Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding

One hundred complexes have been investigated exhibiting D-X center dot center dot center dot A interactions, where X = H, Cl or Li and DX is the `X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized `Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the X center dot center dot center dot A bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X center dot center dot center dot A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared-and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X center dot center dot center dot A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding.

Zeeman effect of chlorine nuclear quadrupole resonance and hydrogen bonding in 2,6-, 2,5- and 3,5-dichlorophenols

The Zeeman effect of chlorine nuclear quadrupole resonance in polycrystalline samples of 2,6-, 2,5 and 3,5-dichlorophenol has been investigated at room temperature in order to study the effect of hydrogen bonding on the electric field gradient asymmetry parameter n. While the two n.q.r. lines in 3,5-dichlorophenol gave an asymmetry parameter of 10%, those in 2,6- and 2,5-dichlorophenol gave different values of n for the two chlorines. The chlorine atom which is ortho to the OH group and involved in hydrogen bonding (i.e., corresponding to the low frequency line) gave an asymmetry parameter of 0.21 in 2,6-dichlorophenol and 0.17 in 2,5-dichlorophenol while the other chlorine (i.e., corresponding to the high frequency line) gave a lower value of 0.12 in 2,6-dichlorophenol and 0.11 in 2,5-dichlorophenol. These values of n are discussed in terms of hydrogen bonding and bond parameters.

Origin of the activation barrier in the process of hydrogen abstraction: the perturbation treatment

The perturbation treatment previously given is extended to explain the process of hydrogen abstraction from the various hydrogen donor molecules by the triplet nπ* state of ketones or the ground state of the alkyl or alkoxy radical. The results suggest that, as the ionization energy of the donor bonds is decreased, the reaction is accelerated and it is not influenced by the bond strength of the donor bonds. The activation barrier in such reactions arises from a weakening of the charge resonance term as the ionization energy of the donor bond increases.

Origin of the activation barrier in the process of hydrogen abstraction: the perturbation treatment

The perturbation treatment previously given is extended to explain the process of hydrogen abstraction from the various hydrogen donor molecules by the triplet nπ* state of ketones or the ground state of the alkyl or alkoxy radical. The results suggest that, as the ionization energy of the donor bonds is decreased, the reaction is accelerated and it is not influenced by the bond strength of the donor bonds. The activation barrier in such reactions arises from a weakening of the charge resonance term as the ionization energy of the donor bond increases.

Vibrational phase relaxation of O–H stretch in bulk water: Role of large amplitude angular jumps and negative cross-correlations among the forces on the O–H bond

The ultrafast vibrational phase relaxation of O–H stretch in bulk water is investigated in molecular dynamics simulations. The dephasing time (T2) of the O–H stretch in bulk water calculated from the frequency fluctuation time correlation function (Cω(t)) is in the range of 70–80 femtosecond (fs), which is comparable to the characteristic timescale obtained from the vibrational echo peak shift measurements using infrared photon echo [W.P. de Boeij, M.S. Pshenichnikov, D.A. Wiersma, Ann. Rev. Phys. Chem. 49 (1998) 99]. The ultrafast decay of Cω(t) is found to be responsible for the ultrashort T2 in bulk water. Careful analysis reveals the following two interesting reasons for the ultrafast decay of Cω(t). (A) The large amplitude angular jumps of water molecules (within 30–40 fs time duration) provide a large scale contribution to the mean square vibrational frequency fluctuation and gives rise to the rapid spectral diffusion on 100 fs time scale. (B) The projected force, due to all the atoms of the solvent molecules on the oxygen (FO(t)) and hydrogen (FH(t)) atom of the O–H bond exhibit a large negative cross-correlation (NCC). We further find that this NCC is partly responsible for a weak, non-Arrhenius temperature dependence of the dephasing rate.

Stereoselectivity in the addition of hydrogen chloride to cyclohex-1-enecarbonitrile: Possible role of chlorine lone pair-nitrile π-orbital pseudoallylic A1, 3 interaction

The (overall trans) addition of hydrogen chloride to cyclohex-1- enecarbonitrile in anhydrous alcoholic media proceeds to give cis-2-chlorocyclohexanecarboxylate (together with some cis-2- chlorocyclohexanecarboxamide): no corresponding products with the trans-configuration are detectable. In anhydrous ether the addition proceeds to give a single isomer, presumably cis-, of 2-chlorocyclohexanecarbonitrile, indicating that the configuration of the products may not be equilibrium-controlled in alcoholic media. An examination of the steric factors indicates that the transition state for protonation of the presumed intermediate, 2-chlorocyclohexylidenemethylideneimine, leading to cis-product is favoured if interaction between the lateral π-orbital of the C-N double bond and the lone-pairs on the chlorine atom at the 2-position is large. Consideration of interactions in the transition states meets Zimmerman's criticism that invoking A1, 3 interaction existing in ground states to explain product configuration takes insufficient account of the Curtin-Hammett principle.

