C-H...O hydrogen bonds in cyclohexenone reveal the spectroscopic behavior of Csp3-H and Csp2-H donors.

C-H...O hydrogen bonds in liquid 2-cyclohexen-1-one are studied to assess the vibrational spectroscopic behavior of the Csp2-H and Csp3-H donors. The presence of a pseudo-isosbestic point in the vC = O region supports the assignment of the two observed bands to two species in equilibrium, considered to be the free and 1:1 associated forms. The values of deltaH degrees =-18.5 +/- 0.6 kJmol(-1) and deltaS degrees = -76 +/- 2 J K(-1) mol(-1) for the dimerization through C-H...O hydrogen bonds were obtained from the dimerization constant at different temperatures. The concentration-dependent intensity of the vCH2 band profile is ascribed to the presence of a blue-shifted band from the hydrogen-bonded Csp3-H group. However, the most surprising result is the absence of concentration- or temperature-dependent intensities in the bands assigned to the stretching modes of the Csp2-H donors.     

Characterization of persistent intramolecular C-H...X(N,O) bonds in solid state and solution

The formation of intramolecular CH...X(N,O) bonds and their persistence in solution were studied by X-ray crystallography and NMR techniques in two different rotamers of a molecule containing the ortho-carborane cage, an amide group and a quinoline ring. Experimental data were confirmed by theoretical ab initio calculations. From the resolved structure of the two forms of this potentially active drug for boron neutron capture therapy, accurate bonding and geometric parameters were extracted for this non-classic hydrogen interaction, and their strength was calculated. These findings provided new insight in the theory of CH...X bonds, which appear stronger and less rare than it was previously thought.     

Homodromic hydrogen bonds in low-energy conformations of single molecule cyclodextrins

Low-energy conformations of β-cyclodextrin under anhydrous conditions in the gas phase were investigated by DFT calculations. In these conformations, two homodromic hydrogen bond rings are formed with very short hydrogen bonds at the narrow side of the cyclodextrin ring and a second one at the wider side. These hypothetical conformations are not comparable to those conformations, which have been studied experimentally, forming inclusion complexes with small and medium-sized guest molecules, but their energy is significantly lower than the open conformations (ΔE = 10 kcal/mol).     

Ab initio studies of electron acceptor-donor interactions with blue- and red-shifted hydrogen bonds.

The features of blue- and red-shifted electron acceptor-donor (ACH/B) hydrogen bonds have been compared by using quantum chemical calculations. The geometry, the interaction energy and the vibrational frequencies of both blue- (ACH=F3CH, Cl3CH with B=FCD3) and red-shifted (ACH=F3CH, Cl3CH with B=NH3 and ACH=CH3CCH with B=FCD3, NH3) complexes were obtained by using ab initio MP2(Full)/6-31+G(d,p) calculations with the a priori basis-set superposition error (BSSE) correction method. One-dimensional potential energy and dipole moment functions of the dimensionless normal coordinate Q1, corresponding to the CH stretching mode of ACH, have been compared for both types of complexes. Contributions of separate components of the interaction energy to the frequency shift and the effect of electron charge transfer were examined for a set of intermolecular distances by using the symmetry-adapted perturbation theory (SAPT) approach and natural bond orbitals (NBO) population analysis.     

Contra-thermodynamic behavior in intermolecular hydrogen transfer of alkylperoxy radicals.

Quantum chemical investigation of bimolecular hydrogen transfer involving alkylperoxy radicals, a key reaction family in the free-radical oxidation of hydrocarbons, was performed to establish structure-reactivity relationships. Eight different reactions were investigated featuring four different alkane substrates (methane, ethane, propane and isobutane) and two different alkylperoxy radicals (methylperoxy and iso-propylperoxy). Including forward and reverse pairs, sixteen different activation energies and enthalpies of reaction were used to formulate structure-reactivity relationships to describe this chemistry. We observed that the enthalpy of formation of loosely bound intermediate states has a strong inverse correlation with the overall heat of reaction and that this results in unique contra-thermodynamic behavior such that more exothermic reactions have higher activation barriers. A new structure-reactivity relationship was proposed that fits the calculated data extremely well: E(A)=E(o)+alphaDeltaH(rxn) where alpha=-0.10 for DeltaH(rxn)<0, and alpha=1.10 for DeltaH(rxn)>0 and E(o)=3.05 kcal mol(-1).     

The properties of weak and strong dihydrogen-bonded D-H...H-A complexes.

