Equatorial Chair Research Articles

Reversible Self-Assembly of an N-Heterocyclic Carbene on Metal Surfaces.

Self-assembly of cyclohexyl cyclic (alkyl)(amino)carbenes (cyCAAC) can be realized and reversibly switched from a close-packed trimer phase to a chainlike dimer phase, enabled by the ring-flip of the cyclohexyl wingtip. Multiple methods including scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT) calculations identified a distinct isomer (axial or equatorial chair conformer) in each phase, and consequently support the conclusion regarding the determination of molecular surface geometry on the self-assembly of cyCAAC. Moreover, various substrates such as Ag (111) and Cu (111) are tested to elucidate the importance of cyCAAC-surface interactions on cyCAAC based nanopatterns. These investigations of patterned surfaces prompted a deep understanding of cyCAAC binding mode, surface geometry and reversible self-assembly, which are of paramount significance in the areas of catalysis, biosensor design and surface functionalization.

Reversible Selbstorganisation eines N‐heterocyclischen Carbens auf Metalloberflächen

AbstractCyclohexyl(alkyl)(amino)carbene (cyCAAC) bilden selbstorganisierende Monolagen, die durch den Ring‐Flip der Cyclohexyl‐Seitengruppe reversibel von einer dicht gepackten Trimer‐Phase in eine kettenartige Dimer‐Phase umgeschaltet werden können. Mehrere Methoden, darunter Rastertunnelmikroskopie (STM), Röntgen‐Photoelektronenspektroskopie (XPS) und Dichtefunktionaltheorie (DFT)‐Berechnungen, identifizierten ein eindeutiges Isomer (axiales oder äquatoriales Sesselkonformer) in jeder Phase und stützen somit die Schlussfolgerung hinsichtlich des Einflusses der molekularen Oberflächengeometrie auf die Selbstorganisation von cyCAAC. Darüber hinaus wurden verschiedene Substrate wie Ag(111) und Cu(111) getestet, um die Bedeutung der Wechselwirkungen zwischen cyCAAC und der Oberfläche für die auf cyCAAC basierenden Nanomuster aufzuklären. Die Untersuchungen von gemusterten Oberflächen führten zu einem tieferen Verständnis der cyCAAC‐Bindungsweise, der Oberflächengeometrie und der reversiblen Selbstorganisation, die in den Bereichen Katalyse, Biosensor‐Design und Oberflächenfunktionalisierung von herausragender Bedeutung sind.

Conformational Analysis of 5-Methyl-1,3-oxathiane

Computer simulation of conformational transformations of 5-methyl-1,3-oxathiane at the DFT PBE/3ζ, RI-MP2/λ2, and HF/6-31++G(d,p) levels of theory has shown that the interconversion between the equatorial (global minimum) and axial chair conformers occurs along several independent pathways through five flexible forms. Nine transition states corresponding to different half-chair forms, as well as symmetrical and unsymmetrical boat conformers, have been localized on the potential energy surface. The free conformational energy of the methyl group has been estimated at 0.9–1.0 kcal/mol by comparison of the calculated and experimental vicinal coupling constants in the 1H NMR spectra.

Vibrational Sum-Frequency Generation Study of Morpholine at Air–Liquid and Air–Solution Interfaces

The structure and orientation of interfacial morpholine molecules have been investigated, using vibrational sum-frequency generation (VSFG) spectroscopy—a nonlinear surface specific technique. The VSFG spectra with SSP and PPP polarizations have been measured in the CH (2800–3000 cm–1) and the OH (3000–3750 cm–1) stretch regions at the air–morpholine and air–solution interfaces. The vibrational frequencies in the CH stretch region could be observed in VSFG spectra, implying presence of morpholine molecules at the interfaces with net polar orientation. The intensities of the CH stretch bands get enhanced at the air–solution interface of morpholine solution in millimolar concentration, in comparison to that at the air–morpholine interface which is attributed to increase in polar orientation of interfacial morpholine molecules induced by water molecules. In pure morpholine, the most predominant conformation of molecules is equatorial chair, both in the bulk and at the air–morpholine interface. But in aqueous solution of morpholine, the contribution from axial chair conformer is known to increase. This effect, and also a probable change from the chair to the boat/twist boat conformation at the air–solution interface, may contribute to the enhanced intensity of VSFG peaks of CH stretch bands in solution. The VSFG intensities of the OH stretching frequencies of interfacial water molecules are also enhanced in the presence of morpholine, suggesting an increase in net polar orientation of water molecules induced by morpholine molecules. The VSFG spectra were also measured in the presence of 300 mM HCl, which showed indications of protonation of the interfacial morpholine molecules. Addition of HCl to aqueous solution of morpholine alters the orientation of interfacial water molecules significantly, and the enhanced VSFG intensities in the OH region induced by morpholine molecules are almost completely obliterated. The result suggests that orientation of interfacial water molecules in the presence of HCl gets random. However, the effects of HCl in the CH region of the VSFG spectra differ for different stretching bands. In presence of readily ionizable HCl molecules, a large number of ions are generated, which are probably responsible for changing the surface orientation of both water and morpholine molecules.

