Hydrogen bonding in dimers of tritolyl and tritosylurea derivatives of triphenylmethanes

The crystal structure of the homodimer formed by the tritolylurea 3a proves the existence of a belt of six bifurcated hydrogen bonds between both NH and the O=C groups of the adjacent urea residues. For the tritosylurea 3b, four additional three-center hydrogen bonds, also involving the SO2 oxygen, are found in the crystalline state. Molecular dynamics simulations in a chloroform box confirm these patterns of the hydrogen bonds and the resulting elongation of the dimer 3b. 3b in comparison to 3a x 3a. The calculated complexation energies for the three dimeric combinations are nearly identical in agreement with the simultaneous formation of heterodimer 3a x 3b in a mixture of 3a and 3b.     

Donor-acceptor interaction-mediated arrangement of hydrogen bonded dimers

The donor-acceptor interaction-driven supramolecular arrangement of a new series of quadruply hydrogen-bonded homo- and heterodimers have been investigated in chloroform with ¹H NMR and UV-Vis spectroscopy. Two kinds of structurally complementary monomers have been prepared. Monomers 3 and 4 are incorporated with one ureidopyrimidone unit and one electron deficient pyromellitic diimide (PDI) or naphthalene diimide (NDI) unit, respectively, monomers 5 and 6 are incorporated with two ureidopyrimidone units and one PDI or NDI unit, respectively, whereas monomers 7 and 8 consist of one electron rich bis-p-phenylene[34]crown-10 unit and one or two 2,7-diamido-1,6-naphthyridine units, respectively. Compounds 3 and 4 exist exclusively as homodimers, respectively. Adding 1 equiv. of 7 to the solution of 3·3 and 4·4 induced them to partially or fully dissociate to produce heterodimers 3·7 and 4·7 due to intermolecular donor-acceptor interaction and the formation of a new binding mode between the ureidopyrimidone of 3 or 4 and the 2,7-diamido-1,6-naphthyridine unit of 7. Both 5 and 6 exist as cyclic monomer and dimer in chloroform. Adding 1 equiv. of 8 to the solution of 5 or 6 in chloroform caused all the cyclic dimer and most of the cyclic monomer to de-cyclize to form new heterodimers 5·8 and 6·8, respectively. ¹H NMR and UV-vis study revealed that heterodimer 5·8 has a structure in which the PDI of 5 is not threaded through the cavity of the bis-p-phenylene[34]crown-10 unit of 8. In contrast, in addition to the heterodimer similar to 5·8, about 40% of heterodimer 6·8 is generated, in which the PDI of 6 is threaded through the cavity of the bis-p-phenylene[3]crown-10 unit of 8 due to the increased donor-acceptor interaction between NDI and bis-p-phenylene[34]crown-10. Steric hindrance and mismatching of the hydrogen bonding moiety play important roles in the arrangement of the new homo- and heterodimers.     

Hydrogen bonded phosphate structures

Abstract

Some phosphate esters form structures containing infinite chains of hydrogen bonded units, others form discrete dimeric units, and still others form columns or chains of dimeric units. We have formed unique hydrogen bonded phosphorus ester systems which incorporate catechol molecules of crystallization, [HOC₆H₄OP(Ph)O₂][PPh₄]· catechol, 1, and [HOC₆H₄OP(Ph)O₂] [C₅H₅NH]· catechol, 2. X-ray analysis shows a chain arrangement in 1 and dimeric phosphonate units in a chain structure for 2 By comparing our results with literature examples, a classification of hydrogen bonding in phosphates results which proves useful in interpreting orientational influences at enzyme active sites.     

Hydrogen bonded homo- and heterodimers of tetra urea derivatives of calix[4]arenes

Calix[4]arene ethers fixed in the cone conformation and substituted at the upper rim by various urea residues have been synthesized by reaction of the amino calix[4]arenes with isocyanates. Their dimerisation in apolar solvents has been established by the formation of mixed dimers consisting of two different urea derivatives.     

Theoretical study on stabilities of multiple hydrogen bonded dimers

A series of self-constituted multiple hydrogen bonded (MHB) complexes has been investigated systematically by density functional theory (PBE1PBE /6-31G**), the Morokuma energy decomposition method (HF/6-31G**) and MP2 (6-31G** and 6-311++G**) calculation. We have discovered that (i) for doubly hydrogen bonded (DHB) complexes, both the interaction energy and stability increase with the charge transfer energy; (ii) for quadruple hydrogen bonded (QHB) complexes, cooperativity is the most important factor determining stability of the complex: stronger cooperative energy correlates well with larger interaction energy and thus more stable complex and vice versa; (iii) correlation energy plays an important role in intermolecular interactions. The correlation energy, mainly consisting of dispersive energy, also exhibits cooperativity in MHB dimers: positive for M-aadd and generally negative for other complexes.     

