Tautomerization‐Mediated Molecular Switching Between Six‐ and Seven‐Membered Rings Stabilized by Hydrogen Bonding

1,3,4,6‐Tetraketones typically undergo keto–enol tautomerism forming bis‐enols stabilized by intramolecular hydrogen bonding in two six‐membered rings. However, 1,3,4,6‐tetraketones derived from the terpene ketone camphor and norcamphor exist as isomers with two distinguishable modes of intramolecular hydrogen bonding, namely, the formation of six‐ or seven‐membered rings. The structural requirements for this so far unknown behavior were investigated in detail by synthesis and comparison of structural analogues. Both isomers of such 1,3,4,6‐tetraketones were fully characterized in solution and in the solid state. Intriguingly, they slowly interconvert in solution by means of tautomerism–rotation cascades, as was corroborated by DFT calculations. The influence of temperature and complexation with the transition metals Pd, Rh, and Ir on the interconversion process was investigated.     

Molecular mechanics investigation of weak complexes: the case of CO:H2O

The structure of the CO:H₂O complex and its isomers have been determined by using the molecular mechanics procedure. The parameters used in atomic pair potentials construction are derived by fitting on ab initio perturbation calculations of atomic or molecular fragments (Symmetry Adapted Perturbation Theory). An intramolecular potential is introduced in order to estimate the frequency shift of the CO stretching mode. Results are compared to recent calculations. The complexes are classified according to the predominant nature of the intermolecular bonding: quasi linear or bifurcated hydrogen bonding, and purely van der Waals bonding.     

Amide–Amide Hydrogen Bonding. Semirubin Amides

Summary. Semirubins are analogs for one-half of the bilirubin structure and capable of intramolecular hydrogen bonding. Semirubin amides of ammonia and primary amines are also capable of intramolecular hydrogen bonding. From a combination of spectroscopic methods (¹H NMR, NOE, and VPO), the primary amide is found to engage very effectively in intramolecular hydrogen bonding. The secondary and tertiary amides engage in both intramolecular (i) and intermolecular (ii) hydrogen bonding: N-methyl (i, monomer + ii, dimer), N-tert-butyl (ii, dimer), N,N-diethyl (i, monomer + ii, dimer). With an oxo-group at C(10), all of the amides are monomeric and most engage in intramolecular hydrogen bonding.     

Amide–Amide Hydrogen Bonding. Semirubin Amides

Semirubins are analogs for one-half of the bilirubin structure and capable of intramolecular hydrogen bonding. Semirubin amides of ammonia and primary amines are also capable of intramolecular hydrogen bonding. From a combination of spectroscopic methods (¹H NMR, NOE, and VPO), the primary amide is found to engage very effectively in intramolecular hydrogen bonding. The secondary and tertiary amides engage in both intramolecular (i) and intermolecular (ii) hydrogen bonding: N-methyl (i, monomer + ii, dimer), N-tert-butyl (ii, dimer), N,N-diethyl (i, monomer + ii, dimer). With an oxo-group at C(10), all of the amides are monomeric and most engage in intramolecular hydrogen bonding.     

The first aldehyde-derived crystalline geminal diol lacking internal electronic stabilization

The first stable crystalline geminal diol of an aldehyde lacking electron-withdrawing groups on the-carbon was synthesized fromd-sorbitol and characterized by¹H and¹³C nuclear magnetic resonance (NMR) and single-crystal x-ray studies. Each hydroxyl is a donor for a single, unique intermolecular hydrogen bond. Only one hydroxyl acts as an acceptor. No intramolecular hydrogen bonding is observed in the crystal.     

Excited-state charge coupled proton transfer reaction via the dipolar functionality of salicylideneaniline

Based on design and synthesis of salicylideneaniline derivatives(1a-1d),we demonstrate a prototypical system to investigate the excited-state intramolecular charge transfer(ESICT) coupled excited-state intramolecular proton transfer(ESIPT) reaction via the dipolar functionality of the molecular framework. In solid and aprotic solvents 1a-1d exist mainly as E conformers that possess an intramolecular sixmembered -ring hydrogen bond.Compounds 1a-1c exhibit a unique proton-transfer tautomer emission, while compound 1d exhibits remarkable dual emission due to the different solvent-polarity environment between ESICT and ESIPT states.Time-dependent density functional theory(TDDFT) calculations are reported on these Schiff bases in order to rationalize their electronic structure and absorption spectra.     

