Conformational pathways of simple six-membered rings

The Influence of the Alkylamino Group on the Solvatochromic Behavior of 5-(4-substituted-arylidene)-1,3-dimethylpyrimidine-2,4,6-triones: Synthesis, Spectroscopic and Computational Studies

Advances in electronics and medical diagnostics have made organic dyes extremely popular as key functional materials. From a practical viewpoint, it is necessary to assess the spectroscopic and physicochemical properties of newly designed dyes. In this context, the condensation of 1,3-dimethylbarbituric acid with electron-rich alkylaminobenzaldehyde derivatives has been described, resulting in a series of merocyanine-type dyes. These dyes exhibit intense blue-light absorption but weak fluorescence. An electron-donating alkylamino group at position C4 is responsible for the solvatochromic behavior of the dyes since the lone electron pair of the nitrogen atom is variably delocalized toward the barbituric ring, which exhibits electron-withdrawing properties. This was elucidated, taking into account the different geometry of the amino group. The intramolecular charge transfer in the molecules is responsible for the relatively high redshift in absorption and fluorescence spectra. Additionally, an increase in solvent polarity moves the absorption and fluorescence to lower energy regions. The observed solvatochromism is discussed in terms of the four-parameter Catalán solvent polarity scale. The differences in the behavior of the dyes were quantified with the aid of time-dependent density functional theory calculations. The obtained results made it possible to find regularities linking the basic spectroscopic properties of the compounds with their chemical structure. This is important in the targeted search for new, practically important dyes.

Experimental and Theoretical Study of the OH-Initiated Degradation of Piperidine under Simulated Atmospheric Conditions

The OH-initiated photo-oxidation of piperidine and the photolysis of 1-nitrosopiperidine were investigated in a large atmospheric simulation chamber and in theoretical calculations based on CCSD(T*)-F12a/aug-cc-pVTZ//M062X/aug-cc-pVTZ quantum chemistry results and master equation modeling of the pivotal reaction steps. The rate coefficient for the reaction of piperidine with OH radicals was determined by the relative rate method to be kOH-piperidine = (1.19 ± 0.27) × 10-10 cm3 molecule-1 s-1 at 304 ± 2 K and 1014 ± 2 hPa. Product studies show the piperidine + OH reaction to proceed via H-abstraction from both CH2 and NH groups, resulting in the formation of the corresponding imine (2,3,4,5-tetrahydropyridine) as the major product and in the nitramine (1-nitropiperidine) and nitrosamine (1-nitrosopiperidine) as minor products. Analysis of 1-nitrosopiperidine photolysis experiments under natural sunlight conditions gave the relative rates jrel = j1-nitrosoperidine/jNO2 = 0.342 ± 0.007, k3/k4a = 0.53 ± 0.05 and k2/k4a = (7.66 ± 0.18) × 10-8 that were subsequently employed in modeling the piperidine photo-oxidation experiments, from which the initial branchings between H-abstraction from the NH and CH2 groups, kN-H/ktot = 0.38 ± 0.08 and kC2-H/ktot = 0.49 ± 0.19, were derived. All photo-oxidation experiments were accompanied by particle formation that was initiated by the acid-base reaction of piperidine with nitric acid. Primary photo-oxidation products including both 1-nitrosopiperidine and 1-nitropiperidine were detected in the particles formed. Quantum chemistry calculations on the OH initiated atmospheric photo-oxidation of piperidine suggest the branching in the initial H-abstraction routes to be ∼35% N1, ∼50% C2, ∼13% C3, and ∼2% C4. The theoretical study produced an atmospheric photo-oxidation mechanism, according to which H-abstraction from the C2 position predominantly leads to 2,3,4,5-tetrahydropyridine and H-abstraction from the C3 position results in ring opening followed by a complex autoxidation, of which the first few steps are mapped in detail. H-abstraction from the C4 position is shown to result mainly in the formation of piperidin-4-one and 2,3,4,5-tetrahydropyridin-4-ol, whereas H-abstraction from N1 under atmospheric conditions primarily leads to 2,3,4,5-tetrahydropyridine and in minor amounts of 1-nitrosopiperidine and 1-nitropiperidine. The calculated rate coefficient for the piperidine + OH reaction agrees with the experimental value within 35%, and aligning the theoretical numbers to the experimental value results in k(T) = 2.46 × 10-12 × exp(486 K/T) cm3 molecule-1 s-1 (200-400 K).