The Mechanism Of The Hydrogen Abstraction Process By Photo-Excited Ketones

Qualitative potential energy surfaces for hydrogen abstraction from alkanes containing primary, secondary and tertiary C-H bonds by a photo-excited ketone have been reported, The results suggest that the activation barriers for these processes decrease in the order primary > secondary > tertiary in agreement with the observed trend in the rate constants. The analysis of the electronic structure of the transition-state reveal that electron-transfer from hydrocarbon to ketone and formation of a new bond are almost synchronous in the hydrogen transfer process. The tunneling of hydrogen is not important in the normal temperature region even though the barriers are small.

Evidence for O-H.cntdot..cntdot..cntdot.C and N-H.cntdot..cntdot..cntdot.C hydrogen bonding in crystalline alkynes, alkenes, and aromatics

Attempts have been made to understand the nature and significance of hydrogen bonds of the type X-H-C (X = 0, N) . These unusual interactions have been discussed recently. Crystallographic studies on 17a-ethynylandrosta- 2,4-dieno[2,3-d]dihydroxazol1-7 8-01 (donazole) provide direct evidence of such an 0-H.0-C interaction. Ab initio computations, IR spectroscopy, and database studies show that these hydrogen bonds, while uncommon, are energetically and structurally significant.

Generation of novel materials for nonlinear optics: Analysis of hydrogen-bonded networks in haloaromatic and aliphatic amine-tartrate complexes

Five tartrate-amine complexes have been studied in terms of crystal packing and hydrogen bonding frameworks. The salts are 3-bromoanilinium-L-monohydrogen tartrate 1, 3-fluoroanilinium-D-dibenzoylmonohydrogen tartrate 2, 1-nonylium-D-dibenzoylmonohydrogen tartrate 3, 1 -decylium-D-dibenzoylmonohydrogen tartrate 4, and 1,4-diaminobutanium-D-dibenzoyl tartrate trihydrate 5. The results indicate that there are no halogen-halogen interactions in the haloaromatic-tartrate complexes. The anionic framework allows accomodation of ammonium ions that bear alkyl chain residues of variable lengths. The long chain amines in these structures remain disordered while the short chain amines form multidirectional hydrogen bonds on either side.

Photochemical intramolecular gamma-hydrogen abstraction in a ketone and an alkene and the role of tunneling of hydrogen

Intramolecular gamma-hydrogen abstraction reactions were examined in pentane-2-one and 2-methyl-1-pentene in their lowest triplet states using the AM1 semi-empirical molecular orbital method with the complete geometry optimization in the unrestricted Hartree-Fock frame. The results reveal that the oxygen atom of the carbonyl group and the end carbon atom of the olefinic bond acquire high free valence and spin density indices in their respective lowest triplet states, leading to abstraction of hydrogen from the gamma-position relative to the carbonyl and olefinic bonds. The theoretical energy profiles fit with a polynomial and the probability of tunneling of hydrogen was estimated by the WKB (Wentzel, Kramer and Brillouin) method. The results, after thermal averaging of the rate constants, reveal that tunneling of hydrogen is significant at room temperature.

Microwave spectroscopic and theoretical studies on the phenylacetylene center dot center dot center dot H(2)O complex: C-H center dot center dot center dot O and O-H center dot center dot center dot pi hydrogen bonds as equal partners

Rotational spectra of five isotopologues of the title complex, C(6)H(5)CCH center dot center dot center dot H(2)O, C(6)H(5)CCH center dot center dot center dot HOD, C(6)H(5)CCH center dot center dot center dot D(2)O, C(6)H(5)CCH center dot center dot center dot H(2)(18)O and C(6)H(5)CCD center dot center dot center dot H(2)O, were measured and analyzed. The parent isotopologue is an asymmetric top with kappa = -0.73. The complex is effectively planar (ab inertial plane) and both `a' and `b' dipole transitions have been observed but no c dipole transition could be seen. All the transitions of the parent complex are split into two resulting from an internal motion interchanging the two H atoms in H(2)O. This is confirmed by the absence of such doubling for the C(6)H(5)CCH center dot center dot center dot HOD complex and a significant reduction in the splitting for the D(2)O analog. The rotational spectra, unambiguously, reveal a structure in which H(2)O has both O-H center dot center dot center dot pi (pi cloud of acetylene moiety) and C-H center dot center dot center dot O (ortho C-H group of phenylacetylene) interactions. This is in agreement with the structure deduced by IR-UV double resonance studies (Singh et al., J. Phys. Chem. A, 2008, 112, 3360) and also with the global minimum predicted by advanced electronic structure theory calculations (Sedlack et al., J. Phys. Chem. A, 2009, 113, 6620). Atoms in Molecule (AIM) theoretical analysis of the complex reveals the presence of both O-H center dot center dot center dot pi and C-H center dot center dot center dot O hydrogen bonds. More interestingly, based on the electron densities at the bond critical points, this analysis suggests that both these interactions are equally strong. Moreover, the presence of both these interactions leads to significant deviation from linearity of both hydrogen bonds.

