Inversion Barrier Research Articles

Stereochemical Behavior of Pairs of P-stereogenic Phosphanyl Groups at the Dimethylxanthene Backbone.

The P-stereogenic bis(phosphanes) 7 and 9, featuring pairs of P(Mes)-ethynyl or vinyl substituents at the dimethyl xanthene backbone show rather low barriers of stereochemical inversion at phosphorus. π-Conjugative effects are probably causing these low inversion barriers. Compound 7 reacted with B(C6 F5 )3 to form the nine-membered heterocyclic product 10, featuring a [P]-C≡C-B(C6 F5 )3 substituent. Compound 7 was converted to the bis[P(Mes)vinyl] xanthene derivative 9, which gave the zwitterionic P(H)(Mes)-CH=CH-B(C6 F5 )3 containing product 16 upon treatment with B(C6 F5 )3 . Thermally induced epimerization barriers at phosphorus of ca. 20 to 27 kcal mol-1 were calculated by DFT for the alkenyl- and alkynyl-P derived systems 6 to 9, 15 and 16 and experimentally determined for the examples 7 and 16.

Synthesis of Dibenzo[h,t]rubicene through Its Internally Dimethoxy-substituted Precursor

Abstract Dibenzo[h,t]rubicene was synthesized from 1,5-dichloroanthraquinone via an internally dimethoxylated intermediate. In contrast to the planar conformation of rubicene, dibenzo[h,t]rubicene adopted a double-helicene-like structure due to the intramolecular steric repulsion around the fused benzene-rings. Theoretical calculation suggests that the helical inversion occurs frequently with an inversion barrier of 4.8 kcal mol−1. The HOMO–LUMO gap of dibenzo[h,t]rubicene is smaller than that of rubicene, resulting in its red-shifted absorption tailing to 690 nm.

Bulky Selenium Ligand Stabilized Trans-Palladium Dichloride Complexes as Catalyst for Silver-Free Decarboxylative Coupling of Coumarin-3-Carboxylic Acids.

This report describes the syntheses of three new trans-palladium dichloride complexes of bulky selenium ligands. These complexes possess a Cl-Pd-Cl rotor spoke attached to a Se-Pd-Se axle. The new ligands and palladium complexes (C1-C3) were characterized with the help of NMR, HRMS, UV-Vis., IR, and elemental analysis. The single-crystal structure of metal complex C2 confirmed a square planar geometry of complex with trans-orientation. The X-ray structure revealed intramolecular secondary interactions (SeCH-Cl) between chlorine of PdCl2 and CH2 proton of selenium ligand. Variable-temperature NMR data shows coalescence of diastereotopic protons, which indicates pyramidal inversion of selenium atom at elevated temperature. The relaxed potential energy scan of C2 suggests a rotational barrier of ∼12.5 kcal/mol for rotation of chlorine atom through Cl-Pd-Cl rotor. The complex C3 possesses dual intramolecular secondary interactions (OCH2 -Cl and SeCH2 -Cl) with stator ligand. Molecular rotor C2 was found to be a most efficient catalyst for the decarboxylative Heck-coupling under mild reaction conditions. The protocol is applicable to a broad range of substrates with large functional group tolerance and low catalyst loading (2.5 mol %). The mechanism of decarboxylative Heck-coupling reaction was investigated through experimental and computational studies. Importantly the reaction works under silver-free conditions which reduces the cost of overall protocol. Further, the catalyst also worked for decarboxylative arylation and decarboxylative Suzuki-Miyaura coupling reactions with good yields of the coupled products.

A New Saddle-Shaped Aza Analog of Tetraphenylene: Atroposelective Synthesis and Application as a Chiral Acylating Reagent

A New Saddle-Shaped Aza Analog of Tetraphenylene: Atroposelective Synthesis and Application as a Chiral Acylating Reagent

Configurational Lability at Tetrahedral Phosphorus: syn/anti‐Isomerization of a P‐Stereogenic Phosphiranium Cation by Intramolecular Epimerization at Phosphorus

AbstractTetrahedral main‐group compounds are normally configurationally stable, but P‐epimerization of the chiral phosphiranium cations syn‐ or anti‐[Mes*P(Me)CH2CHPh][OTf] (Mes*=2,4,6‐(t‐Bu)3C6H2) occurred under mild conditions at 60 °C in CD2Cl2, resulting in isomerization to give a syn‐enriched equilibrium mixture. Ion exchange with excess [NBu4][Δ‐TRISPHAT] (Δ‐TRISPHAT=Δ‐P(o‐C6Cl4O2)3) followed by chromatography on silica removed [NBu4][OTf] and gave mixtures of syn‐ and anti‐[Mes*P(Me)CH2CHPh][Δ‐TRISPHAT]⋅x[NBu4][Δ‐TRISPHAT]. NMR spectroscopy showed that isomerization proceeded with epimerization at P and retention at C. DFT calculations are consistent with a mechanism involving P‐C cleavage to yield a hyperconjugation‐stabilized carbocation, pyramidal inversion promoted by σ‐interaction of the P lone pair with the neighboring β‐carbocation, and ring closure with inversion of configuration at P.