A GH115 α-glucuronidase structure reveals dimerization-mediated substrate binding and a proton wire potentially important for catalysis

The crystal structure of a GH115 α-glucuronidase obtained in complex with xylohexaose and Ca²⁺ reveals that the two molecules constituting the homodimer cooperatively bind the substrate and that a divalent ion is involved in formation of the Michaelis–Menten complex and is likely to contribute to the formation of a protein wire that is essential for catalysis.

Xylan is a major constituent of plant cell walls and is a potential source of biomaterials, and the derived oligosaccharides have been shown to have prebiotic effects. Xylans can be highly substituted with different sugar moieties, which pose steric hindrance to the xylanases that catalyse the hydrolysis of the xylan backbone. One such substituent is α-d-glucuronic acid, which is linked to the O2′ position of the β-1,4 d-xylopyranoses composing the main chain of xylans. The xylan-specific α-glucuronidases from glycoside hydrolase family 115 (GH115) specifically catalyse the removal of α-d-glucuronic acid (GlcA) or methylated GlcA (MeGlcA). Here, the molecular basis by which the bacterial GH115 member wtsAgu115A interacts with the main chain of xylan and the indirect involvement of divalent ions in the formation of the Michaelis–Menten complex are described. A crystal structure at 2.65 Å resolution of wtsAgu115A originating from a metagenome from an anaerobic digester fed with wastewater treatment sludge was determined in complex with xylohexaose, and Asp303 was identified as the likely general acid. The residue acting as the general base could not be identified. However, a proton wire connecting the active site to the metal site was observed and hence a previous hypothesis suggesting a Grotthuss-like mechanism cannot be rejected. Only a single molecule was found in the asymmetric unit. However, wtsAgu115A forms a dimer with a symmetry-related molecule in the crystal lattice. The xylohexaose moieties of the xylohexaose are recognized by residues from both protomers, thus creating a xylohexaose recognition site at the dimer interface. The dimer was confirmed by analytical size-exclusion chromatography in solution. Kinetic analysis with aldouronic acids resulted in a Hill coefficient of greater than 2, suggesting cooperativity between the two binding sites. Three Ca²⁺ ions were identified in the wtsAgu115A structures. One Ca²⁺ ion is of particular interest as it is coordinated by the residues of the loops that also interact with the substrate. Activity studies showed that the presence of Mg²⁺ or Mn²⁺ resulted in a higher activity towards aldouronic acids, while the less restrictive coordination geometry of Ca²⁺ resulted in a decrease in activity.

Dynamics and Entropy of Cyclohexane Rings Control pH-Responsive Reactivity

Activation entropy (ΔS ^‡) is not normally considered the main factor in determining the reactivity of unimolecular reactions. Here, we report that the intramolecular degradation of six-membered ring compounds is mainly determined by the ΔS ^‡, which is strongly influenced by the ring-flipping motion and substituent geometry. Starting from the unique difference between the pH-dependent degradation kinetics of geometric isomers of 1,2-cyclohexanecarboxylic acid amide (1,2-CHCAA), where only the cis isomer can readily degrade under weakly acidic conditions (pH < 5.5), we found that the difference originated from the large difference in ΔS ^‡ of 16.02 cal·mol^-1·K^-1. While cis-1,2-CHCAA maintains a preference for the classical chair cyclohexane conformation, trans-1,2-CHCAA shows dynamic interconversion between the chair and twisted boat conformations, which was supported by both MD simulations and VT-NMR analysis. Steric repulsion between the bulky 1,2-substituents of the trans isomer is one of the main reasons for the reduced energy barrier between ring conformations that facilitates dynamic ring inversion motions. Consequently, the more dynamic trans isomer exhibits much a larger loss in entropy during the activation process due to the prepositioning of the reactant than the cis isomer, and the pH-dependent degradation of the trans isomer is effectively suppressed. When the ring inversion motion is inhibited by an additional methyl substituent on the cyclohexane ring, the pH degradability can be dramatically enhanced for even the trans isomer. This study shows a unique example in which spatial arrangement and dynamic properties can strongly influence molecular reactivity in unimolecular reactions, and it will be helpful for the future design of a reactive structure depending on dynamic conformational changes.

