Kinds Of Intermolecular Interactions Research Articles

An NMR Spectroscopy View on London Dispersion in Catalysis: Detection, Quantification, and Application in Ion Pair and Transition Metal Catalysis.

ConspectusThe energetic contribution of London dispersion (LD) can cover a broad range from very few to hundreds of kJ mol-1 for extended interaction interfaces due to its pairwise additivity. However, for a designed and successful application of LD in chemical catalysis, there are still many obstacles and questions that remain. In principle, LD can be regarded as the attractive part of the van der Waals potential. Thus, considering the whole van der Waals potential, including the repulsive part (steric repulsion), the ideal solution to the problem in catalysis would be to design compatible interaction interfaces at exactly the correct distance. In the case of a self-assembled, flexible structure arrangement, entropic contributions and solvent interactions might be detrimental. In the case of a rigid catalyst pocket, steric hindrance might not allow for large substituents that are usually applied as dispersion energy donors (DEDs). For a working catalytic system, the following question arises: how is it possible to dissect the complex interaction interfaces in terms of energetic contributions? Usually, the energetic contribution of LD to catalysis is addressed by using calculations. However, adequately computing the correct energetic contributions can be extremely challenging for a vast conformational space with all kinds of intermolecular interactions. Thus, experimental data are essential for comparison or benchmarking.Therefore, in this Account, we describe our quest for detailed experimental data obtained via NMR spectroscopy to experimentally dissect and quantify LD in catalytic systems. In addition, we address the question of whether bulky substituents used as DEDs can be used in confined catalytic pockets. With the example of Pd phosphoramidite complexes, we show how it is possible to experimentally dissect and quantify the contribution of individual interaction areas in complicated transition metal complexes. Furthermore, a correlation between conformational rigidity and heterodimer preference clearly reveals that LD can only unfold its full potential in cases where entropic contributions are minimized. This finding can also explain the small contribution of LD in flexible and solvent-exposed molecular balances. In the field of Brønsted acid catalysis, we demonstrated that LD has a strong influence on the structures, stability, and populations of confined catalytic intermediates. LD is key for populating higher aggregates such as dimers. In addition, offsets between the experimental and computational results were observed and attributed to solvent-solute dispersion interactions. We studied the delicate interplay of attractive and repulsive interactions by adding bulky DED substituents onto a substrate, which can function as a molecular balance system. Intriguingly, the effect of LD on the free substrate was straightforwardly transferred onto the highly confined intermediates. Furthermore, this effect could even be read out in the enantioselectivities of the underlying reaction. This conceptualized a general approach regarding how LD can be used beneficially in catalysis to convert from moderate/good to excellent stereoselectivities. It showcased that bulky groups such as tert-butyl must not only be regarded as occupied volumes.

A rational design to improve selective imaging of tau aggregates by constructing side substitution on N,N-dimethylaniline/quinoxaline D-π-A fluorescent probe

Tau aggregation correlates rigorously with the progression and severity of Alzheimer’s disease (AD). However, it is extremely challenging to develop tau-selective imaging probes due to similar β-sheet structures shared with Aβ fibrils. Herein, three new donor-π-acceptor fluorophores (T1-T3) composed of 3,5-dimethoxy-N,N-dimethylaniline-4-yl and quinoxaline, bridged by 1–3 CC bond are rationally designed for selectively imaging tau aggregates. For the first time, we demonstrated the side substitution on D-π-A skeleton is significant for improving the selectivity of tau probes. Molecular docking results revealed that the lateral methoxy groups on molecular rotors could act as antennas to interact with surrounding tau hydrophilic residues via hydrogen-bond and other kinds of intermolecular interactions, improving selective recognition for tau aggregates. Compared with its non-side-substitution precursor T02, T2 exhibited 4.7 times higher tau-over-Aβ selectivity after introducing methoxy substituents. Owing to the improved selectivity, T2 was successfully applied to detect tau aggregates in cells and pathologically relevant regions of AD mice model. This work verifies the pivotal role of side substitution on D-π-A skeleton in increasing the selectivity of tau probes, which provides a rational strategy to design novel tau probes with high selectivity in future.

