Energy Isomers Research Articles

Decomposition of diazomeldrum's acid: a threshold photoelectron spectroscopy study.

Derivatives of meldrum's acid are known precursors for a number of reactive intermediates. Therefore, we investigate diazomeldrum's acid (DMA) and its pyrolysis products by photoionization using vacuum ultraviolet (VUV) synchrotron radiation. The threshold photoelectron spectrum of DMA yields an ionization energy (IE) of 9.68 eV. Several channels for dissociative photoionization are observed. The first one is associated with loss of CH3, leading to a daughter ion with m/z = 155. Its appearance energy AE0K was determined to be 10.65 eV by fitting the experimental data using statistical theory. A second parallel channel leads to m/z = 69, corresponding to N2CHCO, with an AE0K of 10.72 eV. Several other channels open up at higher energy, among them the formation of acetone cation, a channel expected to be the result of a Wolff-rearrangement (WR) in the cation. When diazomeldrum's acid is heated in a pyrolysis reactor, three thermal decomposition pathways are observed. The major one is well-known and yields acetone, N2 and CO as consequence of the WR. However, two further channels were identified: The formation of 2-diazoethenone, NNCCO, together with acetone and CO2 as the second channel and E-formylketene (OCCHCHCO), propyne, N2 and O2 as a third one. 2-Diazoethenone and E-formylketene were identified based on their threshold photoelectron spectra and accurate ionization energies could be determined. Ionization energies for several isomers of both molecules were also computed. One of the key findings of this study is that acetone is observed upon decomposition of DMA in the neutral as well as in the ion and both point to a Wolff rearrangement to occur. However, the ion is subject to other decomposition channels favored at lower internal energies.

Systematic energetics study of graphene nanoflakes: From armchair and zigzag to rough edges with pronounced protrusions and overcrowded bays

Using the PM3 molecular orbit method, we have determined the cohesive energies of 214 fully relaxed hexagonal graphene nanoflakes with different edge structures. The energies of flakes with deep and ultra-deep bays, and protrusions with trio-carbons (C3H3) and quadro-carbons (C4H4) were determined. The pristine hexagonal zigzag flakes (C24H12, C54H18, C96H24, C150H30, C216H36, C294H42, and C384H48) are found to become more energetically stable with size. Yet, the addition of bays or protrusions reduces their relative stability. Inclusion of shallow armchair bays keeps the planar structure of the flakes intact and leads to small changes in energy. HH fjord overcrowding in deep and ultra-deep bays leads to twisting and bending of the flakes and very strong destabilization. For selected flakes, we also calculated the energies of structural isomers where the relative positions of bays or protrusions are systematically varied. We develop structure–energy relationships (SERs) by comparing tendencies for the energetic variability of the structural isomers.

Aromaticity and stability of azaborines.

The influence of the relative boron and nitrogen positions on aromaticity of the three isomeric 1,2-, 1,3-, and 1,4-azaborines has been investigated by computing the extra cyclic resonance energy, NICS(0)πzz index and by visualizing the π-electron (de)shielding pattern as a response of the π system to a perpendicular magnetic field. The origin of the known stability trend, in which the 1,2-/1,3-isomer is the most/least stable, was examined by using an isomerization energy decomposition analysis. The 1,3-arrangement of B and N atoms creates a charge separation in the π-electron system, which was found to be responsible for the lowest stability of 1,3-azaborine. This charge separation can, in turn, be considered as a driving force for the strongest cyclic π-electron delocalization, making this same isomer the most aromatic. Despite the well-known fact that the BN bond attenuates electron delocalization due to large electronegativity difference between the atoms, the 1,4-B,N relationship reduces aromaticity to a greater extent by making the π-electron delocalization more one-directional (from N to B) than cyclic. Thus, 1,4-azaborine was found to be the least aromatic. Its lower stability with respect to the 1,2-isomer was explained by the larger exchange repulsion.

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.