A guinea pig for conformer selectivity and mechanistic insights into dissociative ionization by photoelectron photoion coincidence: fluorocyclohexane

We studied fluorocyclohexane (C₆H₁₁F, FC6) by double imaging photoelectron photoion coincidence spectroscopy in the 9.90-13.90 eV photon energy range. The photoelectron spectrum can identify species isomer and, in this case, even conformer selectively. Ab initio results indicated that the axial conformer has two, close-lying cation electronic states. With the help of Franck-Condon simulations of the vibrational fine structure, we determined the origin of three transitions, (i) axial FC6 → axial FC6⁺ of C₁ symmetry (X[combining tilde]⁺, A'' in C_S), (ii) equatorial FC6 → equatorial FC6⁺ of C₁ symmetry (X[combining tilde]⁺, A'' in C_S), and (iii) axial FC6 → A' axial FC6⁺ of C_S symmetry (Ã⁺) as 10.12 ± 0.01, 10.15 ± 0.01 and 10.15 ± 0.02 eV, respectively. At slightly higher energies, the FC6 cation starts fragmenting by HF loss (E₀ = 10.60 eV), followed by sequential CH₃ (E₀ = 10.71 eV) or C₂H₄ (E₀ = 11.06 eV) loss. Surprisingly, the methyl-loss step has an effective barrier of only 0.11 eV, and yet it is a slow process at threshold. Based on the statistical model, this is explained by isomerization and stabilization of the C₆H₁₀⁺ intermediate. The highest energy channel observed, vinyl fluoride (C₂H₃F) loss yielding C₄H₈⁺ appears in the breakdown diagram at 12 eV, which agrees with the computed threshold to cyclobutane cation formation. However, the model predicted a ca. 1 eV competitive shift for this parallel channel, i.e., an E₀ = 11.23 eV. This led us to explore the potential energy surface to find a lower-lying fragmentation channel including H-transfer steps. Rate constant measurements and statistical modeling thus yield fundamental insights into the reaction mechanism beyond what is immediately seen in the mass spectra.

Hyperpolarization of Pyridyl Fentalogues by Signal Amplification By Reversible Exchange (SABRE)

Fentanyl, also known as 'jackpot', is a synthetic opiate that is 50-100 times more potent than morphine. Clandestine laboratories produce analogues of fentanyl, known as fentalogues to circumvent legislation regarding its production. Three pyridyl fentalogues were synthesized and then hyperpolarized by signal amplification by reversible exchange (SABRE) to appraise the forensic potential of the technique. A maximum enhancement of -168-fold at 1.4 T was recorded for the ortho pyridyl 1H nuclei. Studies of the activation parameters for the three fentalogues revealed that the ratio of ligand loss trans to hydride and hydride loss in the complex [Ir(IMes)(L)3(H)2]+ (IMes=1,3-bis(2,4,6-trimethylphenyl)imidazole-2-ylidene) ranged from 0.52 to 1.83. The fentalogue possessing the ratio closest to unity produced the largest enhancement subsequent to performing SABRE at earth's magnetic field. It was possible to hyperpolarize a pyridyl fentalogue selectively from a matrix that consisted largely of heroin (97 : 3 heroin:fentalogue) to validate the use of SABRE as a forensic tool.

Exhaustive exploration of the conformational landscape of mono- and disubstituted five-membered rings by DFT and MP2 calculations

The conformational landscape of 22 different non, mono-, and disubstituted compounds with a five-membered ring was thoroughly explored by ab initio (MP2) and DFT (B3LYP and M06-2X) methods with the 6-311+G** basis set. Our results showed that the conformational preference of these compounds was governed mainly by the specific characteristics of the substituents, with a minor influence of the level of theory employed. After a detailed analysis of the computational data, we found an interesting preference of the electronegative substituents to take pseudo-axial positions, whereas alkyl groups preferred adopting the pseudo-equatorial locations. Such preferences were pronounced with MP2 and M06-2X and underestimated by B3LYP. Despite each level of theory affording different landscapes in many cases, as a general trend, we noticed that M06-2X afforded much higher correlation with the MP2 results than B3LYP.

The conformational landscape of 22 different non, mono-, and disubstituted compounds with a five-membered ring was thoroughly explored by ab initio (MP2) and DFT (B3LYP and M06-2X) methods with the 6-311+G** basis set.

The conformational preferences of polychlorocyclohexanes

A simple but precise model equation to get accurate conformational energies of polychlorocyclohexane conformations.

Direct Observation of Tetrahydrofuranyl and Tetrahydropyranyl Peroxy Radicals via Cavity Ring-Down Spectroscopy

Room-temperature cavity ring-down (CRD) spectra of the à ← X̃ electronic transition of tetrahydrofuranyl peroxy (THFOO^•) and tetrahydropyranyl peroxy (THPOO^•) radicals were recorded. The peroxy radicals were produced by Cl-initiated oxidation of tetrahydrofuran and tetrahydropyran. Quantum chemical calculations of the lowest-energy conformers of all regioisomers of these two peroxy radicals have been carried out to aid the spectral simulation. Conformational identification and vibrational assignment were achieved by comparing the experimentally obtained spectra to the simulated ones. The absence of α-THPOO^• absorption peaks in the CRD spectrum is attributed to ring opening due to its weak C_α'O bond.

