Structure Of Pyrrole Research Articles

Computational note on the chemical reactivity of pyrrole derivatives

The nanosciences and their companion nanotechnologies are a hot topic all around the world. They promise the development of revolutionary new materials. These materials are based on nanostructures so they could be called Molecular Nanostructured Materials (MNMs). These MNMs have a lot of potential applications, and among them we could mention getting energy and a cleaner environment, creating new sources of energy by generating hydrogen and utilizing our current sources of energy more efficiently at the microscopic level. Organic heterocycles are systems of growing interest in materials science in view of the potential technological applications in fields such as electronics, photonics, sensors, or corrosion protection. The pyrrole-derived MNMs could be the starting materials for Organic Photovoltaics and for High-Performance OLEDs (Organic Light-Emitting Devices). The objective of this work is to perform a detailed calculation of the molecular structure of some pyrrole derivatives as well as of their dimers, and to predict the chemical reactivity of them using concepts derived from Density Functional Theory (or Conceptual DFT) [1] like the electronegativity, hardness, global electrophilicity and the condensed Fukui functions. These compounds have several desirable characteristics related to their use in Organic Photovoltaics and OLEDS: (i) they contain the pyrrole group, with molecular parameters similar to the thiophene derivatives that have been shown to be useful as MNMs; (ii) the p-conjugated derivatives are generally efficient fluorophores, and as such, useful for the fabrication of nanobiosensors; (iii) they can be used as an attractive building block for Organic Molecular Materials. The analysis of the chemical reactivity parameters will help to identify which of the pyrrole derivatives will be more prone to react with functionalized fullerenes in order to be able to design an Organic Photovoltaics device. The studied molecules are phenyl-(4-phenyl-1H-pyrrole-3-yl)methanone (Molecule 1) [2–4], (4-methoxy-phenyl)-(4-phenyl1H-pyrrole-3-yl)-methanone (Molecule 2) [2–4], [4-(4-methoxyphenyl)-1H-pyrrole-3-yl]-phenylmethanone (Molecule 3) [2–4], and their dimers called Molecule 1-1, Molecule 2-2 and Molecule 3-3, respectively. For this reason, we have calculated the molecular structure of the parent molecules pyrrole and anisole through the use of two different theory levels, PBE/DND and PBE/TNP. The molecular structures of the parent molecules obtained from each calculation were compared with the experimental results by aligning both structures and calculating the Root Mean-Square Deviation (RMSD). The agreement is very good: the standard error of the differences between the experimental and the calculated bond lengths and bond angles being very low for both model chemistries (an average value of 0.03). Moreover, the results for both model chemistries are the same. The conclusion is that with the PBE/ DND model chemistry it is possible to obtain accurate values for the molecular structures without the need to resort to other model chemistry with a higher computational cost. The next step in our study was to perform a conformational analysis on every one of the studied molecules in order to obtain the most stable structure at the semiempirical AM1 level. This was performed by modifying the distances angles of the moieties connected to the pyrrole unit. The resulting structures were used as the starting point for geometry optimizations with the PBE/DND model chemistry. The results for the optimized molecular structures of the six molecules are presented in Figs. 1 and 2 of the Supplementary Materials. Listings showing the values of the interatomic bond lengths and bond angles for the six studied molecules are provided in the form of Tables in the Supplementary Materials section accompanying this work.

The Properties of Asphaltenes and Their Interaction with Amphiphiles

The functional groups on asphaltene surfaces of two kinds of Chinese residue oil were analyzed by X-ray photoelectron spectroscopy (XPS). The ζ potential and electrophoretic mobility of asphaltene solutions and residue solutions were measured through phase analysis light scattering (PALS) technique. The ability to stabilize asphaltenes of two typical ionic amphiphiles, dodecyl benzene sulfonic acid (DBSA) and dodecyl trimethyl ammonium bromide (DTAB), were investigated. Karamay asphaltenes contain large amount of carboxyl and calcium and are negatively charged; whereas Lungu asphaltenes are rich in nickel, vanadium, and pyrrolic structures and are positively charged. DBSA has good ability to stabilize Lungu asphaltenes but has no effect on Karamay asphaltenes. Differently, DTAB has good ability to disperse Karamay asphaltenes but has no obvious effect on Lungu asphaltenes. It is concluded from these results that the charges might derive from the dissociation of metal ions and the deprotonation of acid groups (such as COOH, OH, and SH) or basic groups (such as pyridinic groups) on asphaltene surface. The electric property of asphaltenes plays an important role in the interaction between asphaltenes and amphiphiles. The negatively charged asphaltenes tend to be dispersed by cationic amphiphiles, whereas the positively charged asphaltenes tend to be dispersed by anionic amphiphiles.