An ab initio benchmark study of hydrogen bonded formamide dimers

The five singly and doubly hydrogen bonded dimers of formamide are calculated at the correlated level by using resolution of identity M?ller-Plesset second-order perturbation theory (RIMP2) and the coupled cluster with singles, doubles, and perturbative triples [CCSD(T)] method. All structures are optimized with the Dunning aug-cc-pVTZ and aug-cc-pVQZ basis sets. The binding energies are extrapolated to the complete basis set (CBS) limit by using the aug-cc-pVXZ (X = D, T, Q) basis set series. The effect of extending the basis set to aug-cc-pV5Z on the geometries and binding energies is studied for the centrosymmetric doubly N-H...O bonded dimer FA1 and the doubly C-H...O bonded dimer FA5. The MP2 CBS limits range from -5.19 kcal/mol for FA5 to -14.80 kcal/mol for the FA1 dimer. The DeltaCCSD(T) corrections to the MP2 CBS limit binding energies calculated with the 6-31+G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are mutually consistent to within < or =0.03 kcal/mol. The DeltaCCSD(T) correction increases the binding energy of the C-H...O bonded FA5 dimer by 0.4 kcal/mol or approximately 9% over the distance range +/-0.5 Angstrom relative to the potential minimum. This implies that the ubiquitous long-range C-H...O interactions in proteins are stronger than hitherto calculated.     

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 M?ller-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.     

General features of geometries and potential constants of hydrogen bonded dimers

The interaction between theoretical and experimental investigations of hydrogen bonded dimers is examined. The influence on the interaction of the type of information available from current experimental techniqes is discussed, and new areas of profitable interaction are suggested. Dimer geometries, the directional character of hydrogen bonds, bond lengthening, and streching and bending force constants are considered in turn. Emphasis is placed on general features of hydrogen bonding rather than on properties of specific dimers.     

Hydrogen bond cooperativity in dimers of hydroxamic acids

Molecular orbital calculations are performed on various dimeric forms of four tautomers each of thioformohydroxamic acid and formohydroxamic acid. The analysis of stabilization energies associated with the dimerization and their correlation to proton affinities and deprotonation enthalpies of different potential sites present in the molecules indicate that the highest stabilization results when the most basic, site of the molecule acts as hydrogen bond acceptor but combination of the most acidic and the most basic site does not result in the largest stabilization when dimerization occurs. The presence of hydrogen bond cooperativity is indicated and the reasons for the observed cooperativity are explored in this study. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Hydrogen bonded calixarene capsules kinetically stable in DMSO

Half-life times up to 4 days in DMSO at room temperature are observed for the decomposition of dimeric capsules of urea substituted calix[4]arenes held together by a combination of hydrogen bonds, mechanical entanglement and cation-pi interactions.     

Hydrogen bonded OH-stretching vibration in the water dimer

We have calculated the frequencies and intensities of the hydrogen-bonded OH-stretching transitions in the water dimer complex. The potential-energy curve and dipole-moment function are calculated ab initio at the coupled cluster with singles, doubles, and perturbative triples level of theory with correlation-consistent Dunning basis sets. The vibrational frequencies and wavefunctions are found from a numerical solution to a one-dimensional Schr?dinger equation. The corresponding transition intensities are found from numerical integration of these vibrational wavefunctions with the ab initio calculated dipole moment function. We investigate the effect of counterpoise correcting both the potential-energy surface and dipole-moment function. We find that the effect of using a numeric potential is significant for higher overtones and that inclusion of a counterpoise correction for basis set superposition error is important.     

Hydrogen bonded supramolecular polymers in moderately polar solvents

Hydrogen bonded assemblies are usually decomposed by polar organic solvents. However, we have succeeded in preparing a strongly associated supramolecular polymer which forms viscous solutions in competitive solvents such as tetrahydrofuran.     

Rayleigh light scattering from hydrogen‐bonded dimers of small astrophysical molecules

High level ab initio calculations of the Rayleigh scattering activities of the hydrogen‐bonded dimers of formic acid (HCOOH), nitrosyl hydride (HNO), and hydrogen cyanide (HCN) molecules have been performed. All these molecules have already been detected in interstellar space and are of great importance from the astrochemical point of view. The geometries of the homo‐ and hetero‐dimers have been optimized using Hartree–Fock and second‐order Møller‐Plesset perturbation theory. Dipole moment, mean dipole polarizability, and polarizability anisotropy have been calculated utilizing Pople‐type 6‐311++G(d,p) and Dunning's aug‐cc‐pVDZ basis sets for all the complexes. The polarizabilities are then used to calculate and analyze the Rayleigh scattering parameters. The results for the dimers, HCN···HCN, HCOOH···HCOOH, HNO···HNO, HCN···HCOOH, HCN···HNO, and HNO···HCOOH are compared with those of the isolated molecules, HCN, HCOOH, and HNO to see the effect of hydrogen bond formation on the molecular interaction with radiation. © 2011 Wiley Periodicals, Inc.     