Experimental Spectroscopic, Quantum Chemical, Molecular Docking, and Molecular Dynamic Simulation Studies on Hydantoin (Monomer and Dimer)

The quantum chemical properties of hydantoin (imidazolidine-2,4-dione) have been studied by the DFT method (density functional theory) and experimentally by FT-IR, UV–Vis, 1H, and 13 C NMR. The B3LYP technique is used to determine HOMO-LUMO, vibrational frequency, and other parameters as well as to optimize the structure. Along with that vibrational mode assessment, the estimated vibrational frequencies were compared to experimental FT-IR spectra. MEP (molecular electrostatic potential) analysis and a Fukui function analysis were both done to look into the reactive regions of the molecule in order to look into the charge distribution of the molecule. Additionally, the electron localization function (ELF) value was examined to reveal details about the chemical composition, molecular bonding, and reactivity. The calculation of UV–visible spectra using the TD-DFT/PCM approach is done, and the results are contrasted with UV spectra that have been calculated experimentally. From HOMO to LUMO orbitals, electron excitation analysis was carried out. Hole and Electron density distribution (EDD and HDD) maps were created in an excited state using various solvents. The intermolecular interactions on the crystal surface were described and evaluated using fingerprint plots and Hirshfeld surface analyses. The Hirshfeld surface was used to identify different kinds of intermolecular interactions, including N–C, N–H, N–O, O–C, and O–H. The 1H-NMR and 13 C-NMR shifts were calculated using the GIAO method, and the results were compared to experimental spectra. In a biological investigation utilizing several receptors, molecular docking was employed to identify the most effective ligand-protein interactions. The stability of biomolecular systems was investigated using a molecular dynamics simulation.

Investigation of the Nature of Intermolecular Interactions in Tetra(thiocyanato)corrolato-Ag(III) Complexes: Agostic or Hydrogen Bonded?

Tetra(thiocyanato)corrolato-Ag(III) complexes presented here constitute a new class of metallo-corrole complexes. The spectroscopic properties of these complexes are quite unusual and interesting. For example, the absorption spectra of these β-substituted corrolato-Ag(III) complexes are very different from those of the β-unsubstituted corrolato-Ag(III) derivatives. Single-crystal XRD analysis of a representative tetra(thiocyanato)corrolato-Ag(III) derivative reveals C-H···Ag interactions. The C-H···Ag interactions are rarely demonstrated in the crystal lattice of a discrete coordination/organometallic compound. Optimization of the hydrogen positions of the crystal structure discloses the geometrical parameters of the said interaction as a Ag···H distance of 2.597 Å and ∠C-H···Ag of 109.62°. The natural bond orbital analysis provides information about the donor-acceptor orbitals involved in the interactions and their interaction energies. It was observed that the σC-H orbital overlaps with the vacant d-orbital of Ag with an interaction energy of 17.93 kJ/mol. The filled d-orbital of Ag overlaps with the σ*C-H orbital with an interaction energy of 4.79 kJ/mol. The highlights of this work are that the H···Ag distance is outside of the distance range for the typical agostic interaction but fitted with the weak H-bond distance. However, the ∠C-H···Ag angle is within the range of the agostic interaction. Both crystallographic data and electronic structure calculations reveal that these kinds of intermolecular interactions in square-planar d8 Ag(III) complexes are intermediate in nature. Thus, they cannot be categorically called either hydrogen bonding or agostic interaction.

Ultrasonic characterization on fertilizer solutions in view to sustainable agriculture

The volumetric and sound parameters are very helpful tools to predict the different kinds of intermolecular interactions and their strengths associated with them. It is revealed that the soil salinity problem incessantly spreads due to continuous changes in climate, excessive use of groundwater, and bulk use of low-quality water for irrigation. Excessive soil salinity reduces the many agricultural crop production, which is particularly sensitive throughout the development and growth of the plant. The effect of salinity could be controlled or counteracted by the application of suitable fertilizers into the saline soils. In this manuscript, numerous acoustic as well as thermodynamic parameters of ammonium sulphate (AS) fertilizer of different weight fractions at 293.15 K temperature have been studied. The results obtained, from calculated different acoustic and volumetric parameters expose the existence of strong interactions in the system taken for investigation, this depends on the ilk of molecules. The fertilizer: ammonium sulphate shows, maximum molecular interactions at higher concentrations in all the solvents (Water, Sodium Chloride, and Magnesium Chloride), and this can again castoff in view as a remedy for soil salinity using interactions among saline salts and fertilizers.

