Scopine Isolated in the Gas Phase

The rotational spectrum of the tropane alkaloid scopine is detected by Fourier transform microwave spectroscopy in a pulsed supersonic jet. A nonconventional method for bringing the molecules intact into the gas phase is used in which scopine syrup is mixed with glycine powder and the solid mixture is vaporized with an ultrafast UV laser beam. Laser vaporization prevents the easy isomerization to scopoline previously observed with conventional heating methods. A single conformer is unambiguously observed in the supersonic jet and corresponds to the energetically most stable species according to quantum chemical calculations. Rotational and centrifugal distortion constants are accurately determined. The spectrum shows fine and hyperfine structure due to the hindered rotation of the methyl group and the presence of a quadrupolar nucleus (¹⁴N), respectively. This additional information allows the angle of N‐methyl inversion between the N?CH₃ bond and the bicyclic C‐N‐C plane to be determined (131.8–137.8°), as well as the internal rotation barrier of the methyl group (6.235(1) kJ mol^?1).     

The photoinduced isomerization and its implication in the photo-dynamical processes in two simple Schiff bases isolated in solid argon

Two Schiff bases: 2-(1-(methylimino)methyl)-phenol (SMA) and its chlorosubstituted derivative 2-(1-(methylimino)methyl)-6-chlorophenol (SMAC), and SMA complexes with water were studied by infrared matrix isolation spectroscopy and DFT/B3LYP/6-311G++(2d,2p) quantum chemical calculations. SMA and SMAC bases trapped in an argon matrix from the vapor above the liquid and solid samples have the most stable enol conformation with intramolecular O-H···N bonding. Irradiation (λ > 320 nm) leads in both bases to a rotational isomerization reaction in which the scission of the O-H···N bond occurs and the C(H)NCH(3) and OH groups are turned by 180° around the C-C and C-O bonds, respectively. In SMAC a competitive photoreaction channel yields the trans-keto tautomer. The identification of the two SMAC photoproducts evidences that in the excited enol form of this compound two processes compete with each other: the rotational isomerization and intramolecular proton transfer (ESIPT). In the argon matrices doped with SMA and H(2)O the SMA-water complexes were identified and characterized spectroscopically. Interaction of SMA with one or two water molecules does not affect the photochemistry of SMA.     

Reversible Single Molecular Switch Operating at 300 K on a Surface

A single 4‐pyridylazobenzene molecule is observed at room temperature on a Si(111)‐B surface by using scanning tunnel microscopy. The reversible conformational switching of this molecule is induced by tunneling electrons and observed at room temperature. This process is based on an intramolecular rotation of a single phenyl group without isomerization of the N?N double bond.     

Discriminating the structure of exo-2-aminonorbornane using nuclear quadrupole coupling interactions

The intrinsic conformational and structural properties of the bicycle exo-2-aminonorbornane have been probed in a supersonic jet expansion using Fourier-transform microwave (FT-MW) spectroscopy and quantum chemical calculations. The rotational spectrum revealed two different conformers arising from the internal rotation of the amino group, exhibiting small (MHz) hyperfine patterns originated by the (14)N nuclear quadrupole coupling interaction. Complementary ab initio (MP2) and DFT (B3LYP and M05-2X) calculations provided comparative predictions for the structural properties, rotational and centrifugal distortion data, hyperfine parameters, and isomerization barriers. Due to the similarity of the rotational constants, the structural assignment of the observed rotamers and the calculation of the torsion angles of the amino group were based on the conformational dependence of the (14)N nuclear quadrupole coupling hyperfine tensor. In the most stable conformation (ss), the two amino N-H bonds are staggered with respect to the adjacent C-H bond. In the second conformer (st), only one of the N-H bonds is staggered and the other is trans. A third predicted conformer (ts) was not detected, consistent with a predicted conformational relaxation to conformer ss through a low barrier of 5.2 kJ mol(-1).     

Photoinduced oxygen transfer and double-linkage isomerism in a cis-(NO)(NO2) transition-metal complex by photocrystallography, FT-IR spectroscopy and DFT calculations

Photocrystallographic experiments show that laser exposure of crystals of [Ru(bpy)2(NO)(NO2)](PF6)2 at 90 K produces a double isonitrosyl-nitrito linkage isomer and provide the detailed geometry of the metastable species generated. The analysis indicates that the isomerization is accomplished through an intramolecular redox reaction involving oxygen transfer from the nitro to the nitrosyl group. At 200 K only a single (nitrito) linkage isomer is formed with a U-shaped conformation of the nitrito group rather than the Z conformation observed at 90 K. A mechanism for the isomerization is proposed based on the crystallographic results and FTIR data collected at low temperatures during the isomerization process. The study presents the first structural evidence for double linkage isomerization in transition-metal complexes.     

