Isomerization Barrier Research Articles

Accurate CHIPR Potential Energy Surface for the Lowest Triplet State of C3.

We report the first global ab initio-based potential energy surface (PES) for ground-state triplet C3(3A') based on accurate energies extrapolated to the complete basis set (CBS) limit, and using the combined-hyperbolic-inverse-power-representation method for the analytical modeling. By relying on a cost-effective CBS(D,T) protocol, we ensure that the final form reproduces all topographical features of the PES, including its cyclic-linear isomerization barrier, with CBS(5,6)-quality. To partially account for the incompleteness of the N-electron basis and other minor effects, the available accurate experimental data on the relevant diatomics were used to obtain direct-fit curves that replace the theoretical ones in the many-body expansion. Besides describing properly long-range interactions at all asymptotic channels and permutational symmetry by built-in construction, the PES reported here reproduces the proper exothermicities at dissociation regions as well as the spectroscopy of the diatomic fragments. Bound vibrational state calculations in both linear and cyclic isomers have also been carried out, unveiling a good match of the available data on C3(ã 3Πu), while assisting with IR band positions for C3(3A2') that may serve as a guide for its laboratory and astronomical detection.

Forging tools for refining predicted protein structures

Refining predicted protein structures with all-atom molecular dynamics simulations is one route to producing, entirely by computational means, structural models of proteins that rival in quality those that are determined by X-ray diffraction experiments. Slow rearrangements within the compact folded state, however, make routine refinement of predicted structures by unrestrained simulations infeasible. In this work, we draw inspiration from the fields of metallurgy and blacksmithing, where practitioners have worked out practical means of controlling equilibration by mechanically deforming their samples. We describe a two-step refinement procedure that involves identifying collective variables for mechanical deformations using a coarse-grained model and then sampling along these deformation modes in all-atom simulations. Identifying those low-frequency collective modes that change the contact map the most proves to be an effective strategy for choosing which deformations to use for sampling. The method is tested on 20 refinement targets from the CASP12 competition and is found to induce large structural rearrangements that drive the structures closer to the experimentally determined structures during relatively short all-atom simulations of 50 ns. By examining the accuracy of side-chain rotamer states in subensembles of structures that have varying degrees of similarity to the experimental structure, we identified the reorientation of aromatic side chains as a step that remains slow even when encouraging global mechanical deformations in the all-atom simulations. Reducing the side-chain rotamer isomerization barriers in the all-atom force field is found to further speed up refinement.

Fully versus constrained statistical fragmentation of carbon clusters and their heteronuclear derivatives.

The Microcanonical Metropolis Monte Carlo (MMMC) method has been shown to describe reasonably well fragmentation of clusters composed of identical atomic species. However, this is not so clear in the case of heteronuclear clusters as some regions of phase space might be inaccessible due to the different mobility of the different atomic species, the existence of large isomerization barriers, or the quite different chemical nature of the possible intermediate species. In this paper, we introduce a constrained statistical model that extends the range of applicability of the MMMC method to such mixed clusters. The method is applied to describe fragmentation of isolated clusters with high, moderate, and no heteronuclear character, namely, CnHm, CnN, and Cn clusters for which experimental fragmentation branching ratios are available in the literature. We show that the constrained statistical model describes fairly well fragmentation of CnHm clusters in contrast with the poor description provided by the fully statistical model. The latter model, however, works pretty well for both Cn and CnN clusters, thus showing that the ultimate reason for this discrepancy is the inability of the MMMC method to selectively explore the whole phase space. This conclusion has driven us to predict the fragmentation patterns of the C4N cluster for which experiments are not yet available.

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).

