Conformational changes of functionalised indole receptors upon their interaction with anions

The conformational analysis of four C2-amido and C7-ureido functionalised indole anion receptors was performed by a combination of heteronuclear NMR spectroscopy and ab initio quantum mechanical calculations. NOE experiments showed that anti–anti conformation across C2–C2α and C7–N7α bonds is predominant in acetone solution in the absence of anions. Upon anion binding to receptors, syn–syn conformation becomes predominant. The conformational changes upon anion binding are in good agreement with energetic preferences established by ab initio calculations. Chemical shift changes induced by interaction of anions suggest that binding of chloride and bromide anions occurs primarily to H1 and H7α protons. Nitrate anions favour interaction with H7α and H7γ ureido protons, whereas acetate anions interact strongly with all four available hydrogen bond donor groups.     

Oligonucleosides with a Nucleobase‐Including Backbone,Part 7

The conformational analysis of 7 was carried out in (D₆)DMSO and in mixtures of (D₆)DMSO and CDCl₃ to evaluate the syn/anti conformations, relevant to the pairing propensity of this type of nucleotide analogue. The HO−C(5′) of unit I and of unit II of the dimer 7 form an intramolecular H‐bond to N(3). In (D₆)DMSO, the C(5′)−OH⋅⋅⋅N(3) H‐bond in unit I is partially broken, while that in unit II persists to a larger extent. The syn conformation prevails for unit I and particularly for unit II. The furanosyl moieties adopt predominantly a 2′‐endo conformation that is largely independent of the solvent.     

Experimental and Theoretical Charge Density Study on Di‐2‐pyrazylamine (Hdpza) Molecule in Crystal

Electron density distribution of Di‐2‐pyrazylamine ( Hdpza ) is studied both by single‐crystal X‐ray diffraction method at 100K and theoretical calculation. Structural determination reveals that Hdpza molecules crystalize in a syn‐anti conformation with an intramolecular C? H?N hydrogen bond between two pyrazine rings and then gather together via two intermolecular N? H?N and C? H?N hydrogen interaction and π? π stacking interaction between pyrazine rings. Charge density analysis is made in terms of deformation density (Δπ), Laplacian distribution and topological analysis of total electron density based on multipole model and theoretical calculation. The agreement between experiment and theory is good. The topological properties at bond critical points of C? C and C? N bonds reveal a covalent bond character, and those of intermolecular interactions, such as hydrogen bonds and π? π stacking interactions, reveal a closed‐shell interaction. The potential energy curve of Hdpza molecule shows that the syn‐anti conformation is the most stable one (global minima) than the other two of syn‐syn and anti‐anti conformations.     

Exo conformers of N‐(pyridin‐2‐yl)‐ and N‐(pyridin‐3‐yl)norbornene‐5,6‐dicarboximide crystals

Two isomeric pyridine‐substituted norbornenedicarboximide derivatives, namely N‐(pyridin‐2‐yl)‐exo‐norbornene‐5,6‐dicarboximide, (I), and N‐(pyridin‐3‐yl)‐exo‐norbornene‐5,6‐dicarboximide, (II), both C₁₄H₁₂N₂O₄, have been crystallized and their structures unequivocally determined by single‐crystal X‐ray diffraction. The molecules consist of norbornene moieties fused to a dicarboximide ring substituted at the N atom by either pyridin‐2‐yl or pyridin‐3‐yl in an anti configuration with respect to the double bond, thus affording exo isomers. In both compounds, the asymmetric unit consists of two independent molecules (Z′ = 2). In compound (I), the pyridine rings of the two independent molecules adopt different conformations, i.e. syn and anti, with respect to the methylene bridge. The intermolecular contacts of (I) are dominated by C—H...O interactions. In contrast, in compound (II), the pyridine rings of both molecules have an anti conformation and the two independent molecules are linked by carbonyl–carbonyl interactions, as well as by C—H...O and C—H...N contacts.     

Conformational studies of (−)-epicatechin-Mosher ester

An in depth ab initio investigation into the factors governing the conformational behaviour of α-methoxy-α-trifluoromethyl-α-phenylacetic acid (MTPA) esters, extensively utilized to determine the absolute stereochemistry of secondary alcohols and amides, discloses the hyperconjugative interactions responsible for the important syn- and anti-periplanar conformational rigidity and the predominance of the former over the latter. The first flavonoid-Mosher ester crystal structure is reported.     

