Inversion Barrier Research Articles

Synthesis, characterization, catalytic and biological application of half-sandwich ruthenium complexes bearing hemilabile (κ2-C,S)-thioether-functionalised NHC ligands.

A series of cationic Ru(ii)(η6-p-cymene) complexes with thioether-functionalised N-heterocyclic carbene ligands have been prepared and fully characterized. Steric and electronic influence of the R thioether substituent on the coordination of the sulfur atom was investigated. The molecular structure of three of them has been determined by means of X-ray diffractrometry and confirmed the bidentate (κ2-C,S) coordination mode of the ligand. Interestingly, only a single diastereomer, as an enantiomeric couple, was observed in the solid state for complexes 1c, 1i and 1j. DFT calculations established a low energy inversion barrier between the two diastereomers through a sulfur pyramidal inversion pathway with R donating group while a dissociative/associative mechanism is more likely with R substituents that contain electron withdrawing group, thus suggesting that the only species observed by the 1H-NMR correspond to an average resonance position of a fluxional mixtures of isomers. All these complexes were found to catalyse the oxydant-free double dehydrogenation of primary amine into nitrile. Ru complex bearing NHC-functionalised S-tBu group was further investigated in a wide range of amines and was found more selective for alkyl amine substrates than for benzylamine derivatives. Finally, preliminary results of the biological effects on various human cancer cells of four selected Ru complexes are reported.

Cation effects on dynamics of ligand-benzylated formazanate boron and aluminium complexes.

The dynamic processes present in ligand-benzylated formazanate boron and aluminium complexes are investigated using variable temperature NMR experiments and lineshape analyses. The observed difference in activation parameters for complexes containing either organic countercations (NBu4+) or alkali cations is rationalized on the basis of a different degree of ion-pairing in the ground state, and the data are in all cases consistent with a mechanism that involves pyramidal inversion at the nitrogens in the heterocyclic ring rather than homolytic N-C(benzyl) bond cleavage.

Выбор оптимального базисного набора для корректной оценки барьера пирамидальной инверсии триметиламина методом PBE

Выбор оптимального базисного набора для корректной оценки барьера пирамидальной инверсии триметиламина методом PBE

Выбор оптимального базисного набора для корректной оценки барьера пирамидальной инверсии аммиака методом PBE

Выбор оптимального базисного набора для корректной оценки барьера пирамидальной инверсии аммиака методом PBE

Benchmarking the inversion barriers in σ3λ3-phosphorus compounds: a computational study

Benchmark study of three mechanisms for inversion at phosphorus, including parametric criteria for classification and analysis of factors affecting barriers.

Fluorous Corannulenes: Ab initio Predictions and the Synthesis of sym‐Pentafluorocorannulene

AbstractTen sym‐penta and deca‐X substituted corannulenes (1–10; X=H, F, CH3, or CF3) define a library of fluorous compounds comprising high symmetry non‐planar aromatic compunds. They provide a group of structurally similar, yet physically distinct structures manifesting special chemical behavior related to their degree of fluorination. Owing to their bowl forms, corannulene derivatives are distinct from planar polynuclear aromatic compounds; they have relatively high dipole moments, accept 1–4 electrons, and display room temperature fluorescence as well as low temp phosphorescence. Electronic structure theory predicts the bowl inversion barrier and physical properties. The syntheses of sym‐pentafluorocorannulene by an efficient late stage fluorination affords a key derivative to calibrate predictions.

Fluorous Corannulenes: Ab initio Predictions and the Synthesis of sym-Pentafluorocorannulene.

Ten sym-penta and deca-X substituted corannulenes (1-10; X=H, F, CH3 , or CF3 ) define a library of fluorous compounds comprising high symmetry non-planar aromatic compunds. They provide a group of structurally similar, yet physically distinct structures manifesting special chemical behavior related to their degree of fluorination. Owing to their bowl forms, corannulene derivatives are distinct from planar polynuclear aromatic compounds; they have relatively high dipole moments, accept 1-4 electrons, and display room temperature fluorescence as well as low temp phosphorescence. Electronic structure theory predicts the bowl inversion barrier and physical properties. The syntheses of sym-pentafluorocorannulene by an efficient late stage fluorination affords a key derivative to calibrate predictions.