Conformational preferences of non-prolyl and prolyl residues

The conformational study on Ac-Ala-NHMe (the alanine dipeptide) and Ac-Pro-NHMe (the proline dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in the backbone conformational preference and the cis-trans isomerization for the non-prolyl and prolyl residues in the gas phase and in the solutions (chloroform and water). For the alanine and proline dipeptides, with the increase of solvent polarity, the populations of the conformation tC with an intramolecular C(7) hydrogen bond significantly decrease, and those of the polyproline II-like conformation tF and the alpha-helical conformation tA increase, which is in good agreement with the results from circular dichroism and NMR experiments. For both the dipeptides, as the solvent polarity increases, the relative free energy of the cis conformer to the trans conformer decreases and the rotational barrier to the cis-trans isomerization increases. It is found that the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about the non-prolyl and prolyl peptide bonds in both the gas phase and the solutions. The pertinent distance d(N...H-N(NHMe)) can successfully describe the increase in the rotational barriers for the non-prolyl and prolyl trans-cis isomerization as the solvent polarity increases and the higher barriers for the non-prolyl residue than for the prolyl residue, as seen in experimental and calculated results. By analysis of the contributions to rotational barriers, the cis-trans isomerization for the non-prolyl and prolyl peptide bonds is proven to be entirely enthalpy driven in the gas phase and in the solutions. The calculated cis populations and rotational barriers to the cis-trans isomerization for both the dipeptides in chloroform and/or water accord with the experimental values.     

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.     

Geometry‐Retentive C‐Alkenylation of Lithiated α‐Aminonitriles: Quaternary α‐Alkenyl Amino Acids and Hydantoins

α‐Amino nitriles tethered to alkenes through a urea linkage undergo intramolecular C‐alkenylation on treatment with base by attack of the lithionitrile derivatives on the N′‐alkenyl group. A geometry‐retentive alkene shift affords stereospecifically the E or Z isomer of the 5‐alkenyl‐4‐iminohydantoin products from the corresponding starting E ‐ or Z ‐N ′‐alkenyl urea, each of which may be formed from the same N ‐allyl precursor by stereodivergent alkene isomerization. The reaction, formally a nucleophilic substitution at an sp² carbon atom, allows the direct regioselective incorporation of mono‐, di‐, tri‐, and tetrasubstituted olefins at the α‐carbon of amino acid derivatives. The initially formed 5‐alkenyl iminohydantoins may be hydrolyzed and oxidatively deprotected to yield hydantoins and unsaturated α‐quaternary amino acids.     

Deuteron N.M.R. relaxation studies of phospholipid membranes

Bilayers of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), specifically deuteriated at various positions of the sn-2-chain, have been studied by N.M.R. relaxation methods. Analysis of the experiments, employing a density matrix treatment based on the stochastic Liouville equation, provides new information about the dynamic organization of the different membrane phases (liquid-crystalline, intermediate and gel phases). The complex molecular dynamics are characterized by a super-position of inter- and intramolecular motions, comprising overall reorientation of phospholipid molecules and trans-gauche isomerization of individual chain segments. In addition, there is evidence for two-site rotational jumps of the sn-2-chains in the plane of the membrane. The results clearly demonstrate the particular advantage of N.M.R. relaxation studies in characterizing complex chemical and biological systems.     

Photophysics and Rotational Dynamics of a Hydrophilic Molecule in a Room Temperature Ionic Liquid

We have studied the photophysics and rotational diffusion of hydrophilic solute 7‐(N, N′‐diethylamino)coumarin‐3‐carboxylic acid (7‐DCCA) in a room temperature ionic liquid methyltrioctylammonium bis(trifluoromethylsulfonyl) imide ([N₁₈₈₈][NTf₂]). Comparison of activation energies of viscous flow and nonradiative decay shows that the photophysical properties of 7‐DCCA are not guided by the bulk viscosity of the medium but are dependent on the specific solute solvent interaction and structural heterogeneity of the medium. The rotational relaxation behaviour of 7‐DCCA in [N₁₈₈₈][NTf₂] shows significant deviation from the Stokes Einstein Debye hydrodynamic model of rotational diffusion. This is indicative of the influence of specific solute solvent interaction on the rotational relaxation behaviour of 7‐DCCA. Comparison of activation energy of rotational relaxation with activation energy of viscous flow clearly reinforces our assumption that the structural heterogeneity of the medium and specific solute solvent interaction plays a dominant role on the rotational diffusion instead of bulk viscosity.     