Configurational Lability at Tetrahedral Phosphorus: syn/anti-Isomerization of a P-Stereogenic Phosphiranium Cation by Intramolecular Epimerization at Phosphorus.

Tetrahedral main-group compounds are normally configurationally stable, but P-epimerization of the chiral phosphiranium cations syn- or anti-[Mes*P(Me)CH2 CHPh][OTf] (Mes*=2,4,6-(t-Bu)3 C6 H2 ) occurred under mild conditions at 60 °C in CD2 Cl2 , resulting in isomerization to give a syn-enriched equilibrium mixture. Ion exchange with excess [NBu4 ][Δ-TRISPHAT] (Δ-TRISPHAT=Δ-P(o-C6 Cl4 O2 )3 ) followed by chromatography on silica removed [NBu4 ][OTf] and gave mixtures of syn- and anti-[Mes*P(Me)CH2 CHPh][Δ-TRISPHAT]⋅x[NBu4 ][Δ-TRISPHAT]. NMR spectroscopy showed that isomerization proceeded with epimerization at P and retention at C. DFT calculations are consistent with a mechanism involving P-C cleavage to yield a hyperconjugation-stabilized carbocation, pyramidal inversion promoted by σ-interaction of the P lone pair with the neighboring β-carbocation, and ring closure with inversion of configuration at P.

On the Origin of the Non-Planarity in Biarylsilyloxonium Ions.

The structure determination of a series of biphenylsilyloxonium cations through NMR and XRD studies, supported by DFT calculations was carried out, allowing to get insights into the origin of the oxygen pyramidalization in biphenyl and binaphthylsilyl oxoniums. Low barrier of inversion in the oxygenyl series points toward a key role of the biaryl axis in the inversion of configuration at the oxygen center.

Dinuclear Au(I), Au(II) and Au(III) Complexes with (CF2 )n Chains: Insights into The Role of Aurophilic Interactions in the Au(I) Oxidation.

New dinuclear Au(I), Au(II) and Au(III) complexes containing (CF2)n bridging chains were obtained. Metallomacrocycles [Au2{μ‐(CF2)4}{μ‐diphosphine}] show an uncommon figure‐eight structure, the helicity inversion barrier of which is influenced by aurophilic interactions and steric constraints imposed by the diphosphine. Halogenation of LAu(CF2)4AuL (L=PPh3, PMe3, (dppf)1/2, (binap)1/2) gave [Au(II)]2 species, some of which display unprecedented folded structures with Au−Au bonds. Aurophilic interactions facilitate this oxidation process by preorganizing the starting [Au(I)]2 complexes and lowering its redox potential. The obtained [Au(II)]2 complexes undergo thermal or photochemical elimination of R3PAuX to give Au(III) perfluorinated auracycles. Evidence of a radical mechanism for these decomposition reactions was obtained.

Effect of configuration-dependent multi-body forces on interconversion kinetics of a chiral tetramer model

We describe a reformulation of the four-site molecular model for chiral phenomena introduced by Latinwo et al. ["Molecular model for chirality phenomena," J. Chem. Phys. 145, 154503 (2016)]. The reformulation includes an additional eight-body force that arises from an explicit configuration-dependent term in the potential energy function, resulting in a coarse-grained energy-conserving force field for molecular dynamics simulations of chirality phenomena. In this model, the coarse-grained interaction energy between two tetramers depends on their respective chiralities and is controlled by a parameter λ, where λ < 0 favors local configurations involving tetramers of opposite chirality and λ > 0 gives energetic preference to configurations involving tetramers of the same chirality. We compute the autocorrelation function for a quantitative chirality metric and demonstrate that the multi-body force modifies the interconversion kinetics such that λ ≠ 0 increases the effective barrier for enantiomer inversion. Our simulations reveal that for λ > 0 and temperatures below a sharply defined threshold value, this effect is dramatic, giving rise to spontaneous chiral symmetry breaking and locking molecules into their chiral identity.

