Activation Energy For Isomerization Research Articles

Proline Peptide Bond Isomerization in Ubiquitin Under Folding and Denaturing Conditions by Pressure-Jump NMR

Proline isomerization is widely recognized as a kinetic bottleneck in protein folding, amplified for proteins rich in Pro residues. We introduced repeated hydrostatic pressure jumps between native and pressure-denaturing conditions inside an NMR sample cell to study proline isomerization in the pressure-sensitized L50A ubiquitin mutant. Whereas in two unfolded heptapeptides, X-Pro peptide bonds isomerized ca 1.6-fold faster at 1 bar than at 2.5 kbar, for ubiquitin ca eight-fold faster isomerization was observed for Pro-38 and ca two-fold for Pro-19 and Pro-37 relative to rates measured in the pressure-denatured state. Activation energies for isomerization in pressure-denatured ubiquitin were close to literature values of 20 kcal/mole for denatured polypeptides but showed a substantial drop to 12.7 kcal/mole for Pro-38 at atmospheric pressure. For ubiquitin isomers with a cis E18-P19 peptide bond, the 1-bar NMR spectrum showed sharp resonances with near random coil chemical shifts for the C-terminal half of the protein, characteristic of an unfolded chain, while most of the N-terminal residues were invisible due to exchange broadening, pointing to a metastable partially folded state for this previously recognized ‘folding nucleus’. For cis-P37 isomers, a drop in pressure resulted in the rapid loss of nearly all unfolded-state NMR resonances, while the recovery of native state intensity revealed a slow component attributed to cis → trans isomerization of P37. This result implies that the NMR-invisible cis-P37 isomer adopts a molten globule state that encompasses the entire length of the ubiquitin chain, suggestive of a structure that mostly resembles the folded state.

Efficient isomerization of glucose to fructose over Al-loaded functional lignin biopolymer

Al-loaded functional lignin biopolymer (Alx-Lbp) catalysts were synthesized using H2O2 oxidized alkali lignin and aluminum acetate via mechanochemical modification without post-calcination treatment. The Alx-Lbp catalysts exhibited higher hydrophilicity and lower surface energy than lignin-free Al-activated carbon catalysts. Unprecedented high yields (58.5 %) of fructose from glucose were obtained over Al1-Lbp in ethanol at 140 ºC in 30 min reaction time. Al1-Lbp catalyst had Lewis acid sites (47.2 μmol/g), Brønsted acid sites (6.9 μmol/g) and a surface energy of 39.1 mN/m that facilitated glucopyranose ring-opening and gave a glucose isomerization activation energy of 65.2 kJ/mol, which was lower than values reported for Lewis acid-catalyzed systems. Active sites of Al2O3 and Al(OH)3 formed on the Al1-Lbp catalyst in ethanol promoted the formation of an enediol intermediate as confirmed with isotope experiments to achieve efficient isomerization of glucose to fructose. The Al1-Lbp catalyst demonstrated recyclability and maintained its initial activity for eight times reuse.

Ground state properties and infrared spectra of anharmonic vibrational polaritons of small molecules in cavities.

Recent experiments and theory suggest that ground state properties and reactivity of molecules can be modified when placed inside a nanoscale cavity, giving rise to strong coupling between vibrational modes and the quantized cavity field. This is commonly thought to be caused either by a cavity-distorted Born-Oppenheimer ground state potential or by the formation of light-matter hybrid states, vibrational polaritons. Here, we systematically study the effect of a cavity on ground state properties and infrared spectra of single molecules, considering vibration-cavity coupling strengths from zero up to the vibrational ultrastrong coupling regime. Using single-mode models for Li-H and O-H stretch modes and for the NH3 inversion mode, respectively, a single cavity mode in resonance with vibrational transitions is coupled to position-dependent molecular dipole functions. We address the influence of the cavity mode on polariton ground state energies, equilibrium bond lengths, dissociation energies, activation energies for isomerization, and on vibro-polaritonic infrared spectra. In agreement with earlier work, we observe all mentioned properties being strongly affected by the cavity, but only if the dipole self-energy contribution in the interaction Hamiltonian is neglected. When this term is included, these properties do not depend significantly on the coupling anymore. Vibro-polaritonic infrared spectra, in contrast, are always affected by the cavity mode due to the formation of excited vibrational polaritons. It is argued that the quantized nature of vibrational polaritons is key to not only interpreting molecular spectra in cavities but also understanding the experimentally observed modification of molecular reactivity in cavities.