The properties of six dihydrogen-bonded (DHB) dimers with the BeH2 molecule as a proton acceptor were calculated by MP2, CCSD(T) and B3LYP methods. The structural, energetic and spectroscopic parameters are presented and analyzed in terms of their possible correlation with the interaction energy and the intermolecular H...H separation. The symmetry-adapted perturbation theory (SAPT) calculations were performed to gain more insight into the nature of the H...H interactions. The studied complexes are divided into three groups based on the calculated intermolecular distances and the interaction energies which range from approximately -1 to -42 kJ mol(-1). The analysis of the interaction energy components indicates that, in contrast to conventional hydrogen bonds, the induction energy is the most important term in the BeH2NH4+ complex. On the other hand, there is no sharp boundary between the DHB complexes classified as hydrogen bonded and van der Waals systems. The complexation-induced changes in vibrational frequencies and in proton shielding constants show a relationship with the interaction energy. The values of the 2hJXH and 3hJBeX coupling constants correlate well with the interaction energy and with the intermolecular distance.     

On differences between hydrogen bonding and improper blue-shifting hydrogen bonding.

Twenty two hydrogen-bonded and improper blue-shifting hydrogen-bonded complexes were studied by means of the HF, MP2 and B3LYP methods using the 6-31G(d,p) and 6--311 ++G(d,p) basis sets. In contrast to the standard H bonding, the origin of the improper blue-shifting H bonding is still not fully understood. Contrary to a frequently presented idea, the electric field of the proton acceptor cannot solely explain the different behavior of the H-bonded and improper blue-shifting H-bonded complexes. Compression of the hydrogen bond due to different attractive forces-dispersion or electrostatics--makes an important contribution as well. The symmetry-adapted perturbation theory (SAPT) has been utilized to decompose the total interaction energy into physically meaningful contributions. In the red-shifting complexes, the induction energy is mostly larger than the dispersion energy while, in the case of blue-shifting complexes, the situation is opposite. Dispersion as an attractive force increases the blue shift in the blue-shifting complexes as it compresses the H bond and, therefore, it increases the Pauli repulsion. On the other hand, dispersion in the red-shifting complexes increases their red shift.     

Opposing Electronic and Nuclear Quantum Effects on Hydrogen Bonds in H2O and D2O

The effect of extending the O−H bond length(s) in water on the hydrogen-bonding strength has been investigated using static ab initio molecular orbital calculations. The “polar flattening” effect that causes a slight σ-hole to form on hydrogen atoms is strengthened when the bond is stretched, so that the σ-hole becomes more positive and hydrogen bonding stronger. In opposition to this electronic effect, path-integral ab initio molecular-dynamics simulations show that the nuclear quantum effect weakens the hydrogen bond in the water dimer. Thus, static electronic effects strengthen the hydrogen bond in H₂O relative to D₂O, whereas nuclear quantum effects weaken it. These quantum fluctuations are stronger for the water dimer than in bulk water.     

Interaction of carboranes with biomolecules: formation of dihydrogen bonds.

Noncovalent interactions of the polyhedral carborane 1-carba-closo-dodecaborane (CB(11)H(12))(-) with building blocks of biomolecules, modelled by glycine (GLY), serine (SER), phenylalanine (PHE), glutamic acid (GLU), lysine (LYS) and arginine (ARG), were investigated in vacuo by molecular dynamics simulations with the UFF empirical potential. Selected structures were further studied by accurate ab initio quantum chemical procedures. Interactions with a peptide bond (GLY-SER dipeptide) and a nucleic acid building block (guanine) were also considered. The RESP and NPA charges of carboranes and small model systems are compared and their use is discussed. The dominant interaction between carboranes and biomolecules is the formation of unconventional proton-hydride hydrogen bonds (dihydrogen bonds) characterized by a short distance between hydrogen atoms (as close as 1.8 A) and an average strength in the range of 4.2-5.8 kcal mol(-1). The total stabilization energy of complexes investigated is rather large, and the largest value (approximately 15 kcal mol(-1)) was found for the carborane complexes with ARG and the GLY-SER dipeptide. These interactions are ubiquitous under geometrical constraints influencing the strength of the interaction. The carborane forms dihydrogen bonds with biomolecules preferably with the hydrogen atoms of its lower hemisphere (i.e. the part of the cage opposite to the carbon atom). These two geometrical factors can be used to explain the specificity of inhibition of HIV protease by carboranes.     

Ionic hydrogen bonds controlling two-dimensional supramolecular systems at a metal surface

Hydrogen-bond formation between ionic adsorbates on an Ag(111) surface under ultrahigh vacuum was studied by scanning tunneling microscopy/spectroscopy (STM/STS), X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), and molecular dynamics calculations. The adsorbate, 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), self-assembles at low temperatures (250-300 K) into the known open honeycomb motif through neutral hydrogen bonds formed between carboxyl groups, whereas annealing at 420 K leads to a densely packed quartet structure consisting of flat-lying molecules with one deprotonated carboxyl group per molecule. The resulting charged carboxylate groups form intermolecular ionic hydrogen bonds with enhanced strength compared to the neutral hydrogen bonds; this represents an alternative supramolecular bonding motif in 2D supramolecular organization.     