Control of structure and photophysical properties by protonation and subsequent intramolecular hydrogen bonding

Protonation and subsequent intramolecular hydrogen bonding as methods to control chain structure and tune luminescence in heteroatomic conjugated polymers were reported experimentally [A. P. Monkman et al., J. Am. Chem. Soc. 124, 6049 (2002)]. In this paper, the structure and photophysical properties of the model teraryl compound of phenylene-pyridylene copolymer before and after protonation are theoretically studied with quantum chemistry methods. From the optimized ground states, intramolecular hydrogen bonding to the adjacent oxygen atom in the alkoxy substituent planarizes the backbone of the molecules, and the optimized detailed results of compound 9 before and after protonation, such as the dihedral angles between the central benzene and the two pyridyl rings, the bond lengths, and the bond angles, are consistent with the experimental results. From the results of the calculated excited states, the protonation and subsequent intramolecular hydrogen bonding result in the redshifts of the absorption, the increase of the ionization energy, the increase of the electron affinity, the decrease of the energy difference of the highest occupied molecular orbital and lowest unoccupied molecular orbital, the decrease of the binding gap, and the delocalization of the electron-hole coherence. The photophysical properties of compound 9 before and after protonation are further studied with a three-dimensional real-space analysis method of transition and charge difference densities (study transition dipole moment and charge transfer in the absorption and fluorescence processes) and two-dimensional real-space analysis method of transition density matrices (study the electron-hole coherence and the excitation delocalization). The calculated results show theoretically an insight understanding on the influence of the protonation and subsequent intramolecular hydrogen bonding to chain structure and photophysical properties.     

Electron diffraction study of the equilibrium structure of hexamethylenetetramine involving data from quantum chemistry and vibrational spectroscopy

The equilibrium structure of the urotropine molecule is characterized by means of gas electron diffraction (GED) with the involvement of quantum chemistry and vibrational spectroscopy. A structural analysis of the GED data is performed based on the parameters of the intramolecular potential function using of the program complex SYMM/DISP/ELDIFF/LARGE. The quadratic and cubic force constants of the urotropine molecule were obtained earlier on the basis of calculations at the MP2(full)/cc-pVTZ level and assuming molecular symmetry T _d . The values of the equilibrium geometric parameters r _e of the urotropine molecule are found. The experimental structural parameters are in good agreement with those calculated at the MP2(full)/cc-pVTZ level.     

Theoretical study of hyaluronan oligosaccharides

The structure and energetics of hyaluronan oligomers from di- to decasaccharides have been studied by density functional theory calculations at the B3LYP/6-31G** level. The study covered selected conformers of the sodium salt, anionic disaccharides, and neutral acids in the isolated state and in aqueous solution using the PCM model approach. We investigated the structural changes of the hyaluronan chain when the Na⁺ ion is removed or replaced by proton. These processes result in some characteristic changes in the glycosidic torsional angles and hydrogen bonding interactions. We evaluated the folding for the hyaluronan chains and obtained values between 2.2 and 3.2, somewhat smaller than reported for the crystals. We found a contraction of the hyaluronan chains upon enlargement in most derivatives attributed partly to the helical character of hyaluronan. The energy consequences of the enlargement have been modeled by isodesmic reactions. The enlargement processes proved to be exothermal and the energies consistent within the gradual enlargement.     

Electron propagator theory study of N-/O-methylglycine conformers

The low-lying conformers of N-/O-methylglycine are studied by ab initio calculations at the B3LYP, MP3, and MP4(SDQ) levels of theory with the aug-cc-pVDZ basis set. The conformers having the intramolecular hydrogen bonds N-H...O=C or O-H...N are more stable than the others. Vertical ionization energies for the valence molecular orbitals of each conformer predicted with the electron propagator theory in the partial third-order quasiparticle approximation are in good agreement with the experimental data available in the literatures. The relative energies of the conformers and comparison between the simulated and the experimental photoelectron spectra demonstrate that there are at least three and two conformers of N- and O-methylglycine, respectively, in the gas-phase experiments. The intramolecular hydrogen bonding O-H...N effects on the molecular electronic structures are discussed for the glycine methyl derivatives, on the basis of the ab initio electronic structure calculations, natural orbital bond, and atoms-in-molecules analyses. The intramolecular hydrogen bonding O-H...N interactions hardly affect the electronic structures of the O-NH2-CH2-C(=O)-O-CH3 and alpha-methylated NH2-CH2-C(CH3)OOH conformers, while the similar intramolecular interactions lead to the significantly lower-energy levels of the highest occupied molecular orbitals for the N-(CH3-NH-CH2-COOH) and beta-methylated (NH2-CH2-CH2-COOH) conformers.     