Factors that regulate the conformation of m-benziporphodimethene complexes: agostic metal-arene interaction, hydrogen bonding, and η2,π coordination

Group 12 and silver(I) tetramethyl‐m‐benziporphodimethene (TMBPDM) complexes with phenyl, methylbenzoate, or nitrophenyl groups as meso substituents were synthesized and fully characterized. The dimeric silver(I) complex displays an unusual η²,π coordination from the β‐pyrrolic C?C bond to the silver ion. All of the complexes displayed a close contact between the metal ion and the inner C(22)? H(22) on the m‐phenylene ring. The downfield chemical shifts of H(22) and large coupling constants between Cd^II and H(22) strongly support the presence of an agostic interaction between the metal ion and inner C(22)–H(22). Crystal structures revealed that the syn form is the predominant conformation for TMBPDM complexes. This is distinctively different from the exclusive anti conformation observed in m‐benziporphyrin and tetraphenyl‐m‐benziporphodimethene (TPBPDM) complexes. Evidently, intramolecular hydrogen‐bonding interactions between axial chloride and methyl groups stabilize syn conformations. Unlike the merely syn conformation observed in the solid‐state structures of TMBPDM complexes that contain an axial chloride, in solution these complexes display highly solvent‐ and temperature‐dependent syn/anti ratio changes. The observation of dynamic ¹H NMR spectroscopic scrambling between syn and anti conformations from the titration of chloride ion into the solution of the TMBPDM complex suggests that axial ligand exchange is a likely pathway for the conversion between syn and anti forms. Theoretical calculations revealed that intermolecular hydrogen‐bonding interactions between the axial chloride and CHCl₃ stabilizes the anti conformation, which explains the increased ratio for the anti form when dichloromethane or chloroform was used as the solvent.     

Stereoelectronic Aspects of the Anomeric Effect in Fluoromethylamine

High-level ab initio calculations have been made for fluoromethylamine to study structural and energetic effects of the relative orientation of the N lone pair to the C? F bond. The anti-conformer (N lone pair anti-planar to the C? F bond) corresponds to the global energy minimum. It has the longest C? F distance, the shortest C? N distance, and is 7.5 kcal·mol^?1 more stable than the related perpendicular conformation (lone pair perpendicular to the C? F bond). The syn-conformation also shows hallmarks of the anomeric effect: long C? F bond, short C? N bond, and energetic stability when allowance is made for the two pairs of eclipsed hydrogens. The transition state for N inversion is close to the syn-structure; rotation about the C? N bond is strongly coupled with this inversion process. Small bond distance changes of ca. 0.02 Å between parallel and perpendicular conformations are associated with dissociation energy differences of ca. 30 kcal·mol^?1. Various criteria for assessing the strength of the anomeric effect are discussed.     

Dynamics of the glycosidic bond: conformational space of lactose

The dynamics of the glycosidic bond of lactose was studied by a paramagnetic tagging‐based NMR technique, which allowed the collection of an unusually large series of NMR data for a single compound. By the use of distance‐ and orientation‐dependent residual dipolar couplings and pseudocontact shifts, the simultaneous fitting of the probabilities of computed conformations and the orientation of the magnetic susceptibility tensor of a series of lanthanide complexes of lactose show that its glycosidic bond samples syn/syn, anti/syn and syn/anti ?/ψ regions of the conformational space in water. The analysis indicates a higher reliability of pseudocontact shift data as compared to residual dipolar couplings with the presently available weakly orienting paramagnetic tagging technique. The method presented herein allows for an improved understanding of the dynamic behaviour of oligosaccharides.     

