Carboxylic acid to thioamide hydrogen bonding

The lactam groups of dipyrrinones avidly engage in amide-amide hydrogen bonding to form dimeric association complexes in non-polar solvents (in CHCl₃, K_D ∼25,000 M⁻¹ at 22 °C). The corresponding thioamides (dipyrrinthiones), prepared from dipyrrinones by reaction with Lawesson's reagent, also form intermolecularly hydrogen-bonded dimers in non-polar solvents, albeit with much weaker association constants (in CHCl₃, K_D ∼200 M⁻¹ at 22 °C). When a carboxylic acid group is tethered to C(9) of the dipyrrinone, as in the hexanoic acid of [6]-semirubin, tight intramolecular hydrogen bonding between the carboxylic acid group and the lactam moiety (intramolecular K_assoc ?25,000) is found in CHCl₃ with no evidence of dimers. In contrast, the analogous dipyrrinthione, [6]-thiosemirubin, eschews intramolecular hydrogen bonds, as determined using NMR spectroscopy and vapor pressure osmometry, preferring to form intermolecularly hydrogen-bonded dimers of the thioamide-thioamide type.     

Molecular structure of vinylphosphine derivatives. Electron diffraction study of Cl2P−CH=CR2 (R=H,Me)

Internal rotation about the P?C bonds in the Cl₂PCH=CH₂ and Cl₂PCH=CMe₂ molecules is diseussed. It is shown that the cis (with eclipsed C=C bonds and lone electron pair of the phosphorus atom) and eclipsed conformers of the Cl₂PCH=CH₂ molecule are in equilibrium. The geometrical parameters and conformation compositions are refined. The content of the cis conformer is 40%. The Cl?P?C=C torsion angles are ±128.5° for the cis conformer and ?29.6 and ?132.6° for the eclipsed conformer. The Cl₂PCH=CMe₂ molecule occurs only in the cis form. For Cl₂PCH=CMe₂, the geometrical parameters are as follows: bond lengths C?H=1.124(11), C=C=1.322(8), P?C=1.789(3), and P?Cl=2.042(2) Å; bong angles (deg) C?P?Cl=99.1(4), Cl?P?Cl=99.6(6), C=C?CH₃=120.1 and 125.7, and P?C=C=122.3(9); torsion angles Cl?P?C=C=±129.3(3).     

Synthesis of cis-3,4-dibromopyrrolidine and its crystal and molecular structure

Synthesis and structural studies of 3,4-dibromopyrrolidine hydrochloride are reported. The conformation of the dibromopyrrolidine ring is a slightly deformed envelope with ΔC_s(3–4) = 4.03°. The Br atoms have cis conformation. Short Cl?H—N hydrogen bonds link the 3,4-dibromopyrrolidine cations and Cl^? anions along the a-axis.     

Conformational Analysis of Planar Enol Rotamers of 2,4-Pentanedione: an Ab Initio Study

All conformations among different planar enol conformers (rotamers) of 2,4-pentanedione were studied by means of the Hartree-Fock method using the STO-3G** basis set. The calculations were carried out with the Gaussian-98 program. For each conformation, stationary points with the highest energy on the energy curve were found graphically. Several conformations have low energy barriers and correspond to rotations around single bonds. They describe the spatial motion of only one (in most cases, hydrogen) atom or a small molecular fragment. All low energy barriers are in the interval 13-59 kJ·mol^-1. As would be expected, the lowest energy barrier is exhibited by the conformation that leads to the formation of an enol rotamer having an intramolecular H-bond (so-called -shaped form). On the other hand, conformations in which rotation around a bond leads to a break of the intramolecular hydrogen bond have the highest energy barriers. Conformations in which rotation occurs around the double bond have high energy barriers. The influence of the solvents CHCl₃ and CH₃CN on the intramolecular H-bond has also been studied by means of IPCM at the HF/6-31G** level.     

Infrared spectroscopic study of the configuration of some alkylaryl ureas

The conformation of a series of 1-aryl-3-(n-butyl)ureas and 1-aryl-1-methyl-3-(n-butyl)-ureas having an orthohydroxyl group in the aromatic ring is studied by infrared spectroscopy. The spectral data show that in organic solvents (CHCl₃, CH₂Cl₂, CCl₄) the compounds are in a Z,Z-conformation. Conclusive evidence is obtained for the existence of an intramolecular hydrogen bond between the OH and CO groups in all N-methylated ureas.     