Theoretical Study of Ammonolysis of Monobactams: Kinetic Role of the N‐Sulfonate Group

The ammonolysis reaction of 3‐(formylamino)‐4‐methyl‐2‐oxoazetidine‐1‐sulfonate is investigated by quantum‐chemical methods (B3LYP/6‐31+G*) as a model system of the aminolysis reaction of monobactam antibiotics involved in the allergic reaction to these drugs. The influence of the N‐sulfonate group on the β‐lactam ring, reaction intermediates, and transition states is characterized in terms of the geometries and relative energies of the corresponding critical structures located on the B3LYP/6‐31+G* potential‐energy surface. It is shown that the N‐sulfonate group, which has only a moderate impact on the structure and charge distribution of the β‐lactam ring, reduces the rate‐determining ΔG barrier by ca. 20 kcal/mol with respect to a purely uncatalyzed ammonolysis of the unsubstituted system, azetidin‐2‐one. This intramolecular catalytic effect occurs through a −NH−SO↔[−N−SO₃H]⁻ isomerization process, which is involved in the proton relay from the attacking ammonia molecule to the β‐lactam N‐atom. Our theoretical results predict that, in aqueous solution, monobactams will show an intrinsic reactivity against amine nucleophiles more important than that of penicillins.     

The rate enhancement for prolyl cis-to-trans isomerization of cyclic CPFC peptide is caused by an increase in the vibrational entropy of the transition state

The conformational preferences and prolyl cis-trans isomerization of oxidized and reduced Ac-Cys-Pro-Phe-Cys-NH2 (CPFC peptides) have been carried out using the ab initio HF/6-31+G(d) and hybrid density functional B3LYP/6-311++G(d,p) levels of theory. The most preferred conformations of oxidized and reduced CPFC peptides with the trans prolyl peptide bond have a type-I beta-turn for the Pro-Phe sequence in common. In particular, the transition states for both forms are stabilized by the intramolecular hydrogen bonds between the prolyl nitrogen and the N-H group of the Phe3 residue. The rotational barrier DeltaGct to the cis-to-trans isomerization for the oxidized CPFC peptide is calculated to be 19.37 kcal/mol at the B3LYP/6-311++G(d,p)//HF/6-31+G(d) level of theory, which is lower by 0.88 kcal/mol than that of the reduced CPFC peptide. This may indicate that the rate constant kc-->t of the prolyl cis-to-trans isomerization for the oxidized form is about 4 times larger than that of the reduced form, which is reasonably consistent with the value deduced from NMR experiments. In particular, the increase in vibrational entropy for the transition state of the oxidized form over that of the reduced form contributes to enhance the rate constant for the prolyl cis-to-trans isomerization of the oxidized form.     

The shape of beta-alanine

The combination of Fourier transform microwave spectroscopy in a pulsed supersonic jet with laser ablation has made beta-alanine amenable to a structural study in the gas phase. Two new conformers of beta-alanine have been identified together with the two previously observed by McGlone and Godfrey [J. Am. Chem. Soc. 1995, 117, 1043]. The comparison between the experimental rotational and 14N nuclear quadrupole coupling constants and those calculated ab initio provide a definitive test for molecular structures and confirm unambiguously the identification of all conformers. For the two most abundant conformers, an intramolecular hydrogen bond between the amino group and carbonyl oxygen (N-H...O=C) is established, and the COOH adopts a cis-COOH configuration. The next conformer in order of abundance presents an O-H...N intramolecular hydrogen bond with a trans configuration for the COOH group. The high sensitivity of the experiment has allowed us to detect for the first time a conformer uniquely stabilized by an n-pi* hyperconjugative interaction between the nucleophile N: of the amino group and the pi* orbital at the carbonyl group. Partial conformational relaxation has been observed in the supersonic expansion.     

Fluorine Substitution Effects on Flexibility and Tunneling Pathways: The Rotational Spectrum of 2‐Fluorobenzylamine

The effect of ring fluorination on the structural and dynamical properties of the flexible model molecule 2‐fluorobenzylamine has been studied by rotational spectroscopy in free‐jet expansion and quantum chemical methods. The complete potential energy surface originating from the flexibility of the aminic side chain has been calculated at the B3LYP/6‐311++G** level of theory and the stable geometries were also characterized with MP2/6‐311++G**. The rotational spectra show the presence of two of the predicted four stable conformers: the global minimum (I), in which the side chain’s dihedral angle with the phenyl plane is almost perpendicular, is stabilized by an intramolecular hydrogen bond between the fluorine atom and one hydrogen of the aminic group; and a second conformer II (E_II?E_I≈5 kJ mol^?1) in which the dihedral angle is smaller and the amino group points towards the aromatic ortho hydrogen atom. This conformation is characterized by a tunneling motion between two equivalent positions of the amino group with respect to the phenyl plane, which splits the rotational transition. The ortho fluorination increases, with respect to benzylamine, the tunneling splitting of this motion by four orders of magnitude. The motion is analyzed with a one‐dimensional flexible model, which allows estimation of the energy barrier for the transition state as approximately 8.0 kJ mol^?1.     