How the Generalized Anomeric Effect Influences the Conformational Preference

The generalized anomeric effect refers to the conformational preference of a gauche structure over an anti structure for molecules with a R‐X‐C‐Y moiety. Whereas there are conflicting reports regarding the origin of this ubiquitous effect, a general consensus is that both the steric (more specifically electrostatic) and hyperconjugative interactions contribute. Here we employed the block‐localized wavefunction (BLW) method, which is the simplest variant of ab initio valence bond (VB) theory and can define reference electron‐localized states self‐consistently, to evaluate the magnitude of the hyperconjugation effect in a number of acyclic molecules exhibiting the generalized anomeric effect. The BLW‐based energy decomposition analysis revealed that both the steric and hyperconjugation effects contribute to the conformational preferences of methoxymethyl fluoride and methoxymethyl chlorides. But for the other systems under investigation, including methanediol, methanediamine, aminomethanol and dimethoxymethane, the hyperconjugative interactions play a negative role in the conformational preferences and the steric effect is solely responsible for the generalized anomeric effect.     

Molecular conformations of jet-cooled 2-methylindan and 2-phenylindan

The molecular conformations of jet-cooled 2-methylindan (2MI) and 2-phenylindan (2PI) have been studied using resonant-enhanced two-photon ionization spectroscopy in combination with ab initio calculations. Both axial (2MI_ax) and equatorial (2MI_eq) conformers of 2MI have been observed. A 2MI_eq/2MI_ax conformer ratio of 2.3 was estimated at 298 K, leading to the energy difference, \Updelta E = E _{2 \textMI\textax} - E _{2 \textMI\texteq} \Updelta E = E_{{ 2 {\text{MI}}_{\text{ax}} }} - E_{{ 2 {\text{MI}}_{\text{eq}} }} , of 0.49 kcal/mol. Ab initio calculations predicted three stable conformers of 2PI: two equatorial conformers (2PI_eq0 and 2PI_eq90), and one axial conformer (2PI_ax). Only the axial conformer of 2PI (2PI_ax) was experimentally observed. The indan ring of 2PI_ax is slightly more planar than the indan rings of the two equatorial conformers of 2PI because of the intramolecular C_sp2–H/π interactions in 2PI_ax. The equatorial conformers of 2PI relax to the more stable axial conformer because of the high pre-expansion temperature (383 K), and relatively low barrier (1.68 kcal/mol) to axial–equatorial interconversion. The barrier (2.33 kcal/mol) to axial–equatorial interconversion in 2MI is high enough to prevent conformational relaxation at the pre-expansion temperature of 298 K. Intramolecular C–H/π interactions are found to be more important in determining the conformational preference of 2PI than 2MI; this can be attributed to the higher acidity of the C_sp2–H bond than that of C_sp3–H bond.     

Comparative Infrared,Raman, and Natural‐Bond‐Orbital Analyses of King's Sultam

By means of ¹H‐NOESY‐ and Raman‐spectroscopic analyses, we experimentally demonstrated the presence of the equatorial N? Me conformer of King's sultam 4b in solution, resulting from a rapid equilibrium. As a consequence, the value of the N lone‐pair anomeric stabilization should be revised to 1.5–1.6 kcal/mol. Independently from the N tilting, natural bond orbital (NBO)‐comparative analyses suggest that the S d* orbitals do not appear as primordial and stereospecific acceptors for the N lone pair. Second, the five‐membered‐ring sultams do not seem to be particularly well‐stabilized by the S? C σ* orbital in the N‐substituted pseudo‐axial conformation, as opposed to an idealized anti‐periplanar situation for the six‐membered‐ring analogues. In this latter case, the other anti‐periplanar C? C σ* and C(1′)? H/C(2′) σ*orbitals are as important, if not more, when compared to the S? C σ* participation. In the pseudo‐equatorial conformation, γ‐sultams particularly benefit from the N lone‐pair hyperconjugation with the anti‐periplanar S? O₁ σ* and C(2)? H/C or C(1′)? H/C σ* orbitals. This is also the case for δ‐sultams when the steric requirement of the N‐substituent exceeds 1.6 kcal/mol. When both axial and equatorial conformations are sterically too exacting, the N‐atom is prone to sp² hybridization or/and conformational changes (i.e., 12c ). In that case also, the mode of stereoelectronic stabilization differs from γ‐ to δ‐sultams.     

