Range Of Interaction Energies Research Articles

Investigating Recurrent Matere Bonds in Pertechnetate Compounds.

In this manuscript we evaluate the X-ray structure of five new pertechnetate derivatives of general formula [M(H2 O)4 (TcO4 )2 ], M=Mg, Co, Ni, Cu, Zn (compounds 1-5) and one perrhenate compound Zn(H2 O)4 (ReO4 )2 (6). In these complexes the metal center exhibits an octahedral coordination with the pertechnetate units as axial ligands. All compounds exhibit the formation of directional Tc⋅⋅⋅O Matere bonds (MaBs) that propagate the [M(H2 O)4 (TcO4 )2 ], into 1D supramolecular polymers in the solid state. Such 1D polymers are linked, generating 2D layers, by combining additional MaBs and hydrogen bonds (HBs). Such concurrent motifs have been analyzed theoretically, suggesting the noncovalent σ-hole nature of the MaBs. The interaction energies range from weak (~ -2 kcal/mol) for the MaBs to strong (~ -30 kcal/mol) for the MaB+HB assemblies, where HB dominates. In case of M=Zn, the corresponding perrhenate Zn(H2 O)4 (ReO4 )2 complex, has been also synthesized for comparison purposes, resulting in the formation of an isostructural X-ray structure, corroborating the structure-directing role of Matere bonds.

Wolfium bonds in homodimers of MX4Y (M = Mo, W; X = F, Cl, Br; Y = O, S, Se).

The term "wolfium bond" has been recently introduced to describe the noncovalent attraction between an atom of group 6 and a nucleophile via a σ-hole binding site. Crystal structures commonly contain a motif wherein two MX4Y units are arranged in close proximity, where M represents either Mo or W, and X and Y refer to halogen and chalcogen atoms respectively. DFT calculations were thus applied to a wide range of homodimers of these molecules so as to assess their preferred arrangements, and to characterize the types of bonding that are present in each in a systematic manner. The most stable Dual-X configuration is symmetric and contains a pair of equivalent M⋯X bonds. The interaction energies range from -8 to -29 kcal mol-1, and are largest for X = F, Y = O, and M = W. The X electron donor is replaced by Y, and the two wolfium bonds are reduced to one, in the less stable Mono-Y structure, with interaction energies between -2 and -10 kcal mol-1. There is some question as to whether the weaker bonds of this type constitute true wolfium bonds.

Effect of nanocarbon surface curvature on interactions with lithium and its ion

The electronic properties of nanocarbons can be tuned via doping. In this study, the interaction energies of Li with (n,n)-carbon belts (n = 5–20) are investigated using density functional theory to clarify the effect of curvature on doping. The magnitude of the interaction energies range from −20.6 to −14.8 kcal mol−1, with a maximum at n = 8. Essentially, two types of charge transfer occur, depending on the carbon belt diameter. For n ≥ 8, the charge is widely distributed on the carbon belt, whereas for n < 8, back-donation charge transfer to Li occurs.

Adsorption of rare earth elements onto diatomite M45: Experimental investigations and modeling with statistical physics theory

The separation of rare earth elements using diatomite M45 from aqueous solutions was studied. The experimental isotherms for the adsorption of trivalent lanthanum, cerium, and neodymium cations on this adsorbent were quantified under strongly acidic conditions (pH 2) at 298–328 K. The adsorption equilibria of these earth elements were analyzed using two statistical physics models (homogeneous and heterogeneous monolayer models). The results show that the adsorption of these ions implies a multi-ionic mechanism, which is exothermic. Si-containing functional groups are responsible for the adsorption of these rare-earth elements on the diatomite surface. A heterogeneous statistical physics model confirms that two Si-based functional groups participate in the separation of these cations. The calculated adsorption capacities at saturation follow the order: neodymium > cerium > lanthanum. Calculated interaction energies range from 28600 to 40100 J/mol, indicating physical adsorption on diatomite M45. This study demonstrates that diatomite M45 is a promising separation medium that can be used for the recovery of REEs dissolved in aqueous solutions via adsorption.