Conformational analysis of morpholine studied using Raman spectroscopy and density functional theoretical calculations

Morpholine is a very interesting cyclic compound which is an ether as well as a secondary amine. The relative distribution of different conformations of morpholine depends on the medium. Using Raman spectroscopy and theoretical calculations, we found that, equatorial chair conformer is predominant in the pure liquid, but in aqueous solution, contribution from the axial conformer increases. The surface-enhanced Raman scattering (SERS) studies in presence of silver nanoparticles showed change in relative intensities of different vibrational modes of morpholine. It was found that the axial chair conformer is preferentially adsorbed vertically through the NAg bond on the nanoparticle surface.

Conformational analysis of 3-methyltetrahydro-1,3-oxazine

Conformational analysis of 3-methyltetrahydro-1,3-oxazine has been performed using HF/6-31G(d), PBE/3z, and RI-MP2/λ2 simulation approximations. The potential energy surface contains eight minima. Interconversion of the axial and equatorial chair conformers (main minima) occurs via several independent pathways involving six twist forms. The preferred path presumes direct chair-chair transition via pyramidal inversion of the nitrogen atom.

How Sugars Pucker: Electronic Structure Calculations Map the Kinetic Landscape of Five Biologically Paramount Monosaccharides and Their Implications for Enzymatic Catalysis

Glycoside hydrolases (GHs) distort carbohydrate ring geometry along particular "catalytic itineraries" during the cleavage of glycosidic bonds, illustrating the relationship between substrate conformation and reactivity. Previous theoretical studies of thermodynamics of isolated monosaccharides offer insights into the catalytic itineraries of particular sugars. However, kinetic accessibility of carbohydrate puckering conformations and the role of exocyclic groups have not yet been thoroughly addressed. Here we present the first complete library of low-energy local minima and puckering interconversion transition states for five biologically relevant pyranose sugars: β-xylose, β-mannose, α-glucose, β-glucose, and β-N-acetylglucosamine. These were obtained by a thorough theoretical investigation each of the 38 IUPAC designated puckering geometries and all possible conformations of the exocyclic groups. These calculations demonstrate that exocyclic groups must be explicitly considered when examining these interconversion pathways. Furthermore, these data enable evaluation of previous hypotheses of why enzymes perturb ring geometries from the low-energy equatorial chair ((4)C1) conformation. They show that the relative thermodynamics alone do not universally correlate with GH catalytic itineraries. For some sugars, particular puckers offer both catalytically favorable electronic structure properties, such as anomeric carbon partial charge, and low kinetic barriers to achieve a given puckering conformation. However, different factors correlate with catalytic itineraries for other sugars; for β-N-acetylglucosamine, the key N-acetyl arm confounds the puckering landscape and appears to be the crucial factor. Overall, this study reveals a more comprehensive understanding of why particular puckering geometries are favored in carbohydrate catalysis concomitant with the complexity of glycobiology.

Conformational analysis of 2,2-dimethyl-5-alkyl-1,3-dioxa-2-silacyclohexanes

Study of conformational isomerization of 2,2-dimethyl-5-alkyl-1,3-dioxa-2-silacyclohexanes using quantum-chemical HF/6-31G(d) and PBE/3z approximations showed that its route involves an equilibrium between the chair conformers with different orientation of substituent at C5 ring atom and proceeds through a transition state corresponding to the 2,5-twist conformation. Molecular dynamics method showed that at room temperature this conformation transforms into the equatorial or axial chair conformers through 1,4-twist or sofa forms. Based on the experimental and theoretical values of vicinal 1H NMR coupling constants we determined quantitative conformational composition of the molecules of these compounds and the values of ΔG0 of the conformational equilibrium.

