Energy Barrier For Isomerization Research Articles

Impact of Protonation Sites on Collision-Induced Dissociation-MS/MS Using CIDMD Quantum Chemistry Modeling.

Protonation is the most frequent adduct found in positive electrospray ionization collision-induced mass spectra (CID-MS/MS). In a parallel report Lee, J. J. Chem. Inf. Model. 2024, 10.1021/acs.jcim.4c00760, we developed a quantum chemistry framework to predict mass spectra by collision-induced dissociation molecular dynamics (CIDMD). As different protonation sites affect fragmentation pathways of a given molecule, the accuracy of predicting tandem mass spectra by CIDMD ultimately depends on the choice of its protomers. To investigate the impact of molecular protonation sites on MS/MS spectra, we compared CIDMD-predicted spectra to all available experimental MS/MS spectra by similarity matching. We probed 10 molecules with a total of 43 protomers, the largest study to date, including organic acids (sorbic acid, citramalic acid, itaconic acid, mesaconic acid, citraconic acid, and taurine) as well as aromatic amines including uracil, aniline, bufotenine, and psilocin. We demonstrated how different protomers can converge different fragmentation pathways to the same fragment ions but also may explain the presence of different fragment ions in experimental MS/MS spectra. For the first time, we used in silico MS/MS predictions to test the impact of solvents on proton affinities, comparing the gas phase and a mixture of acetonitrile/water (1:1). We also extended applications of in silico MS/MS predictions to investigate the impact of protonation sites on the energy barriers of isomerization between protomers via proton transfer. Despite our initial hypothesis that the thermodynamically most stable protomer should give the best match to the experiment, we found only weak inverse relationships between the calculated proton affinities and corresponding entropy similarities of experimental and CIDMD-predicted MS/MS spectra. CIDMD-predicted mechanistic details of fragmentation reaction pathways revealed a clear preference for specific protomer forms for several molecules. Overall, however, proton affinity was not a good predictor corresponding to the predicted CIDMD spectra. For example, for uracil, only one protomer predicted all experimental MS/MS fragment ions, but this protomer had neither the highest proton affinity nor the best MS/MS match score. Instead of proton affinity, the transfer of protons during the electrospray process from the initial protonation site (i.e., mobile proton model) better explains the differences between the thermodynamic rationale and experimental data. Protomers that undergo fragmentation with lower energy barriers have greater contributions to experimental MS/MS spectra than their thermodynamic Boltzmann populations would suggest. Hence, in silico predictions still need to calculate MS/MS spectra for multiple protomers, as the extent of distributions cannot be readily predicted.

Helical Nanographenes Bearing Pentagon-Heptagon Pairs by Stepwise Dehydrocyclization.

The incorporation of pentagon-heptagon pairs into helical nanographenes lacks a facile synthetic route, and the impact of these pairs on chiroptical properties remains unclear. In this study, a method for the stepwise construction of pentagon-heptagon pairs in helical nanographenes by the dehydrogenation of [6]helicene units was developed. Three helical nanographenes containing pentagon-heptagon pairs were synthesized and characterized using this approach. A wide variation in the molecular geometries and photophysical properties of these helical nanographenes was observed, with changes in the helical length of these structures and the introduction of the pentagon-heptagon pairs. The embedded pentagon-heptagon pairs reduced the oxidation potential of the synthesized helical nanographenes. The high isomerization energy barriers enabled the chiral resolution of the helicene enantiomers. Chiroptical investigations revealed remarkably enhanced circularly polarized luminescence and luminescence dissymmetry factors with an increasing number of the pentagon-heptagon pairs.

