Showing papers on "Conformational isomerism published in 2017"
TL;DR: Two regioisomers of bis(10H-phenothiazin-10-yl)dibenzo[b,d]thiophene-S,S-dioxide, a donor–acceptor–donor thermally-activated delayed fluorescence (TADF) emitter, are studied and it is found that donors or acceptors with more than one conformer have negative repercussions for TADF in organic light-emitting diodes.
Abstract: Regio- and conformational isomerization are fundamental in chemistry, with profound effects upon physical properties, however their role in excited state properties is less developed. Here two regioisomers of bis(10H-phenothiazin-10-yl)dibenzo[b,d]thiophene-S,S-dioxide, a donor–acceptor–donor (D–A–D) thermally-activated delayed fluorescence (TADF) emitter, are studied. 2,8-bis(10H-phenothiazin-10-yl)dibenzo[b,d]thiophene-S,S-dioxide exhibits only one quasi-equatorial conformer on both donor sites, with charge-transfer (CT) emission close to the local triplet state leading to efficient TADF via spin-vibronic coupling. However, 3,7-bis(10H-phenothiazin-10-yl)dibenzo[b,d]thiophene-S,S-dioxide displays both a quasi-equatorial CT state and a higher-energy quasi-axial CT state. No TADF is observed in the quasi-axial CT emission. These two CT states link directly to the two folded conformers of phenothiazine. The presence of the low-lying local triplet state of the axial conformer also means that this quasi-axial CT is an effective loss pathway both photophysically and in devices. Importantly, donors or acceptors with more than one conformer have negative repercussions for TADF in organic light-emitting diodes.
220 citations
TL;DR: A benzo-fused double [7]carbohelicene (D7H) was synthesized through a regioselective cyclodehydrogenation of a tetranaphthyl-p-terphenyl-based precursor, resulting in the excellent conformational stability of D7H.
Abstract: A benzo-fused double [7]carbohelicene (D7H) was synthesized through a regioselective cyclodehydrogenation of a tetranaphthyl-p-terphenyl-based precursor. The twisted (D7H-1) and anti-folded (D7H-2) conformers of D7H were separated by recrystallization, and their double helicene structures with overlapping terminal benzene rings were unambiguously elucidated by X-ray crystallography. A record-high isomerization barrier (46.0 kcal mol−1) in double helicenes was estimated based on density functional theory (DFT) calculation, which resulted in the excellent conformational stability of D7H. The physicochemical properties of D7H-1 and D7H-2 were investigated by UV/Vis absorption spectroscopy and cyclic voltammetry, displaying the variation of electronic structure upon conformational changes. The optical resolution of the racemic D7H-1 was carried out by chiral HPLC, offering enantiopure D7H-1-(P,P) and D7H-1-(M,M), which were further characterized by circular dichroism spectroscopy.
139 citations
TL;DR: The results indicate that in a native-like lipid environment rhodopsin activation is not analogous to a simple binary switch between two defined conformations, but the activated receptor is in equilibrium between multiple conformers that in principle could recognize different binding partners.
Abstract: Conformational equilibria of G-protein–coupled receptors (GPCRs) are intimately involved in intracellular signaling. Here conformational substates of the GPCR rhodopsin are investigated in micelles of dodecyl maltoside (DDM) and in phospholipid nanodiscs by monitoring the spatial positions of transmembrane helices 6 and 7 at the cytoplasmic surface using site-directed spin labeling and double electron–electron resonance spectroscopy. The photoactivated receptor in DDM is dominated by one conformation with weak pH dependence. In nanodiscs, however, an ensemble of pH-dependent conformational substates is observed, even at pH 6.0 where the MIIbH+ form defined by proton uptake and optical spectroscopic methods is reported to be the sole species present in native disk membranes. In nanodiscs, the ensemble of substates in the photoactivated receptor spontaneously decays to that characteristic of the inactive state with a lifetime of ∼16 min at 20 °C. Importantly, transducin binding to the activated receptor selects a subset of the ensemble in which multiple substates are apparently retained. The results indicate that in a native-like lipid environment rhodopsin activation is not analogous to a simple binary switch between two defined conformations, but the activated receptor is in equilibrium between multiple conformers that in principle could recognize different binding partners.
