On the Reliability of Pure and Hybrid DFT Methods for the Evaluation of Halogen, Chalcogen, and Pnicogen Bonds Involving Anionic and Neutral Electron Donors

In this article, we report a comprehensive theoretical study of halogen, chalcogen, and pnicogen bonding interactions using a large set of pure and hybrid functionals and some ab initio methods. We have observed that the pure and some hybrid functionals largely overestimate the interaction energies when the donor atom is anionic (Cl(-) or Br(-)), especially in the halogen bonding complexes. To evaluate the reliability of the different DFT (BP86, BP86-D3, BLYP, BLYP-D3, B3LYP, B97-D, B97-D3, PBE0, HSE06, APFD, and M06-2X) and ab initio (MP2, RI-MP2, and HF) methods, we have compared the binding energies and equilibrium distances to those obtained using the CCSD(T)/aug-cc-pVTZ level of theory, as reference. The addition of the latest available correction for dispersion (D3) to pure functionals is not recommended for the calculation of halogen, chalcogen, and pnicogen complexes with anions, since it further contributes to the overestimation of the binding energies. In addition, in chalcogen bonding interactions, we have studied how the hybridization of the chalcogen atom influences the interaction energies.

Non linear optical analyses of hexamine: phenol cocrystals based on hydrogen bonding: a comparative study

Fourier-Transform Infrared (FT-IR) spectroscopy supported by Raman spectroscopy has been employed to explain the conventional and unconventional hydrogen bonding present in the 4,4'thiodiphenol: hexamine and 4,4'sulfonyldiphenol: hexamine cocrystals. The possible internal and external vibrational modes are predicted through factor group analysis. Influence of intra molecular charge transfer (ICT) interaction caused by the strong ionic ground state hydrogen bonding between charged species, giving rise to a non centro symmetric structure which is a criterion for second harmonic generation (SHG) efficiency has been discussed. Intense low wave number hydrogen bond vibrations in Raman which arise due to electron-phonon coupling are analyzed. Optical quality of adducts is identified through UV-Vis analysis. The second harmonic generation efficiency of both adducts is determined by Kurtz-Perry method.

Dual bonding between H2O/H2S and AgCl/CuCl: Cu/Ag bond, sister bond to Au bond

Recently, Legon et al. reported the first generation and characterization of H2O/H2S···AgCl complexes by rotational spectroscopy and proposed whether there is a silver bond analogous to the more familiar hydrogen and halogen bonds. In this study, a theoretical investigation was performed to answer this question and to deepen the nature of intermolecular interactions for H2O/H2S···M-Cl (M = Cu, Ag, and Au) complexes. NBO analyses reveal that two types of delocalization interactions coexist in these complexes. Apart from the expected σ-donation interaction, the hyperconjugation interaction between H2O/H2S and M-Cl also takes part in the bonding. On the basis of such a dual-bonding mechanism, one class of bond, termed Cu/Ag bond, was defined in this study. In addition, the topological properties at a bond critical point, binding energies, and stretching frequency shifts studied here support that Cu/Ag bond is a sister bond to Au bond put forward previously by Sadlej et al. The Cu/Ag/Au bond is partially covalent and partially electrostatic in nature. Finally, the dual-bonding mechanism of Cu/Ag/Au bond was further discussed. This dual-bonding scheme may be considered a new synergistic bonding model for coordination compounds.

Nano- and microstructuration of supramolecular materials driven by H-bonded uracil·2,6-diamidopyridine complexes

In the last few decades, multiple H-bonded arrays have been shown to be versatile tools to prepare functional supramolecular materials. Supramolecular complexes formed by uracil (Ur) and 2,6-diamidopyridine (DAP) developed by Lehn are the first examples of multiple H-bonded systems governing the formation of supramolecular polymers in solution. Although a large variety of complementary multiple H-bonded complexes has been prepared, the use of the heteromolecular Ur·DAP complex still remains very promising due to its ease of preparation and its intermediate association strength that ensures a dynamical character to the self-assembly and self-organisation processes. In this feature article, we report a detailed account on the results that our group has obtained in this field by designing and engineering a novel library of shape persistent molecular modules able to transfer their geometrical information to the final supramolecular architectures through the formation of Ur·DAP complexes both at the nanoscopic and microscopic levels.