Application of Supra Molecular Immaterialness Adsorbent in Indoor Volatile Organic Compounds Control in Hot and Humid Areas

Supramolecular interaction is a kind of intermolecular interaction with molecular recognition ability. Based on molecular recognition, the design, synthesis, and assembly of novel supramolecular functional materials will provide theoretical guidance and new application systems for analytical science. It has made great contributions to the common development of life sciences, materials sciences, and environmental sciences. This article aims at the application of supramolecular nanomaterial adsorbents in indoor volatile organic pollutants control in hot and humid regions. This article sets up three experimental groups and a control group. The experimental group is to apply supramolecular nanomaterial adsorbents to Northeast China. Among the volatile organic pollutants in cold regions, the experimental group 2 applied the supramolecular nanomaterial adsorbents to indoor volatile organic pollutants in the humid and hot regions of the south. The experimental three groups of supramolecular nanomaterial adsorbents were applied in temperate environments. The control group applied general materials to study the effect of purification, considered purification time, efficiency, and economic benefits, and used mathematical statistics and mathematical analysis to classify and analyze and use big data. Use these methods to fit the data. Experimental data shows that the application of supramolecular nanomaterial adsorbents in indoor volatile organic pollutants control in hot and humid areas has a good effect and can effectively achieve the purpose of purifying organic pollutants. Experimental data shows that the application of supramolecular nanomaterial adsorbents in indoor volatile organic pollutants control in hot and humid areas has a broad application prospect. Its purification efficiency of organic pollutants has increased by about 23.5% and its economic efficiency has increased by about 21.3%. The application plays a guiding rolein the purification of volatile organic pollutants.

Low-temperature dependence on the THz spectrum of CL-20/TNT energetic cocrystal by molecular dynamics simulations.

Based on the unique advantages of terahertz (THz) spectrum on the detection of energetic cocrystals, the low-temperature dependent THz spectra of CL-20/TNT cocrystal were investigated by using molecular dynamics (MD) simulations from 5 to 296K, as well as three different crystal faces, (001), (120), and (010). When the temperature decreases below 95K, we have observed two new peaks for CL-20/TNT cocrystal, at 4.58 and 5.99THz, respectively. Also, the THz peaks below 1.5THz gradually disappear under cooling from 296 to 5K, and they should originate from the lattice thermal vibrations. THz absorption peaks of CL-20/TNT cocrystal reveal frequency shifting, linearly dependent on temperature. Four of them are red shift and other two are blue shift of THz vibrational peaks of CL-20/TNT cocrystal with the temperature increase. The frequency shifts can be attributed to the effects of lattice thermal expansion on inter-/intramolecular vibrational modes as well as their coupling. From the temperature-dependent THz spectra of different crystal faces, we further confirm the response of different kinds of intermolecular interactions on the THz spectrum of CL-20/TNT cocrystal. Graphical abstractThe intermolecular interactions and peak positions of THz spectra of CL-20/TNT cocrystal in the range of 0-6 THz versus temperature.

Solid-State Fluorescence Enhancement of Bromine-Substituted Trans-Enaminone Derivatives

Halogen bonding, as a kind of intermolecular interaction, has rarely been used to tune solid-state emission properties of luminescent materials, especially fluorescent materials. Herein, three trans-enaminone (TE) derivatives (nonbrominated TE, monobrominated BrTE, and tribrominated Br3TE) with aggregation-induced emission property have been designed and synthesized. Two types of BrTE crystals (BrTE-B and BrTE-G) with different fluorescence properties were obtained. It was observed that their solid-state fluorescence has been enhanced by the formation of halogen bonding. In particular, the crystal BrTE-G containing Br…π interactions exhibits a fluorescence quantum yield (9.6%) nearly sevenfold higher than BrTE-B, the crystal without halogen bonding (1.4%), and fivefold higher than the nonbrominated TE derivative (2.1%). By careful inspection of the single-crystal data and theoretical calculations, the high fluorescence quantum yield of BrTE-G appears to be due to halogen-bonding interactions as well as multiple stronger intermolecular interactions which may restrain molecular motions, leading to the reduced nonradiative decay rate and the enhanced radiative decay rate. Additionally, increasing the number of bromine substituents may further promote the radiative decay rate, explaining therefore the higher fluorescence quantum yield (12.5%) of Br3TE.

