Equatorial Forms Research Articles

Conformer-Selective Photoelectron Circular Dichroism.

Conformational flexibility and chirality both play a key role in molecular recognition. It is therefore very useful to develop spectroscopic methods that simultaneously probe both properties. It has been theoretically predicted that photoelectron circular dichroism (PECD) should be very sensitive to conformational isomerism. However, experimental proof has been less forthcoming and only exists for a very few favorable cases. Here, we present a new PECD scheme based on resonance-enhanced two-photon ionization (RE2PI) using UV/Vis nanosecond laser excitations. The spectral resolution obtained thereby guarantees conformer-selectivity by inducing resonant conformer-specific ππ* S1←S0 transitions. We apply this experimental scheme to the study of chiral 1-indanol, which exists in two conformers linked by a ring inversion and defined by the position of the hydroxyl group, namely axial and equatorial. We show that the PECD of the equatorial and axial forms considerably differ in sign, magnitude and shape. We also discuss the influence of the total ionization energy, vibronic excitation of intermediate and final states, and relative polarization of the excitation and ionization lasers. Conformer-specificity adds a new dimension to the applications of PECD in analytical chemistry addressing now the general case of floppy systems.

Conformer‐Selective Photoelectron Circular Dichroism

AbstractConformational flexibility and chirality both play a key role in molecular recognition. It is therefore very useful to develop spectroscopic methods that simultaneously probe both properties. It has been theoretically predicted that photoelectron circular dichroism (PECD) should be very sensitive to conformational isomerism. However, experimental proof has been less forthcoming and only exists for a very few favorable cases. Here, we present a new PECD scheme based on resonance‐enhanced two‐photon ionization (RE2PI) using UV/Vis nanosecond laser excitations. The spectral resolution obtained thereby guarantees conformer‐selectivity by inducing resonant conformer‐specific ππ* S1←S0 transitions. We apply this experimental scheme to the study of chiral 1‐indanol, which exists in two conformers linked by a ring inversion and defined by the position of the hydroxyl group, namely axial and equatorial. We show that the PECD of the equatorial and axial forms considerably differ in sign, magnitude and shape. We also discuss the influence of the total ionization energy, vibronic excitation of intermediate and final states, and relative polarization of the excitation and ionization lasers. Conformer‐specificity adds a new dimension to the applications of PECD in analytical chemistry addressing now the general case of floppy systems.

Revealing the Structure of 6-Aminopenillanic Acid: The Active Nucleus of Penicillins.

6-Aminopenicillanic acid is a penicillanic acid compound and is the active nucleus common to all penicillins. Using laser ablation techniques, we transformed the solid into the gas phase and characterized its conformational panorama by combining supersonic expansions and Fourier transform microwave techniques. Five conformers were determined, adopting different spatial configurations. Among them, the axial and equatorial forms, which are biologically relevant, have been observed. The structural similarity to d-Ala-d-Ala and the detection of both axial and equatorial forms could explain its potential as a penicillin core and its capability as an antibiotic.

Unraveling the secrets of molecular and electronic structures of [Fe(CO)4(GeX)]: A DFT study

The axial, as well as the equatorial forms of [Fe(CO)4(GeX); where X represents chalcogens], were examined using DFT quantum simulations with the B3LYP level of theory. According to the study of total energy, equatorial variants are usually more stable when compared with the axially substituted ones. The bonding characteristics of these complexes were revealed by the NPA and EDA analyses. The bond index for the M-GeX bond was discovered by the WBI analysis. According to the FMO study, the complexes HOMO-LUMO energy gap varied from 4.38 to 4.73 eV, which is less than that of Fe(CO)5. NBO study revealed that the contribution from Fe atoms for the Fe-Ge bond is less than Ge. Additionally, it is revealed that a similar impact is observed on the carbonyl group (in the Fe-C bond); however, the contribution from carbon is greater than the Ge.

Insights into the divergent evolution of the oceanic squid Sthenoteuthis oualaniensis (Cephalopoda: Ommastrephidae) from the Indian Ocean.