80 citations
TL;DR: The conformational preference of the tertiary amide in the starting material leads to intramolecular migration of a range of aryl rings, even those lacking electron-withdrawing activating groups, and provides a method for n→n+4 ring expansion.
Abstract: Analogues of dibenzodiazepines, in which the seven-membered nitrogen heterocycle is replaced by a 9–12-membered ring, were made by an unactivated Smiles rearrangement of five- to eight-membered heterocyclic anthranilamides. The conformational preference of the tertiary amide in the starting material leads to intramolecular migration of a range of aryl rings, even those lacking electron-withdrawing activating groups, and provides a method for n→n+4 ring expansion. The medium-ring products adopt a chiral ground state with an intramolecular, transannular hydrogen bond. The rate of interconversion of their enantiomeric conformers depends on solvent polarity. Ring size and adjacent steric hindrance modulate this hidden hydrophilicity, thus making this scaffold a good candidate for drug development.
54 citations
TL;DR: The lasso peptide benenodin-1 is described, which exhibits conformational switching between two distinct threaded conformers upon actuation by heat, and it is shown that only the native conformer of benenidin-2 is cleaved by its cognate isopeptidase, indicating that thermally induced conformational switched may also be relevant to the biological function of these molecules.
Abstract: Mechanically interlocked molecules that change their conformation in response to stimuli have been developed by synthetic chemists as building blocks for molecular machines. Here we describe a natural product, the lasso peptide benenodin-1, which exhibits conformational switching between two distinct threaded conformers upon actuation by heat. We have determined the structures of both conformers and have characterized the kinetics and energetics of the conformational switch. Single amino acid substitutions to benenodin-1 generate peptides that are biased to a single conformer, showing that the switching behavior is potentially an evolvable trait in these peptides. Lasso peptides such as benenodin-1 can be recognized and cleaved by enzymes called lasso peptide isopeptidases. We show that only the native conformer of benenodin-1 is cleaved by its cognate isopeptidase. Thus, thermally induced conformational switching of benenodin-1 may also be relevant to the biological function of these molecules.
46 citations
TL;DR: The study offers new insights into how the trans conformation is stabilized in TFE clusters of increasing size, and eventually becomes a dominant conformation in the liquid phase.
Abstract: Rotational spectra of the three most stable conformers (I, II, III) of the ternary 2,2,2-trifluoroethanol (TFE) cluster were measured using Fourier transform microwave spectrometers, and unambiguously assigned with the aid of ab initio calculations. The most stable conformer, I, contains one trans-TFE subunit which is unstable in its isolated gas phase form. The study offers new insights into how the trans conformation is stabilized in TFE clusters of increasing size, and eventually becomes a dominant conformation in the liquid phase. A detailed analysis shows that while O-H⋅⋅⋅O-H and O-H⋅⋅⋅F-C hydrogen bonds are the most significant attractive interactions which stabilize all three conformers, the main driving force for the stability of I over III, which has all gauche-TFE subunits, is the attractive interaction of C-F⋅⋅⋅F-C contact pairs. A new type of three-point F⋅⋅⋅F⋅⋅⋅F attractive contact interaction is also identified.
46 citations
TL;DR: The experimental NIR spectra of butyl alcohols were accurately reproduced and explained in a fully anharmonic DFT study by means of generalized second-order vibrational perturbation theory (GVPT2), which leads to the conclusion that the main factor in the temperature-dependent spectral changes of 2νOH band of aliphatic alcohols in the diluted phase is played by the changes in the relative population of their conformations.
Abstract: Conformational isomerism of aliphatic alcohols with respect to the internal rotation of C–O(H) group and its impact on near-infrared (NIR) spectra has been known in the literature. However, no attempt has ever been made to investigate systematically whether and how the conformational flexibility of the aliphatic chain determines the observed NIR data of aliphatic alcohols. In the present study NIR spectra of four kinds of butyl alcohols, 1-butanol, 2-butanol, isobutanol, and tert-butyl alcohol, were investigated in diluted (0.1 M) CCl4 solutions. The experimental NIR spectra of butyl alcohols were accurately reproduced and explained in a fully anharmonic DFT study by means of generalized second-order vibrational perturbation theory (GVPT2). Entire conformational populations were taken into account in each case. On the basis of the theoretical study, influences of conformational flexibility with respect to internal rotations not only about the C–O bond, but also about the C–C bonds have been well evidenced...