A Computational Kinetics Study on the Intramolecular Hydrogen Shift Reactions of Alkylperoxy Radicals in 2‐Methyltetrahydrofuran Oxidation

2‐Methyltetrahydrofuran (2‐MTHF) is one of the potential fuel components based on its combustion behavior, engine efficiency, and emission performance as proposed by the Cluster of Excellence “Tailor Made Fuels from Biomass (TMFB)” at RWTH Aachen University, Germany. Reaction kinetics of intramolecular hydrogen shift (ROO to QOOH) reactions in 2‐MTHF is theoretically investigated in this work. High‐pressure limit rate constants (500–2000 K) are determined from the transition state theory by employing the CBS‐QB3 composite method. Carbon sites neighboring a ring oxygen atom are favorable abstraction sites in 2‐MTHF due to its weak C─H bond strengths. The size of the transition state ring (six‐ and five‐membered) also plays an important role in the isomerization reaction kinetics. Further, effects of ring oxygen and methyl group position in 2‐MTHF are investigated. At 500 K, total rate constants for the isomerization reactions in ROO2 and ROO5t are 51 and 67 times faster in 2‐MTHF than in methylcyclopentane.     

Anti and gauche conformers of an inorganic butane analogue, NH3BH2NH2BH3

The crystal structures of an inorganic butane analogue, NH(3)BH(2)NH(2)BH(3) (DDAB), were determined using single crystal X-ray diffraction, revealing both anti and gauche conformations. The anti conformation is stabilized by intermolecular dihydrogen bonds in the crystal whereas two gauche conformations of DDAB observed in its 18-crown-6 adducts are stabilized by an intramolecular dihydrogen bond. The two gauche conformations show rotational isomerization but whether they are a pair of enantiomers is yet to be defined.     

2,3,7‐Triazabicyclo[3.3.0]octenes Prepared by Tandem Cascade Reaction of Allyl Azides and Olefinic Dipolarophiles

Tandem cascade reactions of allylazides and olefinic dipolarophiles to give cis‐fused 2,3,7‐triazabicyclo [3.3.0]octenes ( 5, 6 or 7 ) are reported. Therein, an intermolecular dipolar cycloaddition of azide and alkene gave a triazoline which was followed by isomerization of the triazoline to a diazoester ( 4 ) and then an intramolecular dipolar cycloaddition from the diazo functional group and the double bond in 4 to give 5 . Compound 5 may further more undergo a Michael addition to give 7‐substituted‐ 2,3,7‐ triazabicyclo [3.3.0]oct‐2‐ene ( 6 ) or a tautomerization to give 2,3,7‐triazabicyclo[3.3.0]oct‐3‐ene ( 7 ). The reaction may be manipulated to stop at a particular stage by adopting a suit able solvent or an appropriate temperature.     

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.     

Theoretical Study of the Intramolecular Proton Transfer in the Tautomers of Cytosine Assisted by Water

Ab initio MP2 and DFT studies on the tautomers of cytosine and the related hydrated tautomers have been carried out. The ground‐state structures of four tautomers of cytosine and related transition states were fully optimized. The vibrational frequency analysis was performed on all the optimized structures. Detailed intrinsic reaction coordinate (IRC) calculations were carried out to guarantee the optimized transition‐state structures being connected to the related tautomers. We obtained the relative stability order for the tautomers of cytosine and the related hydrated tautomers. In the isolated and hydrated condition, the bond types of C(2) O(7) and C(4) N(8) greatly affect the stability of the cytosine tautomers. Moreover, we have explored the influence of the water molecules on the intramolecular proton transfer between the keto and enol forms of the cytosine tautomers. The first water molecule obviously decreases the isomerization activation energy for the monohydrated cytosine tautomers. It is shown that the isomerization energy barrier changes only a little when the second and third water molecules are added in the reaction loop. The solvent effects have an obvious influence on the proton‐transfer barrier of the isolated cytosine. However, the solvent effects seem to be insignificant for the isomerization energy barriers of the monohydrated, dihydrated and trihydrated cytosine. The water molecule in these complexes can be looked on as the explicit water. Therefore, the explicit water model may be more credible to explore the intramolecular proton transfer, in comparison with the PCM which is the implicit water model.