Water-soluble polycarbodiimides and their cytotoxic and antifungal properties

We have successfully synthesized water-soluble neutral and polyelectrolyte helical polycarbodiimides and studied their biological properties. These polymers were prepared by decorating carbodiimide backbones with nonionic, hydrophilic functional groups such as dimethylamine, piperazine, and morpholine. Additionally, the 3° amines present in these functional groups were quaternized using methyl iodide as the alkylating agent to produce their ionic analogs. Polycarbodiimides were chosen as the base polymer used because of their facile chemical modification, pH tolerance in terms of both their helical conformations and degradation behaviors, and tunable helical inversion barriers. Hydrophilic side groups, such as morpholine, dimethylamine, and piperazine, can be used to balance the amphiphilic architecture of the polycarbodiimides along with lipophilic groups, such as alkyl side chains. A chiral R or S BINOL Ti(IV) isopropoxide catalyst was used to control the handedness of the polycarbodiimide helices in these studies. These ionic and neutral polycarbodiimides were subsequently studied for potential antimicrobial and cytotoxic properties. Poly[N-methyl-N’-2-morpholinoethylcarbodiimide], as an example, exhibited significant antifungal properties against Candida albicans. Also, Poly[N-methyl-N’-2-morpholinoethylcarbodiimide] showed significant inhibition of biofilm formation. This suggests that the polymer is a promising candidate for antifungal biomedical applications. Measuring cytotoxicity against urinary bladder cancer cells, poly[N-[3-(dimethylamino)propyl)]-N’-[3-(morpholino)propyl]carbodiimide] (S-cat) and poly[N-[3-(dimethylamino)propyl)]-N’-[3-(morpholino)propyl]carbodiimide]-MeI (S-cat) showed significantly low IC50 values. The IC50 values of poly[N-[3-(dimethylamino)propyl)]-N’-[3-(morpholino)propyl]carbodiimide] (S-cat) and Poly[N-[3-(dimethylamino)propyl)]-N’-[3-(morpholino)propyl]carbodiimide]-MeI (S-cat) are 3.50 μM and 1.27 μM, respectively. The significantly low cancer cell growth inhibition concentration implies the highest cytotoxicity of the polymers, suggesting potential applications as cancer therapeutics. These results also showed that the functionalization and chirality of polycarbodiimides modulate their anticancer and antifungal activity.

Cover Feature: In‐Fjord Substitution in Expanded Helicenes: Effects of the Insert on the Inversion Barrier and Helical Pitch (Chem. Eur. J. 53/2021)

Like the arms of a dancer, which are waved following the rhythm of the music but avoid colliding with her head or her body; the flexible arms of expanded helicenes find different pathways to reverse their position depending on the size and nature of the insert placed in the innermost zone of their fjord. This work presents the synthesis of a series of in-fjord substituted expanded helicenes and an estimation of their inversion barriers through state-of-the-art quantum calculations. Interestingly, the energetic profile of the inversions is intensively affected by the interplay of steric and attractive London dispersion interactions. More information can be found in the Full Paper by R. A. Mata, M. Alcarazo, et al. (DOI: 10.1002/chem.202102585).

In-Fjord Substitution in Expanded Helicenes: Effects of the Insert on the Inversion Barrier and Helical Pitch.

A series of expanded helicenes of different sizes and shapes incorporating phenyl‐ and biphenyl‐substituents at the deepest part of their fjord have been synthesized via sequential Au‐catalyzed hydroarylation of appropriately designed diynes, and their racemization barriers have been calculated employing electronic structure methods. These show that the overall profile of the inversions (energies, number of transition states and intermediates, and their relative position) is intensively affected by the interplay of steric and attractive London dispersion interactions. Hence, in‐fjord substitution constitutes an additional tool to handle the mechanical properties in helicenes of uncommonly large diameter. The photochemical characterization of the newly prepared helical structures is also reported.

Mechanisms of Spontaneous Curvature Inversion in Compressed Graphene Ripples for Energy Harvesting Applications via Molecular Dynamics Simulations.

Electrically conductive, highly flexible graphene membranes hold great promise for harvesting energy from ambient vibrations. For this study, we built numerous three-dimensional graphene ripples, with each featuring a different amount of compression, and performed molecular dynamics simulations at elevated temperatures. These ripples have a convex cosine shape, then spontaneously invert their curvature to concave. The average time between inversion events increases with compression. We use this to determine how the energy barrier height depends on strain. A typical convex-to-concave curvature inversion process begins when the ripple’s maximum shifts sideways from the normal central position toward the fixed outer edge. The ripple’s maximum does not simply move downward toward its concave position. When the ripple’s maximum moves toward the outer edge, the opposite side of the ripple is pulled inward and downward, and it passes through the fixed outer edge first. The ripple’s maximum then quickly flips to the opposite side via snap-through buckling. This trajectory, along with local bond flexing, significantly lowers the energy barrier for inversion. The large-scale coherent movement of ripple atoms during curvature inversion is unique to two-dimensional materials. We demonstrate how this motion can induce an electrical current in a nearby circuit.