Axial–equatorial isomerism and semiexperimental equilibrium structures of fluorocyclohexane

Accuracy vs. computational effort: the mixed estimation method provides very accurate semiexperimental equilibrium structures, as illustrated by the subtle differences between axial/equatorial fluorocyclohexane.

Vapor-Phase Raman Spectra and the Barrier to Planarity of Cyclohexane

The vapor-phase Raman spectra of an atmosphere of cyclohexane vapor heated to 90 and 110 °C collected over a large period of time and utilizing a high laser power of 4 W show hot band series starting at 380.8 cm^-1 and corresponding to the v₆(A_1g) ring-inversion vibration. Fitting this data with a one-dimensional potential energy function allows the barrier to planarity of 8600 cm^-1 (24.6 kcal/mol) to be calculated. Ab initio calculations (MP2/cc-pVTZ) predict a value of 10 377 cm^-1 (29.7 kcal/mol), while DFT (B3LYP/cc-pVTZ) calculations predict 8804 cm^-1 (25.2 kcal/mol).

DFT/PCM theoretical study of the conversion of methyl 4-O-methyl-α-d-galactopyranoside 6-sulfate and its 2-sulfated derivative into their 3,6-anhydro counterparts

Modeling of the conversion of methyl 4-O-methyl-α-d-galactopyranoside 6-sulfate (2) and 2,6-disulfate (1) into methyl 3,6-anhydro-4-O-methyl-α-d-galactopyranoside (4) and its 2-sulfate (3), respectively (Scheme 1) has been carried out using DFT at the M06-2X/6-311 + G(d,p)//M06-2X/6-31 + G(d,p) level with the polarizable continuum model (PCM) in water. The three steps necessary for the alkaline transformation of 6-sulfated (and 2,6-disulfated) galactose units into 3,6-anhydro derivatives were evaluated. The final substitution step appears to be the rate limiting, involving an activation energy of ca. 23 kcal/mol. The other two steps (deprotonation and chair inversion) combined involve lower activation energies (9-12 kcal/mol). Comparison of the thermodynamics and kinetics of the reactions suggest that if the deprotonation step precedes the chair inversion, the reaction should be faster for both compounds. No major differences in reaction rate can be theoretically predicted to be caused by the presence of sulfate on O-2, although one experimental result suggested that O-2 sulfation should increase the reaction rate. The conformational pathways are complex, given the large number of rotamers available for each compound, and the way that some of these rotamers combine into some of the pathways. In any case, the conformation (O)S2 appears as a common intermediate for the chair inversion processes.

Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains

This article describes a revised version 56A6(CARBO_R) of the GROMOS 56A6(CARBO) force field for hexopyranose-based carbohydrates. The simulated properties of unfunctionalized hexopyranoses are unaltered with respect to 56A6CARBO . In the context of both O1 -alkylated hexopyranoses and oligosaccharides, the revision stabilizes the regular (4) C1 chair for α-anomers, with the opposite effect for β-anomers. As a result, spurious ring inversions observed in α(1→4)-linked chains when using the original 56A6(CARBO) force field are alleviated. The (4) C1 chair is now the most stable conformation for all d-hexopyranose residues, irrespective of the linkage type and anomery, and of the position of the residue along the chain. The methylation of a d-hexopyranose leads to a systematic shift in the ring-inversion free energy ((4) C1 to (1) C4 ) by 7-8 kJ mol(-1), positive for the α-anomers and negative for the β-anomers, which is qualitatively compatible with the expected enhancement of the anomeric effect upon methylation at O1. The ring-inversion free energies for residues within chains are typically smaller in magnitude compared to those of the monomers, and correlate rather poorly with the latter. This suggests that the crowding of ring substituents upon chain formation alters the ring flexibility in a nonsystematic fashion. In general, the description of carbohydrate chains afforded by 56A6(CARBO_R) suggests a significant extent of ring flexibility, i.e., small but often non-negligible equilibrium populations of inverted chairs, and challenges the "textbook" picture of conformationally locked carbohydrate rings.

Carbohydrate-protein interactions: molecular modeling insights

The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.