Volumetric, acoustic and transport properties of ternary solutions of l-serine and l-arginine in aqueous solutions of thiamine hydrochloride at different temperatures

The volumetric, acoustic and viscometric properties are used for investigating the interactions of l-serine and l-arginine in aqueous solutions of a vitamin, namely, thiamine hydrochloride, over a temperature range of (293.15–313.15) K and at atmospheric pressure. The limiting apparent molar volume, V0ϕ, and empirical parameter, Sv, is evaluated from apparent molar volume, Vϕ. Similarly, limiting apparent molar isentropic compression, K0ϕ,s, and slope, Sk, is evaluated from apparent molar isentropic compression, Kϕ,s. The corresponding transfer properties (ΔtrV0ϕ and ΔtrK0ϕ,s) from water to aqueous vitamin solutions are also evaluated. The viscosity data has also been used to analyze relative viscosity, ƞr, viscosity B-coefficients and temperature derivative of B-coefficients, dB/dT. The various calculated parameters assist to procure valuable information regarding the presence of different kinds of intermolecular interactions in the ternary (l-serine/l-arginine + water + thiamine-HCl) solutions.

CO2 solubility and mass transfer in water-lean solvents

Shifting from aqueous to water lean solvents has been evaluated as a mean for increasing the mass transfer rates in regular chemical solvents with amines. An array of amines (monoethanolamine, 2-methylpiperazine and N-methyl diethanolamine) and diluents (sulfolane, ethylene glycol, 1-methylimidazole, dimethyl sulfoxide, N-methyl-2-pyrrolidinone) has been analyzed. Addition of organic diluents seem to generally induce both a shift in chemical equilibrium and an increase in mass transfer rates for a fixed CO2 partial pressure, though not necessarily for a fixed CO2 loading. However, these relative advantages in terms of mass transfer rates decrease the more loaded the water lean solvent is. The equilibrium shift caused by organic diluents has been evaluated in terms of de-stabilization of the species in the solvent, which for monoethanolamine-based solvents can be easily related to a decrease in dielectric permittivity. However, this analysis indicates that such treatment is insufficient for other types of water-lean solvents, suggesting that different kinds of intermolecular interactions should also be considered in future studies.

Exploring the enhancement of electron tunneling induced by intermolecular interactions on surface of self-assembled monolayer

The topic of intermolecular interactions enhancing electron tunneling between protein residues on biofilm surface has been investigated by some theoretical studies. However, few of experimental studies could confirm this viewpoint. In this work, the Mercaptopropionic acid self-assembled monolayer (MPA SAM) with terminal carboxyl groups was constructed, as a simplified model for functionalized biomimic membrane. The electron tunneling rate constant of ferrocenylmethanol redox process on SAM was obtained from experimental results of scanning electrochemical microscopy. It is found that the electron tunneling across MPA SAM is faster than that of contrastive Methyl mercaptopropionate SAM. This result is attributed to the intermolecular interactions between the redox and MPA molecules. The conditions of lower pH and weaker ion pair effect all benefit the formation of the intermolecular interactions, resulting the enhancement of electron tunneling more obvious. Based on this, this kind of intermolecular interaction is inferred to be intermolecular hydrogen bond. Our work may have contributions to exploring electron tunneling between protein residues on biofilm surface.

CO2 Solubility and Mass Transfer in Water Lean Solvents

Abstract Shifting from aqueous to water lean solvents has been evaluated as a mean for increasing the mass transfer rates in regular chemical solvents with amines. An array of amines (monoethanolamine, 2-methylpiperazine and N-methyl diethanolamine) and diluents (sulfolane, ethylene glycol, 1-methylimidazole, dimethyl sulfoxide, N-methyl-2-pyrrolidinone) has been analyzed. Addition of organic diluents seem to generally induce both a shift in chemical equilibrium and an increase in mass transfer rates for a fixed CO2 partial pressure, though not necessarily for a fixed CO2 loading. However, these relative advantages in terms of mass transfer rates decrease the more loaded the water lean solvent is. The equilibrium shift caused by organic diluents has been evaluated in terms of de-stabilization of the species in the solvent, which for monoethanolamine-based solvents can be easily related to a decrease in dielectric permittivity. However, this analysis indicates that such treatment is insufficient for other types of water-lean solvents, suggesting that different kinds of intermolecular interactions should also be considered in future studies.