A Chiral Polycyclic Aromatic Hydrocarbon Monkey Saddle

AbstractA contorted polycyclic aromatic hydrocarbon (PAH) in the shape of a monkey saddle has been synthesized in three steps from a readily available truxene precursor. The monkey saddle PAH is consisting of three five‐, seven six‐, and three eight‐membered rings and has been unambiguously characterized by single‐crystal X‐ray diffraction. Owing to the three biaryl axes the monkey saddle PAH is inherently chiral. The inversion of the two enantiomeric structures into each other preferably occurs through a twisting of peripheral rings rather than by a fully planar intermediate, as has been calculated by DFT methods. Enantiomers were separated by chiral HPLC and inversion barriers determined by variable temperature circular dichroism spectroscopy, supporting the twisting mechanism.

A Chiral Polycyclic Aromatic Hydrocarbon Monkey Saddle.

A contorted polycyclic aromatic hydrocarbon (PAH) in the shape of a monkey saddle has been synthesized in three steps from a readily available truxene precursor. The monkey saddle PAH is consisting of three five‐, seven six‐, and three eight‐membered rings and has been unambiguously characterized by single‐crystal X‐ray diffraction. Owing to the three biaryl axes the monkey saddle PAH is inherently chiral. The inversion of the two enantiomeric structures into each other preferably occurs through a twisting of peripheral rings rather than by a fully planar intermediate, as has been calculated by DFT methods. Enantiomers were separated by chiral HPLC and inversion barriers determined by variable temperature circular dichroism spectroscopy, supporting the twisting mechanism.

High-Spin Diradical Dication of Chiral π-Conjugated Double Helical Molecule.

We report an air-stable diradical dication of chiral D2-symmetric conjoined bis[5]diazahelicene with an unprecedented high-spin (triplet) ground state, singlet triplet energy gap, ΔEST = 0.3 kcal mol-1. The diradical dication possesses closed-shell (Kekulé) resonance forms with 16 π-electron perimeters. The diradical dication is monomeric in dibutyl phthalate (DBP) matrix at low temperatures, and it has a half-life of more than 2 weeks at ambient conditions in the presence of excess oxidant. A barrier of ∼35 kcal mol-1 has been experimentally determined for inversion of configuration in the neutral conjoined bis[5]diazahelicene, while the inversion barriers in its radical cation and diradical dication were predicted by the DFT computations to be within a few kcal mol-1 of that in the neutral species. Chiral HPLC resolution provides the chiral D2-symmetric conjoined bis[5]diazahelicene, enriched in (P,P)- or (M,M)-enantiomers. The enantiomerically enriched triplet diradical dication is configurationally stable for 48 h at room temperature, thus providing the lower limit for inversion barrier of configuration of 27 kcal mol-1. The enantiomers of conjoined bis[5]diazahelicene and its diradical dication show strong chirooptical properties that are comparable to [6]helicene or carbon-sulfur [7]helicene, as determined by the anisotropy factors, |g| = |Δε|/ε = 0.007 at 348 nm (neutral) and |g| = 0.005 at 385 nm (diradical dication). DFT computations of the radical cation suggest that SOMO and HOMO energy levels are near-degenerate.

Scattering off molecules far from equilibrium.

Pump-probe gas phase X-ray scattering experiments, enabled by the development of X-ray free electron lasers, have advanced to reveal scattering patterns of molecules far from their equilibrium geometry. While dynamic displacements reflecting the motion of wavepackets can probe deeply into the reaction dynamics, in many systems, the thermal excitation embedded in the molecules upon optical excitation and energy randomization can create systems that encompass structures far from the ground state geometry. For polyatomic molecular systems, large amplitude vibrational motions are associated with anharmonicity and shifts of interatomic distances, making analytical solutions using traditional harmonic approximations inapplicable. More generally, the interatomic distances in a polyatomic molecule are not independent and the traditional equations commonly used to interpret the data may give unphysical results. Here, we introduce a novel method based on molecular dynamic trajectories and illustrate it on two examples of hot, vibrating molecules at thermal equilibrium. When excited at 200 nm, 1,3-cyclohexadiene (CHD) relaxes on a subpicosecond time scale back to the reactant molecule, the dominant pathway, and to various forms of 1,3,5-hexatriene (HT). With internal energies of about 6 eV, the energy thermalizes quickly, leading to structure distributions that deviate significantly from their vibrationless equilibrium. The experimental and theoretical results are in excellent agreement and reveal that a significant contribution to the scattering signal arises from transition state structures near the inversion barrier of CHD. In HT, our analysis clarifies that previous inconsistent structural parameters determined by electron diffraction were artifacts that might have resulted from the use of inapplicable analytical equations.