Anion Recognition by Aliphatic Helical Oligoureas

Anion binding properties of neutral helical foldamers consisting of urea type units in their backbone have been investigated. ¹H NMR titration studies in various organic solvents including DMSO suggest that the interaction between aliphatic oligoureas and anions (CH₃COO^?, H₂PO₄^?, Cl^?) is site‐specific, as it largely involves the urea NHs located at the terminal end of the helix (positive pole of the helix), which do not participate to the helical intramolecular hydrogen‐bonding network. This mode of binding parallels that found in proteins in which anion‐binding sites are frequently found at the N‐terminus of an α‐helix. ¹H NMR studies suggest that the helix of oligoureas remains largely folded upon anion binding, even in the presence of a large excess of the anion. This study points to potentially useful applications of oligourea helices for the selective recognition of small guest molecules.     

Synthesis and Helical Structures of Poly(ω‐alkynamide)s Having Chiral Side Chains: Effect of Solvent on Their Screw‐Sense Inversion

New ω‐alkynamides, (S)‐HC?CCH₂CONHCH₂CH(CH₃)CH₂CH₃ ( 1 ) and (S)‐HC?CCH₂CH₂CONHCH(CH₃)CH₂CH₂CH₂CH₂CH₃ ( 2 ) were synthesized and polymerized with a rhodium catalyst in CHCl₃ to obtain cis‐stereoregular poly(ω‐alkynamide)s (poly( 1 ) and poly( 2 )). Polarimetric, CD, and IR spectroscopic studies revealed that in solution the polymers adopted predominantly one‐handed helical structures stabilized by intramolecular hydrogen bonds between the pendent amide groups. This behavior was similar to that of the corresponding poly(N‐alkynylamide) counterparts (poly( 3 ) and poly( 4 )) reported previously, whereas the helical senses were opposite to each other. The helical structures of the poly(ω‐alkynamide)s were stable upon heating similar to those of the poly(N‐alkynylamide)s, but the solvent response was completely different. An increase in MeOH content in CHCl₃/MeOH resulted in inversion of the predominant screw‐sense for poly( 1 ) and poly( 2 ). Conversely, poly( 3 ) was transformed into a random coil, and poly( 4 ) maintained the predominant screw‐sense irrespective of MeOH content. The solvent dependence of predominant screw‐sense for poly( 1 ) and poly( 2 ) was reasonably explained by molecular orbital studies using the conductor‐like screening model (COSMO).     

Doublet Chirality Transfer and Reversible Helical Transition in Poly(3,5‐disubstituted phenylacetylene)s with Pyrene as a Probe Unit†

A novel doublet chirality transfer (DCT) model was demonstrated in cis poly(3,5‐disubstituted phenylacetylene)s, i.e., S‐I , R‐I , and S‐I‐NMe . The chiral message from the stereocenter of alkylamide substituent at 3‐position induced the polyene backbone to take cis‐transoid helical conformation with a predominant screw sense. And in turn the helical backbone acted as a scaffold to orient the pyrene probes, which was linked to phenyl rings through 5‐position, to array in an asymmetric manner. A combinatory analyses of ¹H NMR, Raman, FTIR, UV‐vis absorption, CD, and computer simulation suggested that the main‐chain stereostructure, solvent nature, and intramolecular hydrogen bonds played important and complex roles on DCT. High cis‐structure content and intramolecular hydrogen bonds were beneficial for the realization of DCT. Reversible helix‐helix transition was observed in S‐I by changing the nature of solvents. In DMF, S‐I adopted a relatively contracted helix, where the main chain exhibited strong optical activity, but that of pyrene was weak. In contrast, a relatively stretched helix formed in CHCl₃, in which the optical activity of pyrene was much larger, whereas that of the polyene backbone was the weakest. This helix‐helix transition was attributed to the intramolecular hydrogen bonds, which was confirmed by solution‐state FTIR spectra and computer calculations.     

