Pyrrole Molecules Research Articles

17O DOR and other solid-state NMR studies concerning the basic properties of zeolites LSX

We demonstrate complementary 1H, 17O, 27Al and 29Si measurements for basic low-silica-X zeolites, which were unloaded and pyrrole and formic acid-loaded. It was found that the acid–base-system is not stabile, if the loading exceeds one pyrrole molecule or two formic acid molecules per supercage. 17O DOR NMR spectra exhibit at least four lines, which are broadened by a distribution of chemical shifts in a similar extend as the 29Si MAS NMR spectra are broadened by distribution of Si–O–Al angles. A strong cation influence upon 17O shifts was observed. But there was no strong influence of the acid molecules on the mean value of the 17O shift of the spectra.

Quantum-chemical investigation of the electrophile affinity of molecules of five-membered heterocycles with one hetero-atom and some model systems

Quantum-chemical calculations have been made of the energy characteristics of the molecules of pyrrole, furan, thiophene, and selenophene, the simplest derivatives of N, O, S, and Se with sp3-and sp2-hybridized C atoms and heteroatoms, and also of the products of addition of proton and certain other electrophiles to these molecules. The calculations were carried out by HF, B3LYP, and MP2 methods with the 6−31+G(d) basis set with corrections to the energy of zero-point vibrations. It was shown that the values of the affinity of the nitrogen-containing systems towards the electrophile were significantly greater than for their analogs, derivatives of chalcogens, while the relative stability of the onium states of the latter depends both on the hybridization of the heteroatoms, and also on the nature of the electrophile. Analysis of the obtained results made it possible to build a stability series of the onium compounds and to interpret the special features of the positional selectivity in electrophilic substitution reactions of five-membered heteroaromatic compounds with one heteroatom.

Structural insight into acute intermittent porphyria

Acute intermittent porphyria (AIP), an inherited disease of heme biosynthesis, is one of the most common types of porphyria. Reduced activity of the enzyme porphobilinogen deaminase (PBGD), which catalyzes the sequential condensation of 4 molecules of porphobilinogen to yield preuroporphyrinogen, has been linked to the symptoms of AIP. We have determined the 3-dimensional structure of human PBGD at 2.2 A resolution. Analysis of the structure revealed a dipyrromethane cofactor molecule covalently linked to C261, sitting in a positively charged cleft region. In addition to the critical catalytic D99, a number of other residues are seen hydrogen bonded to the cofactor and play a role in catalysis. Sequential entry of 4 pyrrole molecules into the active site is accomplished by movement of the domains around the hinges. H120P mutation resulted in an inactive enzyme, supporting the role of H120 as a hinge residue. Interestingly, some of the mutations of the human PBGD documented in patients suffering from AIP are located far away from the active site. The structure provides insights into the mechanism of action of PBGD at the molecular level and could aid the development of potential drugs for the up-regulation of PBGD activity in AIP.

Cluster‐Controlled Photofragmentation: The Case of the Xe–Pyrrole Cluster

In this report we describe a process where chemical control can be used to create a molecular switch. Specifically we demonstrate that the fission of the N-H bond in pyrrole can be “controlled”, i.e., turned ON or OFF, by clustering the system to a single noble gas atom such as Xe. Using slice imaging experiments on the H-atom photofragments in combination with high level quantum mechanical electronic structure calculations, the mechanism underlying the process is unravelled. The effect is general and manifests itself in situations were conical intersections, such as the one present in the pyrrole molecule, a prototype of small DNA bases, are involved in the photochemistry of the system. Hence our observation appears to be a first step towards “biological” control at the molecular level. Part of this work was supported by the Division of Chemical Sciences, Geosciences and Biosciences, Office of Basic Energy Sciences, US Department of Energy. Battelle operates the Pacific Northwest National Laboratory for the US Department of Energy.

Extracting Covalent and Ionic Structures from Usual Delocalized Wave Functions: The Electron-Expansion Methodology

We present easily programmable expansions, allowing the calculation of the weights of local covalent and ionic structures of a chemical bond from usual delocalized wave functions; they are obtained in the framework of the electron-expansion methodology, in which the hole conditions (involved by definition in a covalent or ionic structure) are expanded in terms involving only electrons. From the derived relations, true for both HF and correlated levels, one can also express the covalency/ionicity and the localization of a usual two-electron two-center (2e/2c) bond in terms of electronic populations. The three-electron populations are crucial for bond localization. On the contrary, in 2e/2c bonding, and particularly in Charge-Shift bonds (which show enhanced covalent-ionic interactions) although the three-electron populations can be non-negligible, they are not important for the covalency/ionicity of these bonds. Numerical applications and discussion are given for correlated MO wave functions of butadiene, hexatriene, and pyrrole molecules on the basis of both natural atomic orbitals (NAOs) (orthogonal orbitals) and pre-NAOs (nonorthogonal orbitals).

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.

Photoelectron Angular Distribution in Valence Shell Ionization of Heteroaromatic Molecules Studied by the Continuum Multiple Scattering Xα Method

Photoelectron angular distributions are calculated for the valence shell ionization of heteroaromatic molecules of pyridine, pyrazine, pyrimidine, pyrrole, and furan by the continuum multiple scattering Xalpha method. The asymmetry parameters exhibit strong energy dependences in ionization from pi orbitals but are almost invariant in ionization from sigma orbitals, in good agreement with experimental results. The asymmetry parameters in ionization from nonbonding orbitals appear