Conformational analysis of 5-methyl- and 2,2,5-trimethyl-1,3-dithianes

Conformational isomerization of 5-methyl- and 2,2,5-trimethyl-1,3-dithianes was studied using quantum-chemical HF/6-31G(d), HF/pVDZ, and PBE/3z approximations. The potential energy surface of molecules of both compounds is shown to contain the main minimum corresponding to the equatorial chair conformer C-5e. The calculated potential barriers of the conformational isomerization were found. Based on the experimental (1H NMR) and theoretical vicinal coupling constants the ΔG 0 values were determined of the methyl group at the ring C5 atom. The reasons for the distinctions between the values of this parameter from the ΔG 0, obtained by energy minimizations of the equatorial and axial chair conformers are discussed.

Ab Initio conformational analysis of tetrahydro-1,3-oxazine

Nonempirical RHF/STO-3G and 6-31G(d) studies on conformational behavior of tetrahydro-1,3- oxazine showed that interconversion between the axial (global minimum) and equatorial chair conformers can follow five independent pathways. The potential energy surface contains seven minima corresponding to chair and twist conformers, as well as seven transition states having sofa, half-chair, and symmetrical and unsym- metrical boat conformations. Additional potential barriers to interconversion, resulting from pyramidal inversion of the nitrogen atom, were also revealed.

The conformer resolved ultraviolet photodissociation of morpholine

Distinct sets of resolved photoproducts arising from the photodissociation of two neutral molecule conformers have been observed using H(Rydberg) atom photofragment translational spectroscopy methods. This study focuses on the photodissociation of morpholine, at many wavelengths between 250 nm and 193 nm. Morpholine, a six-membered saturated heterocycle with the molecular formula HN(CH2CH2)2O, exists as two ground state chair conformers that are distinguished by the orientation of the N–H bond (axial or equatorial) relative to the chair ring. Complementary MP2, QCISD and DFT calculations all predict the equatorial chair conformer to be lower in energy by ∼250 cm−1. CASPT2(8/8) calculations confirm that both conformers have similar electronic structures, and share a common first excited singlet state, arising as a result of electron promotion from the nitrogen lone pair orbital (n) to the 3s/σ* orbital centred on the N–H bond, forming a 1nσ* state. Photoexcitation to the 1nσ* potential energy surface (PES) leads to N–H bond extension, with the dissociating flux passing through a conical intersection with the ground state PES en route to morpholinyl radicals and H atom photoproducts. Careful analysis of the resulting H atom time-of-flight spectra reveals peaks attributable to the population of specific vibrational states of morpholinyl products arising from dissociation of both conformers, enabling determination of the energy difference between the two ground conformers of morpholine as 180 ± 50 cm−1, and the N–H bond strengths in both the axial and equatorial conformers as 33200 ± 50 cm−1 and 33380 ± 50 cm−1, respectively.

Pathways of conformational isomerization of 4-phenyl-1,3-dioxane

A study of the potential energy surface of 4-phenyl-1,3-dioxane by non-empirical quantum chemical RHF/STO-3G and 6-31G(d) approximations reveals six energetically inequivalent pathways of conformational isomerization of equatorial and axial chair forms.

Conformational analysis of 4-trifluoromethyl-1,3-dioxane

The interest to the structural investigation of 1,3-dioxanes, six-membered heteroanalogs of cyclohexane, originates from the features of their structure (the presence of two heteroatoms separated by sp3-carbon atoms), from their valuable pharmacological properties, and also from the application to the fine organic synthesis [1–5]. In the last decade computer simulations play an important role in conformationsl studies of such compounds. It was shown in particular that the conformational isomerization of unsubstituted 1,3-dioxane and also of 2,2-, 4,4-, and 5,5-dimethyl-1,3-dioxanes occurred between two degenerate in energy invertomers of chair (C and C*), and of 2-methyl-1,3-dioxane, between the conformers of equatorial and axial chair (Ce and Ca) along two materially equivalent paths [6–9]. This study is dedicated to the computer simulation of the paths of conformational isomerization of 4-trifluoromethyl-1,3-dioxane (I) by nonempirical quantum-chemical approximations RHF//STO-3G and 6-31G(d,p) in the framework of software HyperChem [10] under the conditions simulating the behavior of the molecules of this substance in the gas phase. It follows from the data of 1H NMR spectra of individual stereoisomers of 4-trifluoromethyl-5-methyl1,3-dioxane that the molecules of 1,3-dioxane I exist at room temperature prevailingly in the conformation of equatorial chair (Ce) [11].