Unprecedented SnCl 2·2H 2O-mediated intramolecular cyclization of nitroarenes via C–N bond formation: a new entry to the synthesis of cryptotackieine and related skeletons

A mild, efficient, and one-pot protocol for the intramolecular cyclization of 2-substituted nitroarenes via C–N bond formation using SnCl 2·2H 2O is described. The versatility of the method has been demonstrated by synthesizing two sets of polycyclic structures based on privileged structures of indole and pyrrole, and of the alkaloid cryptotackieine associated with antimalarial activity. Our new approach provides a powerful entry into polycyclic structures related to an alkaloid.

Pyrroles As Antioxidants: Solvent Effects and the Nature of the Attacking Radical on Antioxidant Activities and Mechanisms of Pyrroles, Dipyrrinones, and Bile Pigments

The absolute rate constants, k(inh), and stoichiometric factors, n, of pyrroles, 2-methyl-3-ethylcarboxy-4,5-di-p-methoxyphenylpyrrole, 6, 2,3,4,5-tetraphenylpyrrole, 7, and 2,3,4,5-tetra-p-methoxyphenylpyrrole, 8, compared to the phenolic antioxidant, di-tert-butylhydroxyanisole, DBHA, during inhibited oxidation of cumene initiated by AIBN at 30 degrees C gave the relative antioxidant activities (k(inh)) DBHA > 8 > 7 > 6 and n = 2, whereas in styrene, 8 > DBHA. These results are explained by hydrogen atom transfer, HAT, from the N-H of pyrroles to ROO(*) radicals. The k(inh) values in styrene of dimethyl esters of the bile pigments of bilirubin ester (BRDE), of biliverdin ester (BVDE), and of a model compound (dipyrrinone, 1) gave k(inh) in the order pentamethylhydroxychroman (PMHC) >> BRDE > 1 > BVDE. These antioxidant activities for BVDE and the model compound, 1, and PMHC dropped dramatically in the presence of methanol due to hydrogen bonding at the pyrrolic N-H group. In contrast the k(inh) of BRDE increased in methanol. We now show that pyrrolic compounds may react by HAT, proton-coupled electron transfer, PCET, or single electron transfer, SET, depending on their structure, the nature of the solvent, and the attacking radical. Compounds BVDE and 1 react by the HAT or PCET pathway (HAT/PCET) in styrene/chlorobenzene with ROO(*) and with the DPPH(*) radical in chlorobenzene according to N-H/N-D kH/kD of 1.6, whereas the DKIE with BRDE was only 1.2 with ROO(*). The antioxidant properties of polypyrroles of the BVDE class and model compounds (e.g., 1) are controlled by intramolecular H bonding which stabilizes an intermediate pyrrolic radical in HAT/PCET. According to kinetic polar solvent effects on the monopyrrole, 8, and BRDE, which gave increased rates in methanol, some pyrrolic structures are also susceptible to SET reactions. This conclusion is supported by some calculated ionization potentials. The antioxidant mechanism for BRDE with peroxyl radicals is described by the PCET reaction. Experiments using the 2,6-di-tert-butyl-4-(4'-methoxyphenyl)phenoxyl radical (DBMP(*)) showed this to be a better radical to monitor HAT activities in stopped-flow kinetics compared to the use of the more popular DPPH(*) radical.

Atomic and Electronic Structure of Pyrrole on Ge(100)

We have performed ab initio pseudopotential density-functional calculations for pyrrole adsorbed on the Ge(100) surface in order to investigate its atomic and electronic structure. A large number of the pyrrole/Ge(100) adsorption configurations that could result from cycloadditions and Lewis acid−base reactions were examined. The configuration with both Ge−N and Ge−C linkages was found to be the most stable. The Ge−N linkage is formed by dative bonding after N−H dissociation, and the Ge−C linkage is a weak chemical interaction leading to the loss of aromaticity from the pyrrole ring. The pyrrole molecule bridges two down-Ge atoms in adjacent Ge dimer rows. This configuration was used to explain the experimental scanning tunneling microscopy (STM) images.