Intrinsic photoisomerization dynamics of protonated Schiff-base retinal

The retinal protonated Schiff-base (RPSB) in its all-trans form is found in bacterial rhodopsins, whereas visual rhodopsin proteins host 11-cis RPSB. In both cases, photoexcitation initiates fast isomerization of the retinal chromophore, leading to proton transport, storage of chemical energy or signaling. It is an unsolved problem, to which degree this is due to protein interactions or intrinsic RPSB quantum properties. Here, we report on time-resolved action-spectroscopy studies, which show, that upon photoexcitation, cis isomers of RPSB have an almost barrierless fast 400 fs decay, whereas all-trans isomers exhibit a barrier-controlled slow 3 ps decay. Moreover, formation of the 11-cis isomer is greatly favored for all-trans RPSB when isolated. The very fast photoresponse of visual photoreceptors is thus directly related to intrinsic retinal properties, whereas bacterial rhodopsins tune the excited state potential-energy surface to lower the barrier for particular double-bond isomerization, thus changing both the timescale and specificity of the photoisomerization.

Broadband rotational spectroscopy of trans 3-pentenenitrile and 4-pentenenitrile.

Titan, a moon of Saturn, has a nitrogen- and methane-rich atmosphere that is similar to prebiotic earth, and is replete with organic nitriles. Pentenenitriles have not yet been detected in Titan's atmosphere or in molecular clouds, but are potential precursors to hetero-aromatic compounds such as pyridine. We performed broadband microwave studies in the 8-18 GHz range on the trans isomer of 3-pentenenitrile (3-PN) and 4-pentenenitrile (4-PN) under jet-cooled conditions. Strong-field coherence breaking (SFCB) was used to selectively modulate the intensities of microwave transitions in a conformer-specific manner for 3-PN, aiding analysis. Two conformers of 3-PN and five conformers of 4-PN were identified and the rotational transitions were assigned. Evidence for methyl internal rotation splitting was observed for both the conformers of 3-PN, and the barrier heights of both conformers was determined experimentally. Comparison is made of the conformational preferences, stability and isomerization barriers through the acquired rotational spectra and potential energy surface (PES) calculations of the structural isomers 3-PN and 4-PN.

The possibility of :CNH[formula omitted] within Titan’s atmosphere: Rovibrational analysis of :CNH[formula omitted] and :CCH2

The highest peak in Cassini’s INMS data for stratospheric flybys of Titan’s atmosphere is m/z=28. While this has mostly been attributed to HCNH+, minor contributions from N2+ and C2H2+ are also likely. However, this work shows that :CNH2+ may also be present in a kinetically-favorable potential well based on high-level quantum chemical computations. The ionization energy of N2 is much higher than the isomerization barrier between HCNH+ and :CNH2+. As such, we present computations that provide vibrational and rotational spectroscopic data for the possible remote sensing of this molecule in Titan’s atmosphere. Such data are also computed for the isoelectronic :CCH2 molecule, and comparison to previous laboratory experiments and quantum chemical computations, where available for the hydrocarbon, is excellent. Consequently, the data provided in this work should allow for initial searches for :CNH2+ as well as refinements of data for :CCH2 both in the laboratory and even in Titan’s atmosphere.

Computational characterization of the herbicide metolachlor and its mono-hydroxylated photodegradation products

Electronic structure calculations have been performed for the characterization of the different conformers of the herbicide metolachlor (MC), (2-chloro-N-(2-methyl-6-ethylphenyl)-N-(2-methoxy-1-methylethyl) acetamide), the radical structures obtained through the photo chemical breaking of the C–Cl bond and the most important, experimentally identified mono-hydroxylated photo-fragmentation products. Only the S-metolachlor enantiomer that shows herbicide activity was studied. The goal of the study has been twofold. The first target has been the conformational analysis of the neutral molecule and the corresponding radical. Ten different conformers were identified for the S-metolachlor enantiomer, all of them exhibiting a near perpendicular disposition of the amidyl and the phenyl planes. They were classified into two families of minima depending on the orientation of the carbonyl group (either cis or trans with respect to the phenyl ring). All the minima in the S-cis family were found to lie higher than those in the S-trans family. The free energy of isomerization between the lowest minima of each family was found to be $$ \Delta G_{298}^{0} $$ = 6.2 kcal/mol, while the isomerization barrier around the amide C–N bond causing atropisomerism was calculated to be 34.9 kcal/mol (in good agreement with the experimental energy of activation, 36.9 ± 3 kcal/mol) [45]. The second part of the work is devoted to the computational characterization of the most important isomeric forms of the metolachlor radical and the major photodegradation mono-hydroxylated metabolites formed through the coupling of the metolachlor radical with OH. Reaction enthalpies and free energies for the various hydroxylation pathways have been calculated. Based on their order, the relative significance of the various hydroxylation channels is justified and the preference in the phenyl ring hydroxylation is established. The lowest exothermicity value determined, − 5.8 kcal/mol at the M06/6-31 + G(d,p) level, corresponds to phenyl group hydroxylation at the p-position with regard to C–N bond, in excellent agreement with the experimental findings.

