Theoretical study of cooperativity between hydrogen bond‒hydrogen bond,halogen bond‒halogen bond and hydrogen bond‒halogen bond in ternary FX…diazine…XF (X = H and Cl) complexes

ABSTRACT

In the present work, the cooperativity between hydrogen bond?hydrogen bond, halogen bond?halogen bond and hydrogen bond?halogen bond in ternary FX…diazine…XF (X = H and Cl) complexes is theoretically investigated. The sign of cooperative energy (E_coop) obtained in all of the triads is positive which indicates that the ternary complex is less stable than the sum of the two isolated binary complexes. Moreover, our calculations show that E_coop value in triads increases as FX…pyridazine…XF > FX…pyrimidine…XF > FX…pyrazine…XF. In agreement with energetic, geometrical and topological properties, electrostatic potentials and coupling constants across ¹⁵N…X?¹⁹F (X = ¹H or ³⁵Cl) hydrogen and halogen bonds indicate that hydrogen and halogen bonds are weakened in the considered complexes where two hydrogen and halogen bonds coexist. As compared to N…H hydrogen bond, it is also observed that cooperativity has greater effect on N…Cl halogen bond.     

Electron density characteristics and charge transfer effect of hydrogen bond O–H···Pt(II): atoms in molecules study and natural bond orbital analysis

In this report, we extended the works of Rizzato et al. [Angew. Chem. Int. Ed. 49, 7440 (2010)] on the nature of O–H···Pt hydrogen bond in trans-[PtCl₂(NH₃)(N–glycine)]·H₂O(1·H₂O) complex, by computational study of O–H···Pt interaction in [NBu₄][Pt(C₆F₅)₃(8-hydroxyquinaldine)], with emphasis on charge transfer effect in this interaction of platinum(II) and hydrogen atom. According to the crystallographic geometry reported by José María Casas et al., [NBu₄][Pt(C₆F₅)₃(8-hydroxyquinaldine)] possesses one O–H···Pt hydrogen bridging interaction, similar to the case in trans-[PtCl₂(NH₃)(N–glycine)]·H₂O(1·H₂O) complex. On the basis of topological criteria of electron density, we characterised this O–H···Pt interaction. Charge transferred between platinum(II) and σ^*_O–H orbital in this complex was calculated by using NBO method. The stabilised energy associated to charge transfer was estimated using a direct proportionality, that is 2–3 eV per electron transferred. Charge transfer effects in O–H···Pt hydrogen bonds were studied for these two complexes. Our results indicate that the interaction of O–H···Pt is closed–shell in nature with significant charge transfer, and that charge transfer effect is not negligible in the interaction of O–H···Pt. The second conclusion is different from the result of Rizzato et al.     

The strong OHO hydrogen bond. How much covalency?

In the strong OHO hydrogen bond of the phosphoric acid–urea 1?:?1 complex the proton shifts gradually with temperature from the donor towards the acceptor atom, passing through the center of the hydrogen bond at around 315?K. The AIM parameters were evaluated for the published neutron structures at different temperatures. The values of the electron density, its Laplacian, and the energy densities at both the critical points between the proton and the oxygen atoms in the OHO hydrogen bond were correlated with the OH and HO distances. Changes in the AIM parameters of the strong hydrogen bond were compared with those of the weak NHO bond in this complex.     

Antiproton–hydrogen and antihydrogen–hydrogen annihilation at sub‐Kelvin temperatures

The main properties of the interaction of ultra low‐energy antiprotons (E⩽10^-6 a.u.) and antihydrogen with atomic hydrogen are established. Elastic and inelastic cross‐sections and Protonium formation spectrum are calculated within quantum mechanical coupled channels approach. The results of calculations differ strongly from predictions made by extrapolation of semiclassical models to the energy domain of interest. It is shown that the main feature of the observables behaviour is determined by existence of a family of H, H near‐threshold metastable states. This revised version was published online in July 2006 with corrections to the Cover Date.     

