C−H···O and O−H···O Hydrogen Bonding in Formic Acid Dimer Structures: A QM/MM Study Confirms the Common Origin of Their Different Spectroscopic Behavior

Role of O–H⋯O/S conventional hydrogen bonds in considerable Csp2–H blue-shift in the binary systems of acetaldehyde and thioacetaldehyde with substituted carboxylic and thiocarboxylic acids

The presence of O–H⋯O/S conventional hydrogen bonds in the complex governs a significant blue shift of Csp2–H bonds.

Spectroscopic evidence of a particular intermolecular interaction in iodomethane–ethanol mixtures: the cooperative effect of halogen bonding, hydrogen bonding, and the solvent effect

The particular intermolecular interaction of an iodomethane–ethanol mixture is revealed by NIR, Raman, DFT calculation, and 2D correlation analysis.

Effects of Halogen, Chalcogen, Pnicogen, and Tetrel Bonds on IR and NMR Spectra

Complexes were formed pairing FX, FHY, FH2Z, and FH3T (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) with NH3 in order to form an A⋯N noncovalent bond, where A refers to the central atom. Geometries, energetics, atomic charges, and spectroscopic characteristics of these complexes were evaluated via DFT calculations. In all cases, the A-F bond, which is located opposite the base and is responsible for the σ-hole on the A atom, elongates and its stretching frequency undergoes a shift to the red. This shift varies from 42 to 175 cm-1 and is largest for the halogen bonds, followed by chalcogen, tetrel, and then pnicogen. The shift also decreases as the central A atom is enlarged. The NMR chemical shielding of the A atom is increased while that of the F and electron donor N atom are lowered. Unlike the IR frequency shifts, it is the third-row A atoms that undergo the largest change in NMR shielding. The change in shielding of A is highly variable, ranging from negligible for FSnH3 all the way up to 1675 ppm for FBr, while those of the F atom lie in the 55-422 ppm range. Although smaller in magnitude, the changes in the N shielding are still easily detectable, between 7 and 27 ppm.

Probing Blue-Shifting Hydrogen Bonds with Adiabatic Energy Decomposition Analysis

The physical origin of blue-shifting hydrogen bonds remains a subject of debate, although many plausible explanations have been proposed. Using a molecular property decomposition analysis based on absolutely localized molecular orbitals, we investigated several representative F₃CH···Y (Y = H₂O, NH₃, Cl^-) complexes. We reveal that features of a blue-shifting H-bond already appear on the frozen surface where both polarization and charge transfer (CT) are "turned off", and that the final frequency shift observed depends on the strength of CT. Further decomposition of forces at the frozen level shows that Pauli repulsion is the only component that shortens the C-H bond in the short-range, while both permanent electrostatics and dispersion lengthen the bond. The effects of these forces from the medium to long-range are also discussed. Our analysis provides a complete picture for blue-shifting H-bonds and suggests two necessary conditions for their features to be observed at equilibrium structures: (i) stronger Pauli repulsion than the combination of electrostatic and dispersion forces; (ii) relatively weak CT that is insufficient to compensate for the blue-shifting effect of the frozen interaction.

Conformation dependence of the C(alpha)D(alpha) stretch mode in peptides. II. explicitly hydrated alanine peptide structures

Our previous studies of the potential utility of the C(alpha)D(alpha) stretch frequency, nu(CD), as a tool for determining conformation in peptide systems (Mirkin and Krimm, J Phys Chem A 2004, 108, 10923-10924; 2007, 111, 5300-5303) dealt with the spectroscopic characteristics of isolated alanine peptides with alpha(R), beta, and polyproline II structures. We have now extended these ab initio calculations to include various explicit-water environments interacting with such conformers. We find that the structure-discriminating feature of this technique is in fact enhanced as a result of the conformation-specific interactions of the bonding waters, in part due to our finding (Mirkin and Krimm, J Phys Chem B 2008, 112, 15268) that C(alpha)--D(alpha)...O(water) hydrogen bonds can be present in addition to those expected between water and the CO and NH of the peptide groups. In fact, nu(CD) is hardly affected by the latter bonding but can be shifted by up to 70 cm(-1) by the former hydrogen bonds. We also discuss the factors that will have to be considered in developing the molecular dynamics (MD) treatment needed to satisfactorily take account of the influence of outer water layers on the structure of the first-layer water molecules that hydrogen bond to the peptide backbone.

Peptide C(alpha)D(alpha) stretch frequencies in a hydrated conformation are perturbed mainly by C(alpha)-D(alpha)...O hydrogen bonding

We have shown (J. Phys. Chem. A 2004, 108, 10923; 2007, 111, 5300) that the C(alpha)D(alpha) stretch frequency, nu(CD), can discriminate between uniform alpha(R), beta, and polyproline II conformations of isolated peptides. Similar results for such peptides to which explicit waters are hydrogen bonded exhibit shifts in nu(CD) from those of the isolated structures. We demonstrate that the main source of these frequency shifts is the formation of C(alpha)-D(alpha)...O hydrogen bonds to water. Taking into account C-H...O(water) hydrogen bonding, together with the traditional bonding of peptide groups to water, can be expected to increase our understanding of the interaction of proteins with their aqueous environment.