Sthenoteuthis oualaniensis is known for its complex population structure with three major transoceanic forms (viz. middle-sized, dwarf, and giant forms) whose taxonomic status has been disputed for decades. This integrated taxonomic study examines these prevenient morphotypes gathered on cruises in the Indian Ocean to ascertain their status in the evolutionary history of the species. Molecular analyses employing mitochondrial (COI, ND2) and nuclear (H3) markers revealed four genetically distinct and novel lineages of the species in the Indian Ocean, representing three morphotypes from the Arabian Sea and one from the Southern Indian Ocean. The mitochondrial-based phylograms revealed two distinct clades in the species: "dwarf forms + giant form" and "middle-sized forms," which further branch into geographically structured evolutionary units. Species delimitation analyses recovered five distinct clades, namely, the Arabian Sea giant and dwarf forms, Equatorial, Eastern Typical, and Other Middle-sized forms, representing the consensus molecular operational taxonomic units. H3 being heterozygous could not resolve the phylogeny. Haplotype network and AMOVA analysis of mtDNA genes indicated explicit phylogeographic structuring of haplotypes, whereas these outputs and PCA results were incongruent with the morphological grouping. Phenetic features distinguishing the morphotypes were sometimes plastic and mismatched with the genotypes. The giant form was genetically close to the dwarf forms, contradicting the earlier notion that it descended from the middle-sized form. It may be assumed that the dwarf form evolved following sympatric speciation and adaptation to warm equatorial waters, while the focal features of the Western Arabian Sea guide toward allopatric speciation of the giant form.

The investigation of modification in structural flexibility and coordination modes in a solvent free β-diketone Cu(II) complex by crystal structure and DFT studies

Coordination-driven self-assembly in inorganic complexes is a viable methodology to construct supramolecular coordination complexes. Crystal engineering of β-diketone Cu(II) coordination complexes can be achieved via the host–guest complexation method. The effect of metal–ligand interactions (coordination polyhedra) on the supramolecular framework has been analysed by crystal structure and computational studies. A new crystal form of a Cu(II) complex with 4,4,4-trifluoro-naphthyl butanedione has been identified and characterized using various spectroscopic techniques. X-ray diffraction studies unveiled that complex 1, [Cu(TFNB)2], crystallized in the monoclinic (P21/n) space group and its solvent-induced crystal forms, complex 2, [Cu(TFNB)2DMSO] (Database Identifier: IVAKIC), and complex 3, [Cu(TFNB)2DMF] (Database Identifier: ZOCHOR), which were reported earlier, are in the triclinic (P1¯) crystal system. The previously reported crystal forms (complexes 2 and 3) are examples of a single crystal coordinated solvent exchange (SCCSE) transformation. In complex 1, the β-diketone molecules are attached to the metal ion in an equatorial form with a perfect square planar geometry, whilst complexes 2 and 3 feature a slightly distorted square pyramidal geometry with chelated donor oxygen atoms of the β-diketone ligands in equatorial sites and the crystallizing DMSO and DMF solvents are apically coordinated to the metal centre, respectively. Interestingly, the oxygen donors of the β-diketone ligands in complex 1 are inclined in a trans configuration, whereas in the solvent-induced pseudopolymorphic forms of complexes 2 and 3, a cis configuration is observed. The variation in the supramolecular framework with the coordination geometry in different crystal forms is analysed using the crystal structures and compared with quantum computational (Hirshfeld surface, enrichment ratio, energy framework, NCI index model and DFT) results. Molecular docking analysis was performed for all the complexes against the SARS-CoV2 main protease to explore the structure–property relationship.

Experimental and theoretical studies on coordination of a flexible cyclohexane based C3-symmetric tripodal ligand with iron, aluminum and gallium

The use of a cyclohexane ring in the centre of a C3 symmetric tripodal ligand with a suitable spacer can flip between the axial and equatorial forms due to low transition energy and can facilitate the formation of stable metal complexes. Keeping this perspective in view, a new chelator, N,N′,N″-((1R,3R)-cyclohexane-1,3,5-triyl)tris(8-hydroxyquinoline-2-carboxamide), TACH2COX, comprising of a cis,cis-1,3,5-trisaminocyclohexane(TACH) as central unit and three quinolinols joined through amide linkage is developed. The brown-colored ligand has been characterized through melting point, IR, NMR (1H, 13C), ESI mass, and absorption spectroscopy. The solution coordination chemistry of the newly synthesized ligand is studied by its interaction with three bio-relevant metal ions: iron(III), aluminum (III) and gallium(III) through spectroelectrochemical technique. The high metal–ligand formation constants of the ligand indicate that TACH2COX is one of the strong metal chelators amid synthetic chelators. The structure and bonding of the complexes have been established through DFT studies. The molecular modeling studies reveal that the tripodal ligand binds to the metal ions by coordination of the ligand through three sets of N, O-coordination sites on, each from one pendant showing distorted octahedral geometry. The NBO, EDA, ETS-NOCV analysis, and absorption spectra of the ligand and its metal complexes are also described.