Study of conformations and hydrogen bonds in the configurational isomers of pyrrole‐2‐carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis

The ¹H, ¹³C and ¹⁵N NMR studies have shown that the E and Z isomers of pyrrole‐2‐carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole‐2‐carbaldehyde oxime is stabilized by the N? H···N and N? H···O intramolecular hydrogen bonds, respectively. The N? H···N hydrogen bond in the E isomer causes the high‐frequency shift of the bridge proton signal by about 1 ppm and increase the ¹J(N, H) coupling by ～3 Hz. The bridge proton shows further deshielding and higher increase of the ¹J(N, H) coupling constant due to the strengthening of the N? H···O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by ～3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of ¹H shielding and ¹J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N? H···N and N? H···O hydrogen bondings to be estimated. The NBO analysis suggests that the N? H···N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N? H bond through the N? H···O hydrogen bond occurs in the Z isomer. Copyright © 2010 John Wiley & Sons, Ltd.     

Molecular Self‐Recognition: Rotational Spectra of the Dimeric 2‐Fluoroethanol Conformers

Fluoroalcohols show competitive formation of intra‐ and intermolecular hydrogen bonds, a property that may be crucial for the protein‐altering process in a fluoroalcohol/water solution. In this study, we examine the intra‐ and intermolecular interactions of 2‐fluoroethanol (FE) in its dimeric conformers by using rotational spectroscopy and ab initio calculations. Three pairs of homo‐ and heterochiral dimeric FE conformers are predicted to be local minima at the MP2/6‐311++G(d,p) level of theory. They are solely made of the slightly distorted most stable G+g?/G?g+ FE monomer units. Jet‐cooled rotational spectra of four out of the six predicted dimeric conformers were observed and unambiguously assigned for the first time. All four observed dimeric conformers have compact geometries in which the fluoromethyl group of the acceptor tilts towards the donor and ensures a large contact area. Experimentally, the insertion of the O? H group of one FE subunit into the intramolecular O? H???F bond of the other was found to lead to a higher stabilisation than the pure association through an intermolecular O? H???O? H link. The hetero‐ and homochiral combinations were observed to be preferred in the inserted and the associated dimeric conformers, respectively. The experimental rotational constants and the stability ordering are compared with the ab initio calculations at the MP2 level with the 6‐311++G(d,p) and aug‐cc‐pVTZ basis sets. The effects of fluorination and the competing inter‐ and intramolecular hydrogen bonds on the stability of the dimeric FE conformers are discussed.     

Internal rotation and framework relaxation in ethene thiol

New and existing data on the ground and excited CS torsional states of the stable rotamers of ethene thiol have been analysed to give a potential function for internal rotation around the CS bond. The barrier between the syn and anti rotamers is found to be 800 cm^?1 and that at the planar anti conformation itself to be 12 cm^?1. the syn conformation is 50 cm^?2 more stable than the ‘quasi-planar’ anti conformation Satisfactory reproduction of the observed trends in rotational constants with torsional excitations has been achieved by introducing extensive relaxation of the CCS angle and the CS bond length during internal rotation. The CCS angle reduces by up to 5° v'hilst the CS bond length increases by up to 0.02 A during rotation from the syn to anti conformation. The use of ab initio M.O. calculations to provide an indication of the most significant aspects of structure relaxation is described.     

Conformational preferences of pseudoproline residues

The conformational study on N-acetyl-N'-methylamides of oxazolidine and thiazolidine residues (Ac-Oxa-NHMe and Ac-Thz-NHMe) is carried out using ab initio HF and density functional B3LYP methods with the self-consistent reaction field method to explore the effects of the replacement of the C(gamma)H(2) group in the prolyl ring by oxygen or sulfur atoms on the conformational preferences and prolyl cis-trans isomerization in the gas phase and in solution (chloroform and water). As the solvent polarity increases, the conformations C with the C7 intramolecular hydrogen bonds become depopulated, the PPII- or PPI-like conformations F become more populated, and the cis populations increase for both Oxa and Thz dipeptides, as found for the Pro dipeptide, although the populations of backbone conformations and puckerings are different in pseudoproline and proline dipeptides. As the increase of solvent polarity, the populations of the trans/up conformations decrease for Oxa and Thz dipeptides, but they increase for the Pro dipeptide. It is found that the cis-trans isomerization proceeds through the anticlockwise rotation with omega' approximately -60 degrees about the oxazolidyl peptide bond and the clockwise rotation with omega' approximately +120 degrees about the thiazolidyl peptide bond in the gas phase and in solution, whereas the clockwise rotation is preferred for the prolyl peptide bond. The pertinent distance d(N...H-N(NHMe)) and the pyramidality of the prolyl nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure but the lower rotational barriers for Oxa and Thz dipeptides than those for the Pro dipeptide, which is observed from experiments, cannot be rationalized. The calculated cis populations and rotational barriers to the cis-trans isomerization for both Oxa and Thz dipeptides in chloroform and/or water are consistent with the experimental values.     

