HX Molecules Research Articles

Cooperativity between Intermolecular Hydrogen and Carbon Bonds in ZY···CH3CN/CH3NC···HX Trimers (ZY = H2O, H2S, HF, HCl, HBr, NH3, and H2CO; HX = HF, HCl, and HBr).

Hydrogen-bonding and carbon-bonding interactions are widespread in nature. We studied the cooperativity between these interactions in 42 trimeric complexes ZY···CH3CN/CH3NC···HX, where ZY molecules are H2O, H2S, HF, HCl, HBr, NH3, and H2CO, and HX molecules are HF, HCl, and HBr. Acetonitrile (CH3CN) and isoacetonitrile (CH3NC) act as hydrogen bond acceptors as well as carbon bond donors in these trimers. Various theoretical methods, such as electronic structure calculations, quantum theory of atoms in molecule (QTAIM), natural bond orbital (NBO), and reduced density gradient analysis, are employed to study these trimers, and the results are compared with the corresponding ZY···CH3CN/CH3NC and CH3CN/CH3NC···HX dimers. Electronic structure calculations are performed at the second-order Mo̷ller-Plesset perturbation theory using the 6-311++G(2d,2p) basis set. We show that both the interactions act synergistically in these trimers leading to an increase in their bond strength as compared to the strength in the individual dimers. The cooperative energies for these trimers are in the range of 0.69 to 3.22 kJ/mol. It is seen that the carbon bonds benefit more from the cooperativity than the hydrogen bonds. The trends of cooperativity and correlations of interaction energies and cooperative energies with relevant QTAIM and NBO parameters are reported.

The Acid-Base Through-the-Cage Interaction as an Example of an Inversion in a Cage Isomerism

We define a new inversion in a cage isomerism (ic): X@C⋯Y₪icY@C⋯X, (₪ is the isomerism relation) as an isomerism in the three-component system of molecules X, Y, and a cage C, in which one of the molecules is located inside and the other outside the cage. The ic isomerism is similar to the endo-exo one, which occurs only if either the interior or exterior of C is empty. By contrast, ic occurs only if neither the interior nor the exterior of C is empty. We also discuss the other closely related types of isomerisms are also discussed. Calculations of the XH⋯NH3@C60 and NH3⋯HX@C60ic isomers were performed at the ωB97XD/Def2TZVP level. The calculated energies demonstrated that the systems with the HX acid outside (X = F, Cl) and the NH3 base inside the cage, XH⋯NH3@C60, are more stable than their ic isomers, NH3⋯HX@C60, by about 4–8 kcal/mol. This is because NH3 is more stabilized inside the cage than HX (a matter of 6.5 kcal/mol). In the studied systems and subsystems, the HX molecules are Lewis acids and the NH3 molecule is always a Lewis base. The C60 molecule with HX inside or outside the cage is also an acid for the NH3 base positioned outside or inside the cage. On the other hand, the C60 cage is truly amphoteric because it is simultaneously an acid and a base.

Construction of biosensor for hypoxanthine determination by immobilization of xanthine oxidase and uricase in polypyrrole-paratoluenesulfonate film

A highly selective and stable amperometric biosensor for the determination of the hypoxanthine (Hx) molecule was designed in this study. For this purpose, the enzyme electrode was prepared by immobilizing the xanthine oxidase (XnOx) and uricase (U) enzymes to the surface obtained by electrochemical polymerization in the presence of polypyrrole-paratoluenesulfonate (PPy-pTS) on the platinum (Pt) surface. The determination limit for the Hx molecule of the prepared biosensor was determined as 5 × 10−6 M, and the linear working range was determined as 5 ×10−6–5 × 10−3 M. At the end of 27 measurements, the biosensor preserved 70% of the initial amperometric response. At the end of the fourth 8 days, the enzyme electrode was observed to maintain 26% of the initial amperometric response. The KM value for Pt/PPy-pTS-XnOxU enzyme electrode system prepared by immobilizing XnOxU was found to be 0.05 mM, and Vmax was 0.56 μA/min. The effects of the interventions in biological environments on the biosensor response were examined. Also, since this biosensor has the potential to be used for the determination of Hx in synthetic samples, it can find an important field of study in the biological and food industry.

Relativistic and QED effects on NMR magnetic shielding constant of neutral and ionized atoms and diatomic molecules.