Hydrogen bonding networks and cooperativity effects in the aqueous solvation of trimethylene oxide and sulfide rings by microwave spectroscopy and computational chemistry.

The intermolecular interactions responsible for the microsolvation of the highly flexible trimethylene oxide (TMO) and trimethylene sulfide (TMS) rings with one and two water (w) molecules were investigated using rotational spectroscopy (8-22GHz) and quantum chemical calculations. The observed patterns of transitions are consistent with the most stable geometries of the TMO-w, TMO-(w)2, and TMS-w complexes at the B2PLYP-D3(BJ)/aug-cc-pVTZ level and were confirmed using spectra of the 18O isotopologue. Due to its effectively planar backbone, TMO offers one unique binding site for solvation, while water can bind to the puckered TMS ring in either an axial or equatorial site of the heteroatom. In all clusters, the first water molecule binds in the σv symmetry plane of the ring monomer and serves as a hydrogen bond donor to the heteroatom. The second water molecule is predicted to form a cooperative hydrogen bonding network between the three moieties. Secondary C-H⋯O interactions are a key stabilizing influence in trimers and also drive the preferred binding site in the TMS clusters with the axial binding site preferred in TMS-w and the equatorial form calculated to be more stable in the dihydrate. Using an energy partition scheme from the symmetry-adapted perturbation theory for the O, S, and Se containing mono- and dihydrates, the intermolecular interactions are revealed to be mainly electrostatic, but the dispersive character of the contacts is enhanced with the increasing size of the ring's heteroatom due to the key role of longer-range secondary interactions.

The conformational behavior and structure of monosubstituted-1,3,5-trisilacyclohexanes: 1-N,N-dimethylamino-1,3,5-trisilacyclohexane

1-dimethylamino-1,3,5-trisilacyclohexane was synthesized and its structure and conformational properties have been determined by gas electron diffraction (GED) and quantum chemical (QC) calculations. The molecule may exist in 3 or 4 forms differing from each other by the substituents' position. QC results shows that the equatorial conformers are more stable than axial forms with ratio Eq:Ax=(75–58):(25–42)% (depending on method and basis set). From the GED data, the molar fractions of the conformers were found to be g-Eq:tr-Eq:tr-Ax=40(4):31(8):29(9)% at 272(3) K. In the liquid phase, as follows from IR measurements, the molecule may also exist in equatorial and axial forms.

The Six Isomers of the Cyclohexanol Dimer: A Delicate Test for Dispersion Models

AbstractThe cyclohexanol homodimer acts as a delicate test model of the role of dispersion forces in intermolecular association. Whereas phenol produces a single dimer, the suppression of π interactions and the larger conformational flexibility in cyclohexanol results in multiple isomerism, with six competing dimers of the free molecule being observed in a supersonic jet expansion. Rotational spectroscopy reveals accurate structural data, specifically the formation of homo‐ and heterochiral diastereoisomers and the presence of both equatorial and axial forms in the dimers. Four dispersion‐corrected density‐functional molecular orbital calculations were tested against the experiment, with B3LYP‐D3(BJ) offering good structural reproducibility with an Alrich's triple‐ζ basis set. However, the prediction of the dimer energetics is largely model‐dependent, thus offering a testbed for the validation of dispersion‐corrected computational models.

The Six Isomers of the Cyclohexanol Dimer: A Delicate Test for Dispersion Models.

The cyclohexanol homodimer acts as a delicate test model of the role of dispersion forces in intermolecular association. Whereas phenol produces a single dimer, the suppression of π interactions and the larger conformational flexibility in cyclohexanol results in multiple isomerism, with six competing dimers of the free molecule being observed in a supersonic jet expansion. Rotational spectroscopy reveals accurate structural data, specifically the formation of homo- and heterochiral diastereoisomers and the presence of both equatorial and axial forms in the dimers. Four dispersion-corrected density-functional molecular orbital calculations were tested against the experiment, with B3LYP-D3(BJ) offering good structural reproducibility with an Alrich's triple-ζ basis set. However, the prediction of the dimer energetics is largely model-dependent, thus offering a testbed for the validation of dispersion-corrected computational models.