General framework for calculating spin-orbit couplings using spinless one-particle density matrices: Theory and application to the equation-of-motion coupled-cluster wave functions.

Standard implementations of nonrelativistic excited-state calculations compute only one component of spin multiplets (i.e., Ms = 0 triplets); however, matrix elements for all components are necessary for deriving spin-dependent experimental observables. Wigner-Eckart's theorem allows one to circumvent explicit calculations of all multiplet components. We generate all other spin-orbit matrix elements by applying Wigner-Eckart's theorem to a reduced one-particle transition density matrix computed for a single multiplet component. In addition to computational efficiency, this approach also resolves the phase issue arising within Born-Oppenheimer's separation of nuclear and electronic degrees of freedom. A general formalism and its application to the calculation of spin-orbit couplings using equation-of-motion coupled-cluster wave functions are presented. The two-electron contributions are included via the mean-field spin-orbit treatment. Intrinsic issues of constructing spin-orbit mean-field operators for open-shell references are discussed, and a resolution is proposed. The method is benchmarked by using several radicals and diradicals. The merits of the approach are illustrated by a calculation of the barrier for spin inversion in a high-spin tris(pyrrolylmethyl)amine Fe(II) complex.

Diastereoselective Coordination of P-Stereogenic Secondary Phosphines in Copper(I) Chiral Bis(phosphine) Complexes: Structure, Dynamics, and Generation of Phosphido Complexes.

Diastereoselective coordination of racemic secondary phosphines (PHRR') to Cu(I) precursors containing chiral bis(phosphines) (diphos*) was explored as a potential route to P-stereogenic phosphido complexes. Reaction of [Cu(NCMe)4][PF6] with chiral bis(phospholanes) gave [Cu(diphos*)2][PF6] (diphos* = ( R, R)-Me-DuPhos (1), ( R, R)-Et-DuPhos (2), or ( R, R)-Me-FerroLANE) (3)) or the mono(chelates) [Cu(diphos*)(NCMe) n][PF6] (diphos* = ( R, R)- i-Pr-DuPhos, n = 2 (4); diphos* = ( R, R)-Me-FerroLANE, n = 1 (5)). Treatment of [Cu(NCMe)4][PF6] with diphos* and PHMe(Is) (Is = 2,4,6-( i-Pr)3C6H2) gave mixtures of diastereomers of [Cu(( R, R)- i-Pr-DuPhos)(PHMe(Is))(NCMe)][PF6] (6) and [Cu(( R, R)-Me-FerroLANE)(PHMe(Is))][PF6] (7); two of the three expected isomers of the bis(secondary phosphine) complexes [Cu(( R, R)- i-Pr-DuPhos)(PhHP(CH2) nPHPh)][PF6] ( n = 2 (8); n = 3 (9)) were formed preferentially in related reactions. Reaction of the halide-bridged dimers [Cu(( R, R)- i-Pr-DuPhos)(X)]2 or [Cu(( R, R)-Me-FerroLANE)(I)]2 with PHMe(Is) gave the labile adducts Cu(( R, R)- i-Pr-DuPhos)(PHMe(Is))(X) (X = Cl (10), Br (11), I (12)) and Cu(( R, R)-Me-FerroLANE)(PHMe(Is))(I) (13). Complexes 1, 6, and 8-11 were structurally characterized by X-ray crystallography. Variable temperature NMR studies of 6 and 8 showed that the secondary phosphine ligands underwent reversible dissociation. Deprotonation of 6 or 7 generated the P-stereogenic phosphido complexes Cu(diphos*)(PMeIs) (diphos* = ( R, R)- i-Pr-DuPhos (14) or ( R, R)-Me-FerroLANE) (17)), observed by 31P NMR spectroscopy, but decomposition also occurred. Density functional theory calculations were used to characterize the diastereomers of thermally unstable 17 and the inversion barrier in a model copper-phosphido complex. These observations provided structure-property relationships which may be useful in developing catalytic asymmetric reactions involving secondary phosphines and P-stereogenic copper phosphido intermediates.