45 citations
TL;DR: It is shown that the trans conformer of trifluoromethylhydroxycarbene preferentially rearranges through a facile quantum-mechanical hydrogen tunnelling pathway, while its cis conformer is entirely unreactive, presenting the first example of a conformer-specific hydrogen Tunnelling reaction.
Abstract: Conformational control of organic reactions is at the heart of the biomolecular sciences. To achieve a particular reactivity, one of many conformers may be selected, for instance, by a (bio)catalyst, as the geometrically most suited and appropriately reactive species. The equilibration of energetically close-lying conformers is typically assumed to be facile and less energetically taxing than the reaction under consideration itself: this is termed the ‘Curtin–Hammett principle’. Here, we show that the trans conformer of trifluoromethylhydroxycarbene preferentially rearranges through a facile quantum-mechanical hydrogen tunnelling pathway, while its cis conformer is entirely unreactive. Hence, this presents the first example of a conformer-specific hydrogen tunnelling reaction. The Curtin–Hammett principle is not applicable, due to the high barrier between the two conformers. Control over the selectivity of chemical reactions and biological molecules requires an intimate understanding of how conformation impacts reactivity. It is now shown that the trans conformer of trifluoromethylhydroxycarbene preferentially rearranges through a quantum-mechanical hydrogen-tunnelling pathway, whereas its cis conformer is unreactive.
40 citations
TL;DR: In this paper, the synthesis and coordination chemistry of the (1R,2S,5R)-menthyl-substituted N,N′-diaryl-α-diimine ligands was described.
38 citations
TL;DR: The microwave spectrum of o-methyl anisole (2-methoxytoluene), CH3 OC6 H4 CH3, has been measured by using a pulsed molecular jet Fourier transform microwave spectrometer operating in the frequency range 2-26.5 GHz.
Abstract: The microwave spectrum of o-methyl anisole (2-methoxytoluene), CH3OC6H4CH3, has been measured using a pulsed molecular jet Fourier transform microwave spectrometer operating in the frequency range 2 - 26.5 GHz. Conformational analysis using quantum chemical calculations at the MP2/6-311++G(d,p) level of theory yields only one stable conformer with a Cs structure, which was assigned in the experimental spectrum. A-E splittings due to the internal rotation of the ring methyl group could be resolved and the barrier to internal rotation was determined to be 444.05(41) cm-1. The experimentally deduced molecular parameters such as rotational and centrifugal distortion constants as well as the torsional barrier of the ring methyl group are in agreement with the calculated values.
34 citations
TL;DR: Strong evidence for a significant influence of both wing-tip substituents and conformation on the cytotoxic properties of the applied complexes has been found.
Abstract: The formation of different conformers of dinuclear silver(I) and gold(I) 1,1′-(2-hydroxyethane-1,1-diyl) bridge-functionalized bis(NHC) complexes with various wing-tip substituents (R = methyl, isopropyl and mesityl) has been investigated using multinuclear NMR spectroscopy and SC-XRD as well as DFT calculations. The ratio of anti/syn isomers strongly depends both on wing-tip substituents and the metal. Moreover, the reaction temperature plays a significant role during the transmetallation process for the ratio of gold(I) conformers, which is further affected by purification procedures. All obtained Au(I)–bis(NHC) complexes have been applied in a standard MTT assay performed for screening the antiproliferative activity against human lung and liver cancer cells. Strong evidence for a significant influence of both wing-tip substituents and conformation on the cytotoxic properties of the applied complexes has been found.
TL;DR: For the first time, solid samples of Gly-Gly have been vaporized by laser ablation and three different structures have been revealed in a supersonic expansion by Fourier transform microwave spectroscopy.