Triplex blue-shifting hydrogen bonds of ClO4(-)···H-C in the nanointerlayer of montmorillonite complexed with cetyltrimethylammonium cation from hydrophilic to hydrophobic properties

In this study, molecular interactions of perchlorate (ClO4(-)), an emerging pollutant, with cetyltrimethylammonium(CTMA(+)) complexed in the nanointerlayer of negatively charged montmorillonite were characterized using the zeta potentials, FTIR, Raman, and XRD spectroscopy and quantified using quantum mechanical calculations and sorption experiments. We found that blue-shifting hydrogen bonds assisted in the uptake of ClO4(-) from water into the nanointerlayer spacing of CTMA(+)-montmorillonite and were tunable according to CTMA(+) loading. FTIR spectra presented an obvious 47 cm(-1) blue shift in the C-H vibration coming from the N-terminal methyl group of CTMA(+) when ClO4(-) was absorbed. Quantum mechanical calculations based on density functional theory demonstrated that triplex blue-shifting hydrogen bonds of C-H···O were formed between the three terminal methyl groups of CTMA(+) and three oxygen atoms of ClO4(-). The contribution of blue-shifting hydrogen bonds to perchlorate uptake switched from a ClO4(-)/CTMA(+) ratio of 0.0453 at low CTMA(+) loadings to a ClO4(-)/CTMA(+) ratio of 0.2563 (5.6-fold) at high CTMA(+) loadings, which can be ascribed to the evolution of the nanointerlayer microenvironments from hydrophilic properties to hydrophobic properties. The blue-shifting hydrogen bond of C-H···O that is tunable with the hydrophobic nature of the organic phase should be recognized to elucidate the biochemical behavior of perchlorate in organisms.

Ion-pairing of phosphonium salts in solution: C-H⋅⋅⋅halogen and C-H⋅⋅⋅π hydrogen bonds

The (1) H NMR chemical shifts of the C(α)H protons of arylmethyl triphenylphosphonium ions in CD2 Cl2 solution strongly depend on the counteranions X(-) . The values for the benzhydryl derivatives Ph2 CHPPh3 (+)  X(-) , for example, range from δH =8.25 (X(-) =Cl(-) ) over 6.23 (X(-) =BF4 (-) ) to 5.72 ppm (X(-) =BPh4 (-) ). Similar, albeit weaker, counterion-induced shifts are observed for the ortho-protons of all aryl groups. Concentration-dependent NMR studies show that the large shifts result from the deshielding of the protons by the anions, which decreases in the order Cl(-) > Br(-) ≫ BF4 (-) > SbF6 (-) . For the less bulky derivatives PhCH2 PPh3 (+)  X(-) , we also find CH⋅⋅⋅Ph interactions between C(α)H and a phenyl group of the BPh4 (-) anion, which result in upfield NMR chemical shifts of the C(α)H protons. These interactions could also be observed in crystals of (p-CF3 -C6 H4 )CH2 PPh3 (+)  BPh4 (-) . However, the dominant effects causing the counterion-induced shifts in the NMR spectra are the CH⋅⋅⋅X(-) hydrogen bonds between the phosphonium ion and anions, in particular Cl(-) or Br(-) . This observation contradicts earlier interpretations which assigned these shifts predominantly to the ring current of the BPh4 (-) anions. The concentration dependence of the (1) H NMR chemical shifts allowed us to determine the dissociation constants of the phosphonium salts in CD2 Cl2 solution. The cation-anion interactions increase with the acidity of the C(α)H protons and the basicity of the anion. The existence of CH⋅⋅⋅X(-) hydrogen bonds between the cations and anions is confirmed by quantum chemical calculations of the ion pair structures, as well as by X-ray analyses of the crystals. The IR spectra of the Cl(-) and Br(-) salts in CD2 Cl2 solution show strong red-shifts of the CH stretch bands. The CH stretch bands of the tetrafluoroborate salt PhCH2 PPh3 (+)  BF4 (-) in CD2 Cl2 , however, show a blue-shift compared to the corresponding BPh4 (-) salt.