Helical Nanographenes Bearing Pentagon‐Heptagon Pairs by Stepwise Dehydrocyclization

AbstractThe incorporation of pentagon‐heptagon pairs into helical nanographenes lacks a facile synthetic route, and the impact of these pairs on chiroptical properties remains unclear. In this study, a method for the stepwise construction of pentagon‐heptagon pairs in helical nanographenes by the dehydrogenation of [6]helicene units was developed. Three helical nanographenes containing pentagon‐heptagon pairs were synthesized and characterized using this approach. A wide variation in the molecular geometries and photophysical properties of these helical nanographenes was observed, with changes in the helical length of these structures and the introduction of the pentagon‐heptagon pairs. The embedded pentagon‐heptagon pairs reduced the oxidation potential of the synthesized helical nanographenes. The high isomerization energy barriers enabled the chiral resolution of the helicene enantiomers. Chiroptical investigations revealed remarkably enhanced circularly polarized luminescence and luminescence dissymmetry factors with an increasing number of the pentagon‐heptagon pairs.

Phenylazothiazoles as Visible-Light Photoswitches.

A novel class of photoswitches based on a phenylazothiazole scaffold that undergoes reversible isomerization under visible-light irradiation is reported. The photoswitch, which comprises a thiazole heteroaryl segment directly connected to a phenyl azo chromophore, has very different spectral characteristics, such as a redshifted absorption maximum wavelength and well-separated absorption bands of the trans and cis isomers, than conventional azobenzene and other heteroaryl azo compounds. Substituents at the ortho and para positions of the phenyl ring of the photoswitch resulted in a further shift to longer wavelengths up to 525 nm at the absorption maximum with a small thermal stability compensation. These photoswitches showed excellent photostationary distributions of the trans and cis isomers, thermal half-lives of up to 7.2 h, and excellent reductant stability. The X-ray crystal structure analysis revealed that the trans isomers exhibited a planar geometry and the cis isomers exhibited a T-shaped orthogonal geometry. Detailed ab initio calculations further demonstrated the plausible electronic transitions and isomerization energy barriers, which were consistent with the experimental observations. The fundamental design principles elucidated in this study will aid in the development of a wide variety of visible-light photoswitches for photopharmacological applications.

Theoretical Study on Photothermal Properties of Azobenzene Sulfonate/Magnesium-Aluminum Hydroxide Composite Dye.

The assembly of various azo dyes and pigments with inorganic layered materials could develop new types of intercalation materials. The electronic structures and photothermal properties of composite materials (AbS--LDH) constituted by azobenzene sulfonate anions (AbS-) and Mg-Al layered double hydroxide (LDH) lamella were theoretically studied at the M06-2X/def2-TZVP//M06-2X/6-31G(d,p) level using density functional theory and time-dependent density functional theory. Meanwhile, the influences of LDH lamella on the AbS- in AbS--LDH materials were investigated. The calculated results showed that the addition of LDH lamella could lower the isomerization energy barrier of CAbS- anions (CAbS- stands for cis AbS-). The thermal isomerization mechanisms of AbS--LDH and AbS were related to the conformational change of the azo group, out-of-plane rotation and in-plane inversion. The LDH lamella could reduce the energy gap of the n → π* and π → π* electronic transition and lead to a red-shift in the absorption spectra. When a polar solvent DMSO was applied, the excitation energy of the AbS--LDHs was increased, making its photostability stronger than in nonpolar solvent and solvent-free.

Structure Identification for Force-Induced Reaction Using Single-Molecule Conductance Measurement

Structure Identification for Force-Induced Reaction Using Single-Molecule Conductance Measurement

DFT and dynamic analysis of glucose alcoholysis conversion to 5-ethoxymethylfurfural and ethyl levulinate