Quantum chemical calculation of intrinsic reaction coordinates from trans to cis structure of fluvoxamine

Fluvoxamine is a selective serotonin reuptake inhibitor. Its trans-isomer [(E)-isomer] is pharmacologically active, whereas its cis-isomer [(Z)-isomer] loses its activity. It is a pharmaceutical interest whether the structural change from the (E)-isomer to the (Z)-isomer spontaneously occurs in aqueous solutions without ultraviolet (UV) irradiation. In the present study, the transition state of fluvoxamine was determined by quantum chemical calculation using density functional theory (DFT), and the intrinsic reaction coordinates (IRCs) from the (E)-isomer to the (Z)-isomer were calculated using UB3LYP/6-311++G(d,p) with the integral equation formalism-polarizable continuum model (IEF-PCM). The activation energy of isomerization from the (E)-isomer to the (Z)-isomer was estimated to be 55 kcal/mol. Further, the absorption spectra, the nuclear magnetic resonance chemical shift values, the Raman spectra and the infrared spectra were calculated for the (E) and (Z)-isomers obtained from the reaction coordinate calculation, and these results were in good agreement with the experimental values. The geometrical structures of the (E) and (Z)-isomers proposed in the present study can be used as theoretical models of fluvoxamine for molecular dynamics calculations in future.

Selectivity in carbon–carbon coupling reactions at palladium(IV) and platinum(IV)

The isomerization and reductive elimination reactions from octahedral organometallic complexes of palladium(IV) and platinum(IV) usually occur through five-coordinate intermediates that cannot be directly detected. This paper reports a computational study of five-coordinate complexes of formulae [PtMe3(bipy)]+, [PtMe2Ph(bipy)]+, and [PtMe(CH2CMe2C6H4)(bipy)]+ (M = Pd or Pt, bipy = 2,2′-bipyridine), particularly with respect to reactivity and selectivity in reductive elimination. All of the complexes are predicted to have square pyramidal structures with the bipy and two R groups in the equatorial positions and one R group in the axial position, and axial–equatorial exchange occurs by a pairwise mechanism, with the transition state having a pinched trigonal bipyramidal (PTBP) stereochemistry, with one nitrogen and two R groups in the trigonal plane. The activation energy for isomerization is lower than that for reductive elimination in all cases. For the complexes [MMe2Ph(bipy)]+, the activation energies for reductive elimination with Me–Me or Me–Ph coupling are similar. For the complexes [MMe(CH2CMe2C6H4)(bipy)]+, the reductive elimination with Me–C6H4 bond formation from the isomer with the methyl group in the axial position is predicted and is attributed to it having the best conformation of the Me and C6H4 groups for C–C bond formation. In all cases, the selectivity for reductive elimination is similar for M = Pd or Pt, but reactivity is higher for M = Pd. The relevance of this work to selectivity in catalysis is discussed.

The Effect of trans Ligands in the NO‐Linkage Reverse Isomerization for Ruthenium–Nitrosyl–Tetraammine Complexes: A DFT Study

The rearrangement of the NO ligand in ruthenium–nitrosyl–tetraammine complexes trans‐[Ru(NO)(NH3)4X]2+ (X = F–, Cl–, OH–, SH–) has been studied for metastable oxygen‐coordinated NO complexes by means of DFT. On the basis of obtained data, this rearrangement is concluded to be caused by ligand‐to‐metal charge transfer of the p(X)→π*(Ru–ON) type. The excitation energy for electron transfer from p‐orbital of ligand to LUMO correlates perfectly with the activation energy of isomerization. Found correlations are explained in terms of electronegativity of the trans ligand X.

Volatile Pd–Pb and Cu–Pb heterometallic complexes: structure, properties, and trans-to-cis isomerization under cocrystallization of Pd and Cu β-diketonates with Pb hexafluoroacetylacetonate

Preparation of volatile heterometallic precursors is a significant step on the way to advanced multicomponent materials. Study of molecular transformations in solution upon precursor synthesis is of importance to optimize the preparation of the stable solid product of desired composition. Two new volatile heterobimetallic complexes, cis-PdL2*Pb(hfa)2 and cis-CuL2*Pb(hfa)2, were obtained (L = 2-methoxy-2,6,6-trimethylheptane-3,5-dionate, hfa = 1,1,1,5,5,5-hexafluoropentane-2,4-dionate) under cocrystallization of trans-bis-beta-diketonates of Pd(II) and Cu(II) with Pb(hfa)2 from organic solvents. Crystals of these compounds are built of discrete bimetallic molecules where transition metal complex isomerized from trans-to-cis form. Complexation followed by isomerization was studied by solution NMR. The bimetallic molecular species were formed early in solution. Enthalpy and activation energy of isomerization were estimated to be 49 and 93 kJ mol−1, respectively. A new synthesis technique of Pd(II) beta-diketonates which is distinguished by simplicity and selectivity as well as the crystal structure of trans-PdL2 is described. Volatility of all obtained compounds was confirmed by thermogravimetric analysis and fractional sublimation in vacuum; Pd-containing heterobimetallic complex appeared to be more volatile than both the initial monometallic complexes and Cu-containing complex.