PH-dependent Raman study of pyrrole and its vibrational analysis using DFT calculations

Raman spectra of pyrrole in aqueous medium at different pH values, 2.5, 5.5, 7.5 and 10.5 were recorded in the two spectral regions, 1040–1160 cm −1 and 3300–3360 cm −1 and pH dependence of the linewidth, peak position and intensity of the Raman bands corresponding to the ring breathing and symmetric ν(N–H) stretching modes were examined. A linear pH dependence of the peak positions for the ring breathing mode and a maximum at nearly neutral pH (7.5) for the symmetric ν(N–H) normal mode is observed, whereas the linewidth (FWHM) shows almost no variation with the change of pH. A slight decrease in the wavenumber position of the ν(N–H) mode at pH value >7.5 indicates that the influence of deprotonation is small, which results from a weak interaction between the reference molecule and the surrounding environment. The density functional theory (DFT) calculations were made primarily to obtain the optimized geometry and vibrational spectra of pyrrole in the ground electronic state using B3LYP functional and the highest level basis set 6-311++G(d,p). The assignments of the normal modes of pyrrole were made on the basis of potential energy distribution (PED). The calculations were also performed on protonated and deprotonated structures of pyrrole.

Ground state structures and excited state dynamics of pyrrole-water complexes:Ab initioexcited state molecular dynamics simulations

Structures of the ground state pyrrole-(H2O)n clusters are investigated using ab initio calculations. The charge-transfer driven femtosecond scale dynamics are studied with excited state ab initio molecular dynamics simulations employing the complete-active-space self-consistent-field method for pyrrole-(H2O)n clusters. Upon the excitation of these clusters, the charge density is located over the farthest water molecule which is repelled by the depleted pi-electron cloud of pyrrole ring, resulting in a highly polarized complex. For pyrrole-(H2O), the charge transfer is maximized (up to 0.34 a.u.) around approximately 100 fs and then oscillates. For pyrrole-(H2O)2, the initial charge transfer occurs through the space between the pyrrole and the pi H-bonded water molecule and then the charge transfer takes place from this water molecule to the sigma H-bonded water molecule. The total charge transfer from the pyrrole to the water molecules is maximized (up to 0.53 a.u.) around approximately 100 fs.

A β-Mannoside-Selective Pyrrolic Tripodal Receptor

Acetalic substituents strategically located in a pyrrolic tripodal structure provide a new synthetic receptor endowed with unprecedented affinity for mannosides and the highest selectivity for beta-mannose ever reported for synthetic H-bonding receptors. Binding properties have been determined by NMR, ITC, and ESI-MS techniques, while affinities have been univocally assessed by the BC50(0) parameter, a general descriptor of binding affinity.

Static Normal Coordinate Deformations of the Heme Group in Mutants of Ferrocytochrome c from Saccharomyces cerevisiae Probed by Resonance Raman Spectroscopy

The function of heme proteins is, to a significant extent, influenced by the ligand field probed by the heme iron, which itself can be affected by deformations of the heme macrocycle. The exploration of this field is difficult because the heme structure obtained from X-ray crystallography is not resolved enough to unambiguously identify structural changes on the scale of 10(-2) A. However, asymmetric deformations in this order of magnitude affect the depolarization ratio of the resonance Raman lines assignable to normal vibrations of the heme group. We have measured the dispersion of the depolarization ratios of four structure sensitive Raman bands (i.e., nu4, nu11, nu21, and nu28) in yeast iso-1-ferrocytochrome c and its mutants N52V, Y67F, and N52VY67F with B- and Q-band excitation. The DPR dispersion of all bands indicates the presence of asymmetric in-plane and out-of-plane deformations. The replacement of the polar tyrosine residue at position 67 by phenylalanine significantly increases the triclinic B2g deformation, which involves a distortion of the pyrrole symmetry. We relate this deformation to changes of the electronic structure of pyrrole A, which modulates the interaction between its propionate substituents and the protein environment. This specific heme deformation is eliminated in the double mutant N52VY67F. The additional substitution of N52 by valine induces a tetragonal B1g deformation which involves asymmetric changes of the Fe-N distances and increases the rhombicity of the ligand field probed by the heme iron. This heme deformation might be caused by the elimination of the water-protein hydrogen-bonding network in the heme cavity. The single mutation N52V does not significantly perturb the heme symmetry, but a small B1g deformation is consistent with our data and the heme structure obtained from a 1 ns molecular dynamics simulation of the protein.