Abstract: Among the hundreds of peptide compounds for which conformations have been determined by using different spectroscopic techniques, the structure of the simplest dipeptide glycylglycine (Gly-Gly) is conspicuously absent. Herein, for the first time, solid samples of Gly-Gly have been vaporized by laser ablation and three different structures have been revealed in a supersonic expansion by Fourier transform microwave spectroscopy. The intramolecular hydrogen bonding interactions that stabilize the observed forms have been established based on the 14 N nuclear quadrupole hyperfine structure. We have illustrated how conformer interconversion distorts the equilibrium conformational distribution, giving rise to missing conformers in the conformational landscape.
TL;DR: The parent thioketene S-oxide H2 CCSO has been generated in the gas phase through flash vacuum pyrolysis and decomposes into HCCH/SO and H2 CS/CO in cryogenic Ar matrix via the intermediacy of a novel vinyl sulfinyl radical H2C(Br)-SO (syn and anti conformers).
Abstract: The parent thioketene S-oxide H2 CCSO has been generated in the gas phase through flash vacuum pyrolysis (ca. 1000 K) of vinyl sulfoxide H2 CC(Br)-S(O)CF3 via the intermediacy of a novel vinyl sulfinyl radical H2 C=C(Br)-SO (syn and anti conformers). Upon irradiation at 266 nm, H2 CCSO decomposes into HCCH/SO and H2 CS/CO in cryogenic Ar matrix. Whereas, visible-light irradiations result in syn↔anti conformational interconversion in H2 C=C(Br)-SO. The molecular structures of H2 CCSO and isomers are computationally studied at the CCSD(T)-F12/VTZ-F12 level of theory, and the bonding properties of H2 CCSO are analyzed with the EDA-NOCV method at the M06-2X/TZ2P level.
TL;DR: In this article, the conformational behavior of the hydrogen-bonded cluster ethanol dimer has been investigated by chirped pulse Fourier transform microwave spectroscopy in the 2-8 GHz frequency region.
TL;DR: This study shows an unprecedented example of two conformational isomers with different Ccarbene -element bonds, isolated from the direct reaction between cAAC and phosphorus trichloride, which were further studied by theoretical calculations.
Abstract: The cyclic alkyl(amino) carbene (cAAC) bonded chlorophosphinidene (cAAC)P-Cl (2/2´) was isolated from the direct reaction between cAAC and phosphorus trichloride (PCl3). Compound 2/2´ has been characterized by NMR and mass spectrometry. 31P NMR investigations [~160 ppm (major) and ~130 ppm (minor)] structural determination reveal that there are two different P environments of P-Cl unit. X-ray single crystal determination suggests a co-crystallization of two conformational isomers of (cAAC)P-Cl (2/2´); the major compound possessing a cAAC-PCl unit with CcAAC-P 1.75 A. This C-P bond length is very close to that of (NHC)2P2 [NHC = N-heterocyclic carbene]. The residual density can be interpreted as a conformational isomer with a shorter CcAAC-P bond similar to non-conjugated phosphaalkene [R-P=CR2]. Our study represents an unprecedented example of two conformational isomers with different Ccarbene-element bonds. Additionally, Br (3c/3c´), I (4c/4c´) and H (5c/5c´) analogues [(Me2-cAAC)P-X; X = Br (3), I (4), H (5)] of 2c/2c´[(Me2-cAAC)P-Cl] were also synthesized and characterized by NMR spectroscopy suggesting similar equilibrium in solution. The unique property of cAAC and the required electronegativity of the X (X = Cl, Br, I and H) atom play a crucial role for the existence of the two isomers which are further studied by theoretical calculations.
TL;DR: Qualitative vapor-phase infrared spectra of crotonaldehyde and MVK vapors over the 540-6500 cm-1 range are reported, completing the vibrational analyses of both conformers from the same set of experimental spectra.
Abstract: Methyl vinyl ketone (MVK) and crotonaldehyde are chemical isomers; both are also important species in tropospheric chemistry. We report quantitative vapor-phase infrared spectra of crotonaldehyde and MVK vapors over the 540–6500 cm–1 range. Vibrational assignments of all fundamental modes are made for both molecules on the basis of far- and mid-infrared vapor-phase spectra, liquid Raman spectra, along with density functional theory and ab initio MP2 and high energy-accuracy compound theoretical models (W1BD). Theoretical results indicate that at room temperature the crotonaldehyde equilibrium mixture is approximately 97% s-trans and only 3% s-cis conformer. Nearly all observed bands are thus associated with the s-trans conformer, but a few appear to be uniquely associated with the s-cis conformer, notably ν16c at 730.90 cm–1, which displays a substantial intensity increase with temperature (70% upon going from 5 to 50 o C). The intensity of the corresponding mode of the s-trans conformer decreases with te...
