Cyclic Isomers Research Articles

Chromogenic properties of heterocyclic compounds: Barochromic effect of indoline spiropyrans in the gas phase

Spiropyrans of the indoline and benzothiazole series, which exist under normal conditions in a colored merocyanine form, have been obtained. Solutions of the synthesized compounds exhibit negative photochromism. Previously unknown chromogenic properties were found in the gas phase of the synthesized indoline spiropyrans, namely, the barochromic effect, consisting of the discoloration of a gas containing spiropyran molecules when the pressure of the air is reduced. This effect is due to the conversion of the merocyanine isomers absorbing in the visible region of the spectrum into cyclic isomers absorbing in the UV region of the spectrum. It has been established that solid-phase films of indoline series spiropyrans, which are in a stable merocyanine form under normal conditions, have the properties of negative T- and P-type photochromism. Extremely low values of the rate constants of reverse thermal reactions make it possible to consider them as reverse positive–negative media for recording and processing optical information.

Detection of 1H-Triphosphirene (c-HP3) and 2-Triphosphenylidene (HP3): The Isovalent Counterparts of 1H-Triazirine (c-HN3) and Hydrazoic Acid (HN3).

The hitherto elusive 1H-triphosphirene (c-HP3) and 2-triphosphenylidene (HP3) molecules were prepared in low-temperature matrices and detected isomer selectively through photoionization coupled with reflectron time-of-flight mass spectrometry (PI-ReTOF-MS). Our results reveal a thermodynamically preferred cyclic isomer (c-HP3) compared to the acyclic structure (HP3) in contrast to the isovalent HN3 system favoring hydrazoic acid (HN3) compared to 1H-triazirine (c-HN3). Theoretical computations suggest a ring strain energy of 1H-triphosphirene (c-HP3) of only 35 kJ mol-1, which is significantly lower than the tetrahedral phosphorus molecule (P4) of 74 kJ mol-1. This work provides a fundamental benchmark to understand the electronic structure and chemical bonding of cyclic molecules and offers an unconventional approach to preparing highly strained, still elusive molecules such as 1H-triazirine and tetrahedral tetranitrogen (N4) in the near future involving progressive nonequilibrium chemistries.

Transition Metal-Catalyzed and MAO-Assisted Olefin Polymerization; Cyclic Isomers of Sinn’s Dimer Are Excellent Ligands in Iron Complexes and Great Methylating Reagents

Methylaluminoxane (MAO) is the most commonly used co-catalyst for transition metal-catalyzed olefin polymerization, but the structures of MAO species and their catalytic functions remain topics of intensive study. We are interested in MAO-assisted polymerization with catalysts L(R2)FeCl2 (L = tridentate pyridine-2,6-diyldimethanimine; imine-R = Me, Ph). It is our hypothesis that the MAO species is not merely enabling Fe–Me bond formation but functions as an integral part of the active catalyst, a MAO adduct of the Fe-precatalyst [L(R2)FeCl]+. In this paper, we explored the possible structures of acyclic and cyclic MAO species and their complexation with pre-catalysts [L(R2)FeCl]+ using quantum chemical approaches (MP2 and DFT). We report absolute and relative oxophilicities associated with the Fe ← O(MAO) adduct formation and provide compelling evidence that oxygen of an acyclic MAO species (i.e., O(AlMe2)2, 4) cannot compete with the O-donor in cyclic MAO species (i.e., (MeAlO)2, 7; MeAl(OAlMe2)2, cyclic 5). Significantly, our work demonstrates that intramolecular O → Al dative bonding results in cyclic isomers of MAO species (i.e., cyclic 5) with high oxophilicities. The stabilities of the [L(R2)FeClax(MAO)eq]+ species demonstrate that 5 provides for the ligating benefits of the cyclic MAO species 4 without the thermodynamically costly elimination of TMA. Mechanistic implications are discussed for the involvement of such Fe–O–Al bridged catalyst in olefin polymerization.