Potential energy surfaces of the microhydrated guanine...cytosine base pair and its methylated analogue.

A complete scan of the potential and free-energy surfaces of monohydrated and dihydrated guanine...cytosine and 9-methylguanine...1-methylcytosine base pairs was realized by the molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The most stable and populated structures localized were further fully reoptimized at the correlated ab initio level employing the resolution of identity M?ller-Plesset method with a large basis set. A systematic study of microhydration of these systems using a high-level correlated ab initio approach is presented for the first time. The different behavior of guanine...cytosine and adenine...thymine complexes is also discussed. These studies of nucleic acid base pairs are important for finding binding sites of water molecules around bases and for better understanding of the influence of the solvent on the stability of the structure of DNA.     

On the origin of red and blue shifts of X-H and C-H stretching vibrations in formic acid (formate ion) and proton donor complexes.

Complexes between formic acid or formate anion and various proton donors (HF, H(2)O, NH(3), and CH(4)) are studied by the MP2 and B3LYP methods with the 6-311++G(3df,3pd) basis set. Formation of a complex is characterized by electron-density transfer from electron donor to ligands. This transfer is much larger with the formate anion, for which it exceeds 0.1 e. Electron-density transfer from electron lone pairs of the electron donor is directed into sigma* antibonding orbitals of X--H bonds of the electron acceptor and leads to elongation of the bond and a red shift of the X--H stretching frequency (standard H-bonding). However, pronounced electron-density transfer from electron lone pairs of the electron donor also leads to reorganization of the electron density in the electron donor, which results in changes in geometry and vibrational frequency. These changes are largest for the C--H bonds of formic acid and formate anion, which do not participate in H-bonding. The resulting blue shift of this stretching frequency is substantial and amounts to almost 35 and 170 cm(-1), respectively.     

Geometry of an Isolated Dimer of Imidazole Characterised by Rotational Spectroscopy and Ab Initio Calculations

An isolated, gas‐phase dimer of imidazole is generated through laser vaporisation of a solid rod containing a 1:1 mixture of imidazole and copper in the presence of an argon buffer gas undergoing supersonic expansion. The complex is characterised through broadband rotational spectroscopy and is shown to have a twisted, hydrogen‐bonded geometry. Calculations at the CCSD(T)(F12*)/cc‐pVDZ‐F12 level of theory confirm this to be the lowest‐energy conformer of the imidazole dimer. The distance between the respective centres of mass of the imidazole monomer subunits is determined to be 5.2751(1) Å, and the twist angle γ describing rotation of one monomer with respect to the other about a line connecting the centres of mass of the monomers is determined to be 87.9(4)°. Four out of six intermolecular parameters in the model geometry are precisely determined from the experimental rotational constants and are consistent with results calculated ab initio.     

Car-Parrinello molecular dynamics study of the blue-shifted F3CH...FCD3 system in liquid N2.

Fluoroform, as confirmed by both experimental and theoretical studies, can participate in improper H-bond formation, which is characterized by a noticeable increase in the fundamental stretching frequency nu(C-H) (so-called blue frequency shift), an irregular change of its integral intensity, and a C-H bond contraction. A Car-Parrinello molecular dynamics simulation was performed for a complex formed by fluoroform (F3CH) and deuterated methyl fluoride (FCD3) in liquid nitrogen. Vibrational analysis based on the Fourier transform of the dipole moment autocorrelation function reproduces the blue shift of the fundamental stretching frequency nu(C-H) and the decrease in the integral intensity. The dynamic contraction of the C-H bond is also predicted. The stoichiometry of the solvated, blue-shifted complexes and their residence times are examined.     

Theoretical investigations into the blue-shifting hydrogen bond in benzene complexes.

The benzene...X complexes (X=benzene, antracene, ovalene) were optimised at the MP2/6-31G** level with the C2v symmetry of the complex and planarity of the proton acceptor being preserved. The resulting stabilisation energies amount to 1.2, 2.3 and 2.9 kcal mol(-1), and the C-H bond of the proton donor is contracted by 0.0035, 0.0052 and 0.0055 A, respectively. The contraction is connected with a blue-shift of the C-H stretch vibration frequency. A two-dimensional anharmonic vibration treatment based on a MP2/6-31G** potential energy surface yields the following blue shifts for the complexes studied: 28, 42 and 43 cm(-1). The dominant attraction in the complexes is London dispersion, while the attractive contribution from electrostatic quadrupole-quadrupole interactions is considerably smaller.