Synthesis,binding and fluorescence studies of a new neutral H-bonding receptor for anions based on 3,5-bis(trifluoromethyl)phenylurea

The synthesis and anion binding studies of the new neutral receptor 1,1′-(2,2′-(4,10-dimethyl-1,4,7,10-tetraazacyclododecane-1,7-diyl)bis(2-oxoethane-2,1-diyl))bis(3-(3,5-bis(trifluoromethyl)phenyl)urea) (L1) are reported. L1 is a macrocyclic ligand containing the 3,5-trifluoromethylphenylureido-binding fragment attached as a side arm on the tetraazacyclododecane. L1 is soluble in numerous organic solvents; the binding properties of L1 towards several simple anions (G) were investigated by NMR, UV–vis and fluorescence techniques in DMSO and CH₃CN solutions. L1 is able to bind F^? , Cl^?  and AcO^?  in both solvents; in addition, it binds Br^?  in CH₃CN. Fluoride shows the highest constant values in the halide series (F^?  > Cl^?  > Br^? ) and AcO^?  is the most strongly bound among all the anions investigated. L1 is able to signal the presence of the anions in solution by fluorescence change; in the case of acetate, this occurs in the visible range.     

Spectroscopic studies of the conformational properties of naphthoyl chitosan in dilute solutions

A naphthoyl chitosan derivative was prepared, and its conformations in dilute solutions were characterized with spectroscopic methods, including circular dichroism (CD) spectroscopy and fluorescence emission spectroscopy. The CD spectrum of this polymer showed a negative band at about 295 nm in dimethyl sulfoxide (DMSO), indicating that the polymer adopted a helical secondary structure. A helix reversion occurred at concentrations greater than 1 mg/mL. The intensity of the CD signal decreased with the addition of water to the solution, and this suggested a change from a helical conformation to a looser one as a result of the collapse of intramolecular hydrogen bonds. In the fluorescence emission experiments, two kinds of excimer emission bands were detected at 375 and 425 nm, and they were assigned to a partially overlapped dimer with a twisted geometry and a fully overlapped dimer with a sandwichlike geometry, respectively. Adding water to a solution of naphthoyl chitosan in DMSO resulted in a gradual reduction of the emission intensity at 375 nm, and this implied that the twisted arrangement of the chromophore was destroyed by the presence of water. The relative intensity (i.e., the ratio of the intensity of the excimer emission at 425 nm to that of the excimer emission at 375 nm) depended on the solvent (DMSO, N,N‐dimethylformamide, N,N‐dimethylacetamide, and 1‐methyl‐2‐pyrrolidinone), and this indicated that the conformation of naphthoyl chitosan was solvent‐dependent. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 2747–2758, 2004     

Conformational studies of new pseudotripeptide with pyrazine amidoxime motif and simplified analogs using IR,NMR spectroscopy,and molecular dynamic simulations

Solution structures of new pyrazine-based pseudotripeptide with amidoxime function and simplified pseudodipeptide analogs were determined by a combination of IR and NMR spectroscopic studies and molecular dynamic simulations using explicit chloroform as a solvent. It was found that proline-phenylalanine dipeptide residue and amidoxime moiety in o-position are essential for intramolecular hydrogen bonding including a seven-membered γ-turn formation. In addition, a cis/trans equilibrium study was present for prolyl amides in polar solvents (D₂O and DMSO). A phenylalanine substituent was found to exhibit profound effect on thermodynamic parameters in prolyl peptides. The presence of intramolecular hydrogen bonds dramatically increases the amount of trans isomer in non-hydrogen-bonding CHCl₃ and significantly favor cis isomer in hydrogen-bonding solvents such as DMSO and D₂O. All molecules are not cytotoxic therefore they can be further studied in relation to potent biological activities.

     

Structural comparison of three N‐(4‐halogenophenyl)‐N′‐[1‐(2‐pyridyl)ethylidene]hydrazine hydrochlorides

2‐{1‐[(4‐Chloroanilino)methylidene]ethyl}pyridinium chloride methanol solvate, C₁₃H₁₃ClN₃⁺·Cl⁻·CH₃OH, (I), crystallizes as discrete cations and anions, with one molecule of methanol as solvent in the asymmetric unit. The N—C—C—N torsion angle in the cation indicates a cis conformation. The cations are located parallel to the (02) plane and are connected through hydrogen bonds by a methanol solvent molecule and a chloride anion, forming zigzag chains in the direction of the b axis. The crystal structure of 2‐{1‐[(4‐fluoroanilino)methylidene]ethyl}pyridinium chloride, C₁₃H₁₃FN₃⁺·Cl⁻, (II), contains just one anion and one cation in the asymmetric unit but no solvent. In contrast with (I), the N—C—C—N torsion angle in the cation corresponds with a trans conformation. The cations are located parallel to the (100) plane and are connected by hydrogen bonds to the chloride anions, forming zigzag chains in the direction of the b axis. In addition, the crystal packing is stabilized by weak π–π interactions between the pyridinium and benzene rings. The crystal of (II) is a nonmerohedral monoclinic twin which emulates an orthorhombic diffraction pattern. Twinning occurs via a twofold rotation about the c axis and the fractional contribution of the minor twin component refined to 0.324 (3). 2‐{1‐[(4‐Fluoroanilino)methylidene]ethyl}pyridinium chloride methanol disolvate, C₁₃H₁₃FN₃⁺·Cl⁻·2CH₃OH, (III), is a pseudopolymorph of (II). It crystallizes with two anions, two cations and four molecules of methanol in the asymmetric unit. Two symmetry‐equivalent cations are connected by hydrogen bonds to a chloride anion and a methanol solvent molecule, forming a centrosymmetric dimer. A further methanol molecule is hydrogen bonded to each chloride anion. These aggregates are connected by C—H...O contacts to form infinite chains. It is remarkable that the geometric structures of two compounds having two different formula units in their asymmetric units are essentially the same.     