The Nature of Bond Critical Points in Dinuclear Copper(I) Complexes

Closed-shell contacts between two copper(I) ions are expected to be repulsive. However, such contacts are quite frequent and are well documented. Crystallographic characterization of such contacts in unsupported and bridged multinuclear copper(I) complexes has repeatedly invited debates on the existence of cuprophilicity. Recent developments in the application of Baders theory of atoms-in-molecules (AIM) to systems in which weak hydrogen bonds are involved suggests that the copper(I)copper(I) contacts would benefit from a similar analysis. Thus the nature of electron-density distributions in copper(I) dimers that are unsupported, and those that are bridged, have been examined. A comparison of complexes that are dimers of symmetrical monomers and those that are dimers of two copper(I) monomers with different coordination spheres has also been made. AIM analysis shows that a bond critical point (BCP) between two Cu atoms is present in most cases. The nature of the BCP in terms of the electron density, ?, and its Laplacian is quite similar to the nature of critical points observed in hydrogen bonds in the same systems. The ? is inversely correlated to Cu?Cu distance. It is higher in asymmetrical systems than what is observed in corresponding symmetrical systems. By examining the ratio of the local electron potential-energy density (Vc) to the kinetic energy density (Gc), |Vc|/Gc at the critical point suggests that these interactions are not perfectly ionic but have some shared nature. Thus an analysis of critical points by using AIM theory points to the presence of an attractive metallophilic interaction similar to other well-documented weak interactions like hydrogen bonding.

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

Effect of quantum nuclear motion on hydrogen bonding

This work considers how the properties of hydrogen bonded complexes, X-H center dot center dot center dot Y, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (X) and acceptor (Y) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O-H center dot center dot center dot O complexes is used. The vibrational energy levels of the one-dimensional ground state adiabatic potential of the model are used to make quantitative comparisons with a vast body of condensed phase data, spanning a donor-acceptor separation (R) range of about 2.4-3.0 angstrom, i.e., from strong to weak hydrogen bonds. The position of the proton (which determines the X-H bond length) and its longitudinal vibrational frequency, along with the isotope effects in both are described quantitatively. An analysis of the secondary geometric isotope effect, using a simple extension of the two-state model, yields an improved agreement of the predicted variation with R of frequency isotope effects. The role of bending modes is also considered: their quantum effects compete with those of the stretching mode for weak to moderate H-bond strengths. In spite of the economy in the parametrization of the model used, it offers key insights into the defining features of H-bonds, and semi-quantitatively captures several trends. (C) 2014 AIP Publishing LLC.

Halogen Bonds in Crystal Engineering: Like Hydrogen Bonds yet Different

CONSPECTUS: The halogen bond is an attractive interaction in which an electrophilic halogen atom approaches a negatively polarized species. Short halogen atom contacts in crystals have been known for around 50 years. Such contacts are found in two varieties: type I, which is symmetrical, and type II, which is bent. Both are influenced by geometric and chemical considerations. Our research group has been using halogen atom interactions as design elements in crystal engineering, for nearly 30 years. These interactions include halogen center dot center dot center dot halogen interactions (X center dot center dot center dot X) and halogen center dot center dot center dot heteroatom interactions (X center dot center dot center dot B). Many X center dot center dot center dot X and almost all X center dot center dot center dot B contacts can be classified as halogen bonds. In this Account, we illustrate examples of crystal engineering where one can build up from previous knowledge with a focus that is provided by the modern definition of the halogen bond. We also comment on the similarities and differences between halogen bonds and hydrogen bonds. These interactions are similar because the protagonist atoms halogen and hydrogen are both electrophilic in nature. The interactions are distinctive because the size of a halogen atom is of consequence when compared with the atomic sizes of, for example, C, N, and O, unlike that of a hydrogen atom. Conclusions may be drawn pertaining to the nature of X center dot center dot center dot X interactions from the Cambridge Structural Database (CSD). There is a clear geometric and chemical distinction between type I and type II, with only type II being halogen bonds. Cl/Br isostructurality is explained based on a geometric model. In parallel, experimental studies on 3,4-dichlorophenol and its congeners shed light on the nature of halogen center dot center dot center dot halogen interactions and reveal the chemical difference between Cl and Br. Variable temperature studies also show differences between type I and type II contacts. In terms of crystal design, halogen bonds offer a unique opportunity in the strength, atom size and interaction gradation; this may be used in the design of ternary cocrystals. Structural modularity in which an entire crystal structure is defined as a combination of modules is rationalized on the basis of the intermediate strength of a halogen bond. The specific directionality of the halogen bond makes it a good tool to achieve orthogonality in molecular crystals. Mechanical properties can be tuned systematically by varying these orthogonally oriented halogen center dot center dot center dot halogen interactions. In a further development, halogen bonds are shown to play a systematic role in organization of LSAMs (long range synthon aufbau module), which are bigger structural units containing multiple synthons. With a formal definition in place, this may be the right time to look at differences between halogen bonds and hydrogen bonds and exploit them in more subtle ways in crystal engineering.