Energy Barrier For Isomerization Research Articles

Bidentate Sulfur Dioxide Complexes of Scandium, Yttrium, and Lanthanum Difluorides.

The SO2 complexes of scandium, yttrium, and lanthanum difluorides [MF2(O2S)] were prepared via the reactions of laser-ablated metal atoms and SO2F2 upon UV-vis irradiation in cryogenic matrixes. The presence of bidentate SO2 ligand in the products was demonstrated by the characteristic infrared absorptions as well as isotopic frequency ratios from both S18O2F2 and 34SO2F2 experiments and is further supported by DFT calculations. All three product molecules were predicted to have nonplanar C2 v symmetry with the SO2 ligand bound to the metal center through both oxygens. The computed S-O bond length and stretching frequencies of ligated SO2 approach those of SO2- as a result of electron transfer from metal center to the 1π* orbital of SO2, in agreement with the results from bonding analysis. On the basis of DFT calculations, fluorine transfer from SO2F2 to the metal center to form the MF2(O2S) complexes is highly exothermic. Although a proposed intermediate in the form of MF(O2SF) was predicted to be stable, it was not observed in the experiments, presumably because of the low energy barrier for further isomerization to MF2(O2S).

Shape selectivity in acidic zeolite catalyzed 2-pentene skeletal isomerization from first principles

• The “dimethylcyclopropane” pathway is dominant for 2-pentene isomerization. • The ring-opening step is the rate-determining step for the isomerization reaction. • Van der Waals interactions would change the scaling relations in zeolite catalysis. Periodic density functional theory (DFT) calculations have been performed to examine the monomolecular reaction mechanism for 2-pentene skeletal isomerization catalyzed by acidic zeolite Beta, Mordenite, and ZSM-5. The use of periodic models allows consideration and analysis of zeolite steric constraints that occur within zeolite microspores. Three different reaction pathways, the “dimethylcyclopropane” (DMCP), methyl shift, and ethyl shift mechanisms, have been considered. The DMCP mechanism which includes rearrangement of protonated cyclopropane is proposed as the dominant reaction pathway, and the ring-opening step determines the overall reaction rate. Comparison of the effective energy barriers for 2-pentene isomerization over the three different zeolites reveals that large 12-ring channels of Beta and MOR have little steric hindrance effect on 2-pentene isomerization while small 10-ring of ZSM-5 significantly increases the reaction activation energy. Calculated results also indicate that the adsorption heat of ammonia is a good descriptor for the reactivity of zeolites without taking into account long-range dispersive forces. In contrast, linear scaling relations cannot be obtained by using the BEEF-vdW functional because van der Waals interactions between zeolites framework and guest molecules affects the energetics of the isomerization reaction and changes the transition state energy scaling relation in zeolite catalysis.

Insights into the degradation of (CF3)2CHOCH3 and its oxidative product (CF3)2CHOCHO & the formation and catalytic degradation of organic nitrates

In this work, a systematic investigation of the atmospheric oxidation mechanism of (CF3)2CXOCH3 and their oxidative products (CF3)2CXOCHO (X = H, F) initiated by OH radical or Cl atom is performed by density functional theory. This study reveals that the introduction of NO and O2 promotes the formation of organic nitrates, which are hygroscopic and are inclined to form secondary organic aerosols (SOA) and can affect the air quality. The rate constants of the individual reactions are found to be in agreement with the experimental results. One of the intriguing findings of this work is that the peroxynitrite of (CF3)2CHOCH2OONO formed from the subsequent reactions of (CF3)2CHOCH3 is more favorable to isomerize to organic nitrate (CF3)2CHOCH2ONO2 than to dissociate into alkoxy radical (CF3)2CHOCH2O and NO2 because of the lower energy barrier of isomerization. The second significant observation is that the organic nitrate can be degraded more favorably with the presence of NH3, CH3NH2, and CH3NHCH3 than its naked decomposition reaction (CF3)2CHOCH2ONO2→(CF3)2CHOCHO + HONO. The ammonium salt, a vital part of haze, is harmful to human health and can be formed in the existence of the NH3, CH3NH2, and CH3NHCH3. In addition, the toxic substance of peroxyalkyl nitrate (CF3)2CHOC(O)ONO2 which can reduce the visibility of the atmosphere is produced as the primary subsequent oxidation product of (CF3)2CHOCHO in a NO-rich environment. The main species detected experimentally are confirmed by this study. The computational results are crucial to risk assessment and pollution prevention of the volatile organic compounds (VOCs).

