The Na-23 quadrupolar coupling constant of the Na+ ion in aqueous solution has been predicted using molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics methods for the calculation of electric field gradients. The developed computational approach is generally expected to provide reliable estimates of the quadrupolar coupling constants of monoatomic species in condensed phases, and we show here that intermolecular polarization and non-electrostatic interactions are of crucial importance as they result in a 100% increased quadrupolar coupling constant of the ion as compared to a simpler pure electrostatic picture. These findings question the reliability of the commonly applied classical Sternheimer approximation for the calculations of the electric field gradient. As it can be expected from symmetry considerations, the quadrupolar coupling constants of the 5- and 6-coordinated Na+ ions in solution are found to differ significantly.

The global practical implementation of proton exchange membrane fuel cells (PEMFCs) heavily relies on the advancement of highly effective platinum (Pt)-based electrocatalysts for the oxygen reduction reaction (ORR). To achieve high ORR performance, electrocatalysts with highly accessible reactive surfaces are needed to promote the uncovering of active positions for easy mass transportation. In this critical review, we introduce different approaches for the emerging development of effective ORR electrocatalysts, which offer high activity and durability. The strategies, including morphological engineering, geometric configuration modification via supporting materials, alloys regulation, core-shell, and confinement engineering of single atom electrocatalysts (SAEs), are discussed in line with the goals and requirements of ORR performance enhancement. We review the ongoing development of Pt electrocatalysts based on the syntheses, nanoarchitecture, electrochemical performances, and stability. We eventually explore the obstacles and research directions on further developing more effective electrocatalysts.

Ionic liquids (ILs) are room temperature molten salts that possess preeminent physicochemical properties and have shown great potential in many applications. However, the use of ILs in surface-dependent processes, e.g. energy storage, is hindered by the lack of a systematic understanding of the IL interfacial microstructure. ILs on the solid surface display rich ordering, arising from coulombic, van der Waals, solvophobic interactions, etc., all giving near-surface ILs distinct microstructures. Therefore, it is highly important to clarify the interactions of ILs with solid surfaces at the nanoscale to understand the microstructure and mechanism, providing quantitative structure-property relationships. Atomic force microscopy (AFM) opens a surface-sensitive way to probe the interaction force of ILs with solid surfaces in the layers from sub-nanometers to micrometers. Herein, this review showcases the recent progress of AFM in probing interactions and microstructures of ILs at solid interfaces, and the influence of IL characteristics, surface properties and external stimuli is thereafter discussed. Finally, a summary and perspectives are established, in which, the necessities of the quantification of IL-solid interactions at the molecular level, the development of in situ techniques closely coupled with AFM for probing IL-solid interfaces, and the combination of experiments and simulations are argued.

Ionic liquids (ILs) are a class of salts existing in the liquid state below 100 degrees C, possessing low volatility, high thermal stability as well as many highly attractive solvent and electrochemical capabilities, etc., making them highly tunable for a great variety of applications, such as lubricants, electrolytes, and soft functional materials. In many applications, ILs are first either physi- or chemisorbed on a solid surface to successively create more functional materials. The functions of ILs at solid surfaces can differ considerably from those of bulk ILs, mainly due to distinct interfacial layers with tunable structures resulting in new ionic liquid interface layer properties and enhanced performance. Due to an almost infinite number of possible combinations among the cations and anions to form ILs, the diversity of various solid surfaces, as well as different external conditions and stimuli, a detailed molecular-level understanding of their structure-property relationship is of utmost significance for a judicious design of IL-solid interfaces with appropriate properties for task-specific applications. Many experimental techniques, such as atomic force microscopy, surface force apparatus, and so on, have been used for studying the ion structuring of the IL interface layer. Molecular Dynamics simulations have been widely used to investigate the microscopic behavior of the IL interface layer. To interpret and clarify the IL structure and dynamics as well as to predict their properties, it is always beneficial to combine both experiments and simulations as close as possible. In another theoretical model development to bridge the structure and properties of the IL interface layer with performance, thermodynamic prediction & property modeling has been demonstrated as an effective tool to add the properties and function of the studied nanomaterials. Herein, we present recent findings from applying the multiscale triangle experiment-simulation-thermodynamic modeling in the studies of ion structuring of ILs in the vicinity of solid surfaces, as well as how it qualitatively and quantitatively correlates to the overall ILs properties, performance, and function. We introduce the most common techniques behind experiment-simulation-thermodynamic modeling and how they are applied for studying the IL interface layer structuring, and we highlight the possibilities of the IL interface layer structuring in applications such as lubrication and energy storage. Integrative experiment-simulation-thermodynamic modeling is highly demanded for qualitatively and quantitatively correlating the ionic liquids interface layer structuring to the overall properties, performance, and function.