Meta effect of absorption energy in donor-acceptor substituted benzenoids: a computational study of its dependence on acceptor strength, solvent polarity, and conjugation length.

The present work focuses on theoretical understanding of electronic absorption energies of N,N-dimethylaniline with different ortho-, meta-, and para-substituted acceptor groups. The meta isomers exhibit the lowest absorption energy compared to the ortho and para derivatives. This unusual behavior of absorption energies of the meta isomers is related to the "meta effect" well-known in organic photochemical reactions. The meta effect of absorption energy of the derivatives is found to depend on the strength of acceptors, solvent polarity, and conjugation length. The meta derivatives with strong acceptor groups generally exhibit the lowest absorption energy over the other isomers irrespective of solvent polarity. However, the meta isomers with weak acceptor groups exhibit the meta effect only in highly polar solvents. The trend of the lowest absorption energies of the meta isomers is observed to change if the acceptor group is bridged through π conjugation unit (n) with the core moiety. The normal pattern of absorption energy that is the para isomer is of lowest energy is observed to occur for the derivatives where the repeated conjugation units (n) are between 2 and 4. The normal pattern of absorption energy is continued to observe from n > 4 for all the derivatives.

Investigation on addition and abstraction channels in Cl reactions with 1-butene and isobutene

The reactions of the Cl radical with 1-butene and isobutene have been studied in a flow tube by utilizing photoionization mass spectrometry at the energy range of 9–11eV. The addition C4H7Cl and abstraction C4H7 and C4H6 products were observed in the mass spectra. The experimental ionization energies for C4H7Cl from 1-butene and isobutene were determined to be 9.58±0.10 and 9.56±0.10eV, respectively, consistent with ionization energies of the likely isomers at the MP2/aug-cc-pvtz level. In addition, possible addition and abstraction channels were performed at the MP2/aug-cc-pvtz level. Two addition channels for 1-butene and one for isobutene proceeded via the addition of Cl to the unsaturated bond of the butenes and then led to the chlorobutyl radicals. One abstraction channel for 1-butene and isobutene was identified to be viable, respectively. The observed addition products were established via the secondary reactions of Cl with the forming chlorobutyl compounds.

At What Size Do Neutral Gold Clusters Turn Three-Dimensional?

Recent experiments and calculations have established the transition from two-dimensional (2D) to three-dimensional (3D) structures at a cluster size of 8 and 12 atoms for gold cluster cations and anions. For neutral gold clusters, however, experimental data are scarce, and existing theoretical studies disagree on the 2D–3D crossover point. We present the results of global structure optimizations of neutral gold clusters Aun for n = 9–13 using a genetic algorithm and meta-generalized density functional theory. The relative energies of the lowest-lying isomers are computed using the revTPSS functional and the random phase approximation (RPA). Thermal, scalar relativistic, and spin–orbit effects are included, and basis set extrapolations are performed for the RPA calculations. For the 2D–3D transition of gold cluster cations and anions, this methodology yields near-quantitative agreement with cross section and electron diffraction measurements. For neutral gold clusters, the 2D and 3D structures are predicte...

Valence-Bound and Diffuse-Bound Anions of 5-Azauracil

Structures, isomerization energies, and electron binding energies of 5-azauracil and its anions have been calculated ab initio with perturbative, coupled-cluster, and electron-propagator methods. Tautomeric structures, including those produced by proton transfer to a CH group, have been considered. Dyson orbitals and pole strengths from electron-propagator calculations validated a simple, molecular-orbital picture of anion formation. In one case, an electron may enter a delocalized π orbital, yielding a valence-bound (VB) anion with a puckered ring structure. The corresponding electron affinity is 0.27 eV; the vertical electron detachment energy (VEDE) of this anion 1.05 eV. An electron also may enter a molecular orbital that lies outside the nuclear framework, resulting in a diffuse-bound (DB) anion. In the latter case, the electron affinity is 0.06 eV and the VEDE of the DB anion is 0.09 eV. Another VB isomer that is only 0.02 eV more stable than the neutral molecule has a VEDE of 2.0 eV.