Mixture effects in alkane/cycloalkane hydroconversion over Pt/HUSY: Carbon number impact

Cycloalkanes are known to impact the metal–acid balance of the hydrocracking of n-alkanes with similar carbon number, however, how this impact varies with the carbon number of the components involved is still to be understood in more detail. For this purpose, the hydroconversion of n-octane and tert-butylcyclohexane, and n-decane and methylcyclohexane mixtures was investigated in this work over Pt/HUSY catalyst in both the ideal and the nonideal hydrocracking regime. Irrespective of the hydrocracking regime for pure n-octane, its conversion and isomer yields were significantly lowered upon admixture of tert-butylcyclohexane. On the other hand, n-octane admixture did not impact the tert-butylcyclohexane conversion nor its cyclic isomer yields. Upon methylcyclohexane admixture with n-decane, no impact was observed over the catalyst ensuring ideal hydrocracking of pure n-decane. Over the catalyst with significantly lower Pt loading, which does not ensure ideal hydrocracking of n-decane, methylcyclohexane lowered the n-decane conversion. A slightly negative impact of n-decane admixture on methylcyclohexane conversion was also observed. The observed effects are mainly attributed to the differences in adsorption strengths within the zeolite pores on top of differences in alkane and cycloalkane adsorption on the metal sites.

Polymer nanospheres containing CdSe/ZnS quantum dots and photochromic diaryletenes with photoswitchable luminescence

A study was carried out and a comparative analysis of the spectral-kinetic (absorption and fluorescent) characteristics of nanospheres containing luminescent inorganic quantum dots (QDs) CdSe/ZnS, covered with an amphiphilic polymer shell, which ensures the stability of nanospheres in aqueous colloidal solutions and the possibility of introducing into them hydrophobic photochromic diarylethene molecules with different structure. Photoinduced reversible isomerization of diarylethene molecules causes modulation of the photoluminescence signal of quantum dots, including through the control of the efficiency of resonant energy transfer (FRET) from quantum dots to the cyclic isomer of diarylethene. The FRET efficiency turned out to be the highest in nanospheres with DAE2 and DAE4. The value of the quality index (QF) of the FRET photomodulator (which shows the efficiency of modulation of the quantum yield of QD photoluminescence), introduced in this work, varies for samples with different diarylethenes from 0.003 (for DAE1) to 0.09 (for DAE2). Nanospheres containing luminescent nanoparticles of various shapes can be used in the development of luminescent photocontrolled panels, fluorescent markers, etc. Keywords: quantum dots, fluorescence, Forster resonance energy transfer, nanocomposites, photochromism, diarylethenes.

Фотомодуляция люминесценции наносфер с квантовыми точками CdSe/ZnS в полимерных пленках

The results of studies of the spectral-kinetic (absorption and fluorescent) characteristics of the polymer nanospheres created by us (containing luminescent inorganic CdSe/ZnS quantum dots and photochromic diarylethene molecules) incorporated into a polymer film are presented. A reversible modulation of the fluorescence intensity of quantum dots, caused by the photoisomerization of diarylethene molecules, was found. It is shown that nanospheres in polymer matrices exhibit higher efficiencies of both photoinduced modulation of QD radiation and Förster resonance energy transfer (FRET) from QDs to the cyclic isomer of DAE as compared to solutions. The results can be used, for example, to create luminescent photocontrolled panels based on films containing fluorescent nanoparticles.

Полимерные наносферы, содержащие квантовые точки CdSe/ZnS и фотохромные диарилэтены, с фотопереключаемой люминесценцией

A study was carried out and a comparative analysis of the spectral-kinetic (absorption and fluorescent) characteristics of nanospheres containing luminescent inorganic quantum dots (QDs) CdSe/ZnS, covered with an amphiphilic polymer shell, which ensures the stability of nanospheres in aqueous colloidal solutions and the possibility of introducing into them hydrophobic photochromic diarylethene molecules with different structure. Photoinduced reversible isomerization of diarylethene molecules causes modulation of the photoluminescence signal of quantum dots, including through the control of the efficiency of resonant energy transfer (FRET) from quantum dots to the cyclic isomer of diarylethene. The FRET efficiency turned out to be the highest in nanospheres with DAE2 and DAE4. The value of the quality index (QF) of the FRET photomodulator (which shows the efficiency of modulation of the quantum yield of QD photoluminescence), introduced in this work, varies for samples with different diarylethenes from 0.003 (for DAE1) to 0.09 (for DAE2). Nanospheres containing luminescent nanoparticles of various shapes can be used in the development of luminescent photocontrolled panels, fluorescent markers, etc.

