Noncovalent interactions and internal dynamics in dimethoxymethane-water

The millimeter-wave absorption and Fourier transform microwave spectra of five isotopologues of the 1:1 adduct of dimethoxymethane-water have been measured in supersonic expansions. Each rotational transition appears as a quintuplet, due to the internal rotation of the two methyl groups, which are nonequivalent in the adduct. The water moiety, linked asymmetrically to dimethoxymethane, behaves as a proton donor to one of its oxygen atoms and interferes with the internal rotation of the farther methyl group through a C...HO interaction. From the analysis of the observed splittings, the V(3) barriers to the internal rotation of the two methyl groups have been determined to be 6.83(8) and 6.19(8) kJ mol(-1). The hydrogen bond structural parameters have been determined, the O...HO and C...HO distances being 1.93(1) and 2.78(4) A, respectively.     

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.     

Intermolecular interactions between halothane and dimethyl ether: a cryosolution infrared and Ab initio study.

The complex of halothane (CHClBrCF(3)) and dimethyl ether has been investigated experimentally in solutions of liquid krypton using infrared spectroscopy and theoretically using ab initio calculations at the MP2/6-311++G(d,p) level. The formation of a 1:1 complex was experimentally detected. The most stable ab initio geometry found is the one in which the C--H bond of halothane interacts with the oxygen atom of dimethyl ether. The complexes in which the chlorine or the bromine atom of halothane interacts with the oxygen atom of the ether were found to be local energy minima and were less stable by 14.5 and 9.3 kJ mol(-1), respectively, than the global minimum. The formation of a single complex species was observed in the infrared spectra; the standard complexation enthalpy of this complex was determined to be -12.3(8) kJ mol(-1). Analysis of the observed complexation shifts supports the identification of the complex as the hydrogen-bonded species. The C--H stretching vibration of halothane was found to show a redshift upon complexation of 19(2) cm(-1). The infrared intensity ratios epsilon(complex)/epsilon(monomer) for the fundamental and its first overtone were measured to be 6.5(1) and 0.31(1). The frequency shift was analyzed using Morokuma-type analysis, and the infrared intensity ratios were rationalized using a model including the mechanical and electric anharmonicity of the C--H stretching fundamental.     

Towards a tunable tautomeric switch in azobenzene biomimetics: implications for the binding affinity of 2-(4'-hydroxyphenylazo)benzoic acid to streptavidin

The tautomeric equilibria of 2-(4'-hydroxyphenylazo)benzoic acid (HABA) and 2-(3',5'-dimethyl-4'-hydroxyphenylazo)benzoic acid (3',5'-dimethyl-HABA) have been studied by a combination of spectroscopic and computational methods. For neutral HABA in solvents of different polarity (toluene, chloroform, DMSO, DMF, butanol, and ethanol) the azo tautomer (AT) is largely predominant. For monoanionic HABA, the hydrazone tautomer (HT) is the only detected species in apolar solvents such as toluene and chloroform, while the AT is the only detected species in water and a mixture of both tautomers is detected in ethanol. Comparison of the results obtained for HABA and its 3',5'-dimethylated derivative shows that dimethylation of the hydroxybenzene ring shifts the tautomeric preferences towards the hydrazone species. These findings have been used to examine the differences in binding affinity to streptavidin, as the lower affinity of HABA can be explained in terms of the larger energetic cost associated with the tautomeric shift to the bioactive hydrazone species. Overall, these results suggest that a balanced choice of chemical substituents, embedding environment, and pH can be valuable for exploitation of the azo-hydrazone tautomerism of HABA biomimetics in biotechnological applications.     

Solvent‐Dependent Structure of the I3− Ion Derived from Photoelectron Spectroscopy and Ab Initio Molecular Dynamics Simulations

Ab initio molecular dynamics (MD) simulations of the solvation of LiI₃ in four different solvents (water, methanol, ethanol, and acetonitrile) are employed to investigate the molecular and electronic structure of the I₃^? ion in relation to X‐ray photoelectron spectroscopy (XPS). Simulations show that hydrogen‐bond rearrangement in the solvation shell is coupled to intramolecular bond‐length asymmetry in the I₃^? ion. By a combination of charge analysis and I 4 d core‐level XPS measurements, the mechanism of the solvent‐induced distortions has been studied, and it has been concluded that charge localization mediates intermolecular interactions and intramolecular distortion. The approach involving a synergistic combination of theory and experiment probes the solvent‐dependent structure of the I₃^? ion, and the geometric structure has been correlated with the electronic structure.     