Photo-responsive foam control base on nonionic azobenzene surfactant as stabilizer

A nonionic photo-responsive surfactant (NPS) was synthesized for obtaining photo control of foamability, exposed in ultraviolet (UV) light or visible (Vis) light irradiation. The foamability depended on the surface activity of NPS, which possessed low critical micelle concentration (CMC) and high adsorption capacity compared with the similar type of nonionic surfactants. The azobenzene component in NPS as the light-responsive group, showed high sensitive and reversibility, i.e., the trans → cis isomerization occurred only for 1 s and the time to reach reversible isomerization was 85 s. And the fatigue resistance of isomerization was also outstanding, which remained stable for 14 cycles of alternate irradiation. Due to the lack of free volume and increase of barrier for isomerization, the irradiation time and first-order kinetics of isomerization decreased with the increase of NPS concentration. The foaming ratio and foam stability promoted with the NPS concentration increase, however, the stereospecific blockade amongst cis isomers was stronger than that of trans isomers, resulting in the steep decrease of foam half-life. The sustainable foam stability control of NPS applied into foam dyeing to solve the problem of residual foam.

Predicting the Initial Thermal Decomposition Path of Nitrobenzene Caused by Mode Vibration at Moderate-Low Temperatures: Temperature-Dependent Anti-Stokes Raman Spectra Experiments and First-Principals Calculations.

The lack of understanding of the initial decomposition micromechanism of energetic materials subjected to external stimulation has hindered its safe storage, usage, and development. The initial thermal decomposition path of nitrobenzene triggered by molecular thermal motion is investigated using temperature-dependent anti-Stokes Raman spectra experiments and first-principles calculations to clarify the initial thermal decomposition micromechanism. The experiment shows that the symmetric nitro stretching, antisymmetric nitro stretching, and phenyl ring stretching vibration modes are active as increasing temperature below 500 K. The DFT method is used to examine the effects of the three mode vibrations on the initial decomposition of nitrobenzene by relaxed scan for each relevant change in bond lengths and bond angles to obtain the optimal reaction channel leading to initial thermal decomposition of nitrobenzene. The results demonstrate that the initial thermal decomposition is the isomerization of nitrobenzene to phenyl nitrite. The optimal reaction channel leading to the initial isomerization is the increase or decrease of angle O-N-C from the antisymmetric nitro stretching vibration, which causes the torsion of nitro group and the subsequent oxygen atom attacking carbon atom. The scanning energy barrier related to angle O-N-C is about 62.1 kcal/mol, which is very consistent with the calculated activation barrier of isomerization of nitrobenzene. This proves the reliability of our conclusions.

Density Functional Studies on Secondary Amides: Role of Steric Factors in Cis/Trans Isomerization.