Conformational isomerization of 4-methyl-1,3-dioxane

The whole possible course of conformational isomerization of 4-methyl-1,3-dioxane has been established using empirical (MM+) and nonempirical [STO-3G, 3-21G, 6-31G(d) and 6-31G(d,p)] approximations within the limits of the Hartree-Fock method. It was shown that the potential energy surface of this compound contains a principal (equatorial chair conformer) and local minima corresponding to the axial chair conformer and series flexible forms.

Adsorption changes of cyclohexyl isothiocyanate on gold surfaces

The adsorption and structure of cyclohexyl isothiocyanate (CHIT) on gold surfaces has been investigated by surface-enhanced Raman scattering (SERS) and scanning tunneling microscopy (STM). Depending on the concentration, the spectral changes of the NCS stretching vibration on gold nanoparticles appeared to be more conspicuous than those of cyclohexyl ring modes. Both equatorial and axial chair conformers of CHIT were found to exist at low bulk concentrations near the monolayer coverage limit, whereas the equatorial chair conformer appeared to be dominant at high bulk concentrations. It was also observed that the ring conversion of equatorial to axial conformers can easily occur at higher temperatures, and the mole fraction of the axial form is assumed to increase with increasing temperature from 30 to 60 °C. Alternatively, STM imaging revealed that the adsorption of CHIT molecules on Au(1 1 1) leads to the formation of disordered SAMs with a few vacancy islands, as opposed to the formation of well-ordered self-assembled monolayers (SAMs) by cyclohexanethiols.

Nonempirical study on the potential energy surface of 5-methyl-1,3-dioxane

Quantum-chemical study on the potential energy surface of 5-methyl-1,3-dioxane at the nonempirical RHF//STO-3G, RHF//3-21G, RHF//6-31G(d), RHF//6-31G(d,p), and MP2//6-31G(d,p) levels of theory revealed two energy-equivalent paths of conformational transformation of the equatorial and axial chair conformers. Potential barriers to these processes were estimated. The δG° value for the methyl substituent on C5 in 1,3-dioxane ring, determined on the basis of the experimental (NMR) and calculated vicinal 1H-1H coupling constants, was very consistent with published data

Study of supercooled orientationally disordered binary solid solutions II: cyclohexyl derivatives, neopentanol and neopentylglycol

The main aim of the present investigation is to see how various relaxation processes including the chair-chair transformation (as found by earlier researchers at room temperature in mechanical relaxation spectroscopy) in cyclohexane derivatives evolve as the temperature is lowered. For this purpose, four remarkable (two-component) solid solutions that are orientationally disordered are investigated, where the first three systems are hydrogen (H-) bonded pairs, and the fourth is a non-H bonded pair. The former group is the two-component system of cyclohexanol (CHXOL) + 2,2-dimethyl-1-propanol or neopentanol (NPOL); cyclohexanol (CHXOL) + cycloheptanol (CHPOL) & neopentanol (NPOL) + neopentylglycol (NPGOL) systems, and the lone non H-bonded pair that has been studied is cyanocyclohexane (CNCH) and cyclohexylchloride (CHC). In all these cases, the liquid mixtures on cooling form orientationally disordered phases which are a solid solution of the corresponding pure phases. The feature is common to all the four systems studied here, but in CHXOL + CHPOL, the phase I of CHXOL beyond x(m) > or = 0.1 only forms a solid solution (designated as S(I')) with the phase I of CHPOL. In CNCH + CHC the solid phase is stable for the concentration range 0 < or = x(m) < or = 0.4 (without transition to any other phase). The above solid phase I (or I') has been investigated at low temperatures and for several concentrations, by means of dielectric spectroscopy and differential scanning calorimetry (DSC). Depending upon the concentration, this phase reveals a glass transition in the temperature range 116-150 K and associated with this is a pronounced relaxation process identifiable with the so called alpha-process. The dielectric spectra of this process is found to follow the Havriliak-Negami (HN) equation. In context of the binary system study here, the analysis of the various parameters obtained show an isomorphic relationship between the phases of the pure components through a continuous change of parameters. Another process of much smaller magnitude designated as the alpha'-process was also found in systems consisting of cyclohexyl derivatives above the glass transition temperature T(g) which kinetically freezes around 170 K. This process interestingly, is also non-Arrhenius in nature, becomes increasingly weaker with increase in the second component, and may be identified with (axial) chair-(equatorial) chair transformation. In addition in all these systems, a weak high-frequency process and a clear sub-T(g) process, are found which are designated as the beta- & gamma-processes respectively. The beta-process may be identified with Johari-Goldstein (JG) or beta(JG) process as it is found to follow the predictions of the coupling model proposed by Ngai. However, the identification of the gamma-process with internal degrees of freedom are fraught with some problems in the interpretation of the experimental data that are highlighted. The kinetic freezing of the various dielectric processes have been critically examined in relation to the T(g) found in the DSC experiments.