Understanding sterol-membrane interactions, part II: complete 1H and 13C assignments by solid-state NMR spectroscopy and determination of the hydrogen-bonding partners of cholesterol in a lipid bilayer

The complete assignment of cholesterol 1H and 13C NMR resonances in a lipid bilayer environment (Lalpha-dimyristoylphosphatidylcholine/cholesterol 2:1) has been obtained by a combination of 1D and 2D MAS NMR experiments: 13C spectral editing, ge-HSQC, dipolar HETCOR and J-based HETCOR. Specific chemical shift variations have been observed for the C1-C6 atoms of cholesterol measured in CCl4 solution and in the membrane. Based on previous work (F. Jolibois, O. Soubias, V. Reat, A. Milon, Chem. Eur. J. 2004, 10, preceding paper in this issue: DOI: 10.1002/chem.200400245) these variations were attributed to local changes around the cholesterol hydroxy group, such as the three major rotameric states of the C3-O3 bond and different hydrogen bonding partners (water molecules, carboxy and phosphodiester groups of phosphatidylcholine). Comparison of the experimental and theoretical chemical shifts obtained from quantum-chemistry calculations of various transient molecular complexes has allowed the distributions of hydrogen bonding partners and hydroxy rotameric states to be determined. This is the first time that the probability of hydrogen bonding occurring between cholesterol's hydroxy group and phosphatidylcholine's phosphodiester has been determined experimentally.     

Prevalence of the alkyl/phenyl-folded conformation in benzylic compounds C6H5CH2-X-R (X=O,CH2, CO,S, SO,SO2): significance of the CH/pi interaction as evidenced by high-level ab initio MO calculations

Ab initio MO calculations were carried out to examine the conformational energies of various benzylic compounds C(6)H(5)CH(2)XR (X=O, CH(2), CO, S, SO, SO(2); R=CH(3), C(2)H(5), iC(3)H(7), tC(4)H(9)) at the MP2/6-311G(d,p)//MP2/6-31G(d) level. Rotamers with R/Ph in gauche relationship are generally more stable than the R/Ph anti rotamers. In these stable geometries, the interatomic distance in the interaction of alpha- or beta-CH in the alkyl group and the ipso-carbon atom of the phenyl ring is short. The computational results are consistent with experimental data from supersonic molecular jet spectroscopy on 3-n-propyltoluene and NMR and crystallographic data on structurally related ketones, sulfoxides, and sulfones. In view of this, the alkyl/phenyl-congested conformation of these compounds has been suggested to be a general phenomenon, rather than an exception. The attractive CH/pi interaction has been suggested to be a dominant factor in determining the conformation of simple aralkyl compounds.     

Influence of the Li⋅⋅⋅π Interaction on the H/X⋅⋅⋅π Interactions in HOLi⋅⋅⋅C6H6⋅⋅⋅HOX/XOH (X=F,Cl, Br,I) Complexes

The influences of the Li???π interaction of C₆H₆???LiOH on the H???π interaction of C₆H₆???HOX (X=F, Cl, Br, I) and the X???π interaction of C₆H₆???XOH (X=Cl, Br, I) are investigated by means of full electronic second‐order Møller–Plesset perturbation theory calculations and “quantum theory of atoms in molecules” (QTAIM) studies. The binding energies, binding distances, infrared vibrational frequencies, and electron densities at the bond critical points (BCPs) of the hydrogen bonds and halogen bonds prove that the addition of the Li???π interaction to benzene weakens the H???π and X???π interactions. The influences of the Li???π interaction on H???π interactions are greater than those on X???π interactions; the influences of the H???π interactions on the Li???π interaction are greater than X???π interactions on Li???π interaction. The greater the influence of Li???π interaction on H/X???π interactions, the greater the influences of H/X???π interactions on Li???π interaction. QTAIM studies show that the intermolecular interactions of C₆H₆???HOX and C₆H₆???XOH are mainly of the π type. The electron densities at the BCPs of hydrogen bonds and halogen bonds decrease on going from bimolecular complexes to termolecular complexes, and the π‐electron densities at the BCPs show the same pattern. Natural bond orbital analyses show that the Li???π interaction reduces electron transfer from C₆H₆ to HOX and XOH.     

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.     