As a remarkably powerful analytical technique, surface-enhanced Raman scattering (SERS) continues to find applications from molecular biology and chemistry to environmental and food sciences. In search of reliable and affordable SERS substrates, the development has moved from noble metals to other diverse types of structures, e.g., nano-engineered semiconductor materials, but the cost of the enhancement factors (EF) substantially decreasing. In this work, we employ biocompatible thin films of Ti–Si–Zr–Zn nanometallic glasses as the SERS substrates, while tuning the Zn composition. Aided by quartz crystal microbalance, we find that the composition of 4.3% Zn (Ti–Si–Zr–Zn_4.3) gives an ultrasensitive detection of Cytochrome c (Cyt c) with an EF of 1.38 × 10⁴, 10-fold higher than the previously reported EF in the semiconducting metal oxide nanomaterials, such as TiO₂, and even comparable to the reported noble-metal-assisted semiconducting tungsten oxide hydrate. Ti–Si–Zr–Zn_4.3 exhibits a stronger adhesion force toward Cyt c, which ensures the strong binding of Cyt c to the surface, facilitating the Cyt c adsorption onto the surface and thus enhancing the SERS signal. The high separation efficiency of photoinduced electrons and holes in Ti–Si–Zr–Zn_4.3 is also acknowledged for promoting the SERS activity. 

Nucleic acids are highly charged biopolymers whose secondary structure is strongly dependent on electrostatic interactions. Solvent molecules and ions are also believed to play an important role in mediating and directing both sequence recognition and interactions with other molecules, such as proteins and a variety of ligands. Therefore, to fully understand the biological functions of DNA, it is necessary to understand the interactions with the surrounding counterions. It is well known that monovalent counterions can bind to the minor groove of DNA with consecutive sequences of four, or more, adenine and thymine (A-tracts) with relatively long residence times. However, much less is known about their binding to the backbone and to the major groove. In this work, we used molecular dynamics simulations to both investigate the interactions between the backbone and major groove of DNA and one of its physiological counterions (Na+) and evaluate the relationship between these interactions and the nucleotide sequence. Three dodecamers, namely CGAAAATTTTCG, CGCTCTAGAGCG, and CGCGAATTCGCG, were simulated using the Toukan-Rahman flexible SPC water model and Smith and Dang parameters for Na+, revealing a significant sequence dependence on the ion binding to both backbone and major groove. In the absence of experimental data on the atomistic details of the studied interactions, the reliability of the results was evaluated performing the simulations with additional sets of potential parameters for ions and solvent, namely the A. qvist or the Joung and Cheatham ion parameters and the TIP3P water model. This allowed us to evaluate the results by verifying which features are preserved independently from the parameters adopted.

Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein–protein systems under different physical–chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pK_as for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This “RBD charge rule” should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.

A simple first-principles electronic structure computation, further qc (quantum chemistry) computation, of the methyl radical gives three equal hf (hyperfine) couplings for the three protons with the unpaired electron. The corresponding dipolar tensors were notably rhombic and had different orientations and regular magnitude components, as they should, but what the overall A-tensor was seen by the electron spin is a different story! The final g = (2.002993, 2.002993, 2.002231) tensor and the hf coupling results obtained in vacuum, at the B3LYP/EPRIII level of theory clearly indicate that in particular the above A = (-65.19, -65.19, 62.54) MHz tensor was axial to a first approximation without considering any rotational dynamics for the CH3. This approximation was not applicable, however, for the trifluoromethyl CF3 radical, a heavier and nonplanar rotor with very anisotropic hf coupling, used here for comparison. Finally, a derivation is presented explaining why there is actually no need for the CH3 radicals to consider additional rotational dynamics in order for the electron to obtain an axially symmetric hf (hyperfine) tensor by considering the simultaneous dipolar couplings of the three protons. An additional consequence is an almost isotropic A-tensor for the electron spin of the CH3 radical. To the best of our knowledge, this point has not been discussed in the literature before. The unexpected isotropy of the EPR parameters of CH3 was solely attributed to the rotational dynamics and was not clearly separated from the overall symmetry of the species. The present theoretical results allowed a first explanation of the forbidden satellite lines in the CH3 EPR spectrum. The satellites are a fingerprint of the radical rotation, helping thus in distinguishing the CH3 reorientation from quantum rotation at very low temperatures.