Concentration‐ and temperature‐dependent conformation change of cyclohexyl isocyanide on gold nanoparticle surfaces

AbstractThe conformational changes of cyclohexyl isocyanide (CHNC) on gold nanoparticle surfaces were investigated by means of concentration‐ and temperature‐dependent surface‐enhanced Raman scattering (SERS). The equatorial chair conformer appeared to be dominant at high‐bulk concentrations or low temperatures, whereas both the equatorial and axial chair conformers of CHNC were found to exist at low‐bulk concentrations or high temperatures as in the previous reports of cyclohexanethiol (CHT). Depending on concentrations and temperatures, the spectral changes of the NC stretching vibration on gold nanoparticles appeared to be more conspicuous than those of the cyclohexyl ring modes. A density functional theory (DFT) calculation was performed at the level of B3LYP/6‐31G + + (d,p) to compare the energetic stability of the various conformers of CHT and CHNC. The energy differences between the equatorial and axial chair conformers were predicted to be smaller for CHNC than for CHT by ∼3 kJ mol−1 from the DFT calculation. Copyright © 2008 John Wiley &amp; Sons, Ltd.

Conformational changes of cyclohexanethiol adsorbed on gold surfaces

The conformational changes of cyclohexanethiol (CHT) on gold nanoparticles and gold plate surfaces were investigated by means of surface-enhanced Raman scattering. The equatorial chair conformer appeared to be dominant at high bulk concentrations, whereas, both the equatorial and axial chair conformers of CHT were found to exist at low bulk concentrations corresponding to a near monolayer coverage limit. Molecular-scale scanning tunneling microscopy imaging revealed the existence of two axial and equatorial conformers in the CHT monolayer on an Au(1 1 1) surface as well as the existence of the meta-stable conformer, which may be due to dynamic conformational changes of the cyclic ring. It was also found that the peaks corresponding to the axial bands disappeared below room temperature, indicating the equatorial conformer is dominant at low temperatures. From this result, we found that the conformation of CHT on an Au surface was easily changed by surface temperature.

The Cyclohexasilanes Si6H11X and Si6Me11X with X=F, Cl, Br and I: A Quantum Chemical and Raman Spectroscopic Investigation of a Multiple Conformer Problem

The conformers of the monohalocyclohexasilanes, Si(6)H(11)X (X=F, Cl, Br or I) and the haloundecamethylcyclohexasilanes, Si(6)Me(11)X (X=F, Cl, Br or I) are investigated by DFT calculations employing the B3LYP density functional and 6-31+G* basis sets for elements up to the third row, and SDD basis sets for heavier elements. Five minima are found for Si(6)H(11)X-the axial and equatorial chair conformers, with the substituent X either in an axial or equatorial position-and another three twisted structures. The equatorial chair conformer is the global minimum for the X=Cl, Br and I, the axial chair for X=F. The barrier for the ring inversion is approximately 13 kJ mol(-1) for all four compounds. Five minima closely related to those of Si(6)H(11)X are found for Si(6)Me(11)X. Again, the equatorial chair is the global minimum for X=Cl, Br and I, and the axial chair for X=F. Additionally, two symmetrical boat conformers are found as local minima on the potential energy surfaces for X=F, Cl and Br, but not for X=I. The barrier for the ring inversion is approximately 14-16 kJ mol(-1) for all compounds. The conformational equilibria for Si(6)Me(11)X in toluene solution are investigated using temperature dependent Raman spectroscopy. The wavenumber range of the stretching vibrations of the heavy atoms X and Si from 270-370 cm(-1) is analyzed. Using the van't Hoff relationship, the enthalpy differences between axial and equatorial chair conformers (H(ax-)H(eq.)) are 1.1 kJ mol(-1) for X=F, and 1.8 to 2.8 kJ mol(-1) for X=Cl, Br and I. Due to rapid interconversion, only a single Raman band originating from the "averaged" twist and boat conformers could be observed. Generally, reasonable agreement between the calculated relative energies and the experimentally determined values is found.