A curved host and second guest cooperatively inhibit the dynamic motion of corannulene

Biomolecular systems show how host–guest binding can induce changes in molecular behavior, which in turn impact the functions of the system. Here we report an artificial host–guest system where dynamic adaptation during guest binding alters both host conformation and guest dynamics. The self-assembled cage host employed here possesses concave walls and a chirotopic cavity. Complementarity between the curved surfaces of fullerenes and the inner surface of the host cavity leads the host to reconfigure stereochemically in order to bind these guests optimally. The curved molecule corannulene undergoes rapid bowl-to-bowl inversion at room temperature. Its inversion barrier is increased upon binding, however, and increased further upon formation of a ternary complex, where corannulene and a cycloalkane are both bound together. The chiral nature of the host also leads to clear differences in the NMR spectra of ternary complexes involving corannulene and one or the other enantiomer of a chiral guest, which enables the determination of enantiomeric excess by NMR.

The interrelation between the structural, electronic and energy parameters of nitrogen inversion in ammonia derivatives

The structural, electronic and energy parameters in the ground and transition states of inversion of the amines H2NXHn (XHn=CH3, NH2, OH, F, SiH3, PH2, SH, and Cl) have been calculated by using DFT (PBE96/def2-tzvpp) method. It was established that the increase of electronegativity of the substituents (the X atoms within the same period) leads to stabilization of the ground and transition states of the molecules. The increase in the inversion barriers is due to relative stabilization of the ground states, but not due to relative destabilization of the transition states. The inversion barriers rise with a decrease in conformational energies of the substituents, sums of valence angles at the nitrogen atoms, negative charges on them, energies of the nitrogen lone pairs and with an increase in s-character and population of the nitrogen lone pairs and difference between the energies of the nitrogen lone pairs in the ground and transition states. The main parameters that allow predicting the change of the nitrogen inversion barriers, independently of the type or volume of the XHn substituent, are s-character of the nitrogen lone pairs and difference between the energies of the nitrogen lone pairs. In all other cases, the correlations were found only for the amines containing the elements of the same period at the nitrogen atom. All structural and electronic parameters of amines containing the Х atoms from the second period are more sensitive to the changes of the ХНn substituents than the parameters of amines containing the Х atoms from the third period.

Equation-of-Motion Coupled-Cluster Protocol for Calculating Magnetic Properties: Theory and Applications to Single-Molecule Magnets.

We present a new computational protocol for computing macroscopic magnetic properties of transition-metal complexes using the equation-of-motion coupled-cluster (EOM-CC) framework. The approach follows a two-step state-interaction scheme: we first compute zero-order states using nonrelativistic EOM-CC and then use these states to evaluate matrix elements of the spin-orbit and Zeeman operators. Diagonalization of the resulting Hamiltonian yields spin-orbit- and field-perturbed eigenstates. Temperature- and field-dependent magnetization and susceptibility are computed by numerical differentiation of the partition function. To compare with powder-sample experiments, these quantities are numerically averaged over field orientations. We applied this protocol to several single-molecule magnets (SMMs) with Fe(II) and Fe(III) in trigonal pyramidal, linear, and trigonal bipyramidal coordination environments. We described the underlying electronic structure by the electron-attachment (EOM-EA) and spin-flip (EOM-SF) variants of EOM-CC. The computed energy barriers for spin inversion, and macroscopic magnetization and susceptibility agree well with experimental data. Trends in magnetic anisotropy and spin-reversal energy barriers are explained in terms of a molecular orbital picture rigorously distilled from spinless transition density matrices between many-body states. The results illustrate excellent performances of EOM-CC in describing magnetic behavior of mononuclear transition-metal SMMs.

