified electrode in 0.05M Na2HPO4-KH2PO4 (pH 7.48), confirming the dominant electrostatic interaction between orientin and deoxyribonucleic acid. Moreover, a reliable and sensitive method of reversed-phase high-performance liquid chromatography-electrochemical detection has been developed for simultaneous determination of the isomer pair orientin/isoorientin. Chromatographic separation was carried out on a reversed-phase C18 column and a mobile phase comprised of acetonitrile and acetate (0.5%, pH 2.97) by amperometric detection with a glassy carbon electrode at the working potential of +1.00V. The method was validated for linearity, accuracy, precision, and limit of detection. Under the optimized conditions, linear regression analysis for the calibration curve showed a good linear relationship between peak area and their concentrations in the linear range of 89.2nM to 59.5μM for orientin with detection limit of 14.9nM and 78.0nM to 52.0μM for isoorientin with a detection limit of 13.0nM, respectively. Compared to the method using ultraviolet detection, the detection limits are greatly lowered. Finally, the proposed method has been successfully applied to the determination of orientin and isoorientin in Lophatherum gracile Brongn.

Transport behavior of a single Ca(2+), K(+), and Na(+) in a water-filled transmembrane cyclic peptide nanotube.

Molecular dynamics simulations have been performed to investigate the transport properties of a single Ca(2+), K(+), and Na(+) in a water-filled transmembrane cyclic peptide nanotube (CPNT). Two transmembrane CPNTs, i.e., 8×(WL)n=4,5/POPE (with uniform lengths but various radii), were applied to clarify the dependence of ionic transport properties on the channel radius. A huge energy barrier keeps Ca(2+) out of the octa-CPNT, while Na(+) and K(+) can be trapped in two CPNTs. The dominant electrostatic interaction of a cation with water molecules leads to a high distribution of channel water around the cation and D-defects in the first and last gaps, and significantly reduces the axial diffusion of channel water. Water-bridged interactions were mostly found between the artificially introduced Ca(2+) and the framework of the octa-CPNT, and direct coordinations with the tube wall mostly occur for K(+) in the octa-CPNT. A cation may drift rapidly or behave lazily in a CPNT. K(+) behaves most actively and can visit the whole deca-CPNT quickly. The first solvation shells of Ca(2+) and Na(+) are basically saturated in two CPNTs, while the hydration of K(+) is incomplete in the octa-CPNT. The solvation structure of Ca(2+) in the octa-CPNT is most stable, while that of K(+) in the deca-CPNT is most labile. Increasing the channel radius induces numerous interchange attempts between the first-shell water molecules of a cation and the ones in the outer region, especially for the K(+) system.

Specific recognition mechanism between RNA and the KH3 domain of Nova-2 protein.

The KH3 domain of Nova-2 protein can precisely recognize the sequence-specific target RNA of human glycine receptor α2. However, the recognition mechanism between the protein and its target RNA is still hotly debated. In this study, molecular dynamic simulations in explicit solvent were utilized to understand the recognition mechanism. The structural analysis and the Kolmogorov-Smirnov P-test statistics reveal that the KH3 domain might obey a conformational selection mechanism upon RNA binding. However, the induced fit mechanism could not be completely ruled out. Unfolding kinetics indicates that the folding of RNA and KH3 happens first and then the binding between RNA and KH3 follows. Principle component analysis shows that the invariant Gly-Lys-Gly-Gly loop moves toward to the RNA molecule but the C-terminal domain moves away from the RNA molecule upon binding. These specific dominant motions were hypothesized to stabilize the complex structure. The hydrophobic and hydrogen bonding interactions were found to be the driving forces for the specific recognition, in contrast to the dominant electrostatic interactions for nonspecific recognition.