Calculated vibrational spectra of weak hydrogen bonds

Potential energy and dipole moment surfaces for the H-bond SH... S in the dimeric methanethiol have been calculated by the SCF-MO-LCGO method, and the vibrational spectrum — transition frequencies and IR absorption intensities at 20 °K — computed. This spectrum is compared with that of the monomeric species and with experimental results. The resulting dimerization energy is 1.4 kcal/mole.     

Subtly tuning intermolecular hydrogen bonds in hybrid crystals to achieve ultrahigh-temperature molecular ferroelastic

Molecular-based ferroic phase-transition materials have attracted increasing attention in the past decades due to their promising potential as sensors, switches, and memory. One of the long-term challenges in the development of molecular-based ferroic materials is determining how to promote the ferroic phase-transition temperature (T_c). Herein, we present two new hexagonal molecular perovskites, (nortropinonium)[CdCl₃] (1) and (nortropinium)[CdCl₃] (2), to demonstrate a simple design principle for obtaining ultrahigh-T_c ferroelastic phase transitions. They consist of same host inorganic chains but subtly different guest organic cations featuring a rigid carbonyl and a flexible hydroxyl group in 1 and 2, respectively. With stronger hydrogen bonds involving the carbonyl but a relatively lower decomposition temperature (T_d, 480 K), 1 does not exhibit a crystalline phase transition before its decomposition. The hydroxyl group subtly changes the balance of intermolecular interactions in 2via reducing the attractive hydrogen bonds but increasing the repulsive interactions between adjacent organic cations, which finally endows 2 with an enhanced thermal stability (T_d = 570 K) and three structural phase transitions, including two ferroelastic phase transitions at ultrahigh T_c values of 463 K and 495 K, respectively. This finding provides important clues to judiciously tuning the intermolecular interactions in hybrid crystals for developing high-T_c ferroic materials.

Two new hexagonal molecular perovskites with the same inorganic chain but subtly different organic cations exhibit distinct phase-transition behaviours owing to the different intermolecular interactions.     

The role of weak hydrogen bonds in chiral recognition

Chiral recognition has been studied in neutral or ionic weakly bound complexes isolated in the gas phase by combining laser spectroscopy and quantum chemical calculations. Neutral complexes of the two enantiomers of lactic ester derivatives with chiral chromophores have been formed in a supersonic expansion. Their structure has been elucidated by means of IR-UV double resonance spectroscopy in the 3 μm region. In both systems described here, the main interaction ensuring the cohesion of the complex is a strong hydrogen bond between the chromophore and methyl-lactate. However, an additional hydrogen bond of much weaker strength plays a discriminative role between the two enantiomers. For example, the 1:1 heterochiral complex between R-(+)-2-naphthyl-ethanol and S-(+) methyl-lactate is observed, in contrast with the 1:1 homochiral complex which lacks this additional hydrogen bond. On the other hand, the same kind of insertion structures is formed for the complex between S-(±)-cis-1-amino-indan-2-ol and the two enantiomers of methyl-lactate, but an additional addition complex is formed for R-methyl-lactate only. This selectivity rests on the formation of a weak CHπ interaction which is not possible for the other enantiomer. The protonated dimers of Cinchona alkaloids, namely quinine, quinidine, cinchonine and cinchonidine, have been isolated in an ion trap and studied by IRMPD spectroscopy in the region of the ν(OH) and ν(NH) stretch modes. The protonation site is located on the alkaloid nitrogen which acts as a strong hydrogen bond donor in all the dimers studied. While the nature of the intermolecular hydrogen bond is similar in the homochiral and heterochiral complexes, the heterochiral complex displays an additional weak CHO hydrogen bond located on its neutral part, which results in slightly different spectroscopic fingerprints in the ν(OH) stretch region. This first spectroscopic evidence of chiral recognition in protonated dimers opens the way to the study of the complexes of Cinchona alkaloids involved in enantioselective catalysis. These examples show how secondary hydrogen bonds controlled by stereochemical factors govern molecular recognition processes.     

Azabicyclo[3.3.1]nonanone: a case when weak interactions are preferred over strong hydrogen bonds

Derivatives of azabicyclo[3.3.1]nonanone tend to prefer for weak interactions in the crystal over strong N–H···O hydrogen bonds. The main stabilizing forces in the investigated azatricyclo[7.3.1.0^2,7]trideca-trienone derivatives are C–H···O, N–H···π and C–H···π interactions, leading to interesting structural patterns. The azabicyclo[3.3.1]nonanone ring adopts chair-envelope conformation having exo-C2,C4-aromatic substituents. Amino NH is in trigonal pyramidal configuration. The interesting stereochemistry of azabicyclo[3.3.1]nonanone, driving exceptional preference for weaker interactions over strong hydrogen bonds serves a useful example toward engineering and design strategy, and structure prediction methodologies.     

