Conformational analysis of dicarbonyl(methylcyclopentadienyl)(2-(diethylamino)-2-oxoethyl)iron(II): a spectroscopic and molecular mechanics study

A combination of NMR and IR spectroscopic techniques was used to examine the conformational preferences of the previously unreported oxaallyliron compound dicarbonyl(methylcyclopentadienyl)(2-(diethylamino)-2-oxoethyl)iron(II) (1). IR studies revealed that 1 existed in n-pentane solutions as an equilibrium between two or more exchanging conformers through a rotation about the Fe---C bond. An additional contribution to the conformational dynamics of 1 was identified due to the resonance component of the amide group. The resonance contribution manifested in the observed restricted rotation about the C---N amide bond. Molecular mechanics calculations were used to model the conformational processes. The calculations predicted that the resonance stabilized conformation was the energetically preferred structure of 1. This agrees with the experimental evidence that identified the influence of resonance on the conformation of 1.     

Assignment of absolute configuration of cyclic secondary amines by NMR techniques using Mosher's method: a general procedure exemplified with (-)-isoanabasine

A general procedure to determine the absolute configuration of cyclic secondary amines with Mosher's NMR method is demonstrated, with assignment of absolute configuration of isoanabasine as an example. Each Mosher amide can adopt two stable conformations (named rotamers) caused by hindered rotation around amide C--N bond. Via a three-step structural analysis of four rotamers, the absolute configuration of (-)-isoanabasine is deduced to be (R) on the basis of Newman projections, which makes it easy to understand and clarify the application of Mosher's method to cyclic secondary amines. Furthermore, it was observed that there was an unexpected ratio of rotamers of Mosher amide derived from (R)-isoanabasine and (R)-Mosher acid. This phenomenon implied that it is necessary to distinguish the predominant rotamer from the minor one prior to determining the absolute configuration while using this technique.     

Hindered rotation of the dimethylamino and dimethylthioamide groups in two ortho substituted N,N-dimethylthiobenzamides

Hindered rotation in two o-substituted N,N-dimethylthiobenzamides was investigated by variable temperature ¹H NMR spectroscopy. For one compound, the enthalpies and entropies of activation for (i) thioamide group rotation around the Ar? C bond and (ii) dimethylamino group rotation around the C? N bond were obtained by full line shape analysis; a possible coupling between the two processes is discussed. A new simple method has also been applied to the analysis of dimethylamino exchange and results are in complete agreement with the full line shape analysis with somewhat better precision.     

Identifying the Bond Responsible for the Fluorescence Modulation in an Amyloid Fibril Sensor

An ultrafast intramolecular bond twisting process is known to be the responsible mechanism for the sensing activity of the extensively used amyloid fibril sensor thioflavin T (ThT). However, it is not yet known which one of the two possible single bonds in ThT is actually involved in the twisting process. To resolve this fundamental issue, two derivatives of ThT have been designed and synthesized and subsequently their photophysical properties have been studied in different solvents. It is understood from the present study that the rotation around the central C? C single bond, and not that around the C? N single bond, is primarily responsible for the sensor activity of ThT. Detailed viscosity‐dependent fluorescence studies revealed that the ThT derivative with restricted C? N bond rotation acts as a better sensor than the derivative with free C? N bond rotation. The better sensory activity is directly correlated with a shorter excited‐state lifetime. Results obtained from the photophysical studies of the ThT derivatives have also been supported by the results obtained from quantum chemical calculations.     

Synthesis,Characterization, and Conformational Study of Acylhydrazones of α,β‐Unsaturated Aldehydes

New acylhydrazone derivatives 1–6 have been synthesized by condensation of tert‐butylphenoxyhydrazide and cinnamaldehyde A or β‐chloro‐α,β‐unsaturated aldehydes B–F . They were characterized by IR, (¹H, ¹³C, ¹⁹F) nuclear magnetic resonance (NMR), and high‐resolution mass spectroscopy. The NMR data show the existence of the cis/trans‐amide conformers due to N–C(O) bond rotation in addition to the E/Z isomers around the C=C bond of some of the starting aldehydes. The solvent polarity effects on the ratios of the cis/trans‐amide rotamers have also been investigated. Importantly, rotational barriers around the N–C(O) bond for all compounds 1–6 (62.9–68.8 kJ mol^–1) were calculated using the coalescence‐temperature method according to the Eyring equation. The results are discussed and compared with those previously reported for related acylhydrazones of aryl adehydes and acetone.     

