Direct conformational analysis of a 10 nm long oligothiophene wire

Conformational variations of a 10 nm long oligothiophene wire comprising 24 thiophene rings on Au(111), which are related to the various straight and bent shapes of the long wires, have been directly visualized by scanning tunneling microscopy (STM). The local bending angles within the wire are well characterized as s-cis/s-trans configurations of individual thiophene rings. We find that the partial stabilization of the metastable s-cis conformation results in the wire bending, which should be influenced by solvent and substituents.     

Ab initio studies on the vibrational spectra and conformational isomerism of 2,4-dimethyl-1,3-pentadiene

Ab initio was used to study the structure of various conformational isomers and their vibrational spectra of 2,4-dimethyl-1,3-pentadiene (2,4-PD) in detail. Two stable conformations, s-trans and s-cis, were found in which s-trans is more stable. The geometry of stable conformations and charge distributions were studied, and the effect of different basis sets on geometry optimization is discussed. The results of complete optimization indicate that molecular skeleton is nearly in a plane, its largest deviation is only 0.3 degrees. Therefore, it is reasonable and available to hypothesis that the molecule has Cs symmetry. The thermal dynamics conformations were calculated and compared with experimental values. DeltaH(o) between two conformations of 2,4-PD measured from experiment is 4.36 kJ/mol, deltaS(o) is 2.56 J/mol K., calculated results are slightly different from experimental ones. Vibrational frequencies of 2,4-PD conformers have been studied by ab initio molecular orbital calculations using different basis set. The calculated vibrational frequencies are analyzed and compared with the experimental spectra.     

Conformational thermodynamic and kinetic parameters of methyl-substituted 1,3-butadienes

The s-trans/s-cis conformational equilibria of 10 methyl-substituted 1,3-butadienes [(E)- and (Z)-1,3-pentadiene; 2-methyl-1,3-butadiene; (E)-2-methyl-1,3-pentadiene; 2,3-dimethyl-1,3-butadiene; (E,E)-, (E,Z)-, and (Z,Z)-2,4-hexadiene; 2,5-dimethyl-2,4-hexadiene; and (E,E)-2,4-dimethyl-2,4-hexadiene] were explored by trapping high-temperature conformational equilibria by cryogenic deposition. The vapor state enthalpy differences of these s-trans/s-cis conformers, DeltaH(t equilibrium c), were determined by varying the equilibrating temperature and integrating the resulting matrix isolated IR spectra. The results obtained are in good agreement with ab initio calculations at the G3 level. From these thermodynamic parameters, methyl group nonbonded interactions in conjugated 1,3-butadienes were delineated. Rates of decay of s-cis conformers to their s-trans rotamers were obtained in the solid-state by warming up trapped high-temperature equilibrated samples formed from neat depositions. These data were analyzed in terms of dispersive kinetics with matrix site effects in the solid-state modeled by a Gaussian distribution of activation energies. The activation barriers thus obtained were compared with G3 calculations of the enthalpies of activation.     

Conformational polymorphism of methacrylamide

The industrially important compound methacrylamide crystallizes as concomitant conformational polymorphs; the monoclinic form contains only the s-cis conformer, while the orthorhombic form contains only the s-trans conformer.     

Steric effects in conjugated systems : Part V. methylvinyl ketone and methyl-β-N,N-dimethylaminovinyl ketone

Based on the earlier results on methylated butadienes and acroleins, the conformational analysis of methylvinyl ketone was performed using the Wiberg method. The effect of nonbonded interactions involving the methyl group on the molecular geometry was estimated. In agreement with experimental findings the larger amount of the s-cis than s-trans conformer in methylvinyl ketone vs. acrolein is thought to be due to steric hindrance. Contrary to the situation for other unsaturated compounds, the rotation of the methyl group in the s-trans conformer of methylvinyl ketone seems to be determined mainly by nonbonded interactions. The barrier to internal rotation of the methyl group in the s-cis compared to the s-trans conformation seems to be considerably less. The present analysis of the steric properties of methylvinyl ketone seems to indicate that the spectral arguments in favour of nonplanarity of β-N,N-dimethylaminovinyl ketone are equivocal.     