We show here results of four-component calculations of nuclear magnetic resonance σ for atoms with 10 ≤ Z ≤ 86 and their ions, within the polarization propagator formalism at its random phase level of approach, and the first estimation of quantum electrodynamic (QED) effects and Breit interactions of those atomic systems by using two theoretical effective models. We also show QED corrections to σ(X) in simple diatomic HX and X2 (X = Br, I, At) molecules. We found that the Z dependence of QED corrections in bound-state many-electron systems is proportional to Z5, which is higher than its dependence in H-like systems. The analysis of relativistic ee (or paramagneticlike) and pp (or diamagneticlike) terms of σ exposes two different patterns: the pp contribution arises from virtual electron-positron pair creation/annihilation and the ee contribution is mainly given by 1s → ns and 2s → ns excitations. The QED effects on shieldings have a negative sign, and their magnitude is larger than 1% of the relativistic effects for high-Z atoms such as Hg and Rn, and up to 0.6% of its total four-component value for neutral Rn. Furthermore, percentual contributions of QED effects to the total shielding are larger for ionized than for neutral atoms. In a molecule, the contribution of QED effects to σ(X) is determined by its highest-Z atoms, being up to -0.6% of its total σ value for astatine compounds. It is found that QED effects grow faster than relativistic effects with Z.

Infrared Spectra of the HAnX and H2 AnX2 Molecules (An=Th and U, X=Cl and Br) in Argon Matrices Supported by Electronic Structure Calculations.

Uranium and thorium hydrides are known as functional groups for ligand stabilized complexes and as isolated molecules under matrix isolation conditions. Here, the new molecular products of the reactions of laser-ablated U and Th atoms with HCl and with HBr, namely HUCl, HUBr and HThCl, HThBr, based on their mid and far infrared spectra in solid argon, are reported. The assignment of these species is based on the close agreement between observed and calculated vibrational frequencies. The H-U and U-35 Cl stretching modes of HUCl were observed at 1404.6 and 323.8 cm-1 , respectively. Using DCl instead to form DUCl gives absorption bands at 1003.1 and 314.7 cm-1 . The corresponding bands of HThCl are 1483.8 (H-Th) and 1058.0 (D-Th), as well as 340.3 and 335.8 cm-1 (Th-35 Cl), respectively. HUBr is observed at 1410.6 cm-1 and the BP86 computed shift from HUCl is 6.2 cm-1 in excellent agreement. The U-H stretching frequency increases from 1383.1 (HUF), 1404.6 (HUCl), 1410.6 (HUBr) to 1423.6 cm-1 (UH) as less electronic charge is removed from the U-H bond by the less electronegative substituent. These U-H stretching frequencies follow the Mayer bond orders calculated for the three HUX molecules. A similar trend is found for the Th counterparts. Additional absorptions are assigned to the H2 AnX2 molecules (An=U, Th, X=Cl, Br) formed by the exothermic reaction of a second HX molecule with the above primary products.

Improving the first hyperpolarizability of anthracene through interaction with HX molecules (X[dbnd]F, Cl, Br): A theoretical study

The variations in nonlinear optical activity (NLO) of anthracene (C14H10) was investigated via intermolecular interactions between C14H10 and HX molecules (XF, Cl and Br) using B3LYP-D3 method at 6-311++G(d,p) basis set. The stabilization of those complexes was investigated via vibrational analysis, quantum theory of atoms in molecules, molecular electrostatic potential, natural bond orbitals and symmetry-adapted perturbation theory (SAPT) analysis. Furthermore, the optical spectra and the first hyperpolarizabilities of C14H10⋯HX complexes were computed. The adsorption of hydrogen halide through C14H10⋯HX complex formation, didn't change much the linear optical activities of C14H10 molecule, but the magnitude of the first hyperpolarizability of the C14H10⋯HX complexes to be as much as that of urea.

Synthesis, Structure, and Gas‐Phase Fragmentation of Trinuclear Mo3S4 Clusters Bearing Aminophosphine Ligands: A Combined Experimental and Theoretical Study

Aminophosphine [Mo3S4X3(edpp)3]+ cluster complexes, 1+ (X = Cl) and 2+ (X = Br) {edpp = (2‐aminoethyl)diphenylphosphine} have been quantitatively prepared by treating the [Mo3S7X6]2– anion with the edpp ligand in a one‐pot synthetic procedure. Alternatively, complexes 1+ and 2+ can be synthesized using polymeric {Mo3S7X4}n phases as metal precursors. Their crystal structures show the incomplete cubane‐type Mo3S4 cluster core as well as the formation of a unique isomer in which the nitrogen atoms of the amino group and the halide atoms are located above the trimetallic plane. Gas‐phase reactivity studies on complexes 1+ and 2+ show the subsequent elimination of neutral HX (X = Cl, Br) molecules under collision induced dissociation (CID) conditions. The fragmentation pattern of 1+ and 2+ in combination with gas‐phase DFT calculations are contrary to the general ideas involving the hemilabile character of the aminophosphine ligands and give support to the formation of unsaturated molybdenum/imine Mo=NH species. On the basis of DFT calculations, two competitive mechanisms involving a proton transfer from the amino group to a halide ligand attached to the geminal or to the vicinal molybdenum center are proposed. The first mechanism, which is a proton transfer within the nitrogen and halogen atoms bound to the same metal atom, is energetically favored from a theoretical point of view.