The strengthening effect of a hydrogen or lithium bond on the Z···N aerogen bond (Z = Ar,Kr and Xe): a comparative study

An ab initio study is performed on O₃Z···NCM···NCX (Z = Ar, Kr and Xe; M = H and Li; X = H, F and CH₃) complexes to investigate cooperativity effects between aerogen and hydrogen or lithium bonding interactions in these systems. To understand the cooperative effects, a detailed analysis of the binding distances, interaction energies and bonding properties is performed on these complexes. The results indicate that all Z···N and H/Li···N binding distances in the ternary complexes are shorter than those of corresponding binary systems. For a given M or X, cooperative energies increase as Z = Xe > Kr > Ar. Moreover, O₃Z···NCLi···NCX complexes exhibit a larger cooperative energy than O₃Z···NCH···NCX ones. The non-covalent interaction (NCI) index analysis indicates that the formation of an H/Li···N interaction in the ternary complexes shifts the location of the spike associated with the Z···N interaction towards the negative λ₂ρ values. This indicates that NCI analysis can be regarded as a useful tool for the study of cooperative effects between two different non-covalent interactions. Also, cooperative effects in O₃Z···NCM···NCX complexes make a decrease in ¹⁴N nuclear quadrupole coupling constants of NCH or NCLi molecule.     

A first-principles investigation into the hydrogen bond interaction in β-HMX

A theoretical study of structural and electronic properties of β-HMX crystal is performed using density-functional theory(DFT). The total density of states(TDOS) is presented. The atomic orbit projected density of state(PDOS) from the p-type orbit of C,N,O and the s-type orbit of H is discussed. The study by analyzing the PDOS shows that the structure of β-HMX crystal possesses C-H···O intra- and inter-molecular hydrogen-bonding. There exists a hydrogen bonding between H5 -1s and O12 -2p orbits,between H19 -1s and O28 -2p orbits of intra molecules,and between H19 -1s and O24 -2p orbits of inter molecules. The Mulliken population analysis is also made.     

Can 2‐acylpyrroles form an intramolecular hydrogen bond?

The formation of intramolecular hydrogen bonding by certain N‐substituted 2‐acylpyrroles has been demonstrated by B3LYP/aug‐cc‐pVDZ calculations, the quantum theory of atoms in molecules, and the natural bond orbital method. Total electron energy densities H_BCP at the bond critical point of the H?O bond were applied to analyze the strength of these interactions. The relations between quantum theory of atoms in molecules, carbonyl stretching vibrational modes ν_{C = O}, and natural bond orbital parameters associated with the formation of the C–H?O interaction have been established. The short contacts were found experimentally in the crystal structure of a new 2‐acylpyrrole derivative 5‐chloro‐2‐oxopentyl‐1‐(5‐chloro‐2‐oxopentyl)pyrrolo‐2‐carboxylate. The influence of 2‐ and N‐substitution of 2‐acylpyrroles on C‐H?O interaction energy is discussed. It was found that the methylene group may act as a proton donor leading to a red‐shift or blue‐shift phenomenon of the ν_C–H stretching mode. Copyright © 2015 John Wiley & Sons, Ltd.     

Theoretical investigation of hydrogen atom transfer in the hydrated C–G base pair

Hydrogen atom transfer and the related electronic rearrangement in the hydrated C–G base pair have been studied in order to understand the role of the hydrogen bonds between the bases and those with the water molecules in these processes. The modification of hydrogen transfer due to the first shell and bulk hydration has been analysed. The different structures, when the hydrogen atom moves in a H-bond or in another bond, have been studied. Two naïve schemes, where the water molecules are only indirectly or directly involved in the hydrogen atom transfer, have been considered. The results support the idea that the actual mechanisms are more complex than these schemes. Hydration modifies the potential energy curves of both tautomers and zwitterionic structures, but does not generate new stable structures (minimum PES) of these types. We find a new stable structure due to both a reorganization of the two down water molecules and other global changes of the system. This new system is generated from a zwitterionic structure. The charges, during hydrogen transfer, of the hydrogen donor and of the hydrogen acceptor part of the base pair and of the hydrogen atoms between the bases have been determined and their modifications, due to the first shell and bulk hydration, have been analysed. The qualitative and quantitative behavior has been studied.     

Competition between hydrogen bond and σ-hole interaction in SCS-HArF and SeCSe-HArF complexes

A computational study of the complexes formed between HArF and XCX (X?=?O, S, and Se) has been performed at the MP2/aug-cc-pVTZ level. Two types of complexes were found. One is formed through a hydrogen bond with XCX as the electron donor and the other is formed through the σ-hole interaction with XCX as the electron acceptor. The OCO-FArH complex is more stable than the OCO-HArF complex, whereas the XCX-HArF (X?=?S and Se) complex is more stable than the XCX-FArH complex. The distant H-Ar bond is shortened and exhibits a blue shift, but the associated one displays a red shift in SCS-HArF and SeCSe-HArF complexes. When compared with XCX-HF complex, the structure of the complex suffers a great effect from the inserted noble gas atom. The natural bond orbital (NBO) and atoms in molecules (AIM) have been performed for a better understanding of the interactions.     