Adsorbents with high capacity and selectivity for adsorption of CO2 are currently being investigated for applications in adsorption-driven separation of CO2 from flue gas. An adsorbent with a particularly high CO2-over-N-2 selectivity and high capacity was tested here. Zeolite ZK-4 (Si:Al similar to 1.3:1), which had the same structure as zeolite A (LTA), showed a high CO2 capacity of 4.85 mmol/g (273 K, 101 kPa) in its Na+ form. When approximately 26 at % of the extraframework cations were exchanged for K+ (NaK-ZK-4), the material still adsorbed a large amount of CO2 (4.35 mmol/g, 273 K, 101 kPa), but the N-2 uptake became negligible (<0.03 mmol/g, 273 K, 101 kPa). The majority of the CO2 was physisorbed on zeolite ZK-4 as quantified by consecutive volumetric adsorption measurements. The rate of physisorption of CO2 was fast, even for the highly selective sample. The molecular details of the sorption of CO2 were revealed as well. Computer modeling (Monte Carlo, molecular dynamics simulations, and quantum chemical calculations) allowed us to partly predict the behavior of fully K+ exchanged zeolite K-ZK-4 upon adsorption of CO2 and N-2 for Si:Al ratios up to 4:1. Zeolite K-ZK-4 with Si:Al ratios below 23:1 restricted the diffusion of CO2 and N-2 across the cages. These simulations could not probe the delicate details of the molecular sieving of CO2 over N-2. Still, this study indicates that zeolites NaK-ZK-4 and K-ZK-4 could be appealing adsorbents with high CO2 uptake (similar to 4 mmol/g, 101 kPa, 273 K) and a kinetically enhanced CO2-over-N-2 selectivity.

A novel DPyDB-CN-18C6 compound was synthesised by linking a pyrene moiety to each phenyl group of dibenzo-18-crown-6-ether, the crown ether, through –HCN– bonds and characterized by FTIR, ¹H-NMR, ¹³C-NMR, TGA, and DSC techniques. The quantitative ¹³C-NMR analysis revealed the presence of two position isomers. The electronic structure of the DPyDB-CN-18C6 molecule was characterized by UV-vis and fluorescence spectroscopies in four solvents with different polarities to observe particular behavior of isomers, as well as to demonstrate a possible non-bonding chemical association (such as ground- and excited-state associations, namely, to probe if there were forming dimers/excimers). The interpretation of the electronic structure was realized through QM calculations. The TD-CAM-B3LYP functional, at the 6-311+G(d,p) basis set, indicated the presence of predominant π → π* and mixed π → π* + n → π* transitions, in line with the UV-vis experimental data. Even though DPyDB-CN-18C6 computational studies revealed a π-extended conjugation effect with predominantly π → π* transitions, thorough fluorescence analysis was observed a weak emission, as an effect of PET and ACQ. In particular, the WAXD analysis of powder and thin films obtained from n-hexane, 1,2-dichloroethane, and ethanol indicated an amorphous organization, whereas from toluene a smectic ordering was obtained. These results were correlated with MD simulation, and it was observed that the molecular geometry of DPyDB-CN-18C6 molecule played a defining role in the pyrene stacking arrangement.