An effective catalytic strategy for the conversion of glucose to 5-ethoxymethylfurfural (EMF) catalyzed by ultrastable Y zeolite (USY) in a co-solvent system was developed. Effects of co-solvent and reaction conditions were first investigated. Tetrahydrofuran (THF) with low dipolarity/polarizability (π*) was screened as the appropriate co-solvent, and a higher EMF yield of 41.46% was obtained as the ratio of ethanol to THF was 7:3. The macroscopic reaction kinetic study indicated that THF can protect EMF from easy degradation to EL. Moreover, the reusability and the characterization of USY verified the feasibility of USY as an efficient solid acid catalyst. In this study, density functional theory (DFT) calculations for the catalytic mechanism and solvent effect at the molecular scale were performed for the first time. The extra-framework aluminum species (EFAL), in which Al3+ played an essential role in the reaction as the preferred EFAL species, and THF can reduce the energy barrier of USY-catalyzed glucose isomerization. Meanwhile, the inhibitory effect of THF on EMF alcoholysis was explored via the frontier molecular orbital theory. The results showed that THF increased the LUMO energy of EMF compared with ethanol and γ-valerolactone, which decreased its susceptibility to nucleophilic attack and reduced the adverse alcoholysis of EMF and humins formation. This study provided an enlightening reference for the efficient synthesis of EMF from carbohydrates catalyzed by solid acid catalyst under solvent effect.

Five-Fold Symmetric Pentaindolo- and Pentakis(benzoindolo)Corannulenes: Unique Structural Dynamics Derived from the Combination of Helical and Bowl Inversions.

Peripherally π-extended corannulenes bearing quintuple azahelicene units, 10 and 11, were prepared and their dynamic behaviors were studied experimentally and theoretically. The fused corannulenes were synthesized from sym-pentabromocorannulene in three steps. X-Ray diffraction analysis for 10 displayed a conformer possessing a P(M) bowl chirality and a PPMPM (PMPMM) helical chirality, which was found to be the most stable conformer(s). Variable-temperature NMR measurements of 10 and 11 revealed that their structural isomers can be interconvertible in solution, depending on the steric congestion around the helical scaffolds. Automated search for conformers in the equilibrium and transition states by Artificial Force Induced Reaction (AFIR) method revealed their interconversion networks, including bowl-inversion and helical-inversion. This analysis indicated that the co-existing corannulene and azahelicene moieties influence the conformational dynamics, which leads to mitigation of the activation energy barriers for isomerization.

Five‐Fold Symmetric Pentaindolo‐ and Pentakis(benzoindolo)Corannulenes: Unique Structural Dynamics Derived from the Combination of Helical and Bowl Inversions

AbstractPeripherally π‐extended corannulenes bearing quintuple azahelicene units, 10 and 11, were prepared and their dynamic behaviors were studied experimentally and theoretically. The fused corannulenes were synthesized from sym‐pentabromocorannulene in three steps. X‐Ray diffraction analysis for 10 displayed a conformer possessing a P(M) bowl chirality and a PPMPM (PMPMM) helical chirality, which was found to be the most stable conformer(s). Variable‐temperature NMR measurements of 10 and 11 revealed that their structural isomers can be interconvertible in solution, depending on the steric congestion around the helical scaffolds. Automated search for conformers in the equilibrium and transition states by Artificial Force Induced Reaction (AFIR) method revealed their interconversion networks, including bowl‐inversion and helical‐inversion. This analysis indicated that the co‐existing corannulene and azahelicene moieties influence the conformational dynamics, which leads to mitigation of the activation energy barriers for isomerization.

Structural Diversity of Di-Metalized Arginine Evidenced by Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy in the Gas Phase.

Although metal cations are prevalent in biological media, the species of multi-metal cationized biomolecules have received little attention so far. Studying these complexes in isolated state is important, since it provides intrinsic information about the interaction among them on the molecular level. Our investigation here demonstrates the unexpected structural diversity of such species generated by a matrix-assisted laser desorption ionization (MALDI) source in the gas phase. The photodissociation spectroscopic and theoretical study reflects that the co-existing isomers of [Arg+Rb+K−H]+ can have energies ≥95 kJ/mol higher than that of the most stable one. While the result can be rationalized by the great isomerization energy barrier due to the coordination, it strongly reminds us to pay more attention to their structural diversities for multi-metalized fundamental biological molecules, especially for the ones with the ubiquitous alkali metal ions.