TL;DR: The rotational and quadrupole coupling constants of the two 14N nuclei determined in this work show that this dipeptide exists as a mixture of C7 and C5 conformers in the supersonic expansion, confirming that the polarity/non-polarity of the side chains of the amino acid is responsible for the conformational locking/unlocking.
Abstract: The steric effects imposed by the isopropyl group of valine in the conformational stabilization of the capped dipeptide N-acetyl-l-valinamide (Ac-Val-NH2) have been studied by laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy. The rotational and quadrupole coupling constants of the two 14N nuclei determined in this work show that this dipeptide exists as a mixture of C7 and C5 conformers in the supersonic expansion. The conformers are stabilized by a C[double bond, length as m-dash]OH-N intramolecular hydrogen bond closing a seven- or a five-membered ring, respectively. The observation of both conformers is in good agreement with previous results on the related dipeptides containing different residues, confirming that the polarity/non-polarity of the side chains of the amino acid is responsible for the conformational locking/unlocking. The voluminous isopropyl group is not able to prevent the less stable C5 conformer from forming but it destabilizes the C[double bond, length as m-dash]OH-N interaction.
TL;DR: Experimental infrared and topological data suggest that the strength of IAHB increases for each methyl group addition, and NBO analyses indicate that methyl groups in different positions related to an OH moiety affect the charge transfer energy involved in intramolecular hydrogen bonding.
Abstract: Intramolecular hydrogen bonding (IAHB) is one of the most important intramolecular interactions and a critical element in adopted molecular arrangements. Moreover, slight substitution in a molecule can affect its strength to a great extent. It is well established that alkyl groups play a positive role in IAHB strength. However, the effects that drive it are specific to each system. To investigate the influence of IAHB and its strength dependency on different acyclic compounds, the conformational preferences of propane-1,3-diol, 3-methoxypropan-1-ol, 3-ethoxypropan-1-ol, 3-isopropoxypropan-1-ol, 3-(tert-butoxy)propan-1-ol, butane-1,3-diol, 3-methoxybutan-1-ol, 3-methylbutane-1-diol, and 3-methoxy-3-methylbutan-1-ol were evaluated experimentally using infrared spectroscopy theoretically supported by topological and natural bond orbital analyses. The most stable conformation of each compound exhibited IAHB and these conformers are more populated in the equilibrium for all studied compounds. Experimental infrared and topological data suggest that the strength of IAHB increases for each methyl group addition. NBO analyses indicate that methyl groups in different positions related to an OH moiety affect the charge transfer energy involved in intramolecular hydrogen bonding. This occurs mostly due to an increase in the spn-hybridized lone pair (LP1O) contribution to the charge transfer , which is a result of changes in s-character and orbital energy caused by geometrical rearrangements, rehybridization, and/or electronic effects.
TL;DR: Reactions of the anti-aromatic pentaphenylborole with diazenes indicate that both the substitution and the isomer influence the reaction outcome, and the more aromatic pyridazine proved to be less reactive, forming a resilient adduct.
Abstract: Reactions of the anti-aromatic pentaphenylborole with diazenes indicate that both the substitution and the isomer influence the reaction outcome. With respect to trans isomers, azobenzene underwent coordination and C-H addition across the diene of the borole, and 2',6'-dimethylazobenzene furnished a fused tricyclic system. Under photolytic conditions, both of the aforementioned diazenes generate the first 1,3,2-diazaborepin heterocycles, rationalized through reactivity with the cis isomers. This notion is corroborated by the reaction of pentaphenylborole with benzo[c]cinnoline, the tethered variant of azobenzene, that only exists as the cis conformer as the corresponding 1,3,2-diazaborepin was produced regardless if the reaction is conducted in the dark or light. The more aromatic pyridazine proved to be less reactive, forming a resilient adduct.