Luminescence photomodulation of nanospheres with CdSe/ZnS quantum dots in polymer films

The results of studies of the spectral-kinetic (absorption and fluorescent) characteristics of the polymer nanospheres created by us (containing luminescent inorganic CdSe/ZnS quantum dots and photochromic diarylethene molecules) incorporated into a polymer film are presented. A reversible modulation of the fluorescence intensity of quantum dots, caused by the photoisomerization of diarylethene molecules, was found. It is shown that nanospheres in polymer matrices exhibit higher efficiencies of both photoinduced modulation of QD radiation and Forster resonance energy transfer (FRET) from QDs to the cyclic isomer of DAE as compared to solutions. The results can be used, for example, to create luminescent photocontrolled panels based on films containing fluorescent nanoparticles. Keywords: photochromism, fluorescence, quantum dot, Forster resonance energy transfer, polymer nanospheres, polymer films

15N Chemical Shifts and JNN-Couplings as Diagnostic Tools for Determination of the Azide-Tetrazole Equilibrium in Tetrazoloazines.

Selectively 15N-labeled tetrazolo[1,5-b][1,2,4]triazines and tetrazolo[1,5-a]pyrimidines bearing one, two, or three 15N labels were synthesized. The synthesized compounds were studied by 1H, 13C, and 15N NMR spectroscopy in DMSO and TFA solutions, where the azide-tetrazole equilibrium can lead to the formation of two tetrazole (T, T') isomers and one azide (A) isomer for each compound. Incorporation of the 15N-label(s) leads to the appearance of 15N-15N coupling constants (JNN), which can be easily measured via simple 1D 15N NMR spectra, even at natural abundance between labeled and unlabeled 15N atoms. The chemical shifts for the 15N nuclei in the azole moiety are very sensitive to the ring opening and azide formation, thus providing information about the azido-tetrazole equilibrium. At the same time, the 1-2JNN couplings between 15N-labeled atoms in the azole and azine fragments unambiguously determine the fusion type between tetrazole and azine rings in the cyclic isomers T and T'. Thus, combined analysis of 15N chemical shifts and JNN values in selectively isotope-enriched compounds provides an effective diagnostic tool for direct structural determination of tetrazole isomers and azide form in solution. This method was found to be the most simple and efficient way to study the azido-tetrazole equilibrium.

Synthesis, structure, properties and antimicrobial activity of para trifluoromethyl phenylboronic derivatives

The [2-formyl-4-(trifluoromethyl)phenyl]boronic acid as well as its benzoxaborole and bis(benzoxaborole) derivatives were obtained and their properties studied. The 2-formyl compound displays an unusual structure in the crystalline state, with a significant twist of the boronic group, whereas in DMSO solution it tautomerizes with formation of a cyclic isomer. All the studied compounds exhibit relatively high acidity as well as a reasonable antimicrobial activity. Docking studies showed interactions of all the investigated compounds with the binding pocket of Candida albicans LeuRS. High activity against Bacillus cereus was determined for the 2-formyl compound as well as for the novel bis(benzoxaborole), whereas the studied benzoxaborole shows high antifungal action with MIC values equal to 7.8and 3.9 μg/mL against C. albicans and A. niger respectively. None of the studied compounds exhibits reasonable activity against E. coli.

Putative Nucleotide-Based Second Messengers in the Archaeal Model Organisms Haloferax volcanii and Sulfolobus acidocaldarius.