Synthesis and structure elucidation of allyl Pd(II) complexes of NHC ligands derived from substituted imidazo[1,5-a]quinolin-1(2H)-ylidene

Nine Pd(II) complexes involving N-heterocyclic carbenes (NHCs) derived from 2-substituted and 2- and 7-substituted imidazo[1,5-a]quinolin-1(2H)-ylidene with auxiliary allylic ligands were synthesized and characterized. The structure and configuration of the complexes were elucidated on the basis of combination of dynamic NMR and DFT studies. Conformational studies in respect of hindered rotation around Pd-C bond and η3-η1-η3 pseudo allyl rotation were performed. The results from dynamic NMR and DFT studies confirmed the mechanism of selective η3-η1-η3 isomerization, whose energy barriers are affected by steric hindrance of substituents at nitrogen atom. Energy barriers of isomerization (16.7–18.8 kcal/mol) are slightly influenced by the electronic nature of substituents at seventh position in imidazo[1,5-a]quinolin-1(2H)-ylidene moiety. The results from DFT calculations were in good agreement with the experimental energy barriers.

Stereolability of chiral ruthenium catalysts with frozen NHC ligand conformations investigated by dynamic-HPLC.

The stereolability of chiral Hoveyda-Grubbs II type ruthenium complexes bearing N-heterocyclic carbene (NHC) ligands with Syn-phenyl groups on the backbone and Syn- or Anti-oriented o-tolyl N-substituents was studied by resorting to dynamic high-performance liquid chromatography (D-HPLC). A complete chromatographic picture of the involved stereoisomers (four for Anti- and two for Syn-complexes) was achieved at very low temperatures (-53°C and -40°C respectively), at which the NHC-Ru bond rotations were frozen out. Inspection of the chromatographic profiles recorded at higher temperatures revealed the presence of plateau zones between the couples of either Syn or Anti stereoisomers, attesting to the active interconversion between the eluted species. Such dynamic chromatograms were successfully simulated through procedures based on both theoretical plate and classical stochastic models. The good superimposition achieved between experimental and simulated chromatographic profiles allowed determination of the related isomerization energy barriers (ΔGisom (#) ), all derived by rotation around the NHC-Ru bond. The obtained diastereomerization barriers between the Anti isomers were found in very good agreement with those previously measured by experimental nuclear magnetic resonance (NMR) and assessed through Density Functional Theory (DFT) calculations. With the same approach, for the first time we also determined the enantiomerization barrier of the Syn isomer. Focused changes to the structure of complex Syn, studied by a molecular modeling approach, were found suitable to strongly reduce the stereolability arising from rotation around the NHC-Ru bond.

Excited state free energy calculations of Cy3 in different environments

Cy3, a cyanine dye, is one of the most widely used dyes in investigating the structure and dynamics of biomolecules by means of fluorescence methods. However, Cy3 fluorescence emission is strongly competed by trans-cis isomerization, whose efficiency is dictated by the isomerization energy barrier and the environment of Cy3. The fluorescence quantum yield of Cy3 is very low when the dye is free in homogeneous solution but it is considerably enhanced in an environment that rigidifies the structure, e.g. when it is attached to a DNA strand. In this work, the barriers for isomerization on the excited state of free Cy3, and Cy3 attached to single- and double-stranded DNA in methanol, are presented. The free energy and subsequently the isomerization barrier calculations are performed using the umbrella sampling technique with the weighted histogram analysis method. The hybrid quantum mechanics/molecular mechanics (QM/MM) approach is employed to provide the potential energy surfaces for the excited state dynamics simulations in umbrella sampling. The semiempirical floating occupation molecular orbital configuration interaction method is used for electronic excited state calculations of the QM region (Cy3). From the free energy calculations, the barrier of Cy3 attached to the single-stranded DNA is highest, in agreement with previously reported experimental results. This is likely due to the stacking interaction between Cy3 and DNA. Such a stacking interaction is likely associated with steric hindrance that prevents the rotation around the conjugated bonds of Cy3. If Cy3 experiences high steric hindrance, it has a higher isomerization barrier and thus the efficiency of fluorescence emission increases.