A ring of fire in the pulsar magnetosphere

Contopoulos 2019 proposed that a dissipation zone develops in the magnetosphere of young pulsars at the edge of the closed-line region beyond the light cylinder. This is necessary in order to supply the charge carriers that will establish current closure through the equatorial and separatrix current-sheets. In the present work, we propose to investigate in greater detail this region with a simplified model that we would like to call the `ring-of-fire'. According to this simple model, the dissipation zone is a narrow reconnection layer where electrons and positrons are accelerated inwards and outwards respectively along Speiser orbits that are deflected in the azimuthal direction by the pulsar rotation. After they exit the reconnection layer, the accelerated positrons form the positively charged equatorial current-sheet, and the accelerated electrons form the negatively charged separatrix current-sheet along the boundary of the closed-line region. During their acceleration, particles lose only a small part of their energy to radiation. Most of their energy is lost outside the dissipation region, in the equatorial and separatrix current sheets. Our simple model allows us to obtain high-energy spectra and efficiencies. The radiation emitted by the positrons in the equatorial current-sheet forms a very-high energy tail that extends up to the TeV range.

Impact of Methoxy Substituents on Thermally Activated Delayed Fluorescence and Room-Temperature Phosphorescence in All-Organic Donor-Acceptor Systems.

Thermally activated delayed fluorescence (TADF) and room-temperature phosphorescence (RTP) are known to occur in organic D-A-D and D-A systems where the donor group contains the phenothiazine unit and the acceptor is dibenzothiophene- S, S-dioxide. This study reports the synthesis and characterization of one new D-A and four new D-A-D systems with methoxy groups on the phenothiazine to examine their effect on emission properties in the zeonex matrix. X-ray analysis and highly specialized NMR techniques were used to characterize asymmetric methoxy-substituted derivative 3b, which is chiral at N because of an extremely high flipping barrier at the phenothiazine N atom. Based on hybrid-density functional theory computations, the methoxy substituents tune the relative stabilities of the axial conformers with respect to equatorial conformers of the phenothiazine units, depending on their substitution position. This conformational effect significantly influences both TADF and RTP contributions compared to the parent D-A-D system. It is also demonstrated that the equatorial forms of D-A-D and D-A systems in zeonex exhibit TADF. Additionally, the methoxy groups promote luminescence in D-A-D systems where only axial conformers exist. This work reveals further design opportunities for more efficient TADF and RTP molecules.

Cyanocyclohexane: Axial-to-equatorial “seesaw” parity in gas and condensed phases

Conformational properties and molecular structure of cyanocyclohexane 1 were studied by gas-phase electron diffraction (GED) and dynamic NMR as well as by detailed quantum chemical (QC) computations. This compound violates the so called ‘equatorial rule’ according to which the substituents attached to one of the carbon atom of the ring prefers to occupy an equatorial position relative to the frame of cyclohexane. In case of 1, both conformers contribute nearly equally in gas and liquid phases, with slight domination of the equatorial form as found from the experimental data, Eq:Ax of ca. 3:2. The QC calculations predict contradictive conformer preference depending on method/basis set combination applied. Enthalpy and entropy contributions to Eq↔Ax equilibrium are analyzed.

Semiexperimental and mass-dependent structures by the mixed regression method: Accurate equilibrium structure and failure of the Kraitchman method for ethynylcyclohexane.

The mixed regression method for determination of molecular structures is reviewed and applied to the investigation of ethynylcyclohexane, using both semiexperimental and mass-dependent methods. This methodology provides an efficient and computationally affordable route to obtain accurate molecular reference data, preventing ill-conditioning in the structural least-squares determinations from experimental rotational constants. New supersonic-jet microwave measurements are reported to obtain inertial data for the axial and equatorial species of ethynylcyclohexane, together with all 13C isotopologues of the equatorial form. The semiexperimental equilibrium (reSE) and mass-dependent (rm(2)) structures of the molecule are compared with high-level ab initio optimizations, showing that both methods deliver compatible structures with accuracies of about 0.002 Å for bond lengths and 0.2° for bond angles. We confirm that dependable predicates can be obtained for a large variety of bonds. Finally, we verify that the substitution method completely fails to determine a reliable structure for the title compound.

Rapid Monitoring of Copper Over a Wide Concentration range by High-Sensitive Potentiometric Membrane Electrode Based on 1-cyano-1-piperidino-2(N- piperidino methyl)-cyclo hexane