Bose–Einstein condensation of atomic hydrogen

The recent creation of a Bose–Einstein condensate of atomic hydrogen has added a new system to this exciting field. The differences between hydrogen and the alkali metal atoms require other techniques for the initial trapping and cooling of the atoms and the subsequent detection of the condensate. The use of a cryogenic loading technique results in a larger number of trapped atoms. Spectroscopic detection is well suited to measuring the temperature and density of the sample in situ. The transition was observed at a temperature of 50 μK and a density of 2×10¹⁴ cm^-3. The number of condensed atoms is about 10⁹ at a condensate fraction of a few percent. A peak condensate density of 4.8×10¹⁵ cm^-3 has been observed. Received: 22 June 1999 / Published online: 3 November 1999     

Pulsating one-dimensional detonations in hydrogen–air mixtures

The propagation of one-dimensional detonations in hydrogen–air mixtures is investigated numerically by solving the one-dimensional Euler equations with detailed finite-rate chemistry. The numerical method is based on a second-order spatially accurate total-variation-diminishing scheme and a point implicit time marching algorithm. The hydrogen–air combustion is modelled with a 9-species, 19-step reaction mechanism. A multi-level, dynamically adaptive grid is utilized, in order to resolve the structure of the detonation. Parametric studies for an equivalence ratio range of 0.4–2.0, initial pressure range of 0.2–0.8 bar and different degrees of detonation overdrive demonstrate that the detonation is unstable for low degrees of overdrive, but the dynamics of wave propagation varies with fuel–air equivalence ratio and pressure. For equivalence ratios less than approximately 1.2 and for all pressures, the detonation exhibits a short-period oscillatory mode, characterized by high-frequency, low-amplitude waves. Richer mixtures exhibit a period-doubled bifurcation that depends on the initial pressure. Parametric studies over a degree of overdrive range of 1.0–1.2 for stoichiometric mixtures at 0.42 bar initial pressure indicate that stable detonation wave propagation is obtained at the high end of this range. For degrees of overdrive close to one, the detonation wave exhibits a low-frequency mode characterized by large fluctuations in the detonation wave speed. The McVey–Toong short-period wave-interaction theory is in qualitative agreement with the numerical simulations; however, the frequencies obtained from their theory are much higher, especially for near-stoichiometric mixtures at high pressure. Modification of this theory to account for the finite heat-release time significantly improves agreement with the numerically computed frequency over the entire equivalence ratio and pressure ranges.     

How universal are hydrogen bond correlations? A density functional study of intramolecular hydrogen bonding in low-energy conformers of α-amino acids

Hydrogen bonding is one of the most important and ubiquitous interactions present in Nature. Several studies have attempted to characterise and understand the nature of this very basic interaction. These include both experimental and theoretical investigations of different types of chemical compounds, as well as systems subjected to high pressure. The O–H..O bond is of course the best studied hydrogen bond, and most studies have concentrated on intermolecular hydrogen bonding in solids and liquids. In this paper, we analyse and characterise normal hydrogen bonding of the general type, D–H...A, in intramolecular hydrogen bonding interactions. Using a first-principles density functional theory approach, we investigate low energy conformers of the twenty α-amino acids. Within these conformers, several different types of intramolecular hydrogen bonds are identified. The hydrogen bond within a given conformer occurs between two molecular groups, either both within the backbone itself, or one in the backbone and one in the side chain. In a few conformers, more than one (type of) hydrogen bond is seen to occur.

Interestingly, the strength of the hydrogen bonds in the amino acids spans quite a large range, from weak to strong. The signature of hydrogen bonding in these molecules, as reflected in their theoretical vibrational spectra, is analysed. With the new first-principles data from 51 hydrogen bonds, various parameters relating to the hydrogen bond, such as hydrogen bond length, hydrogen bond angle, bond length and vibrational frequencies are studied. Interestingly, the correlation between these parameters in these bonds is found to be in consonance with those obtained in earlier experimental studies of normal hydrogen bonds on vastly different systems. Our study provides some of the most detailed first-principles support, and the first involving vibrational frequencies, for the universality of hydrogen bond correlations in materials.     