Analyse conformationnelle théorique du biaziridyle

The semi-empirical CNDO and INDO methods are applied to a theoretical conformational analysis of biaziridyl. In agreement with infrared and electron diffraction data, this molecule is found to be in its s-trans conformation. The origins of such a conformation are discussed in terms of Fourier developments. The prediction that some alterations of angles occur when going from the s-trans to the s-cis form, arises from these calculations.     

Highly Enantio- and s-trans C=C bond selective catalytic hydrogenation of cyclic enones: alternative synthesis of (-)-menthol

A highly enantioselective catalytic hydrogenation of cyclic enones was achieved by using the combination of a cationic Rh(I) complex, (S)-5,5'-bis{di(3,5-di-tert-butyl-4-methoxyphenylphosphino)}-4,4'-bi-1,3-benzodioxole (DTBM-SEGPHOS), and (CH2CH2PPh3Br)2. The presence of an s-cis C=C bond isopropylidene moiety on the cyclic enone influenced the enantioselectivity of the hydrogenation. Thus, the hydrogenation of 3-alkyl-6-isopropylidene-2-cyclohexen-1-one, which contains both s-cis and s-trans enones, proceeded in excellent enantioselectivity (up to 98 % ee). To obtain high enantio- and s-trans selectivities, the addition of a halogen source to the cationic Rh complex was the essential step. With the key step of the s-trans selective asymmetric hydrogenation of piperitenone, we demonstrated a new synthetic method for optically pure (-)-menthol via three atom-economical hydrogenations. Moreover, we found that the complete s-trans and s-cis C=C bond selective reactions were also realized by the proper choice of both the chiral ligands and halides.     

Hula-twist within the confinement of molecular crystals

E/Z-photoisomerizations within molecular crystals are varied. Existing cases are summarized. They require crystal lattices that allow for long-range molecular movements in the nontopotactic solid-state mechanism. Reactivity and directionality can be foreseen on the basis of the crystal packing. The reacting crystal changes continuously by phase rebuilding, phase transformation and disintegration. Two possibilities for the chemical mechanism exist: (1) highly space-demanding (cooperative) double-bond rotations; and (2) space-conserving hula-twist (HT) motions while the substituents move within their planes and only one C-H unit undergoes out-of-plane translocation. If internal rotation cannot be reasonably modeled within the crystal lattice, HT remains the only choice, as in the case of trans-1,2-dibenzoylethene. Direct experimental proof is still lacking because the differences in the conformational outcome could not be assessed in the studied examples. Density functional theory calculations of cis-1,2-dibenzoylethene revealed very low differences in energy content of the helical (s-cis, s-cis)- and the almost orthogonal (s-cis, s-trans)-cis-conformers. The almost orthogonal (s-cis, s-trans)-cis-conformer that is found in the pure crystal is very similar to the calculated counterpart. It is suggested that more favorable initial conformers might be obtained by proper vinylic substitution. The stereochemical outcome of highly space-demanding thermal vinylic-bond rotations followed by cyclizations of conjugated bisallenes to give bismethylene cyclobutenes excludes the alternative HT mechanism (double-bond isomerization) in the present cases. But space-conserving HT might be a mechanistic alternative in less-substituted cases under photoexcitation. The stereochemical consequences are discussed.     

Study of the rotational isomerism of 1-vinyl-1,2,4-triazoles by 1H and 13C NMR spectroscopy

Quantitative evaluations of the percentages of rotational isomers in 1-vinyl-1,2,4-triazoles were obtained. The population of the s-cis(N₍₂₎) form in 1-vinyl-1,2,4-triazole is greater by a factor of two than in the s-trans form.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 365–368, March, 1991.     

The low-temperature photochemistry of s-cis acyclic 1,3-dienes

In this article we have examined the very low-temperature photochemistry of three acyclic 1,3-dienes. We have used high-temperature deposition techniques combined with matrix isolation to create samples enriched with the thermally meta-stable s-cis form. This technique has allowed us to examine the separate photochemistry of the s-cis and s-trans conformers. Our results suggest the presence and the absence of barriers on the excited-state surface. In particular, we have found that the electrocyclic closure and s-cis-s-trans photochemical isomerization stops at 15 K for 2,3-dimethyl-1,3-butadiene-d10. The closure occurs at higher temperatures in solution but is slowed by a deuterium isotope effect. The s-trans conformer of EE-2,4-hexadiene shows almost no photoreactivity in a matrix under 254 nm irradiation, but the s-cis conformer is rapidly converted to ZE-2,4-hexadiene (ZE-HXD). The photoreactivity of ZE-HXD is similar in that there is a relatively quick conversion of the s-cis conformer under these conditions, with only a very slow conversion of the s-trans to photoproducts.     