Conformational Stability of Propenoyl Bromide from Temperature-Dependent Infrared Spectra of Krypton Solutions,Ab Initio Calculations,and r 0 Structural Parameters of the Propenoyl Halides (F,Cl, Br)

Variable temperature (–100 to –150°C) studies of the infrared spectra (3500–400 cm^–1) of propenoyl bromide, CH₂=CHCBrO, dissolved in liquid krypton, have been carried out. Utilizing six different conformer pairs, an enthalpy difference of 204 ± 20 cm^–1 (2.44 ± 0.24 kJ/mol) was obtained, with the anti conformer (carbonyl bond trans to C=C bond) the more stable form. At ambient temperature, there is approximately 28 ± 2% of the syn conformer present. The anti conformer also remains in the infrared and Raman spectra of the polycrystalline solid. The optimal geometries, conformational stabilities, harmonic force fields, infrared intensities, Raman activities, depolarization ratios, and vibrational frequencies, are reported for both conformers from MP2/6-31G(d) ab initio calculations. The potential function governing the conformational interchange has been obtained from the MP2/6-31G(d) ab initio calculations. The conformational stabilities were calculated from a variety of basis sets and at the highest level of calculations, MP2/6-311 + (2df,2pd), the anti conformer is predicted to be more stable by 178 cm^–1, which is in excellent agreement with the experimental results. The r ₀ adjusted structural parameters have been obtained for propenoyl fluoride and chloride from a combination of the previously reported microwave rotational constants and ab initio predicted parameters. Several of the parameters for the chloride are significantly different than those proposed from an electron diffraction investigation. The results of these spectroscopic, structural, and theoretical studies are discussed and compared to the corresponding results for some similar molecules.     

N‐(4‐Bi­phenyl­yl)­urea

In the crystal structure of the title compound, C₁₃H₁₂N₂O, N—H(anti)?O hydrogen bonds produce the so‐called urea α‐network and the N—H(syn) donor forms an unconventional N—H?π hydrogen bond.     

A 1H-NMR Spectroscopic Investigation of the Conformation of the Acetamido Group in Some Derivatives of N-Acetyl-D-allosamine and -D-glucosamine

The population of the conformations obtained by rotation around the C(2)? N and the N? C(O) bonds of AllNAc, GlcNAc, and GlcNMeAc derivatives was investigated by ¹H-NMR spectroscopy. The AllNAc-derived α-D -and β-D -pyranosides 4–7 , the AllNAc diazirine 16 , and the GlcNAc-derived axial anomers α-D - 8–10 prefer the (Z)-anti-conformation. A significant population of the (Z)-syn-conformer in the (Z)-syn/(Z)-anti-equilibrium for the equatorial anomers β-D - 8–10 and the GlcNAc diazirine 17 was evidenced by an upfield shift of H? C(2), downfield shifts of H? C(1) and H? C(3), and by NOE measurements. The population of the (Z)-syn-conformation depends on the substituent at C(1) and is highest for the hexafluoroisopropyl glycoside. The population of the (Z)-syn-conformation of β-D - 14 decreases with increasing polarity of the solvent, but a substantial population is still observed for solutions in D₂O. Whereas the α-D -anomers of the hemiacetal 22 and the methyl glycoside 21 prefer the (Z)-anti-conformation in D₂O solution, the corresponding β-D -anomers are mixtures of the (Z)-anti-and (Z)-syn-conformers. The diazirine 17 self-associates in CD₂Cl₂ solution at concentrations above 0.005M at low temperatures. The axial anomers of the GlcNMeAc derivatives α-D - 26–28 are 2:1 to 3:1 mixtures of (Z)-anti-and (E)-anti-conformers, whereas the corresponding β-D -glycosides are ca. 1:3:6 mixtures of (Z)-syn-, (Z)-anti-, and (E)-anti-conformers.