Research on nucleotide-based second messengers began in 1956 with the discovery of cyclic adenosine monophosphate (3′,5′-cAMP) by Earl Wilbur Sutherland and his co-workers. Since then, a broad variety of different signaling molecules composed of nucleotides has been discovered. These molecules fulfill crucial tasks in the context of intracellular signal transduction. The vast majority of the currently available knowledge about nucleotide-based second messengers originates from model organisms belonging either to the domain of eukaryotes or to the domain of bacteria, while the archaeal domain is significantly underrepresented in the field of nucleotide-based second messenger research. For several well-stablished eukaryotic and/or bacterial nucleotide-based second messengers, it is currently not clear whether these signaling molecules are present in archaea. In order to shed some light on this issue, this study analyzed cell extracts of two major archaeal model organisms, the euryarchaeon Haloferax volcanii and the crenarchaeon Sulfolobus acidocaldarius, using a modern mass spectrometry method to detect a broad variety of currently known nucleotide-based second messengers. The nucleotides 3′,5′-cAMP, cyclic guanosine monophosphate (3′,5′-cGMP), 5′-phosphoadenylyl-3′,5′-adenosine (5′-pApA), diadenosine tetraphosphate (Ap4A) as well as the 2′,3′-cyclic isomers of all four RNA building blocks (2′,3′-cNMPs) were present in both species. In addition, H. volcanii cell extracts also contain cyclic cytosine monophosphate (3′,5′-cCMP), cyclic uridine monophosphate (3′,5′-cUMP) and cyclic diadenosine monophosphate (3′,5′-c-di-AMP). The widely distributed bacterial second messengers cyclic diguanosine monophosphate (3′,5′-c-di-GMP) and guanosine (penta-)/tetraphosphate [(p)ppGpp] could not be detected. In summary, this study gives a comprehensive overview on the presence of a large set of currently established or putative nucleotide-based second messengers in an eury- and a crenarchaeal model organism.

Vibrational Spectroscopy of Benzonitrile-(Water)1-2 Clusters in Helium Droplets.

Polycyclic aromatic hydrocarbons are considered as primary carriers of the unidentified interstellar bands. The recent discovery of the first interstellar aromatic molecule, benzonitrile (C6H5CN), suggests a repository of aromatic hydrocarbons in the outer earth environment. Herein, we report an infrared (IR) study of benzonitrile-(D2O)n clusters using mass-selective detection in helium nanodroplets. In this work, we use isotopically substituted water, D2O, instead of H2O because of our restricted IR frequency range (2565-3100 cm-1). A comparison of the experimental and predicted spectra computed at the MP2/6-311++G(d,p) level of benzonitrile-(water)1-2 clusters reveals the formation of a unique local minimum structure, which was not detected in previous gas-phase molecular beam experiments. Here, the solvent water forms a nearly linear hydrogen bond (H-bond) with the nitrile nitrogen of benzonitrile, while the previously reported most stable cyclic H-bonded isomer is not observed. This can be rationalized by the stepwise aggregation process of precooled monomers. The addition of a second water molecule results in the formation of two different isomers. In one of the observed isomers, a H-bonded water chain binds linearly to the nitrile nitrogen similar to the monohydrated benzonitrile-water complex. In the other observed isomer, the water dimer forms a ring-type structure, where a H-bonded water dimer simultaneously interacts with the nitrile nitrogen and the adjacent ortho CH group. Finally, we compare the water-binding motif in the neutral benzonitrile-water complex with the corresponding positively and negatively charged benzonitrile-water monohydrates to comprehend the charge-induced alteration of the solvent binding motif.

The matrix infrared spectra of fulvenone (C5H4=C=O) and its thermal decomposition products

The matrix IR absorbance spectra of fulvenone, a reactive intermediate in the pyrolysis of lignin, and three of its thermal dissociation products were recorded and analysed using a flash pyrolysis microreactor and ab initio calculations. The predicted spectra of fulvenone, penta-1,2-diene-4-yne, penta-1,3-diyne, and n- matched well with the experimentally observed transitions, and are in good agreement with existing literature data. The cyclic isomer, cyclopentadienylidene, could not be conclusively identified, suggesting that fulvenone is the last relatively stable cyclic species in this pyrolytic chain of reactions. The evolution of the IR data with increasing extent of the pyrolysis shows a gradual trend of dissociation of complex organic molecules towards highly unsaturated hydrocarbons. The isomer-specific analysis by IR assignments of these pyrolytic pathways helps pave the way for further study of biomass thermal reactions, towards possible uses of biomass as a renewable source of energy.