Double ring-closing metathesis reaction of nitrogen-containing tetraenes: efficient construction of bicyclic alkaloid skeletons and synthetic application to four stereoisomers of lupinine and their derivatives

The double ring-closing metathesis reaction of nitrogen-containing tetraenes was studied. The selectivity of the fused/dumbbell-type products can be controlled by the electronic/steric effects of the substituents attached to the C[double bond]C bonds and the s-cis/s-trans conformational ratios of the substrates. This methodology has also been successfully applied to the enantioselective synthesis of four stereoisomers of lupinine and their derivatives.     

Conformational preferences of methacrolein in Diels-Alder and 1,3-dipolar cycloaddition reactions

A B3LYP/6-31G* study has been carried out for the reactions of methacrolein with cyclopentadiene, parent nitrone, 1-pyrroline-1-oxide, and (Z)-C,N-diphenylnitrone, in which the coordination of a Lewis acid (borane) and the solvent polarity (dichloromethane) have been taken into account. Calculated activation parameters, regioselectivities (for 1,3-dipolar cycloaddition reactions), and endo/exo stereoselectivities show good agreement with available experimental data. Gas-phase calculations show a varied behavior of the s-cis/s-trans TS stability for noncatalyzed reactions (from the systematic s-cis preference for the cyclopentadiene reaction to the systematic s-trans predilection encountered in the diphenylnitrone cycloaddition). BH3 coordination leads to a preferential stabilization of s-trans TSs in the reactions of cyclopentadiene (exo approach) and diphenylnitrone but a larger stabilization of s-cis structures in the processes involving the parent nitrone or 1-pyrroline-1-oxide. Additionally, a rather systematic preferential stabilization of s-trans structures is induced by solvent polarity in most reactions. As a consequence, an s-trans preference is predicted in solution for both thermal and catalyzed types of reactions in most approaches. Such a conclusion is consistent with some experimental results suggesting a preference for a particular conformation of the methacrolein-Lewis acid complexes.     

Conformational stability, optimized geometries, vibrational and electronic spectra of methacryloyl bromide in ground and excited electronic states

In order to understand conformational isomerism in methacryloyl bromide (MABR) in the ground (S(0)) and the first excited (S(1)) electronic states and to interpret the vibrational and electronic spectra of its conformers in the S(0) state, quantum mechanical calculations using Density Functional Theory (DFT) and RHF methods with extended basis sets 6-31G, 6-31G** and 6-311+G(d,p) have been conducted. In RHF calculations, electron correlation effects have been included at the M?ller-Plesset MP2 level. It is inferred that in both the electronic states the molecule may exist in two isomeric forms-s-trans and s-cis; the former being more stable than the later by about 1.629 kcal mol(-1) in the S(0) state and by about 2.218 kcal mol(-1) in the S(1) state. Electronic transition tends to increase the s-trans/s-cis and s-cis/s-trans, rotational barriers from 7.059 kcal mol(-1) (2468.1 cm(-1)) and 5.428 kcal mol(-1) (1897.8 cm(-1)) in S(0) state to 23.594 kcal mol(-1) (8249.4 cm(-1)) and 21.376 kcal mol(-1) (7473.9 cm(-1)) in the S(1) state. Completely optimized geometries of the two conformers in S(0) state reveal that while there is no significant difference in their bond lengths, some of the bond angles associated with COBr group are appreciably different. Electronic excitation tends to change both the bond lengths and bond angles. Based on suitably scaled DFT and RHF results obtained from the use of 6-31G** and 6-311+G(d,p) basis sets, a complete assignment is provided to the fundamental vibrational bands of both the s-trans and s-cis conformers in terms of frequency, form and intensity of vibrations and potential distribution across the symmetry coordinates in the S(0) state and a comparison has been made with experimental assignments. A theoretical prediction of the electronic transitions in the near UV-region in the two conformers and their tentative assignment has been provided on the basis of CI level calculations using 6-31G basis set.     