Facile Access to Polar-Functionalized Ultrahigh Molecular Weight Polyethylene at Ambient Conditions

Facile Access to Polar-Functionalized Ultrahigh Molecular Weight Polyethylene at Ambient Conditions

What Leads to Aggregation-Induced Emission?

Aggregation-induced emission (AIE), usually referring to the phenomenon in which molecules emit more strongly in the aggregate state than in the solution state, is intriguing and promising in various optoelectronic and biosensing applications. In this Perspective, the basic principles that can lead to AIE and experimental evidence to reveal the AIE mechanism of tetraphenyl ethylene (TPE)-type molecules are discussed. AIE is the consequence of two factors: (1) the fast energy dissipation by crossing a conical intersection (CI) in solutions but not in solids results in low luminescence efficiencies in the solutions, and (2) the weak intermolecular coupling and thus slow intermolecular energy/charge transfers in the AIE solids effectively prevent quenching and result in relatively high luminescence efficiencies. The key to AIE is that the luminescence efficiency is tuned by controlling molecules to cross or not to cross a CI by changing the phase of molecules. How fast a molecule can cross a CI is dependent on the energy barrier of isomerization, which can be tuned in many ways, including mechanical or electrical stimuli, in addition to changing phases. Barrier-dependent crossing CI also results in a very important consequence: excitation-wavelength-dependent fluorescence yield within one electronic excited state, an anti-Vavilov's rule phenomenon. In principle, there can be an alternative way to tune luminescence efficiency by manipulating the formation of CIs instead of crossing or not crossing them. This approach relies on the fact that the electronic ground state and the excited state have many different properties, e.g., dipole moment. By tuning the environment, e.g., dielectric constant, to favor or disfavor one state, one may be able to lift or lower the potential surface of one state so that the potential surfaces of two states can vary between intersected and not contacted.

Effect of Molecular Substitution and Isomerization on Charge-Transport Parameters in Molecular Organic Semiconductors.

Charge transport in an organic semiconductor is strongly dependent on the molecular packing motif, which could be modified by the molecular substitutions and molecular isomerization. We constructed a series of benzodithiophene-based organic semiconductor molecules with different silyethyne substitutions and isomers. The existence of different conformations of these molecules is supported by a low isomerization energy barrier from density functional theory. By using Marcus semiclassical theory calculation, we make a comprehensive assessment for the effect of molecular substitution and isomerization on charge transport. We found that the hole mobility of cis-isomer molecular packing can be enhanced by increasing the length of silylethyne substitutions. We demonstrated that a favorable charge-transport material would possess an identical direction of induced ring currents, stable induced magnetic fields, and dominant π-π stacking interaction in their molecular packing motif to ensure good π-overlap area. Our findings will provide direct guidance for developing organic semiconductor materials.

Effect of Iodine Filler on Photoisomerization Kinetics of Photo-Switchable Thin Films Based on PEO-BDK-MR.

We report the effect of an iodine filler on photoisomerization kinetics of photo-switchable PEO-BDK-MR thin films. The kinetics of photoisomerization and time progression of PEO-BDK-MR/I2 nanocomposite thin films are investigated using UV-Vis, FTIR spectroscopies, and modified mathematical models developed using new analytical methods. Incorporating iodine filler into the PEO-BDK-MR polymeric matrix enhances the isomerization energy barrier and considerably increases the processing time. Our outcomes propose that enhanced photoisomerized and time processed (PEO-BDK-MR)/I2 thin films could be potential candidates for a variety of applications involving molecular solar thermal energy storage media.