The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases

Unraveling the conformational catalytic itinerary of glycoside hydrolases (GHs) is a growing topic of interest in glycobiology, with major impact in the design of GH inhibitors. β-xylanases are responsible for the hydrolysis of glycosidic bonds in β-xylans, a group of hemicelluloses of high biotechnological interest that are found in plant cell walls. The precise conformations followed by the substrate during catalysis in β-xylanases have not been unambiguously resolved, with three different pathways being proposed from structural analyses. In this work, we compute the conformational free energy landscape (FEL) of β-xylose to predict the most likely catalytic itineraries followed by β-xylanases. The calculations are performed by means of ab initio metadynamics, using the Cremer-Pople puckering coordinates as collective variables. The computed FEL supports only two of the previously proposed itineraries, 2SO → [2,5B]ǂ → 5S1 and 1S3 → [4H3]ǂ → 4C1, which clearly appear in low energy regions of the FEL. Consistently, 2SO and 1S3 are conformations preactivated for catalysis in terms of free energy/anomeric charge and bond distances. The results however exclude the OE → [OS2]ǂ → B2,5 itinerary that has been recently proposed for a family 11 xylanase. Classical and ab initio QM/MM molecular dynamics simulations reveal that, in this case, the observed OE conformation has been enforced by enzyme mutation. These results add a word of caution on using modified enzymes to inform on catalytic conformational itineraries of glycoside hydrolases.

Quantum chemical study of the equatorial/axial exchange of different substituents in nitrogen and phosphorous-containing 6-membered rings: Role of charge transfer interactions

Understanding the nature of equatorial/axial conversion in six-membered rings is important because of involvement of these motifs in some biological systems. In this work we have studied the equatorial/axial exchange of nitrogen and phosphorous bearing six-membered rings with different representative substituents by using quantum chemistry methods. Three possible routes, i.e. heteroatom inversion and two ring flipping modes were considered. The feasibility of equatorial/axial conversion (based on ΔE#) for the substituted piperidine rings with substituents was in the following order; H > CH 3> Cl ~ OH ~ F , whereas for the phosphorous bearing six-membered rings it was H ~ F > OH > Cl ~ CH 3. In the piperidine system hydrogen and methyl substituents preferred the atom inversion route while the other substituents ( Cl , F , OH ) favored C4 site ring flipping in equatorial/axial conversion. For the phosphorous bearing rings, however, phosphorous retards the atom inversion mechanism and heteroatom site ring flipping is the preferred route for all substituents. We demonstrate that charge transfer effect is one of the key factors that determines the favored route in the presence of various substituents. We show how wave function analysis by natural bond orbital (NBO) method can be used as a straightforward technique to explain the most favored route in the equatorial/axial conversion of substituted 6-membered rings.

Interconversion study in 1,4-substituted six-membered cyclohexane-type rings. Structure and dynamics of trans-1,4-dibromo-1,4-dicyanocyclohexane

Cyclohexane is an extremely flexible molecule that oscillates, at room temperature, between two clearly distinct and extreme conformations that cannot be distinguished at room temperature; so much so that the NMR spectrum is a single line that includes all 12 protons be they axial or equatorial. This raises the interesting question as to what happens when there are equal substituents at the 1 and 4 carbon atoms of the ring. Therefore substitution in the 1,4-positions in the cyclohexane ring has been the subject of considerable interest because some form of interconversion between extreme conformations could lead to the existence of a rather unusual behavior. To study this problem, the interconversion in (di- or tetra-1,4)-substituted six-membered cyclohexane-type rings, trans-1,4-dibromo-1,4-dicyanocyclohexane, was found to be a particularly suitable candidate. Although X-ray diffraction studies on the crystalline solid found the molecule to be centrosymmetric, it still shows a significant dipole moment μ in solution, as determined with a procedure that leads to the vapor phase values of μ. Furthermore, the low magnetic field proton NMR spectrum at ambient temperature appears as a single line, a situation that changes with increasing field intensity and different solvents. Both these effects are attributed to dynamics, because small distortions can easily disrupt the exact cancellation of the individual dipoles (which are quite strong) associated with each end of the molecule. The molecule can exist in two forms, with both the bromines in an axial geometry or both in an equatorial position. Interconversion between these forms is observed, as in the parent cyclohexane. The single NMR line observed at low magnetic fields is due to fast exchange and requires that the two forms have roughly equal populations. Spectra obtained at low temperature confirm this, and variable-temperature studies allow measurement of the rates, leading to an enthalpy of activation of 62 kJ mol(-1). More details of the interconversion are provided by some new calculation methods. Even for a relatively small molecule like this, calculation of a full potential energy surface is prohibitive. However, methods are now available to follow the molecule along the reaction coordinate in quite an efficient way. The results of these calculations lead to an extremely detailed picture of chair-chair interconversion in a di- and tetrasubstituted six-membered ring of the cyclohexane family.