TL;DR: The results suggest a large difference in the H/D kinetic isotope effects in nitrogen and argon matrices (∼5 and >100, respectively) and the stabilizing effect on cis-DOCO by a nitrogen matrix is much smaller than that on trans-HOCO (estimated to be >104).
Abstract: Conformers of carboxyl radical (HOCO) have been studied by IR spectroscopy in argon and nitrogen matrices. In an argon matrix, only the lower-energy conformer trans-HOCO is observed, whereas both cis and trans conformers are found for deuterated carboxyl radical DOCO. In a nitrogen matrix, both conformers of HOCO and DOCO isotopologues can be prepared, indicating strong stabilization of the higher-energy cis conformer by a nitrogen matrix. Selective vibrational excitation promotes the trans-to-cis and cis-to-trans conversions of DOCO in an argon matrix and HOCO and DOCO in a nitrogen matrix, which is the first conformational photoswitching of an open-shell species. In a nitrogen matrix, the cis-to-trans and trans-to-cis conversions of HOCO is also found upon broadband IR light of the spectrometer, and the ratio of the quantum yields of these processes is about 3.3. The photoswitching peculiarities are in agreement with the available theoretical energy barriers. The higher-energy cis conformer decays to th...
TL;DR: A contrasting computational study of these monosaccharides in their neutral form suggests that the lithium cation coordination with Lewis base oxygens can play a key role in favoring particular structural motifs and disrupting hydrogen bond networks, thus exhibiting specific IR spectral features between these closely related lithium-chelated complexes.
TL;DR: In this article, a conformational, structural and vibrational properties of Methionyl-Serine dipeptide ( l -Methionyl l -Serine, Met-Ser), a biological active molecule, were investigated.
TL;DR: Ytterbium and yttrium complexes of octadentate ligands based on 1,4,7,10-tetraazacyclodododecane with a coordinated pyridyl group and either tricarboxylate (L1) or triphosphinate (L2) donors form twisted-square-antiprismatic structures.
Abstract: Ytterbium and yttrium complexes of octadentate ligands based on 1,4,7,10-tetraazacyclododecane with a coordinated pyridyl group and either tricarboxylate (L1) or triphosphinate (L2) donors form twisted-square-antiprismatic structures. The former crystallizes in the centrosymmetric group P21/c, with the two molecules related by an inversion center, whereas the latter was found as an unusual kryptoracemate in the chiral space group P21. Pure shift NMR and EXSY spectroscopy allowed the dynamic exchange between the (RRR)-Δ-(δδδδ) and (RRR)-Λ-(λλλλ) TSAP diastereomers of the [Y.L2] complex to be detected. The rate-limiting step in the exchange between Δ and Λ isomers involves cooperative ligand arm rotation, which is much faster for [Ln.L1] than for [Ln.L2]. Detailed analysis of NOESY, COSY, HSQC, and HMBC spectra confirms that the major conformer in solution is (RRR)-Λ-(λλλλ), consistent with crystal structure analysis and DFT calculations. The magnetic susceptibility tensors for [Yb.L1] and [Yb.L2], obtained from a full pseudocontact chemical shift analysis, are very different, in agreement with a CASSCF calculation. The remarkably different pseudocontact shift behavior is explained by the change in the orientation of the pseudocontact shift field, as defined by the Euler angles of the susceptibility tensor.
TL;DR: Large oxatub[n]arenes (n = 5, 6) have been synthesized and characterized and their conformational complexity was analyzed and host-guest chemistry was studied, suggesting that there are different binding affinities to C60 or C70 for each conformer of ox atub[6]arene.
TL;DR: The conformer-selected ultraviolet (UV) and infrared (IR) spectra of protonated noradrenaline were measured using an electrospray/cryogenic ion trap technique combined with photo-dissociation spectroscopy and it was found that five conformers coexist under ultra-cold conditions.