The gold-hydrogen bond, Au-H, and the hydrogen bond to gold, Au∙∙∙H-X

In the first part of this review, the characteristics of Au-H bonds in gold hydrides are reviewed including the data of recently prepared stable organometallic complexes with gold(I) and gold(III) centers. In the second part, the reports are summarized where authors have tried to provide evidence for hydrogen bonds to gold of the type Au∙∙∙H-X. Such interactions have been proposed for gold atoms in the Au(-I), Au(0), Au(I), and Au(III) oxidation states as hydrogen bonding acceptors and H-X units with X = O, N, C as donors, based on both experimental and quantum chemistry studies. To complement these findings, the literature was screened for examples with similar molecular geometries, for which such bonding has not yet been considered. In the discussion of the results, the recently issued IUPAC definitions of hydrogen bonding and the currently accepted description of agostic interactions have been used as guidelines to rank the Au∙∙∙H-X interactions in this broad range of weak chemical bonding. From the available data it appears that all the intra- and intermolecular Au∙∙∙H-X contacts are associated with very low binding energies and non-specific directionality. To date, the energetics have not been estimated, because there are no thermochemical and very limited IR/Raman and temperature-dependent NMR data that can be used as reliable references. Where conspicuous structural or spectroscopic effects have been observed, explanations other than hydrogen bonding Au∙∙∙H-X can also be advanced in most cases. Although numerous examples of short Au∙∙∙H-X contacts exist in the literature, it seems, at this stage, that these probably make only very minor contributions to the energy of a given system and have only a marginal influence on molecular conformations which so far have most often attracted researchers to this topic. Further, more dedicated investigations will be necessary before well founded conclusions can be drawn.

Insight into the isoelectronic character of azomethines and vinylenes using representative models: a spectroscopic and electrochemical study

A series of azomethine and vinylene dyad and triad analogues were prepared. Their absorbance, fluorescence, and redox properties were examined experimentally and theoretically using density functional theory (DFT) calculations. These measurements were done to determine the effect of the heteroatom of the azomethine relative to its all-carbon counterpart and to assess the isoelectronic character of the two bonds. The orientation of the azomethine was found to have little effect on the absorbance, fluorescence, and electrochemical properties. In contrast, the spectral and electrochemical properties were highly contingent on the electronic groups and degree of conjugation. The spectral properties could be tuned 200 nm across the visible region. More importantly, the heteroatom in the conjugated bond was found to give rise to only a 20 nm bathochromic shift in the absorbance and fluorescence spectra. The fluorescence quantum yield (ΦFl) of the vinylene derivatives varied between 5% and 20% with fluorescence quenching occurring by photoisomerization from the E to Z isomers. In contrast, the fluorescence of the analogous azomethine derivatives was completely quenched. The collective spectroscopic and electrochemical ab initio DFT data additionally confirmed that the azomethine and its analogous vinylene are isoelectronic. It was also found that a conjugated thiophene vinylene dyad with primary amines in the α,α'-positions could be prepared and isolated. The compound was stable under aerobic conditions providing electron withdrawing (either ester or nitrile) groups were located in the adjacent positions.

1H NMR spectra of alkane-1,3-diols in benzene: GIAO/DFT shift calculations

The proton nuclear magnetic resonance (NMR) spectra of propane-1,3-diol, 2-methylpropane-1,3-diol, 2,2-dimethylpropane-1,3-diol, butane-1,3-diol, 3-methylbutane-1,3-diol, pentane-2,4-diols (dl and meso), 2-methylpentane-2,4-diol and cyclohexane-1,3-diols (cis and trans) in benzene have been analysed. The conformer distribution and the NMR shifts of these diols have been computed on the basis of density functional theory, the solvent being included by means of the integral equation formalism phase continuum model (IEFPCM) implemented in Gaussian 09. Relative Gibbs energies of all conformers are calculated at the Perdew, Burke and Ernzerhof (PBE)0/6-311 + G(d,p) level, and NMR shifts by the gauge-including atomic orbital method with the PBE0/6-311 + G(d,p) geometry and the cc-pVTZ basis set. Vicinal coupling constants for 1,2- and 1,3-diols are rationalised in terms of relative conformer populations and geometries. The NMR shifts of hydrogen-bonded protons in individual conformers of alkane-1,n-diols show a very rough correlation with the OH⋯OH distances. The computed overall NMR shifts for CH protons in 1,2- and 1,3-diols are systematically high but correlate very well with the experimental values, with a gradient of 1.07 ± 0.01. Some values for nonequivalent methylene protons in 1,3-diols are reversed, calculation giving enhanced values for the proton anti to the COH bonds. Errors in the NMR shifts computed for the OH protons of nonsymmetrical diols appear to be related to relative populations of conformers where one or other of the OH groups is the donor. Some results based on the second-order Møller-Plesset approach, the Becke three-parameter Lee-Yang-Parr method and on the IEFPCM solvation model implemented in Gaussian 03 are included.