A new betacoronavirus named SARS-CoV-2 has emerged as a new threat to global health and economy. A promising target for both diagnosis and therapeutics treatments of the new disease named COVID-19 is the coronavirus (CoV) spike (S) glycoprotein. By constant-pH Monte Carlo simulations and the PROCEEDpKa method, we have mapped the electrostatic epitopes for four monoclonal antibodies and the angiotensin-converting enzyme 2 (ACE2) on both SARS-CoV-1 and the new SARS-CoV-2 S receptor binding domain (RBD) proteins. We also calculated free energy of interactions and shown that the S RBD proteins from both SARS viruses binds to ACE2 with similar affinities. However, the affinity between the S RBD protein from the new SARS-CoV-2 and ACE2 is higher than for any studied antibody previously found complexed with SARS-CoV-1. Based on physical chemical analysis and free energies estimates, we can shed some light on the involved molecular recognition processes, their clinical aspects, the implications for drug developments, and suggest structural modifications on the CR3022 antibody that would improve its binding affinities for SARS-CoV-2 and contribute to address the ongoing international health crisis.

Binary alcohol + ether liquid mixtures are of significant importance as potential biofuels or additives for internal combustion engines and attract considerable fundamental interest as model systems containing one strongly H-bonded self-associating component (alcohol) and one that is unable to do so (ether), but that can interact strongly as a H-bond acceptor. In this context, the excess thermodynamic properties of these mixtures, specifically the excess molar enthalpies and volumes (H-E and V-E), have been extensively measured. Butanol isomer + di-n-butyl ether (DBE) mixtures received significant attention because of interesting differences in their V-E, changing from negative (1- and isobutanol) to positive (2- and tert-butanol) with increasing alkyl group branching. With the aim of shedding light on the differences in alcohol self-association and cross-species H-bonding, considered responsible for the observed differences, we studied representative 1- and 2-butanol + DBE mixtures by molecular dynamics simulations and experimental excess property measurements. The simulations reveal marked differences in the self-association of the two isomers and, while supporting the existing interpretations of the H-E and V-E in a general sense, our results suggest, for the first time, that subtle changes in H-bonded topologies may contribute significantly to the anomalous volumetric properties of these mixtures.

Liquid solutions and mixtures are part of our everyday lives and also important for their chemical and industrial applications. While considered fairly unattractive substances when kept in bottles and containers, their behavior as molecules can be completely the opposite, continuously attracting scientists to explain it better. Very strong repulsive and attractive interactions between the molecules can create most intriguing local structures, aggregates and complexes, whose spatial organization is often difficult to rationalize. Also, the same mixture can behave completely differently depending on the composition ratio, affecting strongly its macroscopic properties. To gain insight into the complex world of binary liquid mixtures, deep eutectic solvents and ionic liquid systems, combined theoretical and experimental studies are necessary. In this chapter we introduce the methodology of computer simulations and illustrate with several examples of the often-unexpected behavior of many liquid mixtures. 

An unexpected deficit of the computed hyper fine coupling constant in normal formyl HCO radicals, compared to that expected based on the proton to deuteron gyromagnetic ratio of the DCO species, was observed in experimental electron paramagnetic resonance studies of HCO and DCO radicals in a CO solid matrix at cryogenic conditions. Still, the matrix was found to have only a small effect on the anisotropic parts of the magnetic parameter tensors. The underlying isotope effect between the lighter proton and the heavier deuteron on the motional dynamics was verified and elucidated by quantum chemical calculations. The experimental results obtained within a temperature range of 1.4 K-4.2 K require special attention due to the tunneling motions of the molecule and its constituent particles. The effect from vibrational, rotational, and librational motion observed in the molecular states of formyl as a probe, averaged over the dynamics of the low temperature CO matrix isolation, reveals a clear proton isotope effect under both classical and quantum conditions.

Surface-enhanced Raman scattering (SERS) is an attractive technique for studying trace detection. It is of utmost importance to further improve the performance and understand the underlying mechanisms. An ionic liquid (IL), the anion of which is derived from biomass, [P_6,6,6,14][FuA] was synthesized and used as a trace additive to improve the SERS performance of cytochrome c (Cyt c) on TiO₂ nanotube arrays (TNAs). An increased and better enhancement factor (EF) by four to five times as compared to the system without an IL was obtained, which is better than that from using the choline-based amino acid IL previously reported by us. Dissociation of the ILs improved the ionic conductivity of the system, and the long hydrophobic tails of the [P_6,6,6,14]⁺ cation contributed to a strong electrostatic interaction between Cyt c and the TNA surface, thereby enhancing the SERS performance. Atomic force microscopy did verify strong electrostatic interactions between the Cyt c molecules and TNAs after the addition of the IL. This work demonstrates the importance of introducing the phosphonium-based IL to enhance the SERS performance, which will stimulate further development of more effective ILs on SERS detection and other relevant applications in biology.