Reactions of heterocumulenes with organometallic reagents: XI. Quantum-chemical study on the mechanism of noncatalytic cyclization of methyl 2-methoxy-N-methylbuta-2,3-dienimidothioate (1-aza-1,3,4-triene) into substituted pyrrole

Rotational isomerism of methyl 2-methoxy-N-methylbuta-2,3-dienimidothioate (1-aza-1,3,4-triene), which is readily available from 1-lithio-1-methoxyallene, methyl isothiocyanate, and methyl iodide, was studied by quantum-chemical methods. Four most stable rotamers with the energies of activation of their mutual transformations exceeding 35 kJ/mol were identified. The potential energy surfaces for the formation of pyrrole structure from 1-aza-1,3,4-triene via different ring closure channels were analyzed. According to the results of calculations, the most probable is direct [1,5]-cyclization of 1-aza-1,3,4-triene through a cyclic carbene species.

Anharmonic analysis of vibrational states for five-membered heterocyclic compounds

We have used the DFT/B3LYP method with 6-31G*(**) basis sets for analysis of the vibrational spectra and geometric structure of pyrrole, furan, thiophene, and selenophene in the anharmonic approximation. We have determined the influence of resonance effects on the nature of the vibrational states.

The vibrational structures of furan, pyrrole, and thiophene cations studied by zero kinetic energy photoelectron spectroscopy

The vibrational structures of the electronic ground states ((approximately)X (2)A(2)) of furan, pyrrole, and thiophene cations have been studied by zero kinetic energy (ZEKE) photoelectron spectroscopic method. In addition to the strong excitations of the symmetric a(1) vibrational modes, other three symmetric vibrational modes (a(2), b(1), and b(2)) have been observed unambiguously. These results which cannot be explained by the Franck-Condon principle illustrate that the vibronic coupling and the Coriolis coupling may play important roles in understanding the vibrational structures of the five-membered heterocycle cations. The vibrationally resolved ZEKE spectra are assigned with the assistance of the density function theory calculations, and the fundamental frequencies for many vibrational modes have been determined for the first time. The first adiabatic ionization energies for furan, pyrrole, and thiophene were determined as 8.8863, 8.2099, and 8.8742 eV, respectively, with uncertainties of 0.0002 eV.

Chemical Reactions and Adsorption Geometries of Pyrrole on Ge(100)

The adsorption structures of pyrrole (C(4)H(5)N) on a Ge(100) surface at various coverages have been investigated with both scanning tunneling microscopy (STM) and ab initio density-functional theory (DFT) calculations. Three distinct features are observed in the STM images at low coverages. The comparison of the STM images with the simulation reveals that the most dominant flowerlike feature with a dark side is that the adsorbed pyrrole molecules with H dissociated form bridges between two down Ge atoms of neighboring Ge dimer rows through N-Ge bonding and beta-carbon-Ge interaction. The flowerlike feature without a dark side is also observed as a minority, which is identified as nearly the same structure as the most dominant one where a dissociated H is out of the feature. The third feature showing bright protrusions may be due to a C- and N-end-on (CN) configuration, where the pyrrole molecule is located on one dimer row. At higher coverages, the number of localized configurations increases.

Structure of Pyrrole on Ge(100)

The adsorption structures of pyrrole on a Ge(100) surface at low coverage have been investigated using ab initio density-functional theory (DFT) calculations. The most stable configuration is that the adsorbed pyrrole molecule with H dissociated forms a bridge between two down-Ge atoms of neighboring dimer rows through N–Ge bonding and C–Ge interaction. The corresponding simulated images explain well the flower-like features with a dark side observed in the experiment. Also, C–H dissociative structures are found to contribute as a minority to the features. A similar configuration to the most stable one, but with a dissociated H out of the region of interest, can explain the flower-like feature without a dark side. Finally, a C- and N-end-on configuration may be a possible candidate for bright protrusions in the STM images.

Energy dispersive X-ray diffraction and molecular dynamics meet: The structure of liquid pyrrole

In this work, a coupled experimental–theoretical protocol for the study of molecular liquids is reported. Energy dispersive X-ray diffraction results are successfully interpreted with molecular dynamics. Several models, differing for geometry and force field are presented; their behavior in reproducing experimental data is discussed.