Electronically Nonadiabatic Structural Transformations Promoted by Electron Beams

AbstractThe use of scanning transmission electron microscopes to manipulate substitutional defects in graphene has recently been demonstrated and modeled using ground state molecular dynamics, but the role of electronic excitations induced through inelastic electron scattering in promoting these transformations has so‐far remained unexplored. Here, probed are the effects of electronic excitation on the structural dynamics of graphene quantum dots of differing edge morphologies that are substitutionally doped with silicon or phosphorous. The ground and excited state potential energy barriers for pyramidal inversion of these nonplanar doped species are evaluated using time‐dependent density functional theory. Optically bright excited states in which the barrier is decreased are identified in the low energy region of the electronic spectrum, suggesting that photoexcitation can modulate the reactivity of defects in graphene under electron beam irradiation. Coupling matrix elements between these inversion‐favoring excited states and the ground state and time‐domain simulations of the material's response to a point charge impulse indicate that focusing an electron beam near the defect can also lead to population of these states, suggesting that beam electrons incident on a defect can both excite the material to an inversion‐favoring state and transfer momentum to the defect to initiate the inversion.

Ab initio spectroscopic characterization of the radical CH3OCH2 at low temperatures.

Spectroscopic and structural properties of methoxymethyl radical (CH3OCH2, RDME) are determined using explicitly correlated ab initio methods. This radical of astrophysical and atmospheric relevance has not been fully characterized at low temperatures, which has delayed astrophysical research. We provide rovibrational parameters, excitations to the low energy electronic states, torsional and inversion barriers, and low vibrational energy levels. In the electronic ground state (X2A), which appears "clean" from nonadiabatic effects, the minimum energy structure is an asymmetric geometry whose rotational constants and dipole moment have been determined to be A0 = 46 718.67 MHz, B0 = 10 748.42 MHz, and C0 = 9272.51 MHz, and 1.432D (μA = 0.695D, µB = 1.215D, µC = 0.302D), respectively. A variational procedure has been applied to determine torsion-inversion energy levels. Each level splits into 3 subcomponents (A1/A2 and E) corresponding to the three methyl torsion minima. Although the potential energy surface presents 12 minima, at low temperatures, the infrared band shapes correspond to a surface with only three minima because the top of the inversion Vα barrier at α = 0° (109 cm-1) stands below the zero point vibrational energy and the CH2 torsional barrier is relatively high (∼2000 cm-1). The methyl torsion barrier was computed to be ∼500 cm-1 and produces a splitting of 0.01 cm-1 of the ground vibrational state.

Dynamic polarity of curved aromatic soot precursors

In this paper, we answer the question of whether polar curved aromatics are persistently polar at flame temperatures. We find, using electronic structure calculations and transition state theory, that the inversion barriers of curved aromatics (cPAH) 0.9–1.2 nm in diameter are high and that they are not able to invert over the timescales and at the high temperatures found in sooting flames. We find a transition for smaller curved aromatics between 11–15 ( ≈ 0.8 nm) rings where the increasing strain introduced from the pentagonal ring increases the inversion barrier leading to rigidity. We then performed ab initio quantum molecular dynamics to find the molecular dipole fluctuations of a nanometre sized cPAH at 1500 K. We found the bending mode of the bowl shaped molecule gave rise to the largest fluctuations on the dipole moment by ± 0.5–1 debye about the equilibrium value of 5.00 debye, indicating persistent polarity. We also observed binding of a chemi-ion at 1500 K over 2 ps, suggesting the molecular dipole of cPAH will be an important consideration in soot formation mechanisms.