Different zeroes of interaction energies as the cause of opposite results on the stabilizing nature of C-H···O intramolecular interactions

The interaction energy of the C-H···O intramolecular interaction is estimated by several methods for a large group of systems possessing a quasi-cyclic six-membered ring. In the case of the geometry corrected method (GCM), the related rotamers method (RRM), and Espinosa's method (EM), the linear correlations between interaction energies and the electron density at the bond critical point have close slopes. The first and the last two methods yield almost systematically opposite results concerning the stabilizing/destabilizing character of the interaction, and their main difference is their zero of the interaction energy. An investigation on the limitations of reference energies has led to the introduction of the geometry corrected related rotamers method (GCRRM), estimating both stabilizing and destabilizing C-H···O interactions. An extension of EM is proposed.

Energy Analysis of Competing Non-Covalent Interaction in 1:1 and 1:2 Adducts of Collidine with Benzoic Acids by Means of X-Ray Diffraction

The hydrogen bond pattern and the types of non-covalent interactions in the crystals of the 1:1 and 1:2 adducts of 2,4,6-trimethylpyridine and benzoic acids are studied using high-resolution X-ray diffraction. The geometries of the hydrogen bonds are estimated using a combined XRD/DFT approach that provides the geometrical parameters within the margin of error of neutron diffraction studies. The energies of the non-covalent interactions are estimated on the base of the experimental electron density distribution function. It is shown that the structures of the adducts are governed by the NOH and OHO hydrogen bonds. In turn, C-H...O contacts and stacking interactions define the packing of the adducts in the crystal. On the other hand, it is important to note that the latter interactions affect the competition of the former hydrogen bonds in some 1:2 adducts.

Fundamental and overtone vibrational spectroscopy, enthalpy of hydrogen bond formation and equilibrium constant determination of the methanol-dimethylamine complex

We have measured gas phase vibrational spectra of the bimolecular complex formed between methanol (MeOH) and dimethylamine (DMA) up to about 9800 cm(-1). In addition to the strong fundamental OH-stretching transition we have also detected the weak second overtone NH-stretching transition. The spectra of the complex are obtained by spectral subtraction of the monomer spectra from spectra recorded for the mixture. For comparison, we also measured the fundamental OH-stretching transition in the bimolecular complex between MeOH and trimethylamine (TMA). The enthalpies of hydrogen bond formation (ΔH) for the MeOH-DMA and MeOH-TMA complexes have been determined by measurements of the fundamental OH-stretching transition in the temperature range from 298 to 358 K. The enthalpy of formation is found to be -35.8 ± 3.9 and -38.2 ± 3.3 kJ mol(-1) for MeOH-DMA and MeOH-TMA, respectively, in the 298 to 358 K region. The equilibrium constant (Kp) for the formation of the MeOH-DMA complex has been determined from the measured and calculated transition intensities of the OH-stretching fundamental transition and the NH-stretching second overtone transition. The transition intensities were calculated using an anharmonic oscillator local mode model with dipole moment and potential energy curves calculated using explicitly correlated coupled cluster methods. The equilibrium constant for formation of the MeOH-DMA complex was determined to be 0.2 ± 0.1 atm(-1), corresponding to a ΔG value of about 4.0 kJ mol(-1).