Weak Interactions between Epinephrine and Thymine

Abstract: The weak interactions between epinephrine and thymine were investigated by combining the 6-311+G(d,p) basis set with the M06-2X method based on density functional theory. Results suggest that epinephrine and thymine form 22 steady geometries through weak interactions, which primarily contain hydrogen bonds and π–π stacking. Hydrogen bonding is the main character. In addition, the interaction energies range from −20.98 kJ•mol−1 to −63.14 kJ•mol−1 with the basis set superposition error correction, which are in line with the energy range of the hydrogen bond. Geometrical parameters, frequency analysis, natural bond orbital (NBO) analysis, atoms-in-molecules (AIM) analysis, and reduced density gradient (RDG) analysis were also used to analyze and verify hydrogen bond formation. Most of the hydrogen bonds in optimized structures of the epinephrine–thymine complex are closed-shell interaction and electrostatic dominant, whereas N•••H–N, which exist in geometries 3, 4, 5, and 14, are interacting between the closed-shell and shared-shell. N-H…N is almost linear, which is more conducive to the study of the role of hydrogen bonds in the system.

A Peculiar Binding Characterization of DNA (RNA) Nucleobases at MoOS-Based Janus Biosensor: Dissimilar Facets Role on Selectivity and Sensitivity.

Distinctive properties of Janus monolayer have drawn much interest in biotechnology applications. For this purpose, it has explored theoretically all sensing possibilities of nucleobases molecules (DNA/RNA) by Janus MoOS monolayer on both oxygen and sulfur terminations by means of rigorous first–principles calculation. Indeed, differences in interaction energy between nucleobases indicate that a monolayer can be used for DNA sequencing. Exothermic interaction energy range for DNA/RNA molecules with both oxygen and sulfur sides of the Janus MoOS surfaces have been found to range between (0.61–0.91 eV), and (0.63–0.88 eV), respectively, and the binding distances indicate that these molecules bind to both facets by physisorption. The exchange of weak electronic charges between the MoOS monolayer and the nucleobases molecules has been studied by means of Hirshfeld-I charge analysis. It has been observed that the introduction of DNA/RNA nucleobases molecules alters the electronic properties of both oxygen and sulfur atomic layers of the Janus MoOS complex systems as determined by plotting the 3D Kohn–Sham frontier orbitals. A good correlation has been found between the interaction energy, van der Waals energy, Hirshfeld-I, and d–band center as a function of the nucleobase’s affinity, and the interaction energy, suggesting adsorption dominated by van der Waals interactions driven by molybdenum d–orbital. Moreover, the lowering in the adsorption energy leads to an active interaction of the DNA/RNA with the surfaces, accordingly its conduct to shorter the recovery time. The selectivity of the biosensor modulation device has illustrated a significant sensitivity for the nucleobases on both the oxygen and sulfur layer sides of the MoOS monolayer. This finding reveals that apart from graphene, dichalcogenides–Janus transition metal may also be adequate for identifying DNA/RNA bases in applied biotechnology.

Liquid film rupture beyond the thin-film equation: A multi-component lattice Boltzmann study

Under the condition of partial surface wettability, thin liquid films can be destabilized by small perturbations and rupture into droplets. As successfully predicted by the thin film equation (TFE), the rupture dynamics are dictated by the liquid–solid interaction. The theory describes the latter using the disjoining pressure or, equivalently, the contact angle. The introduction of a secondary fluid can lead to a richer phenomenology, thanks to the presence of different fluid/surface interaction energies but has so far not been investigated. In this work, we study the rupture of liquid films with different heights immersed in a secondary fluid using a multi-component lattice Boltzmann (LB) approach. We investigate a wide range of surface interaction energies, equilibrium contact angles, and film thicknesses. We found that the rupture time can differ by about one order of magnitude for identical equilibrium contact angles but different surface free energies. Interestingly, the TFE describes the observed breakup dynamics qualitatively well, up to equilibrium contact angles as large as 130°. A small film thickness is a much stricter requirement for the validity of the TFE, and agreement with LB results is found only for ratios ε=h/L of the film height h and lateral system size L, such as ε≲×10−3.