Observation of optical activity in polythiourethane obtained by the controlled cationic ring‐opening polymerization of chiral cyclic thiourethane derived from serine

The secondary structure of an optically active polythiourethane [(? CH₂C*H(CO₂Me)NHCOS? )_n] was evaluated with ¹H NMR, IR, and circular dichroism (CD) spectroscopy. Hydrogen bonds between the carbonyl and NH groups in the thiourethane group constrained the main chain of the chiral polythiourethane precisely under the direction of chirality in the main chain, whereas the racemic polymer was also constrained but randomly. The secondary structure of the polythiourethane in CHCl₃ changed noticeably in the presence or absence of trifluoroacetic acid, which eliminated constraining intramolecular hydrogen bonds. IR spectroscopy suggested that the secondary structure was almost identical in solid and solution states. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 1554–1561, 2005     

Triphenylamine-based simple chemosensor for selective fluorometric detection of fluoride, acetate and dihydrogenphosphate ions in different solvents

Triphenylamine-based new chemosensors 1 and 2 have been designed and synthesized for fluorometric detection of anions. The urea-amide conjugates in 1 and 2 are involved in binding of anions via hydrogen bonding. UV?Cvis and fluorescence titration experiments revealed that the sensor 1 has the selectivity for acetate (AcO^?), dihydrogenphosphate (H₂PO₄ ^?) and fluoride (F^?) over the other anions examined in the present study, in CHCl₃. In comparison, receptor 2 is non responsive for the same anions under similar conditions. In more polar solvent CH₃CN containing 0.1% DMSO, the receptor 1 shows a greater selectivity towards fluoride. The color of the solution of 1 is changed from colorless to light yellow and finally to yellowish brown only in the presence of fluoride in CH₃CN containing 10% DMSO. In pure DMSO and CH₃CN solvents, almost colorless solution of 1 is transformed into blood red and reddish brown in the presence of 30 equivalent amounts of F^?, respectively.     

Crystallographic report: 1,4‐Bis[(phenyldichlorostannyl)ethyl]benzene,p‐(Cl2PhSnCH2CH2)2C6H4

An ‘S’ conformation, stabilized by intramolecular C? H···π interactions, is found in centrosymmetric p‐(Cl₂PhSnCH₂CH₂)₂C₆H₄. The dinuclear species features distorted tetrahedral tin centres, with the greatest distortion manifested in the C? Sn? C angle of 134.32(16) °. Copyright © 2002 John Wiley & Sons, Ltd.     

Influence of Hydrogen Bonding and Polarity on the Spectral Properties of 4-Aminophthalimide Clusters Formed with Triethylamine and Dimethyl Sulfoxide in Solution

The time-dependent density functional theory (TDDFT) method has been carried out to study the influences of hydrogen bonding and solvent polarity on the spectral properties of 4-aminophthalimide (4AP) clusters formed with hydrogen-accepting solvents triethylamine (TEA) and dimethyl sulfoxide (DMSO). The ground- and S₁-state geometry structure optimizations, hydrogen bond energies, absorption and emission spectra for both the 4AP monomer and its two triply hydrogen-bonded clusters 4AP + (TEA)₃ and 4AP + (DMSO)₃ have been calculated using DFT and TDDFT methods respectively with the hybrid exchange correlation functional PBE1PBE and split-valence basis set 6-311++G(d,p). It has been demonstrated that the two hydrogen bonds I and II formed with the amine group of 4AP are significantly strengthened while the hydrogen bond III formed with the imide group is slightly weakened due to the intramolecular charge transfer from the amine group to the two carbonyl groups of the 4AP molecule upon photoexcitation. In addition, the hydrogen bonds formed by 4AP with DMSO are stronger than those formed with TEA, which together with its strong polarity, should be the main reasons for the more redshifts of both the absorption and the fluorescence spectra of 4AP in solvent DMSO than those in TEA.     