Intermolecular hydrogen bonds: Comparison of associates in crystals and liquids

The density and sound velocity were measured within wide ranges of temperature for a number of liquids (water, formamide, diols, aliphatic alcohols, cellosolves, ketones), in which various types of H-associate can exist. The temperature dependences of the adiabatic and molar adiabatic compressibility, density, and molar volume are analyzed. The values of the molar adiabatic compressibility permit one to evaluate the dimensionality of H-associates existing in liquids; the values of adiabatic compressibility do not offer this possibility. The terms responsible for the similarity and difference between H-associates in crystals and liquids are discussed.     

Modeling protein-protein interactions through alanine-amide hydrogen bonds

The hydrogen-bonded complexes formed between alanine and formamide and between alanine and N-methylformamide have been completely investigated in the present study using ab initio molecular orbital theory (MP2) and density functional theory (B3LYP) using aug-cc-pVDZ basis set. Geometry optimization and vibrational frequency calculations have been carried out for isolated and hydrogen-bonded systems. The stabilization energies (?E_BSSE) suggest that alanine-N-methylformamide complexes are more stable than alanine-formamide complexes. The tendency of N-H of amide to act as hydrogen bond (HB) donor is found to be much better in relative to the N-H of amino group of alanine. The study suggests that the tendency of carbonyl oxygen of amide to act as HB acceptor towards various sites of alanine decreases in the order O–H?>?N–H?>?C–H. The results are corroborated by natural bond orbital (NBO) analysis, Bader’s theory of atoms in molecules (AIM) and molecular electrostatic potential (MEP) studies. The blue and red shifts in the stretching frequencies of HB donors X-H (X?=?O, N, C) have also been analysed.     

Engineering molecular crystals with abnormally weak cohesion

Adding astutely placed methyl groups to hexaphenylbenzene increases molecular weight but simultaneously weakens key C-H···π interactions, thereby leading to decreased enthalpies of sublimation and showing that materials with abnormally weak cohesion can be made by identifying and then obstructing interactions that help control association.     

"Union is strength": how weak hydrogen bonds become stronger

Recently reported rotational spectroscopic studies on small dimers and oligomers bound by weak hydrogen bonds show that the driving forces, the spatial arrangement and the dynamical features displayed are very different from those involved in stronger and conventional hydrogen bonds. The very small binding energies (similar to those of van der Waals interactions) imply that the stabilization of the dimer is often obtained by networks of weak hydrogen bonds. Even in the presence of multiple bonds the partner molecules show a high degree of internal freedom within the complex. This paper analyses several examples of molecular adducts bound by weak hydrogen bonds formed in free jet expansions and recently characterized by rotational spectroscopy. They include weakly bound complexes of weak donors with strong acceptors (C-H···O,N, S-H···O,N), strong donors (O-H, N-H) with weak acceptors such as the halogen atoms and π systems but also the elusive interactions between weak donors and weak acceptors (C-H···π and C-H···halogen). Examples are also given where rotational spectroscopy highlights that weak hydrogen bonds are extremely important in chiral recognition phenomena and as driving forces of the conformational landscape of important biomolecules.     

Experimental electron density overlapping in hydrogen bonds: topology vs. energetics

We have investigated the relationship between the energetic properties of the hydrogen bond (HB) interaction and the topological overlapping of the electronic clouds at the HO critical point r_CP. This study involves a total of 83 X–HO (X=C, N, O) HBs, which have been described in terms of the topological properties of the electron density ρ(r) at r_CP for a large set of compounds. Kinetic G(r_CP) and potential V(r_CP) contributions to the local energy density of electrons exhibit linear functionalities against, respectively, the positive and negative curvatures of ρ(r) at the critical point, showing an effective deconvolution in the local form of the Virial theorem. The topological variation of the curvatures at r_CP, and therefore changes in the HO overlapping, are related to the onset of the repulsion between the electronic clouds of the basic and acid atoms.     