Theoretical study on Xe⋯N non-covalent interactions: Three hybridization N with XeO3 and XeOF2

The interactions of complexes of XeOF2 and XeO3 with a series of different hybridization N-containing donors are studied by means of DFT and MP2 calculations. The aerogen bonding interaction energies range from 6.5 kcal/mol to 19.9 kcal/mol between XeO3 or XeOF2 and typical N-containing donors. The sequence of interaction for N-containing hybridization is sp3&amp;gt;sp2&amp;gt;sp, and XeO3 is higher than XeOF2. For some donors of sp2 and sp3 hybridization, the steric effect plays a minor role in the interaction with the evidence of reduced density gradient plots. The dominant stable part is the electrostatic interaction. In complex of XeO3, the weight of polarization is larger than dispersion, while the situation is opposite for XeOF2 complexes. Except for the sum of the maximum value of molecular electrostatic potential on Xe atom and minimum value of molecular electrostatic potential on N atom, the otherfive interaction parameters including the potential energy density at bond critical point, the equilibrium distances, interaction energies with the basis set superposition error correction, localized molecular orbital energy decomposition analysis interaction energies, and the electron charge density, show great linear correlation coefficients with each other.

Lattice Model of Multilayer Adsorption of Particles with Orientation Dependent Interactions at Solid Surfaces.

A simple lattice model has been used to study the formation of multilayer films by fluids with orientation-dependent interactions on solid surfaces. The particles, composed of two halves (A and B) were allowed to take on one of six different orientations. The interaction between a pair of differently oriented neighboring particles was assumed to depend on the degrees to which their A and B parts overlap. Here, we have assumed that the AA interaction was strongly attractive, the AB interaction was set to zero, while the BB interaction was varied between 0 and . The ground state properties of the model have been determined for the systems being in contact with non-selective and selective walls over the entire range of BB interaction energies between 0 and . It has been demonstrated that the structure of multilayer films depends on the strengths of surface potential felt by differently oriented particles and the interaction between the B halves of fluid particles. Finite temperature behavior has been studied by Monte Carlo simulation methods. It has been shown that the bulk phase phase diagram is qualitatively independent of the BB interaction energy, and has the swan neck shape, since the high stability of the dense ordered phase suppresses the possibility of the formation of disordered liquid-like phase. Only one class of non-uniform systems with the BB interaction set to zero has been considered. The results have been found to be consistent with the predictions stemming form the ground state considerations. In particular, we have found that a complete wetting occurs at any temperature, down to zero. Furthermore, the sequences of layering transitions, and the structure of multilayer films, have been found to be the same as observed in the ground state.

Universal Fentanyl Sensor for Strip and Wearable Non-Invasive Testing

Current technologies rely on bulkier instruments for detecting small molecule concentration in in the bodyfluids. However, they required time consuming preparation of mixture prior to analysis. In this study, we have demonstrated the new sensing method by using conducting polymer combined with our designed anchor molecule. The sensing interface has secured the ultra-high sensitivity to specific adsorption, which reform the electronic structure of polyaniline substrate by altering the delocalized electrons. Moreover, the PANI structure can be easily tuned for any given sensitivity of detection. Computationally, it was confirmed that the interactions between fentanyl and anchor interface are significantly strong (≈ -1.19 eV). The range of interaction energies is found due to the variation of the positions of key functional groups of fentanyl relative to the PAni-Arg structure. Particularly with strong interactions, spontaneous proton transfer is observed from the sensor to the fentanyl molecule. The sensor showed excellent response when used in different human bodily fluids. In addition to these interactions at the interface, we have demonstrated a new sensing technique as the first type of phase angle detection sensor. Using this technique, the changes at the interface have inherently amplified signals compared to changes in resistance, potential, and/or current signals. The new interface of biocompatible and flexible composite layers can be fabricated via electrochemical approach on variety of surface with minimal maintenance. This approach is particularly useful for assays that requires extremely low sample volume. We showed our designed method and device can be used for testing strip/vial for tear and blood samples and testing patch for in-situ monitoring through skin perspiration. Lastly, electrochemical approach is facile to use, it enables the portability of the sensor for on-site field measurements as well as in clinical settings. This work helped to resolve the challenge of monitoring small molecule drugs accurately and rapidly for point-of-care (POC) diagnosis in current clinical settings.