Assessment of theoretical procedures for a diverse set of isomerization reactions involving double-bond migration in conjugated dienes

We introduce a representative database of 60 accurate diene isomerization energies obtained by means of the high-level, ab initio Wn–F12 thermochemical protocols. The isomerization reactions involve a migration of one double bond that breaks the π-conjugated system. The considered dienes involve a range of hydrocarbon functional groups, including linear, branched, and cyclic moieties. This set of benchmark isomerization energies allows an assessment of the performance of more approximate theoretical procedures for the calculation of π-conjugation stabilization energies in dienes. We evaluate the performance of a large number of density functional theory (DFT) and double-hybrid DFT (DHDFT) procedures. We find that, with few exceptions (most notably BMK-D3 and M05-2X), conventional DFT procedures have difficulty describing reactions of the type: conjugated diene→non-conjugated diene, with root mean square deviations (RMSDs) between 4.5 and 11.7kJmol−1. However, DHDFT procedures show excellent performance with RMSDs well below the ‘chemical accuracy’ threshold.

Serine effects on collision-induced dissociation and photodissociation of peptide cation radicals of the z+●-type

The serine residue displays specific effects on the dissociations of peptide fragment cation-radicals of the z+• type which are produced by electron transfer dissociation. Energy-resolved collision-induced dissociation (ER-CID), time-resolved infrared multiphoton dissociation (TR-IRMPD), and single-photon UV photodissociation at 355 nm revealed several competitive dissociation pathways consisting of loss of OH radical, water, and backbone cleavages occurring at N-terminal and C-terminal positions relative to the serine residue. The activation modes using slow-heating and UV photon absorption resulted in different relative intensities of fragment ions. This indicated that the dissociations proceeded through several channels with different energy-dependent kinetics. The experimental data were interpreted with the help of electron structure calculations that provided fully optimized structures and relative energies for cis and trans amide isomers of the z4+• ions as well as isomerization, dissociation, and transition state energies. UV photon absorption by the z4+• ions was due to Cα-radical amide groups created by ETD that provided a new chromophore absorbing at 355 nm.

Photoionization and pyrolysis of a 1,4-azaborinine: retro-hydroboration in the cation and identification of novel organoboron ring systems.

The photoionization and dissociative photoionization of 1,4-di-tert-butyl-1,4-azaborinine by means of synchrotron radiation and threshold photoelectron photoion coincidence spectroscopy is reported. The ionization energy of the compound was determined to be 7.89 eV. Several low-lying electronically excited states in the cation were identified. The various pathways for dissociative photoionization were modeled by statistical theory, and appearance energies AE0K were obtained. The loss of isobutene in a retro-hydroboration reaction is the dominant pathway, which proceeds with a reverse barrier. Pyrolysis of the parent compound in a chemical reactor leads to the generation of several yet unobserved boron compounds. The ionization energies of the C4 H6 BN isomers 1,2- and 1,4-dihydro-1,4-azaborinine and the C3 H6 BN isomer 1,2-dihydro-1,3-azaborole were determined from threshold photoelectron spectra.

Does prop-2-ynylideneamine, HC≡CCH=NH, exist in space? A theoretical and computational investigation.