The nature of inter- and intramolecular interactions in F2OXe(…)HX (X= F, Cl, Br, I) complexes.

Electronic structure of the XeOF2 molecule and its two complexes with HX (X= F, Cl, Br, I) molecules have been studied in the gas phase using quantum chemical topology methods: topological analysis of electron localization function (ELF), electron density, ρ(r), reduced gradient of electron density |RDG(r)| in real space, and symmetry adapted perturbation theory (SAPT) in the Hilbert space. The wave function has been approximated by the MP2 and DFT methods, using APF-D, B3LYP, M062X, and B2PLYP functionals, with the dispersion correction as proposed by Grimme (GD3). For the Xe-F and Xe=O bonds in the isolated XeOF2 molecule, the bonding ELF-localization basins have not been observed. According to the ELF results, these interactions are not of covalent nature with shared electron density. There are two stable F2OXe…HF complexes. The first one is stabilized by the F-H…F and Xe…F interactions (type I) and the second by the F-H…O hydrogen bond (type II). The SAPT analysis confirms the electrostatic term, Eelst(1) and the induction energy, Eind(2) to be the major contributors to stabilizing both types of complexes.

Heavy Element Effects in the Diagonal Born-Oppenheimer Correction within a Relativistic Spin-Free Hamiltonian.

Methodologies beyond the Born-Oppenheimer (BO) approximation are nowadays important to explain high precision spectroscopic measurements. Most previous evaluations of the BO correction are, however, focused on light-element molecules and based on a nonrelativistic Hamiltonian, so no information about the BO approximation (BOA) breakdown in heavy-element molecules is available. The present work is the first to investigate the BOA breakdown for the entire periodic table, by considering scalar relativistic effects in the Diagonal BO correction (DBOC). In closed shell atoms, the relativistic EDBOC scales as Z(1.25) and the nonrelativistic EDBOC scales as Z(1.17), where Z is the atomic number. Hence, we found that EDBOC becomes larger in heavy element atoms and molecules, and the relativistic EDBOC increases faster than nonrelativistic EDBOC. We have further investigated the DBOC effects on properties such as potential energy curves, spectroscopic parameters, and various energetic properties. The DBOC effects for these properties are mostly affected by the lightest atom in the molecule. Hence, in X2 or XAt molecule (X = H, Li, Na, K, Rb, and Cs) the effect of DBOC systematically decreases when X becomes heavier but in HX molecules, the effect of DBOC seems relatively similar among all the molecules.

The X (X = F, Cl, I) effect on the photoassociation of H+X→HX

This work explores the vibrational state-selective photoassociation (PA) in the ground state of the HX (X = F, Cl, I) molecule by solving the time-dependent Schrödinger equation. For the three systems, the vibrational level of [Formula: see text] is set to be the target state and the PA probability of the target state is calculated and compared by considering different initial collision momentums. It is found that the PA probabilities are in accordance with Franck–Condon overlap integral for the HI and HCl systems, but it is not the case for the HF system. Moreover, for the HF system, it is shown that the PA probability of the target state is largest and the multiphoton transition is more likely to occur.

Computational studies of boron- and nitrogen-doped single-walled carbon nanotubes as potential sensor materials of hydrogen halide molecules HX (X = F, Cl, Br)

Potential applicability of undoped, B-, and N-doped carbon nanotubes (CNTs) for elaboration of the working materials of gas sensors of hydrogen halide molecules HX (X = F, Cl, Br) is analyzed in computational studies of molecular adsorption on the CNTs surfaces. Density Functional Theory (DFT)-based geometry-optimized calculations of the electronic structure of undoped, B-, and N-doped CNTs of (3,3) and (5,5) chiralities with adsorbed HX (X = F, Cl, Br) molecules are performed within molecular cluster approach. Relaxed geometries, binding energies between the adsorbates and the nanotubes, charge states of the adsorbates and the electronic wave function contours are calculated and analyzed in the context of gas sensing applications. Obtained results are supplemented by calculations of adsorption of hydrogen halides on B(N)-doped graphene sheets which are considered as model approximation for large-diameter CNTs. It is found that the B-doped CNTs are perspective for elaboration of sensing materials for detection of HCl and HBr molecules. The undoped and the N-doped CNTs are predicted to be less suitable materials for detection of hydrogen halide gases HX (X = F, Cl, Br). © 2015 Wiley Periodicals, Inc.