Carrot β-Carotene Degradation and Isomerization Kinetics during Thermal Processing in the Presence of Oil

The effect of thermal processing (85-130 °C) on the stability and isomerization of β-carotene in both an olive oil/carrot emulsion and an olive oil phase enriched with carrot β-carotene was studied. During processing, degradation of total β-carotene took place. Initially, total β-carotene concentration decreased quickly, after which a plateau value was reached, which was dependent on the applied temperature. In the oil/carrot emulsion, the total β-carotene concentration could be modeled by a fractional conversion model. The temperature dependence of the degradation rate constants was described by the activation energy and was estimated to be 45.0 kJ/mol. In the enriched oil phase, less degradation took place and the results could not be modeled. Besides degradation, β-carotene isomerization was studied. In both matrices, a fractional conversion model could be used to model total isomerization and formation of 13-Z- and 15-Z-β-carotene. β-Carotene isomerization was similar in both the oil/carrot emulsion and enriched oil phase as the simultaneously estimated kinetic parameters (isomerization reaction rate constant and activation energy) of both matrices did not differ significantly. The activation energies of isomerization were estimated to be 70.5 and 75.0 kJ/mol in the oil/carrot emulsion and enriched oil phase, respectively.

Kinetic Study on the Isomerization of Perindopril by HPLC

The isomerization of perindopril has been investigated using dynamics chromatography and an unified equation introduced by Trapp that was based on stochastic and theoretical plate models to determine the energies. The isomerization rate constants and Gibbs activation energies of isomerization are directly calculated from chromatographic peak parameters, i.e., retention times of the inter-converting species, peak width at half height, and relative plateau height. From the rate constant \( k_{1}^{ue} (T) \), measured at variable temperatures, the kinetic eyring activation parameters ΔG#, ΔH# and ΔS# of isomerization of perindopril were obtained. By variation of the flow rate of the mobile phase, the expected independence of the isomerization barrier from the chromatographic time scale was demonstrated for the first time. The relationships between peak shape and chromatographic conditions, such as flow rate, temperature, pH, organic modifier, and β-cyclodextrin, such as an additive, were investigated. In addition, an NMR investigation on perindopril was described.

Prodrugs of fumarate esters for the treatment of psoriasis and multiple sclerosis—a computational approach

Density functional theory (DFT) calculations at B3LYP/6-31 G (d,p) and B3LYP/6-311+G(d,p) levels for the substituted pyridine-catalyzed isomerization of monomethyl maleate revealed that isomerization proceeds via four steps, with the rate-limiting step being proton transfer from the substituted pyridinium ion to the C=C double bond in INT1. In addition, it was found that the isomerization rate (maleate to fumarate) is solvent dependent. Polar solvents, such as water, tend to accelerate the isomerization rate, whereas apolar solvents, such as chloroform, act to slow down the reaction. A linear correlation was obtained between the isomerization activation energy and the dielectric constant of the solvent. Furthermore, linearity was achieved when the activation energy was plotted against the pKa value of the catalyst. Substituted-pyridine derivatives with high pKa values were able to catalyze isomerization more efficiently than those with low pKa values. The calculated relative rates for prodrugs 1-6 were: 1 (406.7), 2 (7.6×10(6)), 3 (1.0), 4 (20.7), 5 (13.5) and 6 (2.2×10(3)). This result indicates that isomerizations of prodrugs 1 and 3-5 are expected to be slow and that of prodrugs 2 and 6 are expected to be relatively fast. Hence, prodrugs 2 and 3-5 have the potential to be utilized as prodrugs for the slow release of monomethylfumarate in the treatment of psoriasis and multiple sclerosis.