Coherent low-frequency motions of hydrogen bonded acetic acid dimers in the liquid phase

Ultrafast vibrational dynamics of cyclic hydrogen bonded dimers and the underlying microscopic interactions are studied in temporally and spectrally resolved pump-probe experiments with 100 fs time resolution. Femtosecond excitation of the O-H and/or O-D stretching mode gives rise to pronounced changes of the O-H/O-D stretching absorption displaying both rate-like kinetic and oscillatory components. A lifetime of 200 fs is measured for the v=1 state of the O-H stretching oscillator. The strong oscillatory absorption changes are due to impulsively driven coherent wave packet motions along several low-frequency modes of the dimer between 50 and 170 cm(-1). Such wave packets generated via coherent excitation of the high-frequency O-H/O-D stretching oscillators represent a clear manifestation of the anharmonic coupling of low- and high-frequency modes. The underdamped low-frequency motions dephase on a time scale of 1-2 ps. Calculations of the vibrational potential energy surface based on density functional theory give the frequencies, anharmonic couplings, and microscopic elongations of the low-frequency modes, among them intermolecular hydrogen bond vibrations. Oscillations due to the excitonic coupling between the two O-H or O-D stretching oscillators are absent as is independently confirmed by experiments on mixed dimers with uncoupled O-H and O-D stretching oscillators.     

Synthesis of Β-bonded dimers — 1,10,15,20-Tetraphenylporphyrin derivatives

The synthesis of dimers in which the macrocycles are connected by an ester bond was accomplished starting from tetraphenylporphyrin. Dimers containing the metal in one and two porphyrin rings were obtained. It is shown that exclusively the E isomer of 1-(2-carboxyvinyl)-5,10,15,20-tetraphenylporphyrin is formed in the decarboxylation of 1-(2,2-dicarboxyvinyl)-5,10,15,20-tetraphenylporphyrin.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1194–1199, September, 1987.     

Evidence for the formation of singly bonded dimers during the reductive electrochemistry of methanofullerenes

Four methanofullerene derivatives, with phosphonate or sulfone groups attached to a C(60) core through a Bingel procedure, were synthesized to probe their stability upon electrolytic reduction. Derivatives 1 and 2 are the most stable upon electroreduction and do not exhibit retro-cyclopropanation reactions until more than three electrons per C(60) derivative are transferred. The cyclopropane ring is then removed and C(60)(>CH(2))(n) (n=1-3) products result from reactions of the trianion of C(60) with the solvent, CH(2)Cl(2). The situation with diphosphonate 3 or phosphonatecarboxylate 4 is dramatically different. For 3, quantitative retro-cyclopropanation occurs when 2.8 e(-) per molecule are transferred. In the case of 4, when more than two electrons per molecule are transferred, there is evidence of the reversible formation of a very stable intermediate, which is oxidized at a potential 500 mV more positive than the first fullerene-based reduction of the parent compound. Electrolysis of a simple C(70)-Bingel monoadduct (5) also exhibits the formation of a similar intermediate. On the basis of cyclic voltammetry, ESR spectroscopy, and MALDI analysis of products, the intermediate observed during the electrolysis of compounds 4 and 5 is assigned to a dimeric structure.     

Hydrogen bonded oligohydrazide foldamers and their recognition for saccharides

This paper describes the synthesis and characterization of the first series of hydrogen bonding-driven hydrazide foldamers and their recognition for alkyl saccharides in chloroform. Oligomers 1, 2-4, 5, 6, and 7, which contain one, two, four, six, or twelve repeated dibenzoyl hydrazide residues, respectively, have been prepared. The rigid and planar conformations of 1 and 2 or 4 have been established with X-ray analysis and (1)H NMR spectroscopy, whereas the folding and helical conformations of 5-7 have been evidenced by the 1D and 2D (1)H NMR and IR spectroscopy and molecular mechanics calculations. Molecular mechanics calculations also revealed that 5, 6, and 7 possess a rigid cavity with size of ca. 10.6 to 11.1 A, and half of the carbonyl groups in the folding conformations are orientated inwardly inside the cavity. (1)H NMR and CD experiments revealed that 5-7 efficiently complex alkylated mono- and disaccharides 32-35 in chloroform. The association constants (K(assoc)) of the complexes have been determined with the (1)H NMR and fluorescent titration methods. The energy-minimized conformation of 6.34 has been obtained with molecular mechanics calculation. The hydrazide-based folding structures described here represent novel examples of hydrogen bonding-driven foldamers that act as artificial receptors for selective molecular recognition.     

Hydrogen/deuterium exchange of monomers and dimers of leucine enkephalin

Leucine enkephalin has been studied using the combination of electrospray ionization (ESI) with a fast flow technique. ESI of leucine enkephalin produces an isotopic multiplet of peaks beginning at m/z 556. Hydrogen/deuterium exchange of this multiplet with ND₃ has revealed the contribution of two ion populations to this multiplet: The singly protonated monomer and the doubly protonated dimer. These populations were separated through their different kinetic behavior. Whereas the dimers undergo slow exchange the monomers undergo pronounced complexation with ND₃ and display a fast exchange of four labile hydrogens. The results indicate a more compact globular structure for the diprotonated dimer.     

Hydrogen bonded co-crystallised layered isopropanol-pyrogallol[4]arenes

A novel isopropanol-pyrogallol[4]arene forms a layered structure via hydrogen bonding and C–H…π interactions. The layered structure results in encapsulation of one isopropanol molecule. The application of NMR methods to determine solution structures and crystal structures provides insight into host–guest properties and the molecular interactions between them.