MP2, DFT and CCSD methods with 6-311++G** and aug-cc-pvdz basis sets have been used to probe the structural changes and relative energies of E-prop-2-ynylideneamine (I), Z-prop-2-ynylideneamine (II), prop-1,2-diene-1-imine (III) and vinyl cyanide (IV). The energy near-equivalence and provenance of preference of isomers and tautomers were investigated by NBO calculations using HF and B3LYP methods with 6-311++G** and aug-cc-pvdz basis sets. All substrates have Cs symmetry. The optimized geometries were found to be mainly theoretical method dependent. All elected levels of theory have computed I/II total energy of isomerization (ΔE) of 1.707 to 3.707 kJ/mol in favour of II at 298.15 K. MP2 and CCSD methods have indicated clearly the preference of II over III; while the B3LYP functional predicted nearly similar total energies. All tested levels of theory yielded a global II/IV tautomerization total energy (ΔE) of 137.3–148.4 kJ/mol in support of IV at 298.15 K. The negative values of ΔS indicated that IV is favoured at low temperature. At high temperature, a reverse tautomerization becomes spontaneous and II is preferred. The existence of II in space was debated through the interpretation and analysis of the thermodynamic and kinetic studies of this tautomerization reaction and the presence of similar compounds in the Interstellar Medium (ISM).

Thermochemistry, reaction paths, and kinetics on the tert-isooctane radical reaction with O2.

Thermochemical properties of tert-isooctane hydroperoxide and its radicals are determined by computational chemistry. Enthalpies are determined using isodesmic reactions with B3LYP density function and CBS QB3 methods. Application of group additivity with comparison to calculated values is illustrated. Entropy and heat capacities are determined using geometric parameters and frequencies from the B3LYP/6-31G(d,p) calculations for the lowest energy conformer. Internal rotor potentials are determined for the tert-isooctane hydroperoxide and its radicals in order to identify isomer energies. Recommended values derived from the most stable conformers of tert-isooctane hydroperoxide of are -77.85 ± 0.44 kcal mol(-1). Isooctane is a highly branched molecule, and its structure has a significant effect on its thermochemistry and reaction barriers. Intramolecular interactions are shown to have a significant effect on the enthalpy of the isooctane parent and its radicals on peroxy/peroxide systems, the R• + O2 well depths and unimolecular reaction barriers. Bond dissociation energies and well depths, for tert-isooctane hydroperoxide → R• + O2 are 33.5 kcal mol(-1) compared to values of ∼38 to 40 kcal mol(-1) for the smaller tert-butyl-O2 → R• + O2. Transition states and kinetic parameters for intramolecular hydrogen atom transfer and molecular elimination channels are characterized to evaluate reaction paths and kinetics. Kinetic parameters are determined versus pressure and temperature for the chemically activated formation and unimolecular dissociation of the peroxide adducts. Multifrequency quantum RRK (QRRK) analysis is used for k(E) with master equation analysis for falloff. The major reaction paths at 1000 K are formation of isooctane plus HO2 followed by cyclic ether plus OH. Stabilization of the tert-isooctane hydroperoxy radical becomes important at lower temperatures.

Microscopic description of fission in uranium isotopes with the Gogny energy density functional

The most recent parametrizations D1S, D1N, and D1M of the Gogny energy density functional are used to describe fission in the isotopes ${}^{232--280}U$. Fission paths, collective masses, and zero-point quantum corrections, obtained within the constrained Hartree-Fock-Bogoliubov approximation, are used to compute the systematics of the spontaneous fission half-lives ${t}_{\mathrm{SF}}$, the masses and charges of the fission fragments, and their intrinsic shapes. The Gogny-D1M parametrization has been benchmarked against available experimental data on inner and second barrier heights, excitation energies of the fission isomers, and half-lives in a selected set of Pu, Cm, Cf, Fm, No, Rf, Sg, Hs, and Fl nuclei. It is concluded that D1M represents a reasonable starting point to describe fission in heavy and superheavy nuclei. Special attention is also paid to understand the uncertainties in the predicted ${t}_{\mathrm{SF}}$ values arising from the different building blocks entering the standard semiclassical Wentzel-Kramers-Brillouin formula. Although the uncertainties are large, the trend with mass or neutron numbers are well reproduced and therefore the theory still has predictive power. In this respect, it is also shown that modifications of a few percent in the pairing strength can have a significant impact on the collective masses leading to uncertainties in the ${t}_{\mathrm{SF}}$ values of several orders of magnitude.