Cis/trans isomerization of amide bonds is a key step in a wide range of biological and synthetic processes. Occurring through C-N amide bond rotation, it also coincides with the activation of amides in enzymatic hydrolysis. In recently described QM studies of cis/trans isomerization in secondary amides using density functional methods, we highlighted that a peptidic prototype, such as glycylglycine methyl ester, can suitably represent the isomerization and complexities arising out of a larger molecular backbone, and can serve as the primary scaffold for model structures with different substitution patterns in order to assess and compare the steric effect of the substitution patterns. Here, we describe our theoretical assessment of such steric effects using tert-butyl as a representative bulky substitution. We analyze the geometries and relative stabilities of both trans and cis isomers, and effects on the cis/trans isomerization barrier. We also use the additivity principle to calculate absolute steric effects with a gradual increase in bulk. The study establishes that bulky substitutions significantly destabilize cis isomers and also increases the isomerization barrier, thereby synergistically hindering the cis/trans isomerization of secondary amides. These results provide a basis for the rationalization of kinetic and thermodynamic properties of peptides with potential applications in synthetic and medicinal chemistry.

Well-Defined Palladium(II)-NHC Precatalysts for Cross-Coupling Reactions of Amides and Esters by Selective N-C/O-C Cleavage.

Transition-metal-catalyzed cross-coupling reactions represent a most powerful tool for the rapid construction of C-C and C-X bonds available to synthetic chemists. Recently, tremendous progress has been made in the burgeoning area of cross-coupling reactions of amides and esters enabled by regio- and chemoselective acyl C-X (X = N, O) cleavage using well-defined Pd(II)-NHC complexes. The use of N-heterocyclic carbenes as ligands in palladium-catalyzed cross-couplings permits reactions of amides and esters that were previously impossible using palladium or could be achieved only under harsh conditions. These reactions provide an attractive method to synthetic chemists to manipulate the traditionally inert amide and ester bonds with the broad cross-coupling generality inherent to palladium catalysis. Research in the area of cross-coupling of stable acyl electrophiles can be broadly categorized by the type of electrophile undergoing the cross-coupling. Recent studies have shown that cross-coupling of amides by transition-metal catalysis represents one of the most straightforward and wide-ranging ways of manipulating the classically inert amide bonds into generic acyl-metal intermediates that can be systematically exploited in cross-coupling reactions as a new paradigm in organic synthesis. The key to achieving high chemoselectivity of the process is control of amidic resonance (nN to πC═O* conjugation, rotation of ca. 15-20 kcal/mol in planar amides), enabling oxidative addition of the N-C amide bond to a metal in a rational and predictable manner. This mode of catalysis has been extended to C(acyl)-O cross-coupling reactions of aryl esters, where selective C-O bond cleavage is accomplished through a rational match of aryl ester electrophiles and nucleophilic metal catalysts. These two types of transition-metal-catalyzed cross-coupling reactions represent an attractive concept in synthetic chemistry because of the ubiquity of esters and amides as precursors in organic synthesis. Furthermore, the high stability of amides and esters provides unprecedented opportunities for orthogonal cross-coupling strategies in the presence of other electrophiles. In this Account, we highlight advances that have taken place in the past few years in the field of cross-coupling of amides and esters, focusing on both (1) the stereoelectronic properties of well-defined Pd(II)-NHC complexes that have been critical to realize this challenging cross-coupling manifold and (2) the role of the isomerization barrier of the acyl electrophiles undergoing the cross-coupling. In a broader sense, the chemistry described here provides a practical approach to functionalize common amide and ester functional groups in organic synthesis and establishes straightforward access to acyl-metal intermediates that enable nonconventional cross-coupling strategies.

Temperature-Dependent Infrared Photodissociation Spectroscopy of (CO2)3+ Cation.

Infrared photodissociation spectra of He-buffer-gas-cooled (CO2)3+ were measured at ion trap temperatures of 15, 50, 150, and 280 K. Electronic structure calculations at the mPW2PLYPD/aug-cc-pVDZ level were performed to identify the structures of the low-lying isomers and to assign the observed spectral features. The experimental and calculated infrared spectra show that the (CO2)3+ cations formed in the source are primarily dominated by the charge partially delocalized C2O4+ motif, in which the positive charge is partially delocalized over the two CO2 molecules. Thermal heating at elevated internal temperature supplies sufficient energy to overcome the isomerization barriers and gives access to the charge completely delocalized (CO2) n+ ( n = 3) motif, in which the positive charge is almost completely delocalized over all of the constituent CO2 molecules.