Guinier peak analysis for visual and automated inspection of small-angle X-ray scattering data.

The Guinier region in small-angle X-ray scattering (SAXS) defines the radius of gyration, Rg, and the forward scattering intensity, I(0). In Guinier peak analysis (GPA), the plot of qI(q) versus q2 transforms the Guinier region into a characteristic peak for visual and automated inspection of data. Deviations of the peak position from the theoretical position in dimensionless GPA plots can suggest parameter errors, problematic low-resolution data, some kinds of intermolecular interactions or elongated scatters. To facilitate automated analysis by GPA, the elongation ratio (ER), which is the ratio of the areas in the pair-distribution function P(r) after and before the P(r) maximum, was characterized; symmetric samples have ER values around 1, and samples with ER values greater than 5 tend to be outliers in GPA analysis. Use of GPA+ER can be a helpful addition to SAXS data analysis pipelines.

An investigation into the substituent effect of halogen atoms on the crystal structures of indole-3-carboxylic acid (ICA)

An investigation into the substituent effect of halogen atoms (F, Cl, Br) on the crystal structure of indole-3-carboxylic acid (ICA) was prepared in this work. The investigation was done through the aspect of crystal structure, intermolecular interactions and π⋯π stacking motifs with the assistance of infrared spectra, elemental analyses, NMR spectra, differential scanning calorimetry (DSC), thermogravimetric analyses (TGA) and hot stage microscopy (HSM) measurements. The results revealed that the different kinds of halogen atoms and the different substituted positions have a significant effect on the crystal structures, molecular π⋯π stacking motifs and the kinds of intermolecular interactions. We further correlated the melting points of the ICAs with the H–H, O–H and X–H (X = F, Cl, Br) interactions, and found a positive correlation between them.

Inversion gas chromatography in studies of adsorption properties of carbon materials. Specific component of the surface free energy

Inversion gas chromatography was used to determine at extremely low surface coverages the specific component Isp of the surface free energy for various types of carbon blacks. It was demonstrated that the Rohrschneider-McReynolds model can be used to evaluate the capacity of carbon adsorbents for various kinds of intermolecular interactions.

Determination of the charge transport abilities of polymorphs [C6F5Cu]2(4,4′-bipy) with different interactions: a density functional theoretical investigation

Due to the different molecular stacking conformations, two kinds of intermolecular interactions, arene–arene π-stacking interaction and Cu–Cu interaction coexist in the polymorphs of [C6F5Cu]2(4,4′-bipy) crystals, 3-α and 3-β. However, the relative magnitude of the two kinds of intermolecular interactions in 3-α and 3-β is different. With the help of first-principle band structure calculations, the relationship between the charge transport abilities and the intermolecular interactions in the two polymorphs was investigated for the first time. The analysis of band structures and Г point wave functions of the band-edge state in the valence band of crystal 3-α shows that the Cu–Cu interaction so-called cuprophilic interaction determines the hole transport ability, although this interaction is weaker than that in crystal 2 of C6F5Cu(py) discussed in our previous work, which is a promising hole transport material. For polymorph crystal 3-β, the wave functions of LUMO are mainly localized on the bipyridine (bpy) groups, which are result from the arene–arene π-stacking interaction between the bpy groups. Such a π–π stacking interaction dominates the electron transport ability in the conduction band of 3-β and makes the electron main carrier for transporting. The results are also supported by the analysis of effective masses and density of states (DOS). Thus, the charge transport properties are dominated by different intermolecular interactions due to the different molecule stacking in the two polymorphs.