Studies in nuclear magnetic resonance—IX. Rotational barriers in substituted N,N-dimethylbenzamides

The barriers to rotation about the C? N bond in eighteen substituted N,N-dimethylbenzamides have been determined by complete line shape analysis of the NMR spectra of the N,N-dimethyl protons. The barriers have been correlated with the substituent constants σ and σ⁺. It has been shown that polar solvents increase the barrier in N,N-dimethylbenzamide. Acid catalysis of rotation about the amide C? N bond in N-(p-N,N-dimethylcarboxamidobenzyl)-pyridinium bromide has been investigated. ¹⁸O exchange studies show that catalysis is due to N-protonation rather than the formation of a tetrahedral intermediate. The rate of rotation is a function of the Hammett acidity function, H₀, and the water activity, and it is shown that proton exchange between the N- and O-protonated species involves the intermediacy of a water molecule. The differences in chemical shifts for the non-equivalent N, N-dimethyl groups of the benzamides are also a function of the substituents. Possible explanations of this phenomenon are discussed.     

Structures of Highly Twisted Amides Relevant to Amide N−C Cross‐Coupling: Evidence for Ground‐State Amide Destabilization

Herein, we show that acyclic amides that have recently enabled a series of elusive transition‐metal‐catalyzed N?C activation/cross‐coupling reactions are highly twisted around the N?C(O) axis by a new destabilization mechanism of the amide bond. A unique effect of the N‐glutarimide substituent, leading to uniformly high twist (ca. 90°) irrespective of the steric effect at the carbon side of the amide bond has been found. This represents the first example of a twisted amide that does not bear significant steric hindrance at the α‐carbon atom. The ¹⁵N NMR data show linear correlations between electron density at nitrogen and amide bond twist. This study strongly supports the concept of amide bond ground‐state twist as a blueprint for activation of amides toward N?C bond cleavage. The new mechanism offers considerable opportunities for organic synthesis and biological processes involving non‐planar amide bonds.     

Kinetic and thermodynamic characterization of C–N bond rotation by N‐methylacetohydroxamic acid in aqueous media

Hydroxamic acids (HAs) perform tasks in medicine and industry that require bidentate metal binding. The two favored conformations of HAs are related by rotation around the C(=O)–N bond. The conformations are unequal in stability. Recently, we reported that the most stable conformation of a small secondary HA in water places the oxygen atoms anti to one another. The barrier to C–N bond rotation may therefore modulate metal binding by secondary HAs in aqueous media. We have now determined the activation barrier to C–N rotation from major to minor conformation of a small secondary HA in D₂O to be 67.3 kJ/mol. The HA rotational barrier scales with solvent polarity, as is observed in amides, although the HA barrier is less than that of a comparable tertiary amide in aqueous solution. Successful design of new secondary HAs to perform specific tasks requires solid understanding of rules governing HA structural behavior. Results from this work provide a more complete foundation for HA design efforts. Copyright © 2015 John Wiley & Sons, Ltd.     

Mutarotation and isomerization of imines. Substituted N-(1-phenylethyl)-1-benzoylbenzylideneimines.

The mutarotation observed for several benzilmonoimines, having a chiral center, is atributed to the equilibration between two stereoisomers which differ in configuration around the single bond OCCN which, due to restricted rotation, becomes a chiral axis of the imines.     

Triphenylphosphine Mediated Simple Synthesis of Vinyl-Substituted Benzimidazoles

N -isopropenylbenzimidazolone undergoes a smooth reaction with triphenylphosphine and dialkyl acetylenedicarboxylates to produce highly functionalized salt-free phosphorus ylides in good yields. These stabilized phosphorus ylides exist as a mixture of two geometrical isomers as a result of restricted rotation around the carbon-carbon partial double bond resulting from conjugation of the ylide moiety with the adjacent carbonyl group. These ylides are converted to dialkyl 2-(1-isopropenyl-1H-benzimidazol-2-yl)-but-2-enedioates in boiling toluene.     

Synthesis of new functionalized imidazo[2,1‐b]thiazoles and thiazolo[3,2‐a]pyrimidines

5‐Oxo‐5H‐[1,3]thiazolo[3,2‐a]pyrimidine‐6‐carboxylic acid ( 4 ), and 6‐methylimidazo[2,1‐b]thiazole‐5‐carboxylic acid ( 17 ) were reacted with amines 6a‐i by the reaction with oxalyl chloride and N, N‐di methyl‐formamide as a catalyst into primary and secondary amide derivatives 7‐14 and 19‐22. From compound 24 N,N'‐disubstituted ureas 26, 27 and perhydroimidazo[1,5‐c]thiazole 29 derivatives of imidazo[2,1‐b]thiazole were prepared. By nmr analysis of compound 29 , the existence of two stereoisomers resulting from both optical, due to centre of chirality at C7′a, and conformational isomerism, due to restricted C5? N6′ bond rotation were proved.     

Induction of chirality: experimental evidence of atropisomerism in azapeptides

Methylation of the peptide bond in model azadipeptides leads to the E configuration and hence to atropisomerism due to a restricted rotation around the N-N axis.     