Theoretical calculations of photoelectron spectrum of (Au–CO2)− anion

Photoelectron spectra of the (Au–CO2)− anion complex have been calculated using both quantum path-integral and classical molecular dynamics methods to interpret the experimentally measured spectrum, showing a double-peak feature corresponding to two different anion configurations of Au·CO2− and Au−·CO2. The anionic potential energy surfaces have been developed on the basis of density-functional theory calculation results obtained with several different levels. We found that the calculated photoelectron spectra significantly depend on the relative energies of these two isomers and the isomerization barrier heights. Nuclear quantum effects are playing important roles for obtaining reliable spectra through vibrational quantization. The present calculations also suggest that the photoelectron spectrum intensity around the overlap region of the two anion peaks can provide a fingerprint of the Au·CO2− ↔ Au−·CO2 reaction.

Method Calibration or Data Fitting?

We investigate by explicit parameter optimization to what extent basis sets of polarized double-ζ quality can introduce compensating errors in five different density functional methods. It is shown that minor changes in the contraction coefficients of the valence functions in the basis sets can have a significant impact and allow different density functional methods to achieve very similar performances. This holds for nuclear magnetic shielding constants and for isomerization energies, barrier heights, and noncovalent interactions. It is furthermore shown that errors due to neglect of vibrational and solvent effects can be absorbed in the combined method and basis set errors. These findings hold for data sets consisting of 50-150 data points. This raises the question of whether the common practice of identifying combinations of density functional methods and basis sets that have a good performance against a selected set of reference data should be considered as data fitting in the combined parameter space spanned by the method and basis set.

Infrared Spectroscopy of Protonated Phenol-Water Clusters.

To explore the microhydration structures of protonated phenol, size-selective infrared spectroscopy of protonated phenol-(water) n clusters ( n = 1-5) was performed. The protonation of phenol can occur either at the phenyl ring or at the hydroxy group. The coexistence of the two isomer types separated by the high isomerization barrier was reconfirmed for bare protonated phenol. Preferential hydration of the hydroxy group initially occurs in both the two isomer types of protonated phenol. Development of the water hydrogen-bond network is localized around the hydroxy group up to n = 2. Intracluster proton transfer from the phenol moiety to the water moiety was observed in n ≥ 3-4. The water moiety with the H3O+ ion core resides on the phenyl ring, and the water moiety is bound to the phenyl ring with a π-hydrogen bond. Such a structure is in striking contrast to those of phenol+-(water) n radical cation clusters, in which the water moiety is located away from the phenyl ring even when intracluster proton transfer occurs.

Sequential Metal-Free Thermal 1,3-Dipolar Cycloaddition of Unactivated Azomethine Ylides.

The thermal 1,3-dipolar cycloaddition of unactivated azomethine ylides derived from allylamine and aromatic or heteroaromatic aldehydes with maleimides and 1,1- and 1,2-bis(phenylsulfonyl)ethylene affords endo-2,5- trans cycloadducts in moderate to good yields. DFT calculations provide evidence that the diastereoselectivity observed depends on the isomerization between S- and W-ylides according to Curtin-Hammett's principle. DFT calculations also explain the different diastereomeric ratio observed for 2-pyridyl and 2-thienyl derivatives in which the isomerization is not possible due to the competitiveness between isomerization barrier and the rate-limiting step (ylide formation barrier). This methodology is applied to the diastereoselective synthesis of a tricyclic thrombin inhibitor.

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).

Thermal E/ Z Isomerization in First Generation Molecular Motors.

Determination of a thermal E/ Z isomerization barrier of first generation molecular motors is reported. Stable ( E)-1a directly converts to stable ( Z)-1c without photochemical E/ Z isomerization. The activation Gibbs energy of the isomerization was determined to be 123 kJ mol-1 by circular dichroism spectral changes. Density functional theory calculations show that ( Z)-1c is ∼11.4 kJ mol-1 more stable than ( E)-1a.