Abstract: The conformer-selected ultraviolet (UV) and infrared (IR) spectra of protonated noradrenaline were measured using an electrospray/cryogenic ion trap technique combined with photo-dissociation spectroscopy. By comparing the UV photo dissociation (UVPD) spectra with the UV–UV hole burning (HB) spectra, it was found that five conformers coexist under ultra-cold conditions. Based on the spectral features of the IR dip spectra of each conformer, two different conformations on the amine side chain were identified. Three conformers (group I) were assigned to folded and others (group II) to extended structures by comparing the observed IR spectra with the calculated ones. Observation of the significantly less-stable extended conformers strongly suggests that the extended structures are dominant in solution and are detected in the gas phase by kinetic trapping. The conformers in each group are assignable to rotamers of OH orientations in the catechol ring. By comparing the UV–UV HB spectra and the calculated Franck–Condon spectra obtained by harmonic vibrational analysis of the S1 state, with the aid of relative stabilization energies of each conformer in the S0 state, the absolute orientations of catechol OHs of the observed five conformers were successfully determined. It was found that the 0–0 transition of one folded conformer is red-shifted by about 1000 cm−1 from the others. The significant red-shift was explained by a large contribution of the πσ* state to S1 in the conformer in which an oxygen atom of the meta-OH group is close to the ammonium group.
TL;DR: It may be concluded that the an Harmonic GVPT2 method can adequately reproduce the anharmonic effects and vibrational resonances in particular, influencing the IR spectra of aliphatic ethers.
Abstract: Fundamental and non-fundamental vibrational modes, first overtones, and binary combination modes of selected aliphatic ethers (di-n-propylether, di-iso-propylether, n-butylmethyl ether, n-butylethyl ether, di-n-butyl ether, tert-buytlmethyl ether, and tert-amylmethyl ether) were modeled in a fully anharmonic generalized second-order vibrational perturbation theory (GVPT2) approach on the DFT-B2PLYP/SNST level. The modeling procedure of theoretical line shapes took into account conformational isomers of studied molecules. The calculated spectra of the above ethers were compared to the corresponding experimental spectra in the infrared (IR) region (4000–560 cm–1) of the absorption index k(ν) derived from the neat liquid thin-film transmission data. It was found that IR spectra of aliphatic ethers are heavily influenced by the bands originating from non-fundamental modes, particularly from the combination modes in the C–H stretching region (3200–2800 cm–1). Because of the effects of vibrational resonances, t...
TL;DR: In this article, two zinc supramolecular isomers, formulated as α-[Zn(cis-cppca)(H2O)]n (1) and β-[ Zn(trans-CPCA)(H 2O]n (2), have been synthesized under solvothermal conditions and fully characterized (H2cppca = 5-(3-carboxy-phenyl)-pyridine-2-Carboxylic acid).
Abstract: Two zinc supramolecular isomers, formulated as α-[Zn(cis-cppca)(H2O)]n (1) and β-[Zn(trans-cppca)(H2O)]n (2), have been synthesized under solvothermal conditions and fully characterized (H2cppca = 5-(3-carboxy-phenyl)-pyridine-2-carboxylic acid). Solvent-induced conformational isomerism of cppca2− ligand and framework isomerism of 1 and 2 are both observed. Each distorted [Zn(cis-cppca)]2 unit joined four equivalent ones in an abnormal 2D puckered layer in compound 1; however, compound 2 displays a 3-D open framework with larger bi-edge channels constructed by 1D Zn–O–Zn chains and trans-cppca bridges, in which the internal edge is a nearly hexagonal channel with an approximate dimension of 14.51 A and the external edge is a circular channel with an approximate dimension of 19.26 A. Fluorescent properties indicated that compound 1 displays an apparent fluorescence emission in acetone solvent; however, compound 2 was very sensitive to acetone molecules which results in nearly 100% fluorescence quenching. Moreover, compounds 1 and 2 might be promising luminescent probes for the detection of Fe3+. The dye adsorption experiments demonstrated that compound 2 showed good adsorption properties for MB and RhB molecules.
TL;DR: In this article, the hydrogen-bonded complexes of heterocyclic compounds with methanol (MeOH) were studied using matrix isolation FTIR spectroscopy and theoretical calculations based on density functional theory.