Improved direct potential fit analyses for the ground electronic states of the hydrogen halides: HF/DF/TF, HCl/DCl/TCl, HBr/DBr/TBr and HI/DI/TI

The potential energy and Born–Oppenheimer breakdown functions for the X1Σ+ ground electronic states of the hydrogen halides HF, HCl, HBr, and HI are reported in full analytic form. All available pure rotational and vibrational–rotational spectroscopic data for the various isotopologues of the four HX molecules, as well as the B1Σ+→X1Σ+ emission band system data for HF/DF and HCl/DCl, were employed in direct potential fit determinations of the various radial functions. Significant improvements over previous work have been made to the mathematical models for these functions, particularly with respect to the behavior of the potential energy in the long-range region where dispersion forces between the component atoms dominate. The MLR3 model for the potential energy is employed, allowing for constraint of the three leading dispersion coefficients C6, C8, and C10, for the X states of HF and HCl. Quantum-mechanical rotational and centrifugal distortion constants are calculated for all isotopologues considered in the non-linear least-squares fitting procedures. Computer code is provided in order that precise calculation of all functions for all isotopologues is possible for a user-specified radial grid. Precise estimates are obtained for X state equilibrium internuclear separations for the principal isotopologues of all four halides, namely re(HF)=0.91683897±0.00000004Å, re(H35Cl)=1.27454677±0.00000006Å, re(H79Br)=1.4144292±0.0000001Å, and re(HI)=1.6290588±0.0000004Å.

Imaging of hydrogen halides photochemistry on argon and ice nanoparticles.

The photodissociation dynamics of HX (X = Cl, Br) molecules deposited on large ArN and (H2O)N, N̄ ≈ 10(2)-10(3), clusters is investigated at 193 nm using velocity map imaging of H and Cl photofragments. In addition, time-of-flight mass spectrometry after electron ionization complemented by pickup cross section measurements provide information about the composition and structure of the clusters. The hydrogen halides coagulate efficiently to generate smaller (HX)n clusters on ArN upon multiple pickup conditions. This implies a high mobility of HX molecules on argon. On the other hand, the molecules remain isolated on (H2O)N. The photodissociation on ArN leads to strong H-fragment caging manifested by the fragment intensity peaking sharply at zero kinetic energy. Some of the Cl-fragments from HCl photodissociation on ArN are also caged, while some of the fragments escape the cluster directly without losing their kinetic energy. The images of H-fragments from HX on (H2O)N also exhibit a strong central intensity, however, with a different kinetic energy distribution which originates from different processes: the HX acidic dissociation followed by H3O neutral hydronium radical formation after the UV excitation, and the slow H-fragments stem from subsequent decay of the H3O. The corresponding Cl-cofragment from the photoexcitation of the HCl·(H2O)N is trapped in the ice nanoparticle.

A STUDY OF THE STRUCTURES AND VIBRATIONAL SPECTRA OF THE N2O⋯(HX)2 AND ON2⋯(HX)2 WITH X = F, Cl, Br AND CN

Theoretical calculations 6-311++G(d,p) have been performed in order to obtain binding energies and molecular properties of complexes involving nitrous oxide ( N2O ) and two HX (X = F, Cl, Br and CN ) molecules. Our calculations have revealed the existence of eleven stable structures. The vibrational changes which take place in the HX acid after complexation follow the usual behavior: the HX stretching frequency is shifted downward whereas its IR intensity is much enhanced. The new vibrational modes arising upon H-bond formation, were verified, especially, those associated with the out-of-plane and in-plane HX bending modes, which are pure rotations in the HX isolated molecule.