Red-, Blue-, or No-Shift in Hydrogen Bonds: A Unified Explanation

We provide a simple explanation for X-H bond contraction and the associated blue shift and decrease of intensity in IR spectrum of the so-called improper hydrogen bonds. This explanation organizes hydrogen bonds (HBs) with a seemingly random relationship between the X-H bond length (and IR frequency and its intensity) to its interaction energy. The factors which affect the X-H bond in all X-H...Y HBs can be divided into two parts: (a) The electron affinity of X causes a net gain of electron density at the X-H bond region in the presence of Y and encourages an X-H bond contraction. (b) The well understood attractive interaction between the positive H and electron rich Y forces an X-H bond elongation. For electron rich, highly polar X-H bonds (proper HB donors) the latter almost always dominates and results in X-H bond elongation, whereas for less polar, electron poor X-H bonds (pro-improper HB donors) the effect of the former is noticeable if Y is not a very strong HB acceptor. Although both the above factors increase with increasing HB acceptor ability of Y, the shortening effect dominates over a range of Ys for suitable pro-improper X-Hs resulting in a surprising trend of decreasing X-H bond length with increasing HB acceptor ability. The observed frequency and intensity variations follow naturally. The possibility of HBs which do not show any IR frequency change in the X-H stretching mode also directly follows from this explanation.

Hydrogen Bonding in Substituted Formic Acid Dimers

The hydrogen-bonded dimers of formic acid derivatives XCOOH (X = H, F, Cl, and CH3) have been investigated using density functional theory (B3LYP) and second-order Møller-Plesset perturbation (MP2) methods, with the geometry optimization carried out using 6-311++G(2d,2p) basis set. The dimerization energies calculated using aug-cc-pVXZ (with X = D and T) basis have been extrapolated to infinite basis set limit using the standard methodology. The results indicate that the fluorine-substituted formic acid dimer is the most stable one in comparison to the others. Topological analysis carried out using Bader's atoms in molecules (AIM) theory shows good correlation of the values of electron density and its Laplacian at the bond critical points (BCP) with the hydrogen bond length in the dimers. Natural bond orbital (NBO) analysis carried out to study the charge transfer from the proton acceptor to the antibonding orbital of the X-H bond in the complexes reveals that most of the dimers are associated with conventional H-bonding except a few, where improper blue-shifting hydrogen bonds are found to be present.

Structure and Matrix Isolation Infrared Spectrum of Formyl Fluoride Dimer: Blue-Shift of the C−H Stretching Frequency

Infrared spectroscopy (IR) of formyl fluoride (HCOF) dimer is studied in low-temperature argon and krypton matrixes. New IR absorptions, ca. 17 cm(-1) blue shifted from the monomer C-H stretching fundamental, are assigned to the HCOF dimer. The MP2/6-311++G calculations were utilized to define structures and harmonic frequencies of various HCOF dimers. Among the four optimized structures, the dimer having two C-H...O hydrogen bonds possesses strongest intermolecular bonding. The calculated harmonic frequencies of this dimer structure are shifted from the monomer similarly as observed in the experiment. Thus, we suggest that the experimentally observed blue shifted C-H bands belong to the dimer with two C-H...O hydrogen bonds. This observation includes the HCOF dimer to the class of hydrogen bonded complexes showing blue shift in their vibrational energies.

Vibrational dynamics of N–H, C–D, and CO modes in formamide

By means of heterodyned two-dimensional IR photon echo experiments on liquid formamide and isotopomers the vibrational frequency dynamics of the N-H stretch mode, the C-D mode, and the C=O mode were obtained. In each case the vibrational frequency correlation function is fitted to three exponentials representing ultrafast (few femtoseconds), intermediate (hundreds of femtoseconds), and slow (many picoseconds) correlation times. In the case of N-H there is a significant underdamped contribution to the correlation decay that was not seen in previous experiments and is attributed to hydrogen-bond librational modes. This underdamped motion is not seen in the C-D or C=O correlation functions. The motions probed by the C-D bond are generally faster than those seen by N-H and C=O, indicating that the environment of C-D interchanges more rapidly, consistent with a weaker C-D...O=C bond. The correlation decays of N-H and C=O are similar, consistent with both being involved in strong H bonding.

All-Atom Molecular Dynamic Simulations and Relative NMR Spectra Study of Weak C−H···O Contacts in Amide−Water Systems

Amide-water mixtures are studied by all-atom molecular dynamics (MD) simulations and the relative temperature-dependent NMR experiment. The weak C-H...O contacts are found in the amide-water systems theoretically and experimentally. The statistical results of the average numbers of hydrogen bonds indicate that the methyl groups in amide molecules represent different capabilities in forming the weak C-H...O contacts. The statistics also imply that the C-H...O contacts are more obvious in the amide-rich region than those in the water-rich region. The temperature-dependent NMR spectra are also adopted to investigate the weak C-H...O contacts in the amide-water systems. The relative chemical shifts of the methyl groups are in good agreement with the MD simulations.

C[bond]H- - -O hydrogen bonds in beta-sheetlike networks: combined X-ray crystallography and high-pressure infrared study

Close interactions of the C(alpha)[bond]H- - -O type have been analyzed via X-ray crystallography and high-pressure infrared spectroscopy. The results demonstrate that the C(alpha)[bond]H- - -O interactions can offer an additional stability to the beta-sheet formation. X-ray structural data suggest that while 1-acetamido-3-(2-pyrimidinyl)-imidazolium bromide exhibits a bilayer stacking, the PF(6)(-) salt reveals a beta-sheetlike pattern. The appearance of the free-NH infrared absorption indicates that the conventional N[bond]H- - -O or N[bond]H- - -N hydrogen bonds do not fully dominate the packing for the PF(6)(-) salt. The high-pressure infrared study suggests that the C(alpha)[bond]H- - -O hydrogen bonds are the important determinants for the stability of the PF(6)(-) salt. This study also verifies that the imidazolium C[bond]H stretching frequency shifts to a longer wavelength upon the formation of the C[bond]H- - -O hydrogen bonds.