Conformational behaviour, hydrogen bond competition and intramolecular dynamics in vanillin derivatives: acetovanillone and 6-hydroxy-3-methoxyacetophenone

The conformational landscape of the structural isomers acetovanillone (apocynin, AV) and 6-hydroxy-3-methoxyacetophenone (HMAP) has been investigated in a supersonic jet using Fourier transform microwave spectroscopy. Two conformers have been detected in the jet-cooled expansion for each molecule (s-cis and s-trans in AV; s-trans and a-trans for HMAP), differing in the relative orientation of the acetyl and methoxy groups. Both molecules are stabilized by O-H···O or O-H···O=C hydroxyl intramolecular hydrogen bonds, either constraining the local conformations of the methoxy group in AV, or that of the acetyl group in HMAP. Internal rotation splittings have been observed in both conformers of each molecule, originated by the acetyl group, that yield information on the influence of the intramolecular hydrogen bonds on the methyl torsion. The similar internal rotation barriers in both molecules (6.6 and 7.4 kJ mol(-1) in AV; 7.3 and 7.0 kJ mol(-1) in HMAP) suggest that the acetyl torsion is only slightly affected by intramolecular hydrogen bonding. The absence of torsional tunnellings due to the methoxy group indicates torsional barriers above 10.2 and 8.9 kJ mol(-1) for AV conformers, 10.1 and 10.4 kJ mol(-1) for HMAP. Conformational ratios and relative free energies have been estimated from relative intensity measurements of the spectral lines. Ab initio (MP2) and density functional calculations using the recent M05-2X empirical functional have been used to aid the experimental work in describing the structures, internal rotation barriers and isomerization potentials.     

Concerning the “novel intramolecular hydrogen bond to a trans-syn,s-cis formazan system”: solution isomers of 3-carboxymethylthio- and 3-methoxy-carbonyl-1,5-diphenylformazan

Spectroscopic studies of the [1,5-¹⁵N₂]-labelled title compounds demonstrate the presence of the yellow trans-anti,s-trans ($\text{1}$) and the red trans-syn,s-cis ($\text{2}$) isomers in solution. There is no experimental evidence supporting the postulated novel hydrogen bridge $\text{5}$.     

Aspirin. An ab initio quantum-mechanical study of conformational preferences and of neighboring group interactions.

The potential energy surface of acetylsalicylic acid, aspirin, has been explored at the RHF/6-31G* and B3LYP/6-31G* levels, and single-point calculations were performed at levels up to B3LYP/6-311G**//B3LYP/6-31G*. All conformational isomers have been located, the thermochemical functions have been computed, and relative energies and free enthalpies were determined. The conformational space of aspirin is spanned by three internal coordinates, and these are the carboxylic acid C-O conformation (s-trans preferred by about 7 kcal/mol), the C-COOH conformation (Z preferred unless there are H-bonding opportunities), and the ester C-O conformation (s-trans preferred by about 4 kcal/mol). There are nine aspirin isomers since one of the conformers realizes hydrogen-bonding structure isomerism as well. Neighboring group interactions are discussed with reference to the intrinsic properties of benzoic acid and phenyl acetate. The intrinsic conformational preference energies for benzoic acid and phenyl acetate are not additive. The acid s-trans preference energies differ by as much as 9 kcal/mol depending on the Ph-COOH and ester conformations. Similarly, the E-preference energies about the Ph-COOH bond vary by as much as 6 kcal/mol depending on the ester conformation. The structural discussion suggests an overall ortho repulsion between the functional groups in all aspirin isomers including the intramolecularly hydrogen-bonded isomers. The isodesmic reaction between the most stable conformers of benzoic acid and phenyl acetate to form aspirin and benzene is found to be endothermic by 2.7 kcal/mol and provides compelling evidence for and a quantitative measure of ortho repulsion. The ortho repulsion of 2.7 kcal/mol is a lower limit, and the ortho repulsion can increase to as much as 6 kcal/mol in some aspirin isomers.     