The energy components of the extended transition state energy decomposition analysis are path functions: the case of water tetramer

A recent paper (Phys. Chem. Chem. Phys. 2020, 22:22,459) shows that the energy components of the extended transition state energy decomposition analysis (ETS-EDA) are path functions, and therefore, they are not uniquely defined. In this work, we apply the ETS-EDA to analyse all possible dissociation paths of the water tetramer to four free water molecules. Our results confirm that the energy components of the ETS-EDA are path functions. However, they also show that differences among energy components obtained for the different paths are relatively small, and therefore, we conclude that the information obtained from an ETS-EDA can be used to discuss the nature of chemical bonds and analyse the origin of isomerization energies and energy barriers. However, if a given process can be attained by means of different and chemically reasonable paths, we recommend to perform the ETS-EDA of a given reaction for all different paths to confirm that energy components of the ETS-EDA do not differ very much from one path to another.

Absorption and Emission Spectroscopic Investigation of the Thermal Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor Archon2.

Archon2 is a fluorescent voltage sensor derived from Archaerhodopsin 3 (Arch) of Halorubrum sodomense using robotic multidimensional directed evolution approach. Here we report absorption and emission spectroscopic studies of Archon2 in Tris buffer at pH 8. Absorption cross-section spectra, fluorescence quantum distributions, fluorescence quantum yields, and fluorescence excitation spectra were determined. The thermal stability of Archon2 was studied by long-time attenuation coefficient measurements at room temperature (21 ± 1 °C) and at refrigerator temperature (3 ± 1 °C). The apparent melting temperature was determined by stepwise sample heating up and cooling down (obtained apparent melting temperature: 63 ± 3 °C). In the protein melting process protonated retinal Schiff base (PRSB) with absorption maximum at 586 nm converted to de-protonated retinal Schiff base (RSB) with absorption maximum at 380 nm. Storage of Archon2 at room temperature and refrigerator temperature caused absorption coefficient decrease because of partial protein clustering to aggregates at condensation nuclei and sedimentation. At room temperature an onset of light scattering was observed after two days because of the beginning of protein unfolding. During the period of observation (18 days at 21 °C, 22 days at 3 °C) no change of retinal isomer composition was observed indicating a high potential energy barrier of S0 ground-state isomerization.

On the Discrepancy between Experimental and Calculated Raman Intensities for Conjugated Phenyl and Thiophene Derivatives.

Compared with experimental spectra, calculations for conjugated phenyl and thiophene oligomers tend to overestimate the ground state Raman intensities of higher-frequency vibrations (1200-1800 cm-1) relative to the intensities at lower frequencies (<1200 cm-1). The discrepancy was observed in previous benchmarking work that examined the method dependence of the calculated Raman spectra for a series of aromatic molecules. This paper further investigates the nature of the discrepancy by examining the role of anharmonic corrections and the dependence of the calculated Raman spectra on the inter-ring torsion angle for the representative molecules biphenyl (BP), 2-phenylthiophene (PT), and 2,2'-bithiophene (BT). Perturbative anharmonic corrections to the spectra calculated using density functional theory (DFT) provide only slightly better agreement with experiment. On the other hand, calculations at larger torsion angles give up to 30% improvement in the relative Raman intensities compared with the spectra calculated at the optimized geometries. The torsion-angle dependence of the Raman intensities is most pronounced for delocalized C-C and C-S stretching modes, and less pronounced for bending and ring distortion modes that do not involve inter-ring stretching. Higher-level calculations using the coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] method indicate that DFT underestimates the energy barrier for torsion isomerization at small angles, and it overestimates the barriers at large angles, thus predicting minimum geometries at torsion angles that are too small. Therefore, the results suggest that the discrepancy in relative Raman intensities may be related to an overestimation of inter-ring conjugation by DFT, which also tends to favor geometries that are too planar.