Local unitary transformation method for large-scale two-component relativistic calculations. II. Extension to two-electron Coulomb interaction

The local unitary transformation (LUT) scheme at the spin-free infinite-order Douglas-Kroll-Hess (IODKH) level [J. Seino and H. Nakai, J. Chem. Phys. 136, 244102 (2012)], which is based on the locality of relativistic effects, has been extended to a four-component Dirac-Coulomb Hamiltonian. In the previous study, the LUT scheme was applied only to a one-particle IODKH Hamiltonian with non-relativistic two-electron Coulomb interaction, termed IODKH/C. The current study extends the LUT scheme to a two-particle IODKH Hamiltonian as well as one-particle one, termed IODKH/IODKH, which has been a real bottleneck in numerical calculation. The LUT scheme with the IODKH/IODKH Hamiltonian was numerically assessed in the diatomic molecules HX and X(2) and hydrogen halide molecules, (HX)(n) (X = F, Cl, Br, and I). The total Hartree-Fock energies calculated by the LUT method agree well with conventional IODKH/IODKH results. The computational cost of the LUT method is reduced drastically compared with that of the conventional method. In addition, the LUT method achieves linear-scaling with respect to the system size and a small prefactor.

Theoretical study of molecular interactions of phosphorus ylide with HF, HCN, and HN3

The molecular interactions between sulfur ylide (SY) and HX molecules (X = F, CN, and N3) were investigated using the MP2 method at 6-311++G(2d,2p) basis set. Three different patterns including non-classical hydrogen bond (HB) H···C and classical HB H···X were found for complex formation between SY and HX molecules. Stability of the H···C type complexes are greater than H···X complexes. Quantum theories of atoms in molecules, natural bond orbitals, and energy decomposition analysis methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies (SE), the second-order perturbation energy E (2) and the charge transfer qCT in the studied systems.

A simple scheme for magnetic balance in four-component relativistic Kohn–Sham calculations of nuclear magnetic resonance shielding constants in a Gaussian basis

We report the implementation of nuclear magnetic resonance (NMR) shielding tensors within the four-component relativistic Kohn-Sham density functional theory including non-collinear spin magnetization and employing London atomic orbitals to ensure gauge origin independent results, together with a new and efficient scheme for assuring correct balance between the large and small components of a molecular four-component spinor in the presence of an external magnetic field (simple magnetic balance). To test our formalism we have carried out calculations of NMR shielding tensors for the HX series (X = F, Cl, Br, I, At), the Xe atom, and the Xe dimer. The advantage of simple magnetic balance scheme combined with the use of London atomic orbitals is the fast convergence of results (when compared with restricted kinetic balance) and elimination of linear dependencies in the basis set (when compared to unrestricted kinetic balance). The effect of including spin magnetization in the description of NMR shielding tensor has been found important for hydrogen atoms in heavy HX molecules, causing an increase of isotropic values of 10%, but negligible for heavy atoms.

Novel halogen bonding interactions between MH 2 (M = Mg, Be) and HX (X = Cl, Br, I) molecules

In this work, a systematic theoretical investigation on a series of dimeric complexes formed between MH 2 and HX has been carried out by employing correlated ab initio methods. It was shown that besides dihydrogen bonds, there also exists novel noncovalent X⋯H interactions between the two molecules, which have similar characteristics to traditional halogen bonds. Upon complexation, the H X bonds tend to elongate in all cases, concomitant with red-shifts of the H X stretching frequencies. X⋯H interaction energies, calculated at the MP2/aug-cc-pvtz level, range from −2.11 to −11.78 kJ/mol; the interactions are much weaker than corresponding dihydrogen bonds. The major stabilization source of dihydrogen and halogen bonds arises from the electrostatic force, while charge-transfer force plays a minor role in the formation of the complexes. AIM analyses further confirm the presence of X⋯H interactions in the systems, and the electron density at bond critical points correlates fairly well with the interaction energy.

Heterolytic splitting of H–X bonds at a cationic (PNP)Pd center

The (PNP)PdOTf complex is a suitable synthetic equivalent of the [(PNP)Pd](+) fragment in reactions with various HX substrates. The [(PNP)Pd](+) fragment either simply binds HX molecules as L-type ligands (X = NH(2), PCy(2), imidazolyl) or heterolytically splits the H-X bond to produce [(PN(H)P)Pd-X](+) (X = H, CCR, SR). DFT calculations analyze the relative energetics of the two outcomes and agree with the experimental data. Calculations also allow to assess the unobserved Pd(IV) isomer [(PNP)Pd(H)(2)](+) and validate its unfavourability with respect to the Pd(II) isomer [(PN(H)P)PdH](+).

Erratum: “Classical and quantum studies of the photodissociation of a HX (X=Cl, F) molecule adsorbed on ice” [J. Chem. Phys. 127, 164717 (2007)

Erratum: “Classical and quantum studies of the photodissociation of a HX (X=Cl, F) molecule adsorbed on ice” [J. Chem. Phys. 127, 164717 (2007)