Probing the nature of three-centered hydrogen bonds in minor-groove ligand-DNA interactions: the contribution of fluorine hydrogen bonds to complex stability

Double-stranded DNA sequences have been prepared in which single atoms (the O2-carbonyls of selected thymines) have been replaced by fluorine or methyl. To maintain normal Watson-Crick hydrogen bonding with the complementary purines, these analogue derivatives have been prepared as C-nucleosides. The O2-carbonyls of interest for this study are those involved in a bifurcated (or three-centered) hydrogen bond with the minor groove binding ligand 4',6-diamidino-2-phenylindole (DAPI). TM studies of the duplexes illustrate that the DNA duplexes are destabilized when fluorine or methyl replaces one or both of the minor groove O2-carbonyls, which can in part be explained by changes in minor groove hydration. In the presence of DAPI, most of the duplexes exhibit an increased TM due to the presence of DAPI bound in the minor groove. The extent of helix overstabilization negatively correlates with the presence of one or both methyl groups in the minor groove, suggesting that ligand binding is weakened in the presence of the non-carbonyl functional groups. The presence of single fluorine appears to promote helix stabilization, and native-like stabilization occurs when both fluorines are present. KD values quantitate binding effects between DAPI and the native and analogue sequences. Sequences with one or both methyl groups exhibit very poor binding with DAPI, while those containing a single fluorine behave essentially like native carbonyl-containing sequences. With both fluorines present, KD values were observed to increase by a moderate 3-fold at 100 mM NaCl and somewhat more at 200 mM NaCl. Binding affinities with both methyl groups present were 500-1000-fold weaker than native. The results suggest that organofluorines can function as hydrogen-bond acceptors, at least in the bifurcated interaction that contributes to minor groove binding by DAPI.     

Facile activation of H-H and Si-H bonds by boranes

The borane B(C(6)F(5))(3) is a precatalyst for H/Dexchange between H(2) and deuterium-labeled silanes (D(3)SiPh, D(2)SiMePh, DSiMe(2)Ph, DSiEt(3)). Experimental and DFT studies reveal that B(C(6)F(5))(3) itself cannot activate dihydrogen but converts to HB(C(6)F(5))(2) under the action of hydrosilane. The latter species easily activates H-H and Si-H bonds by a σ-bond metathesis mechanism, which was further confirmed by the reactions of BD(3)·THF with H(2).     

The nature and energy characteristics of intramolecular hydrogen bonds in crystals

The review concerns the results of systematic X-ray diffraction studies of the electron density distribution in the crystals of compounds with strong intramolecular hydrogen bonds N-H...O, O-H...O, O-H...N, and N-H...S. The advantages of the topological analysis of the electron density distribution function in the analysis of the nature and estimation of the H-bond energies directly from experimental data are discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 1–14, January, 2006.     

An ab initio molecular dynamics study on hydrogen bonds between water molecules

The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance d(H···H) between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance r(O···H) between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When d(H···H) and r(O···H) are small (e.g., d(H···H) < 2.0 ? and r(O···H) < 1.62 ?), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They show that the majority of the H-bonds counted by using the conventional criteria combined with the d(H···H) criterion and the restriction of r(O···H) match what is identified by the binding energy criteria (e.g., E ≤ -10 kJ/mol), while some of them still have a binding energy that exceeds the energy criterion, indicating that the complicated quantum effects in H bonding can only be described by the three geometric parameters to a certain extent.     

Supramolecular self-assembly of new thiourea derivatives directed by intermolecular hydrogen bonds and weak interactions: crystal structures and Hirshfeld surface analysis

Research on Chemical Intermediates - We synthesized and characterized a series of four closely related thiourea derivatives (1–4) obtained by reaction of 4-R-benzoyl chloride (R: H, Cl, CH3,...     

Quantum chemical study of molecular ion complexes with hydrogen bonds (Review)

Institute of Bioorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated from Zhurnal Strukturnoi Khimii, Vol. 33, No. 6, pp. 157–183, November–December, 1992.     

Phonon driven proton transfer in crystals with short strong hydrogen bonds

Recent work on understanding why protons migrate with increasing temperature in short, strong hydrogen bonds is extended here to three more organic, crystalline systems. Inelastic neutron scattering and density functional theory based simulations are used to investigate structure, vibrations, and dynamics of these systems as functions of temperature. The mechanism determined in a previous work on urea phosphoric acid of low frequency vibrations stabilizing average crystal structures, in which the potential energy well of the hydrogen bond has its minimum shifted towards the center of the bond, is found to be valid here. The new feature of the N-H...O hydrogen bonds studied in this work is that the proton is transferred from the donor atom to the acceptor atom. Molecular dynamics simulations show that in an intermediate temperature regime, in which the proton is not completely transferred, the proton is bistable, jumping from one side of the hydrogen bond to the other. In the case of 3,5-pyridine dicarboxylic acid, which has been studied in most detail, specific phonons are identified, which influence the potential energy surface of the proton in the short, strong hydrogen bond.