Abstract: Acting as hydrogen bond acceptors, heterocyclic compounds could interact with a hydrogen bond donor, where either the heteroatom or the π system is the bonding site. The hydrogen bonded complexes of heterocyclic compounds with methanol (MeOH) were studied using matrix isolation FTIR spectroscopy and theoretical calculations based on density functional theory. Four heterocyclic compounds, furan (Fu), 2,5-dihydrofuran (DHF), pyrrole (Py) and thiophene (Th) were selected as representative examples for acceptors. For each of the MeOH–Fu, MeOH–DHF and MeOH–Th complexes, the O–H⋯π and O–H⋯Y (YO, S) hydrogen bonded structures were obtained, while an N–H⋯O instead of O–H⋯N hydrogen bonded conformer was found in the MeOH–Py complex. The measured OH-stretching transitions of the complexes in the IR spectra were assigned to the O–H⋯O bonded MeOH–Fu (b) and MeOH–DHF (b) conformers and the N–H⋯O bonded Py–MeOH (b) conformer, respectively. However, it was hard to assign the spectra to the exact MeOH–Th conformer, because all the hydrogen bond characteristic features obtained for different MeOH–Th conformers are too close. DHF forms a stronger O–H⋯O hydrogen bond than furan, and the O–H⋯O hydrogen bonded MeOH–Fu complex is more stable than the O–H⋯S bonded MeOH–Th complex. Atoms in molecules analysis was also performed to understand the nature of interaction in the MeOH complexes. This analysis allowed us to characterize the new bond critical point generated in the complexes. The present results help to evaluate the atmospheric behavior of some heterocyclic compounds, and indicate their importance in the pre-nucleation mechanism at the molecular level.
TL;DR: This contribution lists all the conformationally stable cyclic peptoids reported up to the year 2017 and proposes a simple method to define their geometric arrangement in terms of planar chirality.
Abstract: Most of the structural studies made on the secondary structure of peptoids describe their geometric attributes in terms of the classic Ramachandran plot (based on the local analysis of ω, ψ, χ, φ dihedral angles). However, little intuitive understanding is available from internal coordinates when stereochemistry is involved. In this contribution we list all the conformationally stable cyclic peptoids reported up to the year 2017 and propose a simple method to define their geometric arrangement in terms of planar chirality. Evidence of conformational isomerism (due to the long average time of single bond rotation) and conformational chirality (induced by the absence of roto-reflection axes) in this promising class of synthetic macrocycles is provided by NMR spectroscopy (using Pirkle's alcohol as chiral solvating agent) and careful evaluation of X-ray crystallographic studies. The full understanding of the oligomeric macrocycles' structural properties and the clear framing of their conformational isomerism in a proper conceptual scheme is fundamental for future application of peptoids in asymmetric synthesis, chiral recognition and supramolecular chemistry.
TL;DR: One-photon vacuum ultraviolet mass-analyzed threshold ionization (VUV-MATI) spectroscopy was used to characterize the essential conformations of tetrahydrofuran (THF) and thus determine the stereochemistry of the furanose ring constituting the backbones of DNA and RNA.
Abstract: One-photon vacuum ultraviolet mass-analyzed threshold ionization (VUV-MATI) spectroscopy was used to characterize the essential conformations of tetrahydrofuran (THF) and thus determine the stereochemistry of the furanose ring constituting the backbones of DNA and RNA. Since the VUV-MATI spectrum of THF exactly corresponds to the vibrational spectrum of the gas-phase THF cation, the above cation was detected using time-of-flight mass spectrometry featuring the delayed pulsed-field ionization of the target in high Rydberg states by scanning the wavelength of the VUV pulse across the region of the vibrational spectrum. The position of the 0-0 band in the recorded VUV-MATI spectrum was extrapolated to the zero-field limit, allowing the adiabatic ionization energy of THF to be accurately estimated to be 9.4256 ± 0.0004 eV. The above ionization was assigned to a transition between C2-symmetric neutral (S0) and cationic (D0) ground states. The potential energy surfaces associated with molecular pseudorotation in the above states were constructed at the B3LYP/aug-cc-pVDZ level, being in good agreement with experimental observations. The twisted (C2-symmetric) and bent (CS-symmetric) conformers of the S0 state were predicted to be separated by a small interconversion barrier, whereas the D0 state exclusively existed in the C2 conformation. Based on the above, the peaks in the MATI spectrum were successfully assigned based on the Franck-Condon factors and vibrational frequencies calculated by varying the geometrical parameters of the C2 conformation, which determines the precise molecular structure of the THF cation.