Interaction of Zn2+ with extraframework aluminum in HBEA zeolite and its role in enhancing n-pentane isomerization

The electrodeposition method was used to produce Zn2+ cation precursors, followed by the introduction of Zn2+ cation precursors to HBEA by the ion exchange technique. The introduction of Zn2+ cations slightly changed the specific surface area and crystallinity of HBEA. IR, XPS and solid state MAS NMR results showed that Zn2+ cations interacted with (AlO)+ extraframework aluminum to form Zn(OAl)2 and simultaneously induced the formation of bridging hydroxyl groups, Si(OH)Al. The pyridine adsorbed IR study revealed that the presence of Zn2+ cations fully eliminated weak and partially eliminated strong Brønsted acid sites. As a result, strong and relatively weak Lewis acid sites were formed in which the pyridine probe molecule desorbed at 623K and below. The presence of Zn2+ cations enhanced the catalytic activity of HBEA in n-pentane isomerization due to the presence of strong Lewis acid sites; the sites may facilitate the formation and maintenance of active protonic acid sites through a hydrogen spillover mechanism. At 598K, the yield of isopentane for Zn-HBEA was 25.7% higher than that of HBEA. Within a reaction temperature range of 373–648K, the apparent activation energy for isomerization of n-pentane over HBEA and Zn-HBEA was 118.76 and 90.79kJ/mol, respectively.

Exploring the unexpected pyridine- and 4,4′-bipyridine-catalyzed isomerization of maleic acid: A DFT approach

DFT at B3LYP/6-31G(d,p) and B3LYP/6-311+G(d,p) levels calculations for the pyridine- and 4,4′-bipyridine-catalyzed isomerization of maleic acid demonstrated that the mechanism involves four steps: (1) a proton transfer from one of maleic acid carboxyl groups onto the amine nitrogen (pyridine or 4,4′-bipyridine) to yield an ion pair INT1. (2) Proton transfer from INT1 to the C–C double bond to give INT2. (3) Rotation about the central C–C single bond followed by proton abstraction by an amine molecule to yield INT3, and (4) proton transfer from the ammonium cation into the carboxylate anion of the fumarate thus formed to furnish the trans isomer, fumaric acid. Moreover, the calculations revealed that an abstraction of a proton from INT2 (step 3) was found to be the rate limiting step. However, the activation energy difference between steps 2 and 3 was not significant. Furthermore, it was found that the solvent dielectric constant has a profound impact on both the isomerization activation energy and the free energy difference between the cis and trans isomers (maleic and fumaric acids). While, polar solvents such as DMSO tend to lower the isomerization activation energy and to increase the free energy difference between the two isomers, apolar solvents such as chloroform behave in an opposite manner. In addition, linear correlation was found between the activation energy and the solvent dielectric constant.

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

AbstractAb 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.

The Isomerization of Methoxy Radical: Intramolecular Hydrogen Atom Transfer Mediated through Acid Catalysis

The catalytic ability of water, formic acid, and sulfuric acid to facilitate the isomerization of the CH(3)O radical to CH(2)OH has been studied. It is shown that the activation energies for isomerization are 30.2, 25.7, 4.2, and 2.3 kcal mol(-1), respectively, when the reaction is carried out in isolation and with water, formic acid, or sulfuric acid as a catalyst. The formation of a doubly hydrogen bonded transition state is central to lowering the activation energy and facilitating the intramolecular hydrogen atom transfer that is required for isomerization. The changes in the rate constant for the CH(3)O-to-CH(2)OH isomerization with acid catalysis have also been calculated at 298 K. The largest enhancement in the rate, by over 12 orders of magnitude, is with sulfuric acid. The results of the present study demonstrate the feasibility of acid catalysis of a gas-phase radical isomerization reaction that would otherwise be forbidden.

Reversible isomerization of a zwitterionic polysquaraine induced by a metal surface

The variation of visible and IR absorption spectra and of small-angle X-ray scattering of poly(3-octylpyrrole)squaraine in trichloromethane solution indicates that, for this zwitterionic conducting polymer (CP), a reversible change of conformation is induced by contact of the solution with the surface of an active metal. The structure of the target polymer might switch from being linear to being folded. For a copper surface, the activation energy of isomerization between the two forms, whatever their nature, is 18.9 ± 0.7 kJ mol−1, whereas for the reverse process the activation energy is 38 ± 6 kJ mol−1. In a folding transformation, formation of intramolecular hydrogen bonds might play a key role. This observation of a reversible conformation for a zwitterionic polymer induced by a metallic surface provides an impetus to investigate both such a structural modification of other CP and applications of this phenomenon.