Insights into the ultraviolet spectrum of liquid water from model calculations: the different roles of donor and acceptor hydrogen bonds in water pentamers

With a view toward a better understanding of changes in the peak position and shape of the first absorption band of water with condensation or temperature, results from electronic structure calculations using high level wavefunction based and time-dependent density functional methods are reported for water pentamers. Excitation energies, oscillator strengths, and redistributions of electron density are determined for the quasitetrahedral water pentamer in its C(2v) equilibrium geometry and for many pentamer configurations sampled from molecular simulation of liquid water. Excitations associated with surface molecules are removed in order to focus on those states associated with the central molecule, which are the most representative of the liquid environment. The effect of hydrogen bonding on the lowest excited state associated with the central molecule is studied by adding acceptor or donor hydrogen bonds to tetramer and trimer substructures of the C(2v) pentamer, and by sampling liquid-like configurations having increasing number of acceptor or donor hydrogen bonds of the central molecule. Our results provide clear evidence that the blueshift of excitation energies upon condensation is essentially determined by acceptor hydrogen bonds, and the magnitudes of these shifts are determined by the number of such, whereas donor hydrogen bonds do not induce significant shifts in excitation energies. This qualitatively different role of donor and acceptor hydrogen bonds is understood in terms of the different roles of the 1b(1) monomer molecular orbitals, which establishes an intimate connection between the valence hole and excitation energy shifts. Since the valence hole of the lowest excitation associated with the central molecule is found to be well localized in all liquid-like hydrogen bonding environments, with an average radius of gyration of ~1.6 Å that is much lower than the nearest neighbor O-O distance, a clear and unambiguous connection between hydrogen bonding environments and excitation energy shifts can be established. Based on these results, it is concluded that peak position of the first absorption band is mainly determined by the relative distribution of single and double acceptor hydrogen bonding environments, whereas the shape of the first absorption band is mainly determined by the relative distribution of acceptor and broken acceptor hydrogen bonding environments. The temperature dependence of the peak position and shape of the first absorption band can be readily understood in terms of changes to these relative populations.

Cellular and molecular investigations of the adhesion and mechanics of Listeria monocytogenes lineages' I and II environmental and epidemic strains

Atomic force microscopy (AFM) was used to probe the mechanical and adherence properties of eight Listeria monocytogenes' strains representative of the species' two phylogenetic lineages I and II. From a functional perspective, lineage' I strains were characterized by lower overall adhesion forces and higher specific and nonspecific forces compared to lineage' II strains. From a structural perspective, lineage' II strains were characterized by higher Young's moduli and longer and stiffer biopolymers compared to lineage' I strains. Both lineages' I and II strains were similar in their grafting densities. Finally, our results indicated that epidemic and environmental strains of L. monocytogenes and irrespective of their lineage group were characterized by similar Young's moduli of elasticities and adhesion forces at the cellular level. However, at the molecular level, epidemic strains were characterized by higher specific and nonspecific forces, shorter, denser, and more flexible biopolymers compared to environmental strains.

Communication: Frequency shifts of an intramolecular hydrogen bond as a measure of intermolecular hydrogen bond strengths

Infrared-ultraviolet double resonance spectroscopy has been applied to study the infrared spectra of the supersonically cooled gas phase complexes of formic acid, acetic acid, propionic acid, formamide, and water with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. In these complexes each binding partner to 9HFCA can function as both proton donor and acceptor. Relative to its frequency in free 9HFCA, the 9-hydroxy (9OH) stretch is blue shifted in complexes with formic, acetic, and propionic acids, but is red shifted in the complexes with formamide and water. Density functional calculations on complexes of 9HFCA to a variety of H bonding partners with differing proton donor and acceptor abilities reveal that the quantitative frequency shift of the 9OH can be attributed to the balance struck between two competing intermolecular H bonds. More extensive calculations on complexes of glycolic acid show excellent consistency with the experimental frequency shifts.

1H NMR spectra of ethane-1,2-diol and other vicinal diols in benzene: GIAO/DFT shift calculations

The proton NMR spectra of several 1,2-diols in benzene have been analysed so as to associate each magnetically nonequivalent proton with its chemical shift. The shifts and coupling constants of the OH and methylene protons of ethane-1,2-diol have been determined in a wide range of solvents. The conformer distribution and the proton NMR shifts of these 1,2-diols in benzene have been computed on the basis of density functional theory. The solvent is included using the integral-equation-formalism polarizable continuum model implemented in Gaussian 09. Relative Gibbs energies for all stable conformers are calculated at the Perdew, Burke and Enzerhof (PBE)0/6-311 + G(d,p) level, and shifts are calculated using the gauge-including atomic orbital method with the PBE0/6-311 + G(d,p) geometry but using the cc-pVTZ basis set. Previous calculations on ethane-1,2-diol and propane-1,2-diol have been corrected and extended. New calculations on tert-butylethane-1,2-diol, phenylethane-1,2-diol, butane-2,3-diols (dl and meso) and cyclohexane-1,2-diols (cis and trans) are presented. Overall, the computed NMR shifts are in good agreement with experimental values for the OH protons but remain systematically high for CH protons. Some results based on the Gaussian 03 solvation model are included for comparison.