Effect of Different Ionic Liquids on 5‐Hydroxymethylfurfural Preparation from Glucose in DMA over AlCl3: Experimental and Theoretical Study

AbstractIn this work, effect of different ionic liquids (ILs) on 5‐hydroxymethylfurfural (HMF) preparation from glucose in N,N‐dimethylacetamide (DMA) over AlCl3 was revealed by a combined experimental and computational study. ILs used as cocatalysts in this work included N‐methyl‐2‐pyrrolidone hydrogen sulfate ([NMP]HSO4), N‐methyl‐2‐pyrrolidone methyl sulfate ([NMP]CH3SO3), N‐methyl‐2‐pyrrolidone chlorine ([NMP]Cl) and N‐methyl‐2‐pyrrolidone bromide ([NMP]Br) which were endowed with the same cation but different anions. According to the conclusion that fructose was intermediate product from glucose to HMF, we found fructose was transformed to more by‐products by [NMP]HSO4, making HMF yield decline significantly when glucose was treated as substrate. Neither glucose nor fructose could be converted by [NMP]CH3SO3 efficiently, leading to its no influence on glucose conversion to HMF. [NMP]Br had a higher selectivity for HMF from fructose than [NMP]Cl and AlCl3. Besides, Al3+ preferred to combine with Br−, slightly decreasing both the overall free energy barrier for glucose isomerization and activation barrier for H‐shift at 393.15 K. So a high HMF yield of 57% was obtained from glucose catalyzed by AlCl3 together with [NMP]Br under mild conditions.

Direct measurement of the isomerization barrier of the isolated retinal chromophore.

Isomerizations of the retinal chromophore were investigated using the IMS-IMS technique. Four different structural features of the chromophore were observed, isolated, excited collisionally, and the resulting isomer and fragment distributions were measured. By establishing the threshold activation voltages for isomerization for each of the reaction pathways, and by measuring the threshold activation voltage for fragmentation, the relative energies of the isomers as well as the energy barriers for isomerization were determined. The energy barrier for a single cis-trans isomerization is (0.64±0.05) eV, which is significantly lower than that observed for the reaction within opsin proteins.

Conformational preferences of 3,4-dihydroxyphenylacetic acid (DOPAC)

The conformational space of 3,4-dihydroxyphenylacetic acid (DOPAC), an important dopamine metabolite, has been investigated by quantum chemical methods (B3LYP and MP2, with the 6-311++G(d,p) basis set) and matrix-isolation infrared spectroscopy. Detailed analysis of the calculated potential energy surfaces of the molecule led to identification of thirteen unique conformers, all of them showing the acetic acid side chain out of the aromatic ring plane by 60–95°. According to the calculated Gibbs energies, the five lowest energy conformers make up 99.7% of the conformational mixture at 298.15K, exhibiting individual populations falling between 16% and 24%. The main conformational trends of this molecule were interpreted on the grounds of a thorough analysis of the structural parameters and by the application of the Natural Bond Orbital theory. The role of the intramolecular interactions on the relative stability and structure of the conformers was also investigated. The infrared spectrum of DOPAC was registered after isolation of its monomers in argon and xenon matrices. Only one of DOPAC forms populated in the gas phase could be trapped in both matrix gases. This result is in agreement with the predicted low energy barriers for conformational isomerization and is also supported by annealing experiments. The spectra of matrix-isolated model compounds, phenylacetic acid and catechol, were studied under the same experimental conditions. These data were used as references and assisted in the interpretation of the results obtained for DOPAC.

Theoretical investigation of the effect of the solvent, hydrogen bond and amino group on the isomerization of Rhodamines

The isomerization between two forms of Rhodamine dyes, namely the lactone and zwitterion, have been investigated theoretically in solution phase at the B3LYP/6-31+G(d,p) level of theory with the polarizable continuum model (PCM). The isomerization energy barrier between the lactone and zwitterion of Rhodamine 110 in solvents of different polarity is calculated. The solvent polarity has little effect on the isomerization energy barrier of Rhodamine 110, though a linear correlation between the energy barrier and solvent polarity is found. The effect of the hydrogen bonds at five sites of Rhodamine 110 on the energy barrier of isomerization is investigated by the inclusion of an explicit methanol molecule in addition to the PCM approach. The energy barrier of Rhodamine dyes with different amino groups is calculated at the PCM-B3LYP/6-31+G(d,p) level of theory to clarify the role of the amino groups in the isomerization of Rhodamines. The change of the energy barrier is explained by the electrostatic repulsion between the xanthene ring and the carboxyl group as evidenced by the linear relation between the energy barrier of the isomerization and the lactonic C–O distance under different conditions. The relative energies of lactone and zwitterion, which are affected by solvent, hydrogen bonds and the amino groups, are also discussed.