High-performance liquid chromatographic-nuclear magnetic resonance investigation of the isomerization of alachlor-ethanesulfonic acid

The metabolism of the acetanilide herbicide alachlor in soils leads to the formation of alachlor-ethanesulfonic acid (alachlor-ESA) as one of the major transformation products of this compound. The unique structure of alachlor and its metabolites allows the formation of two diastereomers (s-trans and s-cis) due to the hindered rotation of the amide bond connected to a rigid aromatic ring. Although these stereoisomers do interconvert by rotation about the amide bond, the rate of interconversion is slow allowing separation of the isomers on the chromatographic time scale. Once separated, the unique nuclear magnetic resonance signals of each isomer can be used to monitor the rate of isomerization. This paper reports the on-line separation and detection of the rotational diastereomers using high-performance liquid chromatography-nuclear magnetic resonance (HPLC-NMR) to efficiently measure the isomerization rate of alachlor-ESA.     

The interplay of thio(seleno)amide/vinylogous thio(seleno)amide "resonance" and the anisotropic effect of thiocarbonyl and selenocarbonyl functional groups

Amino-substituted thio(seleno)acrylamides 1-4 were synthesized and their 1H and 13C NMR spectra assigned. Both the NMR data and the results of theoretical calculations at the ab initio level of theory were employed to elucidate the adopted structures of the compounds in terms of E/Z isomerism and s-cis/s-trans configuration. In the case of the asymmetrically N(Me)Ph-substituted compounds, ab initio GIAO-calculated ring current effects of the N-phenyl group were applied to successfully determine the preferred conformer bias. The restricted rotations about the two C-N partial double bonds were studied by DNMR and the barriers to rotation (DeltaG(c)++) determined at the coalescence temperatures, and these were discussed with respect to the structural differences between the compounds. The barriers to rotation were also calculated at the ab initio level of theory where the best results (R(2) = 0.8746) were obtained only with inclusion of the solvent at the SCIPCM-HF/6-31G* level of theory. The calculations also provided means of assessing structural influences which were not available due to inaccessible rotation barriers. By means of natural bond orbital (NBO) analysis of 1-4, the occupation numbers of nitrogen lone pairs and bonding/antibonding pi/pi orbitals were shown to quantitatively describe thio(seleno)amide/vinylogous thio(seleno)amide "resonance". Finally, the thio(seleno)carbonyl anisotropic effect was quantitatively calculated by the GIAO method and visualized by isochemical shielding surfaces (ICSS). Only marginal differences between the two anisotropic effects were calculated and are therefore of questionable utility for previous and future applications with respect to stereochemical assignments.     

Synthesis and Characterization of Rhenium(V) Oxo Complexes with a New Thiol-Amide-Thiourea Ligand System. X-ray Crystal Structure of [1-Phenyl-3-[2-((2-thioacetyl)amino)ethyl]thioureato]oxorhenium(V)

General methods for preparing Re(V)O complexes with a novel series of thiol-amide-thiourea (TATU) ligands, a new class of N(2)S(2) chelates, were developed. The TATU ligands, the first multidentate systems designed with a bidentate thiourea moiety, have been used to prepare the first high-valent transition metal complexes with bidentate thiourea coordination. Direct reaction of N-(2-aminoethyl)-2-((triphenylmethyl)thio)acetamide (1) with phenyl, 4-methoxyphenyl, 4-chlorophenyl, and methyl isothiocyanate afforded ready access to the corresponding S-protected TATU ligands in one step. A two-step preparation of the N,N-dimethylthiourea TATU ligand derived from 1 was also developed. Deprotection of thiols in trifluoroacetic acid with triethylsilane followed by a ligand exchange reaction with Re(V)O precursors yielded neutral ReO(TATU) complexes. The structure of [1-phenyl-3-[2-((2-thioacetyl)amino)ethyl]thioureato]oxorhenium(V) (6a) was determined by X-ray diffraction methods. Crystal data for 6a: C(11)H(12)N(3)O(2)ReS(2), fw 468.6, orthorhombic, Pca2(1); a = 22.605(5) ?, b = 13.029(3) ?, c= 9.698(2) ?; V = 2856.3(11) ?(3); Z = 8. The coordination environment of 6a was pseudo-square-pyramidal with a deprotonated thiol S, deprotonated amide N, deprotonated thiourea N, and thiocarbonyl S coordinated in the basal plane and the oxo ligand in the apical position. The thiourea function forms a four-membered chelate ring in the multidentate TATU ligands. The two N-C and the S-C bond distances within the monodeprotonated thiourea moiety were typical of bonds with multiple-bond character. Solution (1)H NMR data for all five complexes were consistent with the solid-state structure of 6a. A broad singlet attributable to the uncoordinated NH group of thiourea was observed for the monosubstituted thiourea complexes but was not present for the N,N-dimethylthiourea derivative. Instead, two singlets of equal intensity were observed for the two methyl groups, indicating that there is restricted rotation around the C-N(CH(3))(2) bond and an extended pi system in the thiourea moiety. The four-membered ring might cause difficulty because the M-S distance would be relatively long in an undistorted ligand. This may be the reason such chelate ligands have not been previously investigated. However, the N-C-S angle narrows to approximately 105 degrees, permitting a Re-S bond with a typical bond length to be formed. We conclude that such a ring represents a versatile new building block to create multidentate ligands.     