A theoretical and experimental chemist's joint view on hydrogen bonding in ionic liquids and their binary mixtures

A combined experimental and theoretical approach including quantum chemistry tools and computational simulation techniques can provide a holistic description of the nature of the interactions present in ionic liquid media. The nature of hydrogen bonding in ionic liquids is an especially intriguing aspect, and it is affected by all types of interactions occurring in this media. Overall, these interactions represent a delicate balance of forces that influence the structure and dynamics, and hence the properties of ionic liquids. An understanding of the fundamental principles can be achieved only by a combination of computations and experimental work. In this contribution we show recent results shedding light on the nature of hydrogen bonding, for certain cases the formation of a three-dimensional network of hydrogen bonding, and its dynamics by comparing 1-ethyl-3-methylimidazolium based acetate, chloride and thiocyanate ionic liquids.A particularly interesting case to study hydrogen bonding and other interactions is the investigation of binary mixtures of ionic liquids of the type [cation1][anion1]/[cation1][anion2]. In these mixtures, competing interactions are to be expected. We present both a thorough property meta-analysis of the literature and new data covering a wide range of anions, i.e., mixtures of 1-ethyl-3-methylimidazolium acetate with either trifluoroacetate, tetrafluoroborate, methanesulfonate, or bis(trifluoromethanesulfonyl)imide. In most cases, ideal mixing behavior is found, a surprising result considering the multitude of interactions present. However, ideal mixing behavior allows for the prediction of properties such as density, refractive index, surface tension, and, in most cases, viscosity as function of molar composition. Furthermore, we show that the prediction of properties such as the density of binary ionic liquid mixtures is possible by making use of group contribution methods which were originally developed for less complex non-ionic molecules. Notwithstanding this ideal mixing behavior, several exciting applications are discussed where preferential solvation via hydrogen bonding gives rise to non-additive effects leading to performance improvements. The assessment of the excess properties and (1)H NMR spectroscopic studies provide information on these structural changes and preferential interactions occurring in binary mixtures of ionic liquid, that clearly support the conclusions drawn from the computational studies.

Terminology for aggregation and self-assembly in polymer science (IUPAC Recommendations 2013)

In the past, aggregation and self-assembly have been associated principally with micellar and colloidal systems of molecules; however, with the advent of supramolecular chemistry, molecular self-assembly has been opened to a much wider understanding that has facilitated access to a variety of different shapes and sizes, along with the construction of new and fascinating molecular topologies. This document aims at defining more than 150 terms related to aggregation and self-assembly in the particular case of macromolecules. The list is restricted to the most commonly encountered terms.

1,2-Bis{4-[1-(anthracen-9-ylmeth-yl)-1H-1,2,3-triazol-4-yl]phen-yl}-1,2-bis-[4,5-bis-(methyl-sulfan-yl)-1,3-dithiol-2-yl-idene]ethane

The title mol-ecule, C58H44N6S8, has point symmetry 2 (in the Schönfliess notation C2). The related crystallographic twofold axis bis-ects the central ethane bond while it is parallel to the monoclinic unique axis of the unit cell. The dithiole=C-C=dithiole torsion angle is 103.7 (4)° and the triazole-anthracene moieties adopt a pincer-like conformation. The crystal structure features C-H⋯S and C-H⋯N contacts. The distance between the stacked anthracene fragments [centroid-centroid separations of 3.6871 (19) Å, off-set by 1.516 (3) Å and mean anthracene plane-plane separations of 3.361 (2) Å], which are parallel to (101) and (-101), indicates inter-molecular anthracene-anthracene π-π contacts. One of the terminal methyl-sulfanyl groups was modelled as being disordered with two refined orientations that converged to occupancies of 0.809 (5) and 0.191 (5).