IRMPD Spectra of Protonated Hydroxybenzaldehydes: Evidence of Torsional Barriers in Carboxonium Ions

Protonation at the formyl oxygen atom of benzaldehydes leading to the formation of carboxonium ions yields two distinct isomers, depending on the relative orientation of the proton either cis or trans with respect to the hydrogen atom on the adjacent carbon. In this context, the IR multiple photon dissociation (IRMPD) spectra of protonated ortho, meta, and para-hydroxybenzaldehydes (OH-BZH+ ), delivered into the gas phase by electrospray ionization of hydro-alcoholic solutions, are reported in the 3200-3700 cm-1 spectral range. This range is characteristic of O-H stretching modes and thus able to differentiate cis and trans carboxonium isomers. Comparison between IRMPD spectra and DFT calculations at the B3LYP/6-311++G(2df2p) level suggests that for both p-OH-BZH+ and m-OH-BZH+ only cis conformers are present in the ion population analyzed. For o-OH-BZH+ , IRMPD spectroscopy points to a mixture comprising one trans and more than one cis conformers. The energy barrier for cis-trans isomerization calculated for each OH-BZH+ isomer is a measure of the degree of π-electron delocalization. Furthermore, IRMPD spectra of p-OH-BZH+ , m-OH-BZH+ and protonated phenol (this last used as reference) were recorded also in the fingerprint range. Both the observed C-O and O-H stretching vibrations appear to be a measure of π-electron delocalization in the ions.

Experimental and kinetic modeling investigation on ethylcyclohexane low-temperature oxidation in a jet-stirred reactor

In this work, the oxidation of ethylcyclohexane was studied in a jet-stirred reactor at 780 Torr, 480–780 K and equivalence ratios of 0.5, 1.0 and 2.0. Synchrotron vacuum ultraviolet photoionization mass spectrometry (SVUV-PIMS) was used for the detection of oxidation products, including a series of reactive intermediates such as cycloalkylhydroperoxides, keto-hydroperoxides, alkenal-hydroperoxides and highly oxygenated molecules. Quantum chemistry calculations were performed to obtain ionization energies for the identification of some important intermediates and energy barriers of several important pathways. On the other hand, this work presents the first efforts on developing a low-temperature oxidation model of ethylcyclohexane. The present model can reasonably capture the low-temperature oxidation reactivities and negative temperature coefficient behaviors observed in both present and previous experimental work of ethylcyclohexane oxidation. Modeling analyses were performed to provide insight into the low-temperature oxidation chemistry of ethylcyclohexane. The two-stage O2 addition mechanism is concluded to dominate the chain-branching process in the low-temperature region. The concerted elimination reactions of cycloalkylperoxy radical and “formally direct” chemically activated reactions of cycloalkyl+O2 result in cycloalkenes and HO2 formation at the negative temperature coefficient region and serve as main chain-termination pathways. Compared with smaller cycloalkanes like cyclohexane and methylcyclohexane, the ethyl sidechain structure in ethylcyclohexane reduces the energy barriers of cycloalkylperoxy radical isomerization and facilitates the formation of keto-hydroperoxides which leads to more pronounced low-temperature oxidation reactivity of ethylcyclohexane.

Ab initio structure and vibration-rotation dynamics of the formyl and isoformyl cations, HCO+/HOC.

Accurate structure and potential energy surface of the formyl and isoformyl cation system, HCO+/HOC+, in its ground electronic state X̃ 1Σ+ have been determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent basis sets up to septuple-zeta quality. Both the isomers are confirmed to be linear at equilibrium, with the total energy minimum of HOC+ lying 14 120 cm-1 above that of HCO+ and the HCO+ → HOC+ isomerization energy barrier being 26 870 cm-1 (in the Born-Oppenheimer approximation). The equilibrium structural parameters for HCO+ are estimated to be re(HC) = 1.0919 Å and re(CO) = 1.1058 Å, whereas those for HOC+ are estimated to be re(HO) = 0.9899 Å and re(CO) = 1.1544 Å. The vibration-rotation energy levels were predicted for various isotopologues using a variational approach and compared with the experimental data. For the spectroscopically well characterized formyl cation, the observed vibration-rotation energies and the effective rotational constants are reproduced to within about 2.3 cm-1 and 1.7 MHz, respectively. The role of the core-electron correlation, higher-order valence-electron correlation, scalar relativistic, and adiabatic effects in determining the structure and vibration-rotation dynamics of both the isomers is discussed.