A systematic study of the hydride reduction of cyclopropyl ketones with structurally simplified substrates. highly stereoselective reductions of trans-substituted cyclopropyl ketones via the bisected s-cis conformation

The stereoselective hydride reduction of the cis- and trans-substituted cyclopropyl ketones was systematically investigated using a series of structurally simplified substrates, trans-[tert-butyldiphenylsilyloxymethyl]cyclopropyl ketones 1a-e and trans-(benzyloxymethyl)cyclopropyl methyl ketone (2), and the corresponding cis congeners 3a,b,e and 4. The results showed that, not only in the reduction of the cis-substituted cyclopropyl ketones but also in that of the trans-substituted ketones, high stereoselectivity can be realized when the substrate has a bulky substituent on the cyclopropane ring, even though it is attached to the position trans to the acyl moiety. Ab initio calculations based on the density functional theory (DFT) of cyclopropyl ketones showed that (1) the bisected s-cis and s-trans conformers were the only two minimum energy conformers, while the s-cis conformer was more stable than the s-trans and (2) a bulky alkyl group in the acyl moiety and a cis substituent on the cyclopropane ring made the bisected s-cis conformer much more stable. On the basis of these calculations and experimental results, it is likely that the more stable the bisected s-cis conformer of the substrate, the more stereoselective the hydride reduction. Thus, the stereochemistry can be explained by hydride attack on the bisected s-cis conformation of the substrate from the less-hindered face. The predictability of the stereochemical results is predicated on the bisected s-cis transition-state model, which is very important from the viewpoint of synthetic organic chemistry.     

Development of Molecular Mechanics Torsion Parameters for alpha,beta-Cyclopropyl Ketones and Conformational Analysis of Bicyclo[m.1.0]alkan-2-ones

Conformations of cyclopropyl methyl ketone have been studied using ab initio methods in an effort to quantify the effects of conjugative overlap between the cyclopropane ring and an adjacent ketone carbonyl. Results were comparable with previous experimental and theoretical studies. Cyclopropyl methyl ketone exhibits a global energy minimum in the s-cis conformer and a local energy minimum near the s-trans conformer. The potential energy curve obtained was used to derive torsion parameters which were employed in molecular mechanics studies of the conformations of the set of bicyclo[m.1.0]alkan-2-ones having larger ring sizes from five- to 16-membered. Similar conformations for the cyclopropyl ketone substructure are observed for all the medium and large ring systems examined. Possible synthetic ramifications of local conformational anchoring by this functional group array are discussed.     

On the valence excited states of conjugated dienes

Electron impact spectroscopic results are reported for the lowest-energy A_g and B_u valence excited states of several conjugated dienes. In all cases, the B_u state was found to lie below the A_g state. The B_u state of the s-cis compounds was found to be ≈ 0.5 eV lower in energy than that of the s-trans compounds. Correlations of these results with those obtained for several s-trans and s-cis polyenes leads to a new possible interpretation of the state observed below the B_u state in intermediate length polynes.     

Synthesis of unsymmetrical substituted 1,4-dihydropyridines through thermal and microwave assisted [4+2] cycloadditions of 1-azadienes and allenic esters

Thermal and microwave assisted [4+2] cycloadditions of 1,4-diaryl-1-aza-1,3-butadienes with allenic esters lead to cycloadducts, which after a 1,3-H shift afford variedly substituted unsymmetrical 2-alkyl-1,4-diaryl-3-ethoxycarbonyl-1,4-dihydropyridines in high yields. Reactions carried out under microwave irradiation are cleaner and give higher yields with much shortened reaction times. Density functional theory (DFT) at the B3LYP/6-31G* level has been used to calculate geometric features of the reactants, barrier for s-trans to s-cis and reverse isomerization of azadienes (5a-d, 10a-e), dihedral angles between N(1), C(2), C(3), and C(4) atoms of azadienes along with various indices such as chemical hardness (eta), chemical potential (micro), global electrophilicity (omega), and the difference in global electrophilicity (Deltaomega) between the reacting pairs and Fukui functions (f (+) and f(-)). The results revealed that s-trans is the predominant conformation of azadienes at ambient temperature and the barrier for conversion of the s-trans rotamer of 1-azadienes to s-cis may be the major factor influencing the chemoselectivity, i.e., [4+2] verses [2+2] cycloaddition. The regiochemistry of the observed cycloadditions is collated with the obtained local electrophilicity indices (Fukui functions). Transition states for the formation of both [4+2] and [2+2] cycloadducts as located at the PM3 level indicate that the transition state for the formation of [4+2] cycloadducts has lower energy, again supporting the earlier conclusion that preferred formation of [4+2] cycloaaducts at higher temperature may be a consequence of barrier for s-trans to s-cis transformation of 1-azadienes.