The disappearance of the stable slightly-bent isomer of germasilaallenes and the appearance of its cyclic isomer

Systematic density functional theory (DFT) calculations and natural bond orbital (NBO) analyses were carried out to understand the reason behind the disappearance of linear and slightly-bent isomer of germasilaallenes and the bond-stretch phenomenon of their cyclic isomer, unusual electronic properties of highly-bent isomers of germasilaallenes. Our results show that in contrast to trisilaallene and trigermaallene, 1,3-digermasilaallene and 1-germadisilaallene do not have stable cyclic isomers, due to increased ring strains. DFT calculations and NBO analyses indicate that the stability of highly-bent isomers of germasilaallenes arise from three parts: p(terminal) → p(central) donor–acceptor interaction, p(terminal)-p(terminal) partial overlapping and the aromatic delocalization along the ring. Different from mono- and di-germasilaallene, DFT and CCSD calculations indicate that there is no stable minimum along the first half, from 180° to 90.0°, of the potential energy surface of trigermasilaallene. For trigermasilaallene, for bending angle α > 120.0°, π-π* orbital delocalization effect dominates the stability and when α < 120.0°, aromatic delocalization of the conformer becomes the main factor. With the bending angle lighter, the stable energy becomes larger. Thus, the germasilaallenes gradually become more stable along the bending PES from 180° to 90.0° and no barrier stabilizes the slightly-bent isomer. DFT calculations indicate that strong donor effect from substituents attached to terminal Si (Ge) to central Si (Ge) can stabilize the slightly-bent isomer of germasilaallenes.

Theoretical research on reaction of solid sulfur allotropes with elemental mercury

Element sulfur has proven to be active material for hazardous elemental mercury (Hg0) removal. However, the underlying mechanism of elemental sulfur reacting with Hg0 was still unclear. Generally, solid elemental sulfur exists mainly composed of crown-shaped S8 molecules and traces of S6, S7, and S9 molecules. This research employed quantum chemical calculations and electronic wavefunction analysis to investigate the reaction between branched and cyclic Sn isomers (n = 6–9) with Hg0 at the molecular level. Thermodynamic data and kinetics were also computed. It was found that Hg0 react with branched Sn isomers would proceed spontaneously with heat release by analyzing reaction Gibbs free energies and enthalpies. Reaction rate constants of branched Sn molecules are several orders of magnitude higher than those of cyclic Sn molecules. Moreover, the electronic wavefunction analysis was conducted. The Mayer bond order along the reaction pathway could characterize Hg-S and S-S bonds breaking and formation quantitively. Localized molecular orbitals isosurface maps reflect Hg-S bonds show typical σ bond characteristics in the products. Localized orbital locator color-filled maps reveal electrons begin to concentrate in the region between Hg and S atoms as reactions proceeding forward. In summary, this research would help develop sulfur contained adsorbents with superior Hg0 removal performance in the future.

Some DADNE Originated Cyclic Isomers - A DFT Study

Diaminodinitroethylene (DADNE) has three constitutional isomers, geminal, cis and trans. The geminal one is the well known FOX-7 explosive. It is a push-pull type molecule. In the present study, within the restrictions of density functional theory at the level of B3LYP/6-311++G(d,p), two cyclic dimeric structures of DADNE are investigated quantum chemically. Also their mono ionic forms have been investigated (unrestricted treatment). All the structures are found to be stable. Various quantum chemical and spectral data are collected computationally and discussed.

Probing the fuel-specific intermediates in the low-temperature oxidation of 1-heptene and modeling interpretation

In this work, low temperature (low-T) oxidation of 1-heptene was investigated in a jet-stirred reactor (JSR) over the temperatures of 450–800 K, 770 Torr and equivalence ratios of 0.5–2.0. The intermediates were identified and quantified using synchrotron vacuum ultraviolet photoionization mass spectrometry (SVUV-PIMS) and gas chromatography combined with mass spectrometry (GC–MS). The SVUV-PIMS experiment combined with quantum chemistry calculation of ionization energy enables the identification of fuel-specific intermediates, including C7 alkenylperoxy radical and hydroperoxides, such as diolefinic-hydroperoxide, alkenylhydroperoxide, alkenyl-ketohydroperoxide and cyclic ether hydroperoxide. Among them, alkenylperoxy radical, diolefinic-hydroperoxide and cyclic ether hydroperoxide have not been detected in alkene oxidation before. In order to accurately identify and quantify other fuel-specific intermediates such as aldehyde and cyclic ether isomers, the GC–MS experiment was conducted under the same conditions as the SVUV-PIMS experiment. On the other hand, a detailed low-T oxidation model of 1-heptene was developed, which can reasonably capture the fuel oxidation rate and negative temperature coefficient behaviors observed in this work. The present model can not only interpret the formation of different kinds of hydroperoxides and predict their temperature windows, but also capture the formation of 2-heptenal, hexanal and heptanal, and branched tetrahydrofurans, which are derived from the H-abstraction by OH, OH addition and H addition reactions of 1-heptene, respectively, revealing that the competition between these reactions can be well characterized.