Fluorine Substitution Effects on Flexibility and Tunneling Pathways: The Rotational Spectrum of 2‐Fluorobenzylamine

The effect of ring fluorination on the structural and dynamical properties of the flexible model molecule 2‐fluorobenzylamine has been studied by rotational spectroscopy in free‐jet expansion and quantum chemical methods. The complete potential energy surface originating from the flexibility of the aminic side chain has been calculated at the B3LYP/6‐311++G** level of theory and the stable geometries were also characterized with MP2/6‐311++G**. The rotational spectra show the presence of two of the predicted four stable conformers: the global minimum (I), in which the side chain’s dihedral angle with the phenyl plane is almost perpendicular, is stabilized by an intramolecular hydrogen bond between the fluorine atom and one hydrogen of the aminic group; and a second conformer II (E_II?E_I≈5 kJ mol^?1) in which the dihedral angle is smaller and the amino group points towards the aromatic ortho hydrogen atom. This conformation is characterized by a tunneling motion between two equivalent positions of the amino group with respect to the phenyl plane, which splits the rotational transition. The ortho fluorination increases, with respect to benzylamine, the tunneling splitting of this motion by four orders of magnitude. The motion is analyzed with a one‐dimensional flexible model, which allows estimation of the energy barrier for the transition state as approximately 8.0 kJ mol^?1.     

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.     

Preparing Gold(I) for Interactions with Proton Donors: The Elusive [Au]⋅⋅⋅HO Hydrogen Bond

MP2 and DFT calculations with correlation consistent basis sets indicate that isolated linear anionic dialkylgold(I) complexes form moderately strong (ca. 10 kcal mol^?1) Au???H hydrogen bonds with single H₂O molecules as donors in the absence of sterically demanding substituents. Relativistic effects are critically important in the attraction. Such bonds are significantly weaker in neutral, strong σ‐donor N‐heterocyclic carbene (NHC) complexes (ca. 5 kcal mol^?1). The overall association (>11 kcal mol^?1), however, is strengthened by co‐operative, synergistic classical hydrogen bonding when the NHC ligands bear NH units. Further manipulation of the interaction by ligands positioned trans to the carbene, is possible.     

How Good is Fluorine as a Hydrogen‐Bond Acceptor in Fluorinated Single‐Walled Carbon Nanotubes?

Ab initio (RI-MP2/TZVPP) computations were employed to investigate the interaction between hydrogen-bond donors H2O and CH3OH and covalently bound fluorine in organofluorine compounds. While the CFHO interaction energy is around 3 kcal mol(-1) for unstrained systems, the linear correlation between pyramidalization angle at the carbon atom and the interaction energy suggests that increased binding can be obtained in strained systems. This is confirmed for the dihydrodifluoropyrene-methanol pair, but a large portion of the binding energy is due to the interaction of the pi system with the oxygen atom. Density functional periodic boundary condition computations (PBC-PBE/6-31G*) of the structures of (5,5) and (10,10) armchair (C2F)n fluorinated SWNTs (F-SWNTs) indicate that the pyramidalization at the fluorine-binding carbon atoms are too similar to that of CH3F to enhance the hydrogen-bond acceptor properties of fluorine significantly. The solubility of F-SWNTs in alcohols therefore could be due to a combination of hydrogen bonds and van der Waals interactions with the pi systems.     

The Role of Intramolecular Hydrogen Bonds vs. Other Weak Interactions on the Conformation of Hyponitrous Acid and Its Mono- and Dithio-Derivatives

High level ab initio and density functional theory calculations have been carried out to investigate the relative stability of the different conformers of hyponitrous acid and its mono- and dithio-derivatives. Geometries and vibrational frequencies were obtained at the B3LYP/6-311+G(d,p) level and final energies through B3LYP/6-311++G(3df,2pd) single point calculations. The reliability of this theoretical scheme has been assessed by comparing these DFT results with those obtained at the G3 level of theory, for some suitable cases. The cis conformers of hyponitrous acid and its mono- and dithio-derivatives are systematically more stable than the trans ones because in the cis conformation a dative interaction between the nitrogen-lone pairs and the σ_NX^* antibonding orbital is significantly favored. Quite interestingly, in general, the conformers presenting an intramolecular hydrogen bond (IHB) are not the global minima of the corresponding potential energy surfaces and only for hyponitrous acid the conformer with a OH ⋅s O IHB is slightly more stable than the cis conformer without IHB. The low stability of the tautomers with IHB is closely related with another weak intramolecular interaction which involves the lone-pairs of the chalcogen atoms and the π_NN^* antibondig orbital, and which is significantly perturbed when the IHB is formed.     

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).