Detecting the small amounts of proteins interacting effectively with the solid film electrodes surface still remains a challenge. To address this, in this work, a new approach was proposed by the combination of the adhesion forces and the molecular interaction measured with AFM. Cytochrome c (Cyt C) interacting effectively with TiO2 nanotube arrays (TNAs) was chosen as a probe. The amounts of Cyt C molecules interacting effectively on TNAs surface (C-TNA) range from 5.5x10(-12) to 7.0x10(-12) mol/cm(2) (68.2-86.8 ng/cm(2)) and they are comparable with the values obtained by the electrochemistry method in the literature, in evidence of the accuracy of this AFM-based approach. The reliability of the proposed approach was further verified by conducting Surface Enhanced Raman Scattering (SERS) measurements and estimating the enhancement factor (EF). This interaction-based AFM approach can be used to accurately obtain the small amounts of adsorbed substances on the solid film electrodes surface in the applications such as biosensors, biocatalysis, and drug delivery, etc.

Enhancing molecular interaction is critical for improving the immobilization and stability of proteins on TiO2 surfaces. In this work, mesoporous TiO2 materials with varied pore geometries were decorated with phenyl phosphoric acid (PPA), followed by a thermal treatment to obtain chemically heterogeneous C-TiO2 samples without changing the geometry and crystalline structure, which can keep the advantages of both carbon and TiO2. The molecular interaction force between the protein and the surfaces was measured using atomic force microscopy by decomposing from the total adhesion forces, showing that the surface chemistry determines the interaction strength and depends on the amount of partial carbon coverage on the TiO2 surface (similar to 40-80%). Samples with 58.3% carbon coverage provide the strongest molecular interaction force, consistent with the observation from the detected friction force. Surface-enhanced Raman scattering and electrochemical biosensor measurements for these C-TiO2 materials were further conducted to illustrate their practical implications, implying their promising applications such as in protein detection and biosensing.

The effect of pH-induced electrostatic conditions on the molecular interaction force of a single lysozyme molecule with TiO2 is investigated using atomic force microscopy (AFM). The force between the charged or neutral lysozyme molecule and the TiO2 surface is measured at different pH from 3.6 to 10.8. It is found to be directly proportional to the contact area, given by an effective diameter of the lysozyme molecule, and is further qualitatively verified by the AFM-measured friction coefficients. The results of the Derjaguin-Landau-Verwey-Overbeek theory show that the pH can change the surface charge densities of both lysozyme and TiO2, but the molecular interaction force at different pH is only dependent on the pH-induced effective diameter of lysozyme. The molecular interaction forces, quantified at the nanoscale, can be directly used to design high-performance liquid chromatography measurements at macroscale by tuning the retention time of a protein under varied pH conditions. They can also be applied to develop a model for predicting and controlling the chromatographic separations of proteins.

By adjusting the ionic strengths through changing the concentration of the buffer ions, the molecular force and the interfacial behavior of cytochrome c (Cyt c) and TiO2 are systematically studied. The molecular forces determined by combining the adhesion force and adsorption capacity are found to first increase and then decrease with the increasing ionic strength, with a peak obtained at an ionic strength between 0.8 and 1.0 M. The mechanism is explained based on the dissociation and hydration of ions at the interfaces, where the buffer ions could be completely dissociated at ionic strengths of <0.8 M but were partially associated when the ionic strength increased to a high value (>1.2 M), and the strongest hydration was observed around 1.0 M. The hydrodynamic size and the zeta potential value representing the effective contact area and protein stability of the Cyt c molecule, respectively, are also affected by the hydration and are proportional to the molecular forces. The interfacial behavior of Cyt c molecules on the TiO2 surface, determined through surface-enhanced Raman scattering (SERS), is extremely affected by the ionic strength of the solution as the ion dissociation and hydration also increase the electron transfer ability, where the best SERS enhancement is observed at the ionic strength of around 1.0 M, corresponding to the largest molecular force. Our results provide a detailed understanding at the nanoscale on controlling the protein interfacial behavior with solid surfaces, adjusted by the buffer ions.