\hbox {FeF}_{3} catalyzed cascade C–C and C–N bond formation: synthesis of differentially substituted triheterocyclic benzothiazole functionalities under solvent-free condition

A series of diverse polyfunctionalized triheterocyclic benzothiazoles were easily prepared in excellent yields via the Biginelli reaction of 2-aminobenzothiazole with substituted benzaldehydes and $\upalpha $ -methylene ketones using $\hbox {FeF}_{3}$ as an expeditious catalyst under solvent-free conditions. The protocol provides a practical and straightforward approach toward highly functionalized triheterocyclic benzothiazole derivatives in excellent yields. The reaction was conveniently promoted by $\hbox {FeF}_{3}$ and the catalyst could be recovered easily after the reaction and reused without any loss of its catalytic activity. The advantageous features of this methodology are high atom economy, operational simplicity, shorter reaction time, convergence, and facile automation.     

Chalcogen bonds tuned by an N–H···π or C–H···π interaction: investigation of substituent,cooperativity and solvent effects

In the present work, ab-initio calculations are performed to investigate cooperativity effects between chalcogen bond and H···π interactions in XHY···NCH···C₆H₆ and XHY···CNH···C₆H₆ complexes, where X = F, Cl, Br, CN, NC, and Y = S, Se. The nature of these interactions and the mechanism of cooperativity are studied by means of quantum theory of atoms in molecules, noncovalent interaction index, many-body analysis of interaction energy and electron density shift analysis. For each ternary complex, the shortening of the Y···N(C) distance is more pronounced than that of the H···π. The cooperative energies of these complexes are all negative which demonstrate a positive cooperativity between the Y···N(C) and H···π interactions. The many-body analysis of interaction energy reveals that the two-body energy term has the largest contribution to the total interaction energies of ternary complexes. A good linear correlation is established between the three-body energy and cooperative energy values in the ternary systems. The cooperative energies of XHY···CNH···C₆H₆ complexes indicate a larger sensitivity on the polarity of solvent than XHY···NCH···C₆H₆ ones.     

Investigation of hydrogen storage in MWCNT–TiO2 composite

The hydrogen storage capacity of MWCNT–TiO₂ composite has been evaluated in the present work. The composite has been prepared by means of ultrasonication followed by drop casting on substrates. Morphology, structural and functional group studies of the prepared samples are carried out by transmission electron microscopy (TEM), scanning electron microscopy (SEM), powder X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and Raman spectroscopy. Then, the samples are hydrogenated in the hydrogenation chamber as a function of time. Hydrogen storage capacity of the composite sample is found to be 0.9 wt% at 100 °C. Hydrogen uptake of the composite is accounted for the spillover mechanism in CNTs–metal oxide composite. Desorption temperature range, activation energy of desorption, binding energy of hydrogen are determined from thermogravimetric (TG) analysis.     

Influence of the Si–O–C interplayer on the flexural behaviors of C/Si–C–N composites

Carbon fiber reinforced Si–C–N matrix composite(C/Si–C–N) with a Si–O–C interlayer (C/Si–O–C/Si–C–N) was fabricated via CVI and PIP process. The flexural behaviors of C/Si–O–C/Si–C–N were investigated using the three-point-bending method and the SEM technique. The results indicated that the flexural strengh of the C/Si–O–C/Si–C–N increases with increasing temperature and the modulus of the composite is essentially unchanged. The strength of C/Si–O–C/Si–C–N is comparable to that of C/PyC/Si–C–N, and the role of Si–O–C interlayer in C/Si–C–N can rival that of the PyC interlayer. The weaker interfacial bonding and the larger thickness of Si–O–C interlayer make a contribution to this at RT while the thinner interlayer and unstable structure of Si–O–C interphase do it above 1300 °C.     