Halogen Atoms in the Modern Medicinal Chemistry: Hints for the Drug Design

A significant number of drugs and drug candidates in clinical development are halogenated structures. For a long time, insertion of halogen atoms on hit or lead compounds was predominantly performed to exploit their steric effects, through the ability of these bulk atoms to occupy the binding site of molecular targets. However, halogens in drug - target complexes influence several processes rather than steric aspects alone. For example, the formation of halogen bonds in ligand-target complexes is now recognized as a kind of intermolecular interaction that favorably contributes to the stability of ligand-target complexes. This paper is aimed at introducing the fascinating versatility of halogen atoms. It starts summarizing the prevalence of halogenated drugs and their structural and pharmacological features. Next, we discuss the identification and prediction of halogen bonds in protein-ligand complexes, and how these bonds should be exploited. Interesting results of halogen insertions during the processes of hit-to-lead or lead-to-drug conversions are also detailed. Polyhalogenated anesthetics and protein kinase inhibitors that bear halogens are analyzed as cases studies. Thereby, this review serves as one guide for the virtual screening of libraries containing halogenated compounds and may be a source of inspiration for the medicinal chemists.

Crystal structure of cis-2,5-bis(3-pyridyl)-1,3,4-thiadiazole, C12H8N4S

Article Crystal structure of cis-2,5-bis(3-pyridyl)-1,3,4-thiadiazole, C12H8N4S was published on September 1, 2008 in the journal Zeitschrift für Kristallographie - New Crystal Structures (volume 223, issue 3).

Excess molar enthalpies and volumes of binary mixtures of nonafluorobutylmethylether with ketones at T = 298.15 K

Excess molar enthalpies, H m E , and volumes, V m E , were reported for binary mixtures of {nonafluorobutylmethylether, (FBME, C 4F 9OCH 3) + 2-propanone, or + 2-butanone, or + 3-pentanone} at 298.15 K. Results of H m E and V m E were positive over a whole range of concentrations for all the mixtures. The magnitude was in order: 2-propanone > 3-pentanone > 2-butanone for H m E and 3-pentanone > 2-butanone = 2-propanone for V m E at the maximum point. However, the difference in the maximum values of H m E and V m E by the increase in the number of carbon atoms in the ketones, n C is not so large. From these results, partial molar quantities ( H m , i E , ∞ , V m , i E , ∞ , and V m , i ∞ ) of the i component at infinite dilution, and apparent molar enthalpies of solvation, Δ solv H i of the i component were evaluated. The dependence of these thermodynamic quantities on the n C were discussed in consideration of various kinds of intermolecular interactions in pure component liquids and solutions.

Excess molar enthalpies and volumes of binary mixtures of nonafluorobutylmethylether with ethylene glycol ethers at T = 298.15 K

Excess molar enthalpies, H m E and volumes, V m E were reported for binary mixtures of {nonafluorobutylmethylether, (NFBME, C 4F 9–O–CH 3)} + [five ethylene glycol ethers, EGE n, m-R, {C m H 2 m + 1 -(OCH 2CH 2) n -R, n = 1 and 2, m = 1 to 4, R = OH and OCH 3}] at 298.15 K. Results of excess molar enthalpies and volumes were positive over whole range of concentrations for all the mixtures. The magnitude was in order: EGE1,4-OH > EGE1,3-OH > EGE1,2-OH > EGE1,1-OH > EGE2,1-OH > EGE2,1-OCH 3 for H m E and EGE2,1-OCH 3 > EGE1,4-OH > EGE1,3-OH > EGE1,2-OH > EGE1,1-OH > EGE2,1-OH for V m E at the maximum point. The curves of H m E and V m E for the EGE2,1-OH system were depressed in the middle mole fraction of NFBME, x 1 suggesting a quasi-stable state in the solution. We observed occurrences of the stable emulsification state in solutions in concentrations range of 0.35 < x 1 < 0.55. From these results, excess partial molar enthalpies, H m , 2 E , ∞ , and volumes, V m , 2 E , ∞ , of EGE n, m-R at infinite dilution, apparent molar enthalpies of solvation, Δ solv H 2, of the EGE n, m-R in NFBME were evaluated. The dependence of these thermodynamic quantities on the number of carbon atoms in the alkyl group, m, the number of the ethylene oxide group, n, and the difference of R group were discussed in consideration of various kinds of intermolecular interactions in pure component liquids and solutions.