Electrical properties and structural defects of p-type GaN layers grown by halide vapor phase epitaxy

The electrical properties and structural defects of p-type GaN layers with Mg concentrations from 8.0 × 1018 to 8.3 × 1019 cm−3 grown by halide vapor phase epitaxy (HVPE) were investigated. In all samples, p-type conduction was confirmed at room temperature. The hole concentration at room temperature decreased in a heavily Mg-doped sample. By analyzing the results of Hall-effect measurements at various temperatures, the acceptor concentration decreased in a heavily Mg-doped sample, whereas the compensating donor concentration increased. These results affect the decrease in the hole concentration. The hole mobility decreased with increasing acceptor concentration. In the heavily Mg-doped sample, pyramidal inversion domains (PIDs) were formed. The size of each PID in an HVPE-grown sample is in good agreement with that Mg-doped GaN layers grown by metalorganic vapor phase epitaxy (MOVPE). Thus, the formation mechanism of PIDs in HVPE-grown samples is possibly the same as that in MOVPE-grown samples. Energy-dispersive X-ray spectroscopy shows that Mg atoms accumulate in PIDs, which suggests that Mg atoms in PIDs are electrically inactive, inhibiting the increase in the acceptor concentration. These results are useful guidelines for fabricating p-type GaN layers with higher hole concentrations by HVPE.

Reversible Stereoisomerization of 1,3-Diphosphetane Frameworks Revealed by a Single-Electron Redox Approach.

The discovery of pyramidal inversion has continued to impact modern organic and organometallic chemistry. Sequential alkylation reactions of an N-heterocyclic carbene (NHC) ligated dicarbondiphosphide 1 with RI (R = Me, Et, or iBu) and ZnMe2 give rise to the highly stereoselective synthesis of cis-1,3-diphosphetanes 3. cis-3 is conformationally favorable at room temperature, whereas inversion to trans-3 is observed at 110 °C. One-electron oxidation of cis-3 with Fc+(BArF) (Fc = [Fe(C5H5)2]; BArF = [B(3,5-(CF3)2C6H3)4)]-) leads to the stereoselective formation of trans-1,3-diphosphetane radical cation salts 3•+(BArF), which can be reversibly transformed to cis-3 upon one-electron reduction. Salts 3•+(BArF) represent the first examples of 1,3-diphosphetane radical cations. These results provide a potential application of planar four-membered heterocycle-based building blocks for electrically fueled molecular switches.

Effect of confinement on ammonia inversion

The effect of confinement on ammonia inversion inside $$\hbox {C}_{50}$$ ( $$D_{5h}$$ ) and $$\hbox {C}_{60}$$ ( $$I_h$$ ) fullerenes has been investigated. Calculations at the DFT(M06-2X)/6-311G** level of theory suggest that $$\hbox {NH}_{3}$$ is stable inside both $$\hbox {C}_{50}$$ and $$\hbox {C}_{60}$$ by $$-8.6$$ and $$-23.8~\hbox {kcal mol}^{-1}$$ , respectively. While the barrier for inversion of the free $$\hbox {NH}_{3}$$ molecule is estimated to be $$1896~\hbox {cm}^{-1}$$ , it increases to $$1972~\hbox {cm}^{-1}$$ and $$2108~\hbox {cm}^{-1}$$ , respectively, inside $$\hbox {C}_{50}$$ and $$\hbox {C}_{60}$$ . The results also reveal that the magnitude of splitting of the bound states below the barrier in the symmetric double-well potential decreases inside both the $$\hbox {C}_{50}$$ and $$\hbox {C}_{60}$$ cages.

Molecular docking, spectroscopic, and quantum chemical studies on aromatic heterocycle tetrakis(4-pyridyl)cyclobutane regioisomers: potential membrane-permeable inhibitors.

Aromatic heterocyclic compounds are commonly used in pharmaceutical and agrochemical products. The usage has been also extended in the production of corrosion inhibitors and electronic, opto-electronic, and NLO devices. The four regioisomers of the aromatic heterocyclic molecule, tetrakis(4-pyridyl)cyclobutane (tpcb), were optimized, and their chemical, electronic, and biological properties were examined. The rctt and rtct isomers were isolated and further characterized by the infrared and Raman spectroscopic techniques, and their vibrational modes with attention on important functional groups were discussed. The theoretical vibrational data obtained by DFT/B3LYP/6-311++G(d,p) were in very good agreement with the experimental ones. The occupancy, bond polarization, hybridization of the N-C bond, bonding characteristics between the pyridyl carbon and cyclobutane moiety, and distribution of electron density for the four tpcb isomers have been explored through NBO analysis. The inversion barrier of the cyclobutane moiety was obtained based on the optimized structures of the planar and puckered configurations of the isomers. The rccc isomer exhibited the least electrophilic character compared to the other tpcb isomers. The chemical significance of tpcb has been further explained by the wave function analyses. Molecular docking results revealed that the tpcb ligand would possess a potential anti-viral and anti-bacterial activity via a membrane-permeable mechanism.