Theoretical investigation of para amino‐dichloro chalcone isomers, part I: A DFT structure—stability study

AbstractChalcones are versatile compounds with various biological activities and nonlinear optical applications. This study investigated the trans and cis isomers of 3‐(x,y‐dichlorophenyl)‐1‐(4′‐NH2‐phenyl)‐2‐propen‐1‐one, where (x) and (y) represent the positions of the two chlorine atoms [(2,3), (2,4), (2,5), (2,6), (3,4) and (3,5)] and their cyclic chromene isomers. The B3LYP density functional theory (DFT) method was used, with a 6‐311G (d,p) basis set. Calculations revealed that trans chalcones prefer s‐cis conformations. The syn conformation, in which chlorine atoms at carbon (2) or (3) is parallel to the carbonyl group, was more stable than the anti‐syn in trans chalcones. However, in cis chalcones, the opposite result was obtained. In contrast, (3,4) chalcones behaved in the opposite manner, for both trans and cis isomers. This order of conformation stability did not change when dispersion correction (DC) was incorporated in the calculations. Geometry optimisation with DC revealed that the trans (3,5) chalcone is the most stable, and the cis (2,3) chalcone is the least stable isomer in both chalcone series. However, (2,6) chromene was the most stable in chromene series isomers and the (3,4) chromene as the least stable. Calculated heat of hydrogenations for cis and trans isomers revealed that trans and cis (3,4) chalcones are the most stable in each series. However, trans and cis (2,6) chalcones are the least stable in each series. The stability of the three isomers, with and without DC, was determined as the following order: trans &gt; cis &gt; chromene.

5-Trifluoromethyl-2-formylphenylboronic Acid.

2-Formylphenylboronic acids display many interesting features, not only from synthetic but also from an application as well as structural points of view. 5-Trifluoromethyl-2-formyl phenylboronic acid has been synthesized and characterized in terms of its structure and properties. The presence of an electron-withdrawing substituent results in a considerable rise in the acidity in comparison with its analogues. In some solutions, the title compound isomerizes with formation of the corresponding 3-hydroxybenzoxaborole. Taking into account the probable mechanism of antifungal action of benzoxaboroles, which blocks the cytoplasmic leucyl-tRNA synthetase (LeuRS) of the microorganism, docking studies with the active site of the enzymes have been carried out. It showed possible binding of the cyclic isomer into the binding pocket of Candida albicans LeuRS, similar to that of the recently approved benzoxaborole antifungal drug (AN2690, Tavaborole, Kerydin). In case of Escherichia coli LeuRS, the opened isomer displays a much higher inhibition constant in comparison with the cyclic one. The antimicrobial activity of the title compound was also investigated in vitro, showing moderate action against Candida albicans. The compound reveals higher activity against Aspergillus niger as well as bacteria such as Escherichia coli and Bacillus cereus. In case of Bacillus cereus, the determined Minimum Inhibitory Concentration (MIC) value is lower than that of AN2690 (Tavaborole). The results confirm potential of 2-formylphenylboronic acids as antibacterial agents and give a hint of their possible mechanism of action.

Inducing molecular isomerization assisted by water

Light is not the only stimulus that can induce linear-to-cyclic isomerization of donor-acceptor Stenhouse adducts (DASAs). Here we demonstrate the water-induced linear-to-cyclic isomerization of DASAs. The mechanism of the water-induced linear-to-cyclic isomerization of DASAs is investigated by density functional theory (DFT) calculations. Water molecules coordinate with DASAs and stabilize the intermediates and cyclic isomers, which favors cyclization thermodynamically. Moreover, the linear-to-cyclic isomerization is reversible. Heating removes the coordinated H2O molecules, which further triggers cyclic-to-linear isomerization. DASAs have been applied in information hiding/displaying and color switching under water vapor and heating control.