Kinetics and equilibria of cis/trans isomerization of backbone amide bonds in peptoids

The biological activities of N-substituted glycine oligomers (peptoids) have been the subject of extensive research. As compared to peptides, both the cis and trans conformations of the backbone amide bonds of peptoids can be significantly populated. Thus, peptoids are mixtures of configurational isomers, with the number of isomers increasing by a factor of 2 with each additional monomer residue. Here we report the results of a study of the kinetics and equilibria of cis/trans isomerization of the amide bonds of N-acetylated peptoid monomers, dipeptoids, and tripeptoids by NMR spectroscopy. Resonance intensities indicate the cis conformation of the backbone amide bonds of the peptoids studied is more populated than is generally the case for the analogous secondary amide bond to proline residues in acyclic peptides. Rate constants were measured by inversion-magnetization transfer techniques over a range of temperatures, and activation parameters were derived from the temperature dependence of the rate constants. The rate of cis/trans isomerization by rotation around the amide bonds in the peptoids studied is generally slower than that around amide bonds to proline residues and takes place on the NMR inversion-magnetization transfer time scale only by rotation around the amide bond to the C-terminal peptoid residue.     

Elucidating Atropisomerism in Nonplanar Porphyrins with Tunable Supramolecular Complexes

Atropisomerism is a fundamental feature of substituted biaryls resulting from rotation around the biaryl axis. Different stereoisomers are formed due to restricted rotation about the single bond, a situation often found in substituted porphyrins. Previously NMR determination of porphyrin atropisomers proved difficult, if not almost impossible to accomplish, due to low resolution or unresolvable resonance signals that predominantly overlapped. Here, we shed some light on this fundamental issue found in porphyrinoid stereochemistry. Using benzenesulfonic acid (BSA) for host-guest interactions and performing 1D, 2D NMR spectroscopic analyses, we were able to characterize all four rotamers of the nonplanar 5,10,15,20-tetrakis(2-aminophenyl)-2,3,7,8,12,13,17,18-octaethylporphyirin as restricted H-bonding complexes. Additionally, X-ray structural analysis was used to investigate aspects of the weak host–guest interactions. A detailed assignment of the chemical signals suggests charge-assisted complexation as a key to unravel the atropisomeric enigma. From a method development perspective, symmetry operations unique to porphyrin atropisomers offer an essential handle to accurately identify the rotamers using NMR techniques only.     

Structural Characterization of N‐Alkylated Twisted Amides: Consequences for Amide Bond Resonance and N−C Cleavage

Herein, we describe the first structural characterization of N‐alkylated twisted amides prepared directly by N‐alkylation of the corresponding non‐planar lactams. This study provides the first experimental evidence that N‐alkylation results in a dramatic increase of non‐planarity around the amide N?C(O) bond. Moreover, we report a rare example of a molecular wire supported by the same amide C=O‐Ag bonds. Reactivity studies demonstrate rapid nucleophilic addition to the N?C(O) moiety of N‐alkylated amides, indicating the lack of n_N to π^*_C=O conjugation. Most crucially, we demonstrate that N‐alkylation activates the otherwise unreactive amide bond towards σ N?C cleavage by switchable coordination.     

Stereocontrolled synthesis of iminocyclitols with an ether bridge

Nor-tropane related bicyclic (6+5) iminocyclitols with an ether bridge and different substituents (hydroxymethyl, aminomethyl, and aminoethyl) on C-1 are prepared starting from a β-d-psicofuranosyl cyanide. The method involves an internal nucleophilic attack of a stabilized amide ion on a 5-mesyloxy derivative. The intermediate N-acetyl O-protected iminocyclitols present atropoisomerism due to restricted rotation of the N-CO amido bond. Conformational aspects of the prepared compounds are discussed.     

Conformational studies by nuclear magnetic resonance?VI: C?C and C?N rotation barriers in various enamine derivatives

Delocalisation of the nitrogen lone electron pair by an acyl and acylvinylogue group simultaneously, results in a lowering of both C? N rotational barriers. MeC(O)CBr?CHNMe₂ and MeC(O)C(OCOMe)?CHNMe₂ exhibit restricted rotation around what is formally a double bond C?C.