Solvent-Enhanced Conformational Flexibility of Cyclic Tetrapeptides

Solvent and temperature can affect the structural properties of cyclic peptides by controlling their flexibility. Here, we investigate two cyclic peptides, featuring beta turns. Using temperature-dependent NMR and FT-IR, we observed a pronounced temperature effect on the conformation of the cyclic peptide D-1 in CHCl₃ but a much smaller effect in CH₃CN. Almost no effect was observed for its diastereomer L-1 within a similar temperature range and using the same solvents. With the aid of Replica Exchange Molecular Dynamics simulations and Quantum Mechanics/Molecular Mechanics calculations, we were able to explain this behavior based on the increased flexibility of D-1 (in CHCl₃) in terms of intramolecular hydrogen bonding. The largest temperature dependence is observed for D - 1 in CHCl₃, while the temperature effect is less pronounced for L-1 in CHCl₃ and for both peptides in CH₃CN. This work provides new insights into the role of the environment and temperature on the conformations of cyclic peptides.     

Charge transfer molecular complexes of arylidene anthranilic acid derivatives with π-electron acceptors

X-Benzylidenesanthranilic acid molecular complexes with π-acceptors, tetracyanoethylene, 2,3-dichloro-5,6-dicyano-p-benzoquinone and chloranil, have been studied. The intramolecular hydrogen bonding that exists in such compounds greatly inhibits the transition of the nitrogen azomethine n-electrons. The formation constant values and molar extinction coefficients of the p-dimethyl-aminobenzylidenean-thranilic acid-DDQ CT complexes have been determined in CH₂Cl₂, C₂H₄Cl₂ and CHCl₃ in the temperature range 10–30°C. Such CT complexes are of strong n-π type.     

The Ozonolysis of Longifolene: A Tool for the Preparation of Useful Chiral Compounds. Configuration Determination of New Stereogenic Centers by NMR Spectroscopy and X‐Ray Crystallography

The ozonolysis of (+)‐longifolene ( 1 ) in different solvents (Et₂O, CH₂Cl₂, CHCl₃, acetone) at ?80° provided quantitatively longifolene epoxide ( 3 ) as a single diastereoisomer in which the O‐atom is endo‐positioned (Scheme 2). Upon warming to room temperature, the epoxide remained stable only in acetone and was isolated as a low‐melting crystalline compound. In CH₂Cl₂, Et₂O, or CHCl₃ solution, epoxide 3 rapidly rearranged to the isomeric enols 4 and 5 , which underwent further rearrangement to give the exo‐aldehyde 6 . On standing for several weeks in CH₂Cl₂ solution, or in CHCl₃ and Et₂O as well, at room temperature, aldehyde 6 slowly rearranged into its epimer 7 . The aldehydes 6 and 7 were isolated on the preparative scale for further synthetic use. The addition of methylmagnesium iodide to 6 and 7 provided the corresponding alcohols 13 / 14 and 15 / 16 , respectively, which were isolated as pure diastereoisomers (Scheme 4). The configurations of the new chiral centers in 13 – 16 were determined by NMR methods and X‐ray crystallography.     

Hydrogen‐bonded bilayers in ­piperazinium(2+) bis(mandelate) bis(methanol) solvate

In the title compound, C₄H₁₂N₂²⁺·2C₈H₇O₃^?·2CH₄O, the cations lie across centres of inversion and are disordered over two orientations with equal occupancy; there are equal numbers of (R)‐ and (S)‐mandelate anions present (mandelate is α‐hydroxy­benzene­acetate). The anions and the neutral water mol­ecules are linked by O—H?O hydrogen bonds [O?O 2.658 (3) and 2.682 (3) Å, and O—H?O 176 and 166°] into deeply folded zigzag chains. Each orientation of the cation forms two symmetry‐related two‐centre N—H?O hydrogen bonds [N?O 2.588 (4) and 2.678 (4) Å, and N—H?O 177 and 171°] and two asymmetric, but planar, three‐centre N—H?(O)₂ hydrogen bonds [N?O 2.686 (4)–3.137 (4) Å and N—H?O 137–147°], and by means of these the cations link the anion/water chains into bilayers.