Electrochemical and theoretical investigation of functionalized reduced graphene aerogel modified electrode for lead ions sensing

In this work, we have incorporated 4,4′-methylenedianiline into reduced graphene oxide (F-rGO Aerogel) with high surface area and increased conductivity. The modified electrode with F-rGO Aerogel presents a sensitive Pb(II) sensor performance with good properties, such as excellent conductivity, high effective surface area and high adsorption ability for lead (II) ions. After the deposition process, the amount of lead on the working electrode surface can be increased due to easily coordination of the –NH2 groups present in F-rGO Aerogel/CPE with Pb(II). Molecular geometry optimization, structural calculations, as well as molecular system electronic state were carried out to obtain suitable information about adsorption process. The range of interaction energies in the cationic complexes (−659.80 kJ mol−1 to −763.15 kJ mol−1) represents the establishment of a covalent bond, by sharing π-electron with d-orbitals of lead cations. The strong cation-π interaction with high adsorption energy helps to remain the Pb2+ ions on the graphene surface through chemical adsorption that do not collapse with time. This strong chemisorption interaction allows the graphene species, especially the newly presented one, to be one of the most powerful adsorbent for adsorbing lead cation atoms. Under optimized condition, the built active electrode system could present a low detection limit of 0.03 μM concentration and a detection range of 0.01–0.3 μM. Furthermore, the reproducibility and stability of the sensor exhibited satisfactory results.

Water-silanol interactions on the amorphous silica surface: A dispersion-corrected DFT investigation

Interpreting the interaction between the amorphous silica surface and water is a key step to understand its physicochemical properties. However, due to the flexibility of the structure and the distribution of types and geometries of the silanols one can obtain a broad range of interaction energies, as was already shown in former studies. This time we were able to investigate the distribution of silanols in relation with the calculated interaction energies, and thus designate those different silanols sites. Different dispersion-correction PBE-D (PBE + D2, D3, D3-BJ, TS, TS-HI, MBD, and FI-MBD) and meta-GGA SCAN methods has been used to quantify the interactions between water and defined silanols sites of the surface. All the methods give similar interaction energies, showing equivalent performances of SCAN and PBE-D methods to describe week interactions in our system. Following various routes, we identified a protocol of calculation in order to compute the interaction energies more accurately, taking into consideration the van der Waals (vdW) forces. Once different silanols are correctly described within the calculation level, it is clear that the geometry and environment determine its chemistry. Furthermore, the possible deformation of the silica surface affected by the water interaction is studied. The quantification of the interaction energies is important in order to correctly scale the results and confront with the experiments. With this information in mind, one can think about synthesis techniques that modify the silanols distribution of the silica surface in a way to tune its hydrophobicity and acidity.

Carbon nitride 2-D surface as a highly selective electrochemical sensor for V-series nerve agents

Herein, carbon nitride 2-D surface (C2N) was studied as an electrochemical sensor for chemical warfare agents (CWA; A-230, A-232, A-234, and VR). The deep insight of analytes@C2N complexation was obtained by interaction energy, SAPT0, NCI, QTAIM, EED, and FMO analyses. The interaction energies results indicate that these CWAs are physisorbed onto the surface where BSSE corrected interaction energies range from −14.42 kcal/mol to −15.99 kcal/mol. Moreover, SAPT0 analysis revealed that dispersion interactions are the dominant component which amount to nearly 61% of overall SAPT0 interaction energies. SAPT0 analysis results are consistent with interaction energies. The nature of interactions was also quantified by NCI and QTAIMs analysis. NBO analysis showed that the highest amount of charge transfer is observed in A232@C2N (−0.018 e−), while the least amount of charge transfer is seen in VR@C2N. The EDD analysis also verified the results of NCI, QTAIM and NBO analyses. A short recovery time of 0.027 s at 298 K for desorption of VR from C2N surfaces was calculated. VR adsorption onto C2N surface caused the highest change in the HOMO-LUMO energy gap (2.68 eV) compared to bare C2N (3.71 eV), which reveals the potential of C2N as an electrochemical sensor for VR. The complexation of A-230, A-232, and A-234 had a negligible effect on the HOMO-LUMO energy gap. Among all complexes, HOMO-LUMO excitation is associated with charge transfer from analytes to the C2N surface.