Preferential etching of Si–Si bond in the microcrystalline silicon germanium

Hydrogenated microcrystalline silicon germanium (μc-Si_1?xGe_x:H) films were investigated as a bottom cell absorber in multi-junction solar cells. μc-Si_1?xGe_x:H films were prepared using very high frequency (VHF, 60 MHz) plasma enhanced chemical vapor deposition (PECVD) systems working pressure of about 1.5 Torr. The precursor flow rates were carefully controlled to determine the phase transition point and to improve the crystallinity of μc-Si_1?xGe_x:H. A relatively high plasma power was necessary to have the high hydrogen (H₂) dilution. Raman spectroscopy study showed transition steps from amorphous to microstructure morphology as hydrogen dilution increasing. Crystallite Si–Ge and Ge–Ge bonds were occurred at relatively higher H₂ dilution compare to crystallite Si–Si bond. The rapidly increased Ge content as increasing the H₂ dilution is believed mainly due to the different decomposition rate of silane (SiH₄) and germane (GeH₄). The other reason of high Ge content even at the low GeH₄ precursor flow rate is probably due to the preferential etching of silicon atom by H₂. The preferential etching of Si–H possibly occurred in very highly concentrated H₂ plasma due to the preferential attachment of Si–H. The compositions of μc-Si_1?xGe_x:H films measured using RBS were Si_0.83Ge_0.17, Si_0.67Ge_0.33 and Si_0.59Ge_0.41 at H₂/SiH₄ flow rate of 60, 80 and 100, respectively. μc-Si_1?xGe_x:H films showed the dark (σ_d) and photo conductivity (σ_p) of about 10^?7 and 10^?5 S/cm, respectively and photo response (σ_p/σ_d) was about 10². This study will present the comprehensive evaluation of crystallization behavior of μc-Si_1?xGe_x:H films.     

The pion–nucleon scattering lengths from pionic hydrogen and deuterium

This is the final publication of the ETH Zurich–Neuchatel–PSI collaboration on the pionic hydrogen and deuterium precision X-ray experiments. We describe the recent hydrogen 3p–1s measurement, report on the determination of the Doppler effect correction to the transition line width, analyze the deuterium shift measurement and discuss implications of the combined hydrogen and deuterium results. From the pionic hydrogen 3p–1s transition experiments we obtain the strong-interaction energy level shift eV and the total decay width eV of the state. Taking into account the electromagnetic corrections we find the hadronic s-wave scattering amplitude for elastic scattering and for single charge exchange, respectively. We then combine the pionic hydrogen results with the 1s level shift measurement on pionic deuterium and test isospin symmetry of the strong interaction: our data are still compatible with isospin symmetry. The isoscalar and isovector scattering lengths (within the framework of isospin symmetry) are found to be and , respectively. Using the GMO sum rule, we obtain from a new value of the coupling constant () from which follows the Goldberger–Treiman discrepancy . The new values of and imply an increase of the nucleon sigma term by at least 9 MeV. Received: 20 April 2001 / Revised version: 6 July 2001 / Published online: 24 August 2001     

Softening and hardening of yield stress by hydrogen–solute interactions

Abstract

Hydrogen atoms have a wide variety of effects on the mechanical performance of metals, and the underlying mechanisms associated with effects on plastic flow and embrittlement remain to be discovered or validated. Here, the reduction in the plastic flow stress (softening) due to hydrogen atoms in solute-strengthened metals, previously proposed by Sofronis et al. is demonstrated at the atomistic level. Glide of an edge dislocation through a field of solutes in a nickel matrix, both in the absence of hydrogen and in the presence of H bound to the solutes, is modelled. The ‘solutes’ here are represented by vacancies, enabling use of accurate binary Ni–H interatomic potentials. Since vacancies have a misfit strain tensor in the Ni matrix and also bind hydrogen atoms, they are excellent surrogates for study of the general phenomenon. The binding of H to the solute (vacancy) reduces the misfit volume to nearly zero but also creates a non-zero tetragonal distortion. Solute strengthening theory is used to establish the connection between strength and solute/hydrogen concentration and misfit strain tensor. Simulations show that when a dislocation moves through a field of random vacancy ‘solutes’, the glide stress is reduced (softening) when H is bound to the solutes. Trends in the simulations are consistent with theory predictions. Trends of softening or hardening by H in metal alloys can thus be made by computing the misfit strain tensor for a desired solute in the chosen matrix with and without bound hydrogen atoms. Pursuing this, density functional theory calculations of the interaction of H with carbon and sulphur solutes in a Ni matrix are presented. These solutes/impurities do not bind with H and the complexes have larger misfit strains, indicative of H-induced strengthening rather than softening for these cases. Nonetheless, H/solute interactions are the only mechanism, to date, that shows nanoscale evidence of plastic softening due to hydrogen associated with the hydrogen-enhanced localised plasticity concept in fcc metals.