Molecular Dynamics Simulations on Relaxed Reduced-Dimensional Potential Energy Surfaces.

Molecular dynamics (MD) simulations with full-dimensional potential energy surfaces (PESs) obtained from high-level ab initio calculations are frequently used to model reaction dynamics of small molecules (i.e., molecules with up to 10 atoms). Construction of full-dimensional PESs for larger molecules is, however, not feasible since the number of ab initio calculations required grows rapidly with the increase of dimension. Only a small number of coordinates are often essential for describing the reactivity of even very large systems, and reduced-dimensional PESs with these coordinates can be built for reaction dynamics studies. While analytical methods based on transition-state theory framework are well established for analyzing the reduced-dimensional PESs, MD simulation algorithms capable of generating trajectories on such surfaces are more rare. In this work, we present a new MD implementation that utilizes the relaxed reduced-dimensional PES for standard microcanonical (NVE) and canonical (NVT) MD simulations. The method is applied to the pyramidal inversion of a NH3 molecule. The results from the MD simulations on a reduced, three-dimensional PES are validated against the ab initio MD simulations, as well as MD simulations on full-dimensional PES and experimental data.

Azaindenocorannulenes: Synthesis, Properties, and Chirality.

Palladium-catalyzed intramolecular arylation provides bowl-shaped azaindenocorannulenes 7-9. Crystals of 8 show bowl-in-bowl columnar stacking. A substituent model rationalizes the first reduction potential of 18 related molecular bowls. The absolute configurations of bowls 7 and 9 are correlated with VCD and ECD spectra. The bowl inversion barrier of 9 (>190 kJ/mol) shows it to be more inert configurationally than chiral biaryl, phosphenes, or [ n]helicenes.

Dicyclopenta[ghi,pqr]perylene as a Structural Motif for Bowl-Shaped Hydrocarbons: Synthetic and Conformational Studies.

Dicyclopenta[ghi,pqr]perylene (DCPP) is a substructural fragment on the surface of C70 yet not on C60. Unlike its intensely investigated buckybowl cousins, corannulene and sumanene, DCPP is largely ignored due to the lack of synthetic accessibility. This communication describes the first preparation of a DCPP derivative from bay substituted perylene bis(4-(trifluoromethyl)phenyl)methanol as the key cyclization precursor. Further incorporation of indeno substitutions at peri positions was accomplished through Suzuki-Heck benzannulation. DCPP derivatives 4 adopts a planar structure in crystal. On the contrary, indeno DCPP 5 and bis-indeno DCPP 6 adopt the bowl-shaped conformation in both the solid state and solution. Density functional theory (DFT) calculation reveals that the lowest-energy conformations of 4, 5, and 6 are all bowl-shaped. Nevertheless, small bowl-to-bowl inversion barrier for 4 (3.4 kcal/mol) is overcome by the crystal packing force, which leads to its observed planar structure. However, the bowl-shaped structures of 5 and 6 are affirmed by DFT calculation with intermediate and high bowl-to-bowl inversion barriers (10.4 and 18.5 kcal/mol, respectively).

Conformational Analysis of (1,1′-Phenyl-1,1′-silacyclohex-1-yl)disiloxane. DFT and Low-Temperature 13C NMR Spectroscopy Study

The DFT and MP2 theoretical conformational analysis of the recently synthesized (1,1′-phenyl-1,1′-silacyclohex-1-yl)disiloxane has revealed the energetic preference of the Phax,Phax conformer. The Phax,Phax: Phax,Pheq: Pheq,Pheq conformers ratio has been estimated as of 46.6: 33.1: 20.3 from the M062X/6-311G(d,p) free energy simulation, suggesting the possibility of detecting individual conformers experimentally, e.g., by low-temperature 1H and 13C NMR spectroscopy. However, only the presence of several conformers has been detected by means of 1H NMR spectroscopy at 113 K; determination of the Δν (Hz) and ΔG# (kcal/mol) parameters for the 6-membered ring interconversion has been impossible due to the signals broadening at low temperature, signal temperature shifts, and extremely low barrier of ring inversion at Tc < 113 K.