On the Role of Interacting Particles and Limited Resources in the Regulation of Lattice Length Dynamics

Motivated by the significant effect of particle–particle interactions on the driven stochastic transport system, we examine how interacting particles control the lattice polymerization and depolymerization dynamics under the restricted supply of involved resources. We carried out a theoretical analysis based on the simple mean-field and cluster mean-field theory to predict the fundamental role of interactions on the steady-state length dynamics. It has been detected that there is a strong correlation between the lattice length dynamics and the concentration of the total number of lattice sites in the reservoir. For lower and higher values of available resources, depolymerization and polymerization process dominates the lattice dynamics, respectively, while for intermediate values of resources we observe a competition between polymerization and depolymerization kinetics. Further, it is examined that for a specific range of interaction energy E, the system remains in low density phase, on the contrary, for its significantly higher value, the system transits to high-density phase. In contrast to the high density phase, it is observed that in low density phase, lattice length decreases with an increase in interaction strength. Finally, the theoretical outcomes are validated with extensive Monte Carlo simulations.

Approaches for machine learning intermolecular interaction energies and application to energy components from symmetry adapted perturbation theory.

Accurate prediction of intermolecular interaction energies is a fundamental challenge in electronic structure theory due to their subtle character and small magnitudes relative to total molecular energies. Symmetry adapted perturbation theory (SAPT) provides rigorous quantum mechanical means for computing such quantities directly and accurately, but for a computational cost of at least O(N5), where N is the number of atoms. Here, we report machine learned models of SAPT components with a computational cost that scales asymptotically linearly, O(N). We use modified multi-target Behler-Parrinello neural networks and specialized intermolecular symmetry functions to address the idiosyncrasies of the intermolecular problem, achieving 1.2 kcal mol-1 mean absolute errors on a test set of hydrogen bound complexes including structural data extracted from the Cambridge Structural Database and Protein Data Bank, spanning an interaction energy range of 20 kcal mol-1. Additionally, we recover accurate predictions of the physically meaningful SAPT component energies, of which dispersion and induction/polarization were the easiest to predict and electrostatics and exchange-repulsion are the most difficult.

A theoretical investigation of the interaction between substituted pyridines and CS2. Versatility of the CS2 molecule

Abstract The interaction between carbon disulfide and para-substituted pyridines (X = NH2, CH3, H, F, CN, NO2) are investigated by theoretical methods. Four different stable structures are detected for the complexes at the MP2 = full/aug-cc-pVDZ level of theory. The A structures having bonding energies between −9.34 and −11.57 kJ/mol are characterized by N⋯S chalcogen bonds. In the B structures, the interaction energies range between −8.86 and −9.37 kJ/mol and the complexes are bonded by N⋯C tetrel bonds. In the C structures, characterized by interaction energies between −12.20 and −15.03 kJ/mol, the molecules are bonded by S…π interactions. The D complexes involve, in addition to N⋯S chalcogen bonds, a direct participation of the substituents in the bonding process. They have the largest binding energies, between −18.06 and −24.22 kJ/mol. The nature and properties of the four complexes are analyzed by natural bond orbitals (NBO) calculations, atoms in molecules (AIM) analysis and energy decomposition (SAPT) calculations. The role of the basicity of the pyridines and the influence of the electrostatic potential of the pyridines on the charge transfer is outlined.

Explicit Inclusion of Polarizing Electric Fields in σ- and π-Hole Interactions.

The interactions between a wide variety of molecules having σ-holes or π-holes and several nitrogen bases have been analyzed computationally. The σ- and π-hole atoms span groups III-VII of the periodic table. The interaction energies range from quite weak, typical of non-covalent bonding, to unusually strong: from -4.6 to -22.0 kcal/mol for σ-hole bonding and from -4.0 to -42.4 kcal/mol for π-hole bonding. The markedly greater strengths of some bonds does not imply that any new factors or types of bonding are involved; they simply reflect higher degrees of the polarization that is part of any Coulombic interaction. To explain the stronger bonding, this polarization must be explicitly taken into account. We show that the interaction energies can be related quite well to (a) the maximum positive electrostatic potentials associated with the σ- or π-holes on their molecular surfaces, (b) the polarizabilities of the nitrogen bases, and especially (c) the polarizing electric fields of the σ- or π-hole molecules at the positions of the nitrogens.

Hydrogen Bond Enhanced Halogen Bonds: A Synergistic Interaction in Chemistry and Biochemistry.