Identification of the 11- cis- specific retinyl-ester synthase in retinal Müller cells as multifunctional O- acyltransferase (MFAT)

Absorption of a photon by a rhodopsin or cone-opsin pigment isomerizes its 11-cis-retinaldehyde (11-cis-RAL) chromophore to all-trans-retinaldehyde (all-trans-RAL), which dissociates after a brief period of activation. Light sensitivity is restored to the resulting apo-opsin when it recombines with another 11-cis-RAL. Conversion of all-trans-RAL to 11-cis-RAL is carried out by an enzyme pathway called the visual cycle in cells of the retinal pigment epithelium. A second visual cycle is present in Müller cells of the retina. The retinol isomerase for this noncanonical pathway is dihydroceramide desaturase (DES1), which catalyzes equilibrium isomerization of retinol. Because 11-cis-retinol (11-cis-ROL) constitutes only a small fraction of total retinols in an equilibrium mixture, a subsequent step involving selective removal of 11-cis-ROL is required to drive synthesis of 11-cis-retinoids for production of visual chromophore. Selective esterification of 11-cis-ROL is one possibility. Crude homogenates of chicken retinas rapidly convert all-trans-ROL to 11-cis-retinyl esters (11-cis-REs) with minimal formation of other retinyl-ester isomers. This enzymatic activity implies the existence of an 11-cis-specific retinyl-ester synthase in Müller cells. Here, we evaluated multifunctional O-acyltransferase (MFAT) as a candidate for this 11-cis-RE-synthase. MFAT exhibited much higher catalytic efficiency as a synthase of 11-cis-REs versus other retinyl-ester isomers. Further, we show that MFAT is expressed in Müller cells. Finally, homogenates of cells coexpressing DES1 and MFAT catalyzed the conversion of all-trans-ROL to 11-cis-RP, similar to what we observed with chicken-retina homogenates. MFAT is therefore an excellent candidate for the retinyl-ester synthase that cooperates with DES1 to drive synthesis of 11-cis-retinoids by mass action.

Theoretical study of isomerism of compounds of CO and CO2 molecules with aluminum clusters Al13, Al12Ti, and Al12Ni

Structural characteristics, vibrational frequencies, and energies of isomers of compounds of CO and CO2 molecules with the centered aluminum cluster Al13 and its doped analogues Al12M (M = Ti and Ni) have been calculated by the density functional theory method. For the Al12MCO compounds, the most favor-able are two “fragment” isomers in which the C and O atoms are separated and built into the cluster cage, completing it to a 14-vertex polyhedron. In one of them, the C and O atoms are in the capping positions over adjacent trigonal MAl2 faces; in the second isomer, there is the five-coordinate C* atom located in the center of a tetragonal MAl3 face and bound to the central Al atom through the long fifth bond. The “coordinated” isomers, in which the CO molecule is coordinated as a ligand to a cluster vertex, edge, or face, are unstable to removal of CO for Al13CO, close in energy to the fragment isomers for Al12NiCO, and considerably higher on the energy scale than the fragment isomers but remain stable to CO removal for Al12TiCO. For the Al12MCO2 compounds, the most favorable is the fragment isomer in which both oxygen atoms are in the capping positions over adjacent faces and the C* atom is five-coordinate. The alternative oxo carbonyl isomer Al12MO(CO) is close to the lowest-lying one in the case of M = Ni and is ∼56 kcal/mol higher on the energy scale in the case of M= Ti. The less stable Al12M(CO2) isomer is the complex in which the CO2 ligand is coordinated to an M-Al edge. According to calculations, addition of CO to Al12MO and addition of CO2 to Al12M to form, respectively, Al12MO(CO) and Al12M(CO2) can occur without noticeable barrier. The Al12M(CO2) and Al12MO(CO) isomers are separated by a barrier, moderate for M = Ti (∼16 kcal/mol) and small for M = Ni (∼6 kcal/mol).