Theoretical Study on the Isomerization Reaction Mechanism of the Chain-Isomers of N<sub>9</sub>H<sub>9</sub>

Density functional theory B3LYP method with 6-311++G** basis set has been used to optimize Chain-isomers of N9H9. Sixteen species are found, the structures, stabilities, thermochemical properties, and their tautomerism are studied and discussed. The ten corresponding transition states have been found. The experimental results indicated that the reaction energy barriers of isomerization of these isomers were between 139.56 kJ/mol and 236.67kJ/mol. The activation energies is higher, the isomerization of these isomers is relatively difficult. The isomerization processes of these chain-isomers of N9H9 are all completed by the H transfer.

Ab initio studies of isomerization and dissociation reactions of methyl peroxynitrate

Using the CCSD(T)/cc-pVDZ//B3LYP/6-311G(2d,2p) method, we calculated the detailed potential energy surfaces (PESs) for the unimolecular isomerization and decomposition of methyl peroxynitrate (CH3O2NO2). The results show that there are the two most stable isomers, IS1a and IS1b, which are a pair of mirror image isomers. From IS1a and IS1b, different isomerization and unimolecular decomposition reaction channels have been studied and discussed. Among them, the predominant thermal decomposition pathways are those leading to CH3O2 + NO2 and cis-CH3ONO + O2. The former is the lowest-energy path through the direct O–N bond rupture in IS1a or IS1b. The PES along the O–N bond in IS1a has been scanned, where the energy of IS1a reaches maximum value of 23.5 kcal/mol when the O–N bond is stretched to about 2.8 A. This energy is 2.7 kcal/mol larger than the O–N bond dissociation energy (BDE) and 2.8 kcal/mol larger than the experimental active energy. In addition, because the energy barriers of IS1a isomerization to IS2a are 23.8 kcal/mol, close to the 20.8 kcal/mol O–N BDE in IS1a or IS1b, the isomerization reaction may compete with the direct bond rupture dissociation reaction.

Mechanisms on electrical breakdown strength increment of polyethylene by acetophenone and its analogues addition: a theoretical study

A theoretical investigation is completed on the mechanism of electrical breakdown strength increment of polyethylene. It is shown that it is one of the most important factors for increasing electrical breakdown strength of polyethylene through keto-enol isomerization of acetophenone and its analogues at the ground state S0 and the lowest triplet state T1. The minimum structures and transition states of the keto- and the enol-tautomer of acetophenone and its analogues at the S0 and T1 states are obtained at the B3LYP/6-311+G(d,p) level, as well as the harmonic vibration frequencies of the equilibrium geometries and the minimum energy path (MEP) by the intrinsic reaction coordinate (IRC) theory at the same level. The two C-C bond cleavage reaction channels have been identified in acetophenone. The calculated results show that the energy barriers of keto-enol isomerization of acetophenone and its analogues at S0 and T1 states are much smaller than the average C-C bond energy of polyethylene, and the acetophenone doping or bond linked into polyethylene can increase the electrical breakdown strength and inhibit polyethylene electrical tree initiation and aging.

Wilcox Molecular Torsion Balance with Rigid Side Arm and Separable Atropisomers for Investigating CH−π Interactions

A new variant of the Wilcox molecular torsion balance featuring a naphthyl-alkyl side arm was synthesized. The energy barrier for axial isomerization in the new balance was sufficiently high to allow for separation of the two rotamers and to observe their isomerization kinetics. The CH-π interaction energies in derivatives of the new and the original ester balance were in close agreement, suggesting that the motion in ester linkage is not an important factor in folding in the ester balance.

The tautomerism influence on the antioxidant prediction of oxederavone

A detailed theoretical prediction of oxedaravone (a hydro-soluble derivative of edaravone) as antioxidant was performed. The DFT method with B3LYP/6-31G(d) basis sets was used for the tautomerism study in gas phase and solvent medium (water and methanol) and the antioxidant capacity was predicted from HOMO, ionization energy (IE), and bond dissociation energies (BDE). All calculations showed that the keto–enol tautomerism of oxedaravone is thermodynamically more favored than the imine–enamine tautomerism and the solvent effect reduced the isomerization energy barriers for the O–H or N–H tautomers. HOMO and IE values showed that the N–H tautomer is a better antioxidant, while the BDE values showed that the O–H tautomer is the better antioxidant. Our results showed that the oxedaravone may be a good strategy for designing polar derivatives of edaravone.