A Two-Layer ONIOM Study on Initial Reactions of Catalytic Cracking of 1-Butene To Produce Propene and Ethene over HZSM-5 and HFAU Zeolites

Two-layer ONIOM calculations were carried out to study initial reactions of catalytic cracking of 1-butene to produce propene and ethene on HZSM-5 and HFAU zeolites. Direct cracking and dimerization cracking mechanisms were evaluated. The calculated data indicate that the dimerization cracking is more favorable than the direct cracking based on both kinetic and thermodynamic considerations. HZSM-5 is catalytically more effective than HFAU for the cracking reactions. ONIOM energy analysis shows that the effectiveness of zeolite is due to long-range van der Waals interaction energies that stabilize all reaction intermediates, and short-range interaction between the zeolite and the reacting species that reduce the activation energies. For the dimerization process, stepwise and concerted mechanisms are similar in energy changes. Generally speaking, dimerizations appear to be exothermic reactions with modest activation energies. The activation energies for isomerization, β-scission, and deprotonation are lower for larger molecular fragments than for smaller ones.

Z/E (C=C)-isomerization and fluorescence modulation of imines of 7-N,N-dialkylamino-4-hydroxy-3-formylcoumarins in organic solvents

Imines of 7-dialkylamino-3-formyl-4-hydroxycoumarins have been found to exist in Z-ketoenamine form in crystal state and undergo Z/E-isomerization around C=C bond in organic solvents at room temperature. Activation energies of isomerization have been measured experimentally and calculated by the DFT B3LYP method. Transition of ketoenamine form of p-nitrophenylimines into (hydroxy)imine form at low concentration (10-5 m) in polar solvents is accompanied by strong increase in fluorescence.

Theoretical studies on the mechanism of 1,3-dipolar cycloaddition of methyl azide to [50]fullerene

The 1,3-dipolar cycloaddition of methyl azide to C 50 and the subsequent nitrogen elimination from the formed triazoline intermediate to yield the aziridine adduct have been studied using semiempirical AM1 methods. The results show that the cycloaddition of methyl azide to a [5,5] bond of C 50 leading to a closed [5,5]-triazoline intermediate takes place through two stepwise pathways a and b: both of them starting from the formation of one C–N bond followed by the formation of the other C–N bond. The two pathways are competitive and the activation energy of each path is about 22 kcal mol −1. The subsequent thermal loss of N 2 from the closed [5,5]-triazoline takes place through two paths, I and II: path I includes three steps while path II includes two steps. And path I is the preferred one with a total activation energy of approximately 41 kcal mol −1. There is also a pathway without the formation of triazoline, in which the formation of C–N bond between N 3CH 3 and C 50 to give an intermediate is followed by the elimination of N 2 together with the formation of the other C–N bond to form the closed [5,6]-C 50NCH 3, which is the preferred pathway among all the pathways with a total activation energy of about 14.5 kcal mol −1. It is expected that the closed [5,6]-C 50NCH 3 is the main product from addition of N 3CH 3 to C 50. The closed [5,6]-C 50NCH 3 isomer is more stable than its closed [5,5] isomer. The isomerization activation energy from the closed [5,6] isomer to the [5,5] isomer is 53.6 kcal mol −1, and that for the reverse isomerization is 35.7 kcal mol −1. This result indicates that the conversion of the two isomers can hardly take place at room temperature and some day both of them can have the chance to be actually isolated experimentally.

Comparison of Large Pore Zeolites for n‐Octane Hydroisomerization: Activity, Selectivity and Kinetic Features

AbstractThe hydroisomerization of n‐octane has been catalyzed by different zeolitic structures with large pore size (12 MR). It has been seen that channel topology, chemical composition, crystal size, and adsorption properties are of paramount importance for improving the isomerization activity and selectivity. Nanocrystalline beta zeolite (30 nm) with large pore size (0.66 × 0.67 and 0.56 × 0.56 nm), and high aluminum content (Si/Al = 16), was the best catalyst to produce multibranched isomers. Cracking reactions also occur together with isomerization and the product distribution will depend on the rate constant and relative activation energies of isomerization, desorption, and cracking. Furthermore, a complete kinetic study of n‐octane isomerization has been carried out with beta zeolite, and kinetic rate constants, heats of adsorption, and activation energies have been determined for each individual isomerization step. The rate of isomerization of n‐octane to monobranched products was found to be faster than the rate of cracking of dibranched products and the rate of isomerization of mono‐ to dibranched products. It should be possible to obtain high yields of dibranched alkanes by distillation and recycling units, or by using membrane reactors.

Theoretical studies of carbon dioxide catalysis of peroxynitrite isomerizations

The carbon dioxide mediated isomerization of peroxynitrite to nitrate is investigated theoretically using density functionals methods. It is found that carbon dioxide, as a catalyst, lowers the activation energy by about 100 kJ/mol relative to the uncatalyzed reaction. Likewise, the activation energy for isomerization of the syn/anti peroxynitrite conformers is reduced by about 30 kJ/mol. These reductions make both processes feasible at physiological conditions.