n this paper, 1-cyano-1-piperidino-2(N- piperidino meth-yl)-cyclohexane was synthesized. The lowest-energy conformer of this molecule (Ligand) with axial and equatorial forms of cyanide toward cyclohexane and local minima corresponding to their complexes with various ions were obtained using Monte Carlo procedure by Molecular Mechanics with MMFF94 method. The calculated results of the Gibbs free energy of the reaction using density functional theory (DFT) show that the thermodynamic reactivity of complexation of copper ion with studied ligand is the best. Finally, a selective and sensitive copper-ion selective liquid membrane electrode for potentiometric monitoring of ultra-trace amounts of Cu2+ was prepared by using 1-cyano-1-piperid-ino-2(N- piperidino methyl)-cyclohexane as an excellent ionophore. This electrode exhibits a Nernstian response for Cu2+ ions over a con-centration range (1.5 × 10-2 to 1.0 × 10-8 mol L-1) with a slope of 28.4±0.4 mV per decade. The limit of detection of the sensor is 6.3 × 10-9 mol L-1. The sensor has a relatively fast response time (<10 s) and a useful working pH range of 5.0–8.5. Interference of some cations was also evaluated. The practical utility of the Cu2+ ion sensor has been demonstrated by using it as an indicator electrode in potentiomet-ric titration of Cu2+ with EDTA and for direct determination of Cu2+ in well water samples.

Orbital interaction between electron lone pair and carbonyl group in N-trifluoroacetylpiperidine and N-piperidine amides: Planar and non-planar nitrogen bond configurations

Molecular structure of N-trifluoroacetylpiperidine (NFAPi) was studied by synchronous gas-phase electron diffraction/mass spectrometry (GED/MS), IR spectroscopy and quantum chemical (QC) calculations. Due to the influence of strong conjugation between the electron lone pair on the nitrogen atom and the double bond of the carbonyl group, NFAPi may exist as only one conformer, in which the trifluoroacetyl group is located in an intermediate, between axial and equatorial, position. Nine atoms (two Cα atoms along with their Heq atoms, the nitrogen atom, the carbonyl group and one CF fragment of the trifluoromethyl group) form a single plane.In contrast, partition of the conjugation between the double CO bond and the two lone pairs leads to coexisting intermediate and axial, in 1-piperidinecarboxamide, and axial and equatorial forms in N, N-dimethyl-1-piperidinecarboxamide and 1,1′-carbonyldipiperidine. The conformational ratio for the latter ones is Eq:Ax≈50:50%. The steric effect and conjugation stabilize the axial conformer.

A comparative study of two novel unsymmetrically substituted triazacyclohexanes

Novel unsymmetrically N-substituted N,N′-R1N″-R2-1,3,5-triazacyclohexanes (1b and 2b; R1 = p-chlorophenyl or p-methoxyphenyl and R2 = butyl or cyclohexyl) have been synthesized in a good yield from condensation reaction by excess amine. Both triazacyclohexane rings have chair conformation. However, 1b adopts diaxial orientation of aryl groups and an equatorial form of alkyl group whereas 2b prefers an axial orientation of the alkyl group and diequatorial forms of aryl groups. 1b is consolidated by weak C-H⋯π interactions. Intra-molecular C-H⋯O or C-H⋯N hydrogen bonds and C-H⋯π may be effective in the stabilization of 2b. Both compounds have showed moderate antimicrobial activity, but 1b exhibits higher activity than 2b. All experimental results are found in good support to theoretical data. Findings of research may be helpful guide for the medicinal chemists and the field is further open for pharmacokinetics studies.

New unsymmetrically substituted triazacyclohexanes: Synthesis, characterisation, antimicrobial properties and DFT study

New five unsymmetrically substituted 1,3,5-triazacyclohexanes compounds, carrying aliphatic as well as aromatic substituent, were synthesized and structural analyses were performed by FTIR, 1H NMR and single crystal X-ray techniques. Experimental research was complemented by quantum mechanical calculations. The present triazacyclohexane rings adopt a chair conformation by both R1 substituents in axial positions and R2 group in an equatorial form. Further, all compounds were screened for their anti-bacterial and anti-fungal properties. By revealing further insight into triazacyclohexanes systems, the data theoretically predicted and experimentally obtained in current research may be helpful guide for the medicinal chemists.

Vapor-phase infrared and Raman spectra and ab-initio calculations of the axial and equatorial forms of cyclohexane-d1 and d11

The vapor-phase infrared and Raman spectra of cyclohexane-d11 in the C–H stretching region show two bands at 2891 and 2921cm−1 corresponding to the axial and equatorial C–H stretching modes respectively. Similarly, cyclohexane-d1 has two C–D stretching modes at 2145 and 2164cm−1 (Mátrai and Gal, 1984) corresponding to the two forms. Force constants were calculated for these vibrations and these confirm the theoretical calculations, which show the equatorial bonds to be shorter and stronger. The force constant for the equatorial C–H stretching is 2% higher than for the axial.