Characterizing New Molecular Species: A Systematic Study of Stationary States on the Singlet [H, Se, Br] Potential Energy Surface

Structural characterization, infrared spectra, relative stability, dissociation energies and energy barrier for isomerization of new molecular species, HSeBr and HBrSe, were investigated at a high level of theory, CCSD(T)/CBS. HSeBr is predicted to be 44.95 kcal mol-1 more stable than HBrSe, with a barrier (ΔG#) for isomerization of 52.24 kcal mol-1. Due to the much smaller barrier for the reverse reaction, if formed, the less stable isomer is expected to be readily converted to HSeBr, except at cryogenic temperatures. The possibility of dissociation into atomic Se and HBr is also a likely one by a spin-orbit coupling mechanism. Heats of formation of SeBr and HSeBr were estimated to be 31.54 and 12.31 kcal mol-1, respectively, at 298.15 K. The effect of core-valence correlation on the structural parameters and harmonic frequencies was also evaluated, as well as the contribution of anharmonicity to the frequencies. Additional calculations performed with explicitly correlated wavefunctions showed promising results of fast convergence to the complete basis set (CBS) limit with relatively smaller basis sets.

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.

Activation parameters of supercritical and gas-phase β-pinene thermal isomerization

New data on enthalpy and entropy contributions to the energy barrier of β-pinene thermal isomerization were obtained. The rate of β-pinene conversion is higher in supercritical EtOH (P = 120 atm) than in the gas phase (P ≤ 1 atm, without solvent, or for inert carrier gas N2) at equal temperatures. The highest activation energy EΣ of total β-pinene conversion is also observed in reactions in the supercritical (sc) condition. Activation parameters ΔHΣ#, ΔSΣ#, and ΔGΣ# depend strongly on the reaction pressure. Thus, at P ≤ 1 atm (gas-phase reaction) the values of ΔSΣ# are negative, while at sc conditions at P = 120 atm is positive. The linear dependences lnkΣ0 − EΣ and ΔSΣ# − ΔSΣ# indicate an isokinetic relation (IKR) and enthalpy-entropy compensation effect (EEC). The isokinetic temperature was calculated (Tiso = 605.5 ± 22.7 K). It was shown that elevation of temperature reduces the value of ΔGΣ#(T) upon sc thermolysis only, whereas in all gas-phase reactions ΔGΣ#(T) increases. At equal reaction temperatures, the greatest values of Keq#(T) proved to be typical for thermolysis in sc-EtOH. We hypothesize that the rate of total β-pinene conversion increases dramatically due to a considerable shift in equilibrium toward higher concentrations of activated complex yTS#. A detailed analysis of activation parameters shows that the IKR and EEC coincide, evidence of a common mechanism of β-pinene conversion observed under different reaction conditions, including thermolysis in sc-EtOH.

Switching of non-helical overcrowded tetrabenzoheptafulvalene derivatives

This study explores a series of non-helical overcrowded tetrabenzoheptafulvalene derivatives, which are different from the parent tetrabenzoheptafulvalene (1) by avoiding terminal C–C double bonds, detailing their synthesis, characterization and syn/antiisomerization. The most interesting findings from this study are that the syn and anti isomers of three overcrowded tetrabenzoheptafulvalene derivatives (3–5) can be switched by photo- and thermal isomerizations both in very high yields. The predominance of syn isomer in the photoisomerization has been explained with DFT calculations in terms of the arrangement of the excited- and ground-state potential energy surfaces. The less stable syn isomer of an overcrowded tetrabenzoheptafulvalene derivative thermally isomerizes to the corresponding anti isomer through seven-membered ring flipping, and the energy barrier of thermal isomerization is found to be directly related to the rigidity and crowdedness of the seven-membered rings. These findings suggest that overcrowded tetrabenzoheptafulvalene derivatives are promising building blocks for molecular switches and machines. In addition, the new synthesis and unambiguous characterization of hexabenzoheptafulvalene (4) have also led to correction of the previously claimed synthesis of hexabenzooctalene.

Comparison of two thioxopeptide bond photoswitches in insect kinin

The photoisomerization abilities of secondary thioxopeptide bond (CS–NH) and thioxo prolyl bond (CS–N) incorporated into the C-terminal pentapeptide of insect kinin were compared. H-Phe-Phe- ψ[CS–NH]- d-Ala-Trp-Gly-NH 2 and H-Phe-Tyr- ψ[CS–N]-Pro-Trp-Gly-NH 2 were studied by UV–vis absorption. The isomerization energy barriers of the two segments, Ac-Phe- ψ[CS–NH]- d-Ala-NH 2 and Ac-Tyr- ψ[CS–N]-Pro-NH 2 picked from the two peptides, were calculated using ab initio method. The cis isomer of CS–N is more stable than that of CS–NH due to higher energy barrier, so the former is more suitable in peptide structure–activity relationship studies.