Influence of the octupole mode on nuclear high-K isomeric properties

The influence of quadrupole–octupole deformations on the energy and magnetic properties of high-K isomeric states in even–even actinide (U, Pu, Cm, Fm, No), rare-earth (Nd, Sm and Gd), and superheavy ( nuclei is examined within a deformed shell model with pairing interaction. The neutron two-quasiparticle (2qp) isomeric energies and magnetic dipole moments are calculated over a wide range in the plane of quadrupole and octupole deformations. In most cases the magnetic moments exhibit a pronounced sensitivity to the octupole deformation. At the same time, the calculations outline three different groups of nuclei: with pronounced, shallow, and missing minima in the 2qp energy surfaces with respect to the octupole deformation. The result indicates regions of nuclei with octupole softness as well as with possible octupole deformation in the high-K isomeric states. These findings show the need for further theoretical analysis as well as of detailed experimental measurements of magnetic moments in heavy deformed nuclei.

Studies of Structural Isomers o-, m-, and p-Fluorophenylacetylene by Two-Color Resonant Two-Photon Mass-Analyzed Threshold Ionization Spectroscopy

We report the vibrational spectra of o-fluorophenylacetylene (OFPA), m-fluorophenylacetylene (MFPA), and p-fluorophenylacetylene (PFPA) in the electronically excited S1 and cationic ground D0 states. These new data show that the relative location of the fluorine atom with respect to the acetylenic group can influence the transition energy and molecular vibration. The adiabatic ionization energies of these structural isomers follow the order: PFPA < OFPA < MFPA. It is found that the molecular geometries of these molecules in the D0 state resemble those in the S1 state. Detailed spectral analysis suggests that the in-plane ring deformation vibrations are slightly "harder" in the D0 state than the corresponding ones in the S1 state.

On the Structures and Growing Mechanisms of the Ti@C2n (2n = 26 - 50) Endohedral Fullerenes

During the last years, several mechanisms have been suggested in relation to the formation of fullerenes. One of them involves the ingestion of a C2 unit by an already formed fullerene. In this communication, we summarize the theoretical investigations carried out for the series of Ti@C2n endohedral fullerenes, with 2n = 26 to 50. After a thorough exploration of the most favorable isomers, potential energy surfaces associated with the C2 addition, and the topology of the involved structures we have concluded that in contrast to large endohedral metallofullerenes (2n>60) in which the empty cage is different to the optimal cage that hosts a metal ion or a small cluster, in small endohedral fullerenes encapsulating a tetravalent ion the empty and hosting cage often coincides. The addition of a C2 unit to an already formed Ti@C2n fullerene is always an exergonic reaction. Most of the lowest in energy isomers are formally linked by a C2 addition and a Stone-Wales transformation. Car-Parrinello Molecular Dynamics calculations show that after the attack of a C2 unit to one of the C atoms of the Ti@C2n system, the formation of the second C-C bond that closes the cage is an improbable event and must be accelerated using Metadynamics or via an external collision, for example with He atoms that are present in the sample.

Computational design of mixed-ligand adducts of Co aminovinyl ketonates with redox-active o-quinones and their derivatives

The adducts of cobalt aminovinyl ketonates with o-benzoquinones, o-benzoquinone imines, and o-benzoquinone diimines were studied by the density functional theory method (B3LYP*/6-311++G(d,p)). For all of the compounds, the ground states are low-spin structures containing a trivalent cobalt atom and a redox-active ligand in the semiquinonate form. The bulky substituents at the bis-chelate and ligand nitrogen atoms favor a decrease in the energy difference between the low-spin and high-spin isomers of the adducts containing LSCoIII and HSCoII atoms, respectively. These compounds can exhibit valence tautomerism in the crystalline state, but the relatively low stabilization energies of the high-spin isomers in solutions may induce a competing process: dissociation into the original bis-chelate and redox-active ligand.