The effect of electron-withdrawing groups on 15N and 13C chemical shifts: a density functional study on a series of pyrroles

Electron-withdrawing groups (EWGs) on the nitrogen atom of pyrroles have significant effects on the properties of the pyrrole. It has been suggested that the experimental 13C chemical shifts show a general increase in deshielding effect with the increase of N-EWGs strength [A. Thompson, S. Gao, G. Modzelewska, D.S. Hughes, B. Patrick, D. Dolphin, Org. Lett., 2, 3587 (2000)]. However, recently observed 15N chemical shifts of pyrroles do not correlate with the N-EWG strength. To elucidate the relationship between the electronic structures of pyrroles and their nitrogen and carbon chemical shifts, density functional theory calculations were performed on pyrroles with various substituents. A correlation between the paramagnetic shift and the 15N chemical shift was observed for the pyrroles, indicating that the nitrogen chemical shift trend for the pyrroles arises entirely from variations of the paramagnetic shift contribution. However, a general correlation between the 15N chemical shifts and the EWG strength does not exist. Natural chemical shielding (NCS) analysis shows that the changes in the σ(N5–R)–π* transitions and changes in the sum of the σ(C1–N5)–π* and σ(C4–N5)–π* transitions account for the nitrogen chemical shift trend observed in the pyrroles.

Elucidating the porous and chemical structures of ZnCl2-activated polyacrylonitrile on a fiberglass substrate

ZnCl2-activated polyacrylonitrile (PAN) coated onto a fiberglass substrate was prepared in N2 at 450 °C. The porous and chemical structures were characterized by using N2 adsorption at 77 K, XPS, FTIR, competitive adsorption of CO2/CH4 and the adsorption of Cs+, Sr2+ and Ag+. The activated PAN displays a high BET surface area up to 1012 m2 g−1, a broad mesopore size distribution as well as a major micropore size distribution. Up to 19.3 wt% of nitrogen, which is probably in the form of pyridinic and pyrrolic structures, is incorporated in the chemically activated PAN. HCl uptake results show that such a material has a higher amount of weakly basic functional groups compared to a commercially available ACF15. The activated PAN also exhibits a higher selectivity coefficient for CO2/CH4 at STP and higher adsorption amounts for Cs+, Sr2+ and Ag+ than ACF15. It is proposed that nitrogen-containing, weakly basic functional groups positioned on the suitable-sized pore walls improve the adsorption ability of the activated PAN toward CO2, Cs+, Sr2+ and Ag+.

Reactions of Heterocumulenes with Organometallic Reagents: X. Quantum-Chemical Study of the Reaction of Aliphatic Isothiocyanates with Lithiated Allenes. Intramolecular Rearrangements of 1,3,4-Azatrienes

Study of the potential energy surface for the reaction of isothiocyanates with α-lithiated allenes showed that the formation of 1,3,4-azatriene occurs in one step through a four-center transition state. [1,5]-Sigmatropic rearrangements of 1,3,4-azatrienes and electrocyclizations of the resulting conjugated 1,3,5-azatriene systems lead to formation of dihydropyridine ring. Pyrrole structures are more likely to arise from protonation of 3-alkoxy-1,3,4-azatriene.

Trofimov Reaction with Oximes Derived from Ketosteroids: Steroid—Pyrrole Structures.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Comparative study of chemically synthesized and plasma polymerized pyrrole and thiophene thin films

Pyrrole and thiophene polymers prepared via chemical means or plasma polymerization at different radio frequency (RF) power input on different substrates were compared using X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, scanning electron microscopy and UV–visible absorption spectroscopy. These polymers were deposited as thin films on either low-density polyethylene (LDPE) or LDPE surface graft copolymerized with acrylic acid (AAc). The results indicate that the structures of plasma polymerized pyrrole and thiophene are rather different from those of polymers synthesized by conventional chemical methods, due to a higher degree of crosslinking and branching reactions in plasma polymerization. A higher and more stable conductivity can be obtained with chemically synthesized polypyrrole and polythiophene, but the thin films generated from the plasma polymerization process are much smoother and more uniform. The lack of stability in the plasma polymerized samples’ conductivity may be due to the unstable nature of the charge transfer complex with the dopant (iodine) resulting in a greater ease of diffusion of the iodine from the film. Under the conditions tested, the thickness of plasma polymerized pyrrole and thiophene thin layers increases almost linearly with the RF power. The modification of the LDPE substrates using AAc-graft copolymerization can enhance the growth and adhesion of the thin film and its conductivity.