The structure of trisformamidomethane in dimethyl sulphoxide-d6, hexamethylphos-phortriamide and trifluoroacetic acid

The PMR spectrum of trisformamidomethane in dimethyl sulphoxide-d₆ and hexamethyl-phosphortriamide has been explained by postulating four major structures in solution: two rotamers and two structural isomers, all of which are stabilized by intramolecular hydrogen bonding to form six membered rings. The spectrum in trifluoroacetic acid is also described.     

Beta-turn mimic in tripeptide with Phe(1)-Aib(2) as corner residues and beta-strand structure in an isomeric tripeptide: an X-ray diffraction study

A single crystal X-ray diffraction study of the tripeptide Boc-Phe-Aib-Leu-OMe (Aib = alpha-aminoisobutyric acid) reveals that it forms structurally one of the best type II beta-turns so far reported in tripeptides, stabilized by 10 atom intramolecular hydrogen bonding. In contrast, the isomeric tripeptide Boc-Phe-Leu-Aib-OMe adopts a beta-strand like conformation. Interestingly, a previously reported structure of another isomeric tripeptide, Boc-Leu-Aib-Phe-OMe, shows a double bend conformation without any intramolecular hydrogen bonding. These results demonstrate an example of the creation of structural diversities in the backbone of small peptides depending upon the co-operative steric interactions amongst the amino acid residues.     

Structure effects of the protonated lincomycin molecule on the mechanism of its complexation with organic compounds

The mechanism of complexation of the protonated lincomycin molecule with para-substituted nitrobenzenes in the gas phase is analyzed by quantum chemical methods. The regioselectivity of lincomycin protonation is treated in a B3LYP/6-31G(d′, p) approximation; the geometrical structure and conformation of the molecule are analyzed. The lincomycin molecule is protonated at the nitrogen atom of the pyrrolidine cycle. In stable conformers, a pseudovoid is formed and stabilized by intramolecular hydrogen bonding. The cross section of the pseudovoid (1.77–2.62 Å) is too small for the protonated lincomycin molecule to participate in host guest complexation with organic compounds. According to B3LYP/6-31G(d′, p) calculations, complexation of the protonated lincomycin molecule with nitrobenzenes occurs through hydrogen bonding.     

UV-vis, IR and 1H NMR spectroscopic studies of some mono- and bis-azo-compounds based on 2,7-dihydroxynaphthalene and aniline derivatives

The absorption spectra of mono- and bis-azo-derivatives obtained by coupling the diazonium salts of aromatic amines and 2,7-dihydroxynaphthalene have been studied in six organic solvents. The different absorption bands have been assigned and the effect of solvents on the charge transfer band is also discussed. The diagnostic IR spectral bands and 1H NMR signals are assigned and discussed in relation to molecular structure. Also, semi-empirical molecular orbital calculations using the atom superposition and electron delocalization molecular orbital (ASED-MO) theory have been performed to investigate the molecular and electronic structures of these compounds. According to these calculations, an intramolecular hydrogen bonding is essential for stabilization of such molecules.     

Gelation‐Induced Enhanced Fluorescence Emission from Organogels of Salicylanilide‐Containing Compounds Exhibiting Excited‐State Intramolecular Proton Transfer: Synthesis and Self‐Assembly

Self‐assembly structure, stability, hydrogen‐bonding interaction, and optical properties of a new class of low molecular weight organogelators (LMOGs) formed by salicylanilides 3 and 4 have been investigated by field‐emission scanning electron microscopy (FESEM), X‐ray diffraction (XRD), UV/Vis absorption and photoluminescence, as well as theoretical studies by DFT and semiempirical calculations with CI (AM1/PECI=8) methods. It was found that salicylanilides form gels in nonpolar solvents due to π‐stacking interaction complemented by the presence of both inter‐ and intramolecular hydrogen bonding. The supramolecular arrangement in these organogels predicted by XRD shows lamellar and hexagonal columnar structures for gelators 3 and 4 , respectively. Of particular interest is the observation of significant fluorescence enhancement accompanying gelation, which was ascribed to the formation of J‐aggregates and inhibition of intramolecular rotation in the gel state.     