The halogen bond (XB) has become an important tool for molecular design in all areas of chemistry, including crystal and materials engineering and medicinal chemistry. Its similarity to the hydrogen bond (HB) makes the relationship between these interactions complex, at times competing against and other times orthogonal to each other. Recently, our two laboratories have independently reported and characterized a synergistic relationship, in which the XB is enhanced through direct intramolecular HBing to the electron-rich belt of the halogen. In one study, intramolecular HBing from an amine polarizes the iodopyridinium XB donors of a bidentate anion receptor. The resulting HB enhanced XB (or HBeXB) preorganizes and further augments the XB donors. Consequently, the affinity of the receptor for halogen anions was significantly increased. In a parallel study, a meta-chlorotyrosine was engineered into T4 lysozyme, resulting in a HBeXB that increased the thermal stability and activity of the enzyme at elevated temperatures. The crystal structure showed that the chlorine of the noncanonical amino acid formed a XB to the protein backbone, which augmented the HB of the wild-type enzyme. Calorimetric analysis resulted in an enthalpic contribution of this Cl-XB to the stability of the protein that was an order of magnitude greater than previously determined in biomolecules. Quantum mechanical (QM) calculations showed that rotating the hydroxyl group of the tyrosine to point toward rather than away from the halogen greatly increased its potential to serve as a XB donor, equivalent to what was observed experimentally. In sum, the two systems described here show that the HBeXB concept extends the range of interaction energies and geometries to be significantly greater than that of the XB alone. Additionally, surveys of structural databases indicate that the components for this interaction are already present in many existing molecular systems. The confluence of the independent studies from our two laboratories demonstrates the reach of the HBeXB across both chemistry and biochemistry and that intentional engineering of this enhanced interaction will extend the applications of XBs beyond these two initial examples.

A first principle evaluation of the adsorption mechanism and stability of volatile organic compounds into NaY zeolite

Abstract Removal of volatile organic compounds (VOCs) from indoor or outdoor environments is an urgent challenge for the protection of human populations. Inorganic sorbents such as zeolites are a promising solution to tackle this issue. Using dispersion corrected periodic DFT calculations, we have studied the interaction between sodium-exchanged faujasite zeolite and a large set of VOCs including aromatics, oxygenates and chlorinated compounds. The computed interaction energies range from about −25 (methane) to −130 kJ/mol (styrene). Methane is by far the less interacting specie with the NaY zeolite. All other VOCs present interaction energies higher in absolute value than 69 kJ/mol. Most of them show a similar adsorption strength, between −70 and −100 kJ/mol. While the electrostatic interactions are important in the case of oxygenates and acrylonitrile, van der Waals interactions predominate in hydrocarbons and chlorides. By monitoring the variation of molecular bond lengths of the different VOCs before and after adsorption, we have then evaluated the tendency of adsorbate to react and form by-products, since a significant stretching would evidently lead to the activation of the bond. While hydrocarbons, tetrachloroethylene and acrylonitrile seem to be not activated upon adsorption, all oxygenates and 1,1,2-trichloroethane could possibly react once adsorbed.

Increase of the Charge Transfer Rate Coefficients for NO+ and O2+• Reactions with Isoprene Molecules at Elevated Interaction Energies

Atmospheric concentrations of isoprene (2-methylbutadiene) in environmental research and in exhaled breath for medical research are usually measured by soft chemical ionization mass spectrometry that relies on a knowledge of the kinetics of the gas phase reactions of H3O+, NO+ or O2+• ions with isoprene molecules. Thus, we have carried out an experimental study of the rate coefficients, k, and product ions distributions for such reactions over a range of ion-molecule interaction energy, Er, (0.05-0.8 eV) in a helium-buffered selected ion flow-drift tube, SIFDT. It is found that contrary to the ion-induced dipole capture model, k for the NO+ and O2+• charge transfer reactions almost doubled over the E r range, while k for the H3O+ proton transfer reaction did not significantly change with E r, as predicted. These results reveal that the reaction mechanism involving ion-molecule capture forming an intermediate complex does not properly describe charge transfer to isoprene molecules. It is important to account for this increase in k with E r in these isoprene charge transfer reactions, and probably for other such reactions, when using drift tube reactors for trace gas analysis.