Studies of intramolecular hydrogen bonding in protonated and non-protonated hexahydropyridinobenzodioxins

The conformational stability of hexahydropyridobenzodioxin and related derivatives in both protonated and non-protonated forms have been investigated by means of ab initio molecular orbital methods as well as semi-empirical AM1 and PM3 methods. One of the cis conformers (cis2e) has been found to be most stable due to the formation of an intramolecular hydrogen bond, other conformers including the trans isomer cannot form this interaction but are of different stability because of the orientation of the polar oxygens and the nitrogen. The effect of the intramolecular hydrogen bonding on the stability of hexahydropyridobenzodioxin and its methylated derivatives has been examined using various basis sets levels. In protonated form, both the semi-empirical and ab initio calculations give excellent agreement in energetic order; however, different orderings of conformer stabilities are observed by different computational methods in non-protonated form. The results provide insight into the intramolecular hydrogen bonding in computational studies of biologically important molecules.     

Intramolecular Hydrogen Bonds in Low‐Molecular‐Weight Polyethylene Glycol

We used static DFT calculations to analyze, in detail, the intramolecular hydrogen bonds formed in low‐molecular‐weight polyethylene glycol (PEG) with two to five repeat subunits. Both red‐shifted O?H???O and blue‐shifting C?H???O hydrogen bonds, which control the structural flexibility of PEG, were detected. To estimate the strength of these hydrogen bonds, the quantum theory of atoms in molecules was used. Car–Parrinello molecular dynamics simulations were used to mimic the structural rearrangements and hydrogen‐bond breaking/formation in the PEG molecule at 300 K. The time evolution of the H???O bond length and valence angles of the formed hydrogen bonds were fully analyzed. The characteristic hydrogen‐bonding patterns of low‐molecular‐weight PEG were described with an estimation of their lifetime. The theoretical results obtained, in particular the presence of weak C?H???O hydrogen bonds, could serve as an explanation of the PEG structural stability in the experimental investigation.     

Understanding the mechanism of cellulose dissolution in 1-butyl-3-methylimidazolium chloride ionic liquid via quantum chemistry calculations and molecular dynamics simulations

While N,N′-dialkylimidazolium ionic liquids (ILs) have been well-established as effective solvents for dissolution and processing of cellulose, the detailed mechanism at the molecular level still remains unclear. In this work, we present a combined quantum chemistry and molecular dynamics simulation study on how the ILs dissolve cellulose. On the basis of calculations on 1-butyl-3-methylimidazolium chloride, one of the most effective ILs dissolving cellulose, we further studied the molecular behavior of cellulose models (i.e. cellulose oligomers with degrees of polymerization n = 2, 4, and 6) in the IL, including the structural features and hydrogen bonding patterns. The collected data indicate that both chloride anions and imidazolium cations of the IL interact with the oligomer via hydrogen bonds. However, the anions occupy the first coordination shell of the oligomer, and the strength and number of hydrogen bonds and the interaction energy between anions and the oligomer are much larger than those between cations and the oligomer. It is observed that the intramolecular hydrogen bond in the oligomer is broken under the combined effect of anions and cations. The present results emphasize that the chloride anions play a critically important role and the imidazolium cations also present a remarkable contribution in the cellulose dissolution. This point of view is different from previous one that only underlines the importance of the chloride anions in the cellulose dissolution. The present results improve our understanding for the cellulose dissolution in imidazolium chloride ILs.     

Molecular structures and properties of the complete series of bromophenols: Density functional theory calculations

The complete series of 19 bromophenols have been studied by density functional theory (DFT) calculations at the B3LYP/6-311G++(d,p) level. The molecular structures and properties of bromophenols are strongly influenced by intramolecular hydrogen bonding of ortho-bromine, steric and inductive effects of substituted bromine, and other intramolecular electrostatic interactions. Systematic trends in several structural parameters and molecular properties of bromophenols have been found with the increasing number of bromine substitutions, including increase in O-H bond length, decrease in C-O bond length, red shift in O-H stretching frequency, and blue shift in O-H torsional frequency. Correlations among several key molecular parameters as well as those with available aqueous pKa values are examined. Comparisons with chlorophenols have indicated that the inductive effect of substituted bromine appears larger and bromophenols are slightly stronger acids than chlorophenols.     

Synthesis of structure-defined branched hyaluronan tetrasaccharide glycoclusters

Hyaluronan is a glycosaminoglycan with a large number of biological activity. Hyaluronan of different molecular weight often shows different biological activity, sometimes even completely opposite, but the mechanism is not clear. Herein, the hyaluronan tetrasaccharide glycoclusters using hyaluronan tetrasaccharide obtained by enzymolysis of natural hyaluronan were firstly synthesized in high yield. The structurally determined and diverse glycoclusters were of wide molecular weight range and might be used for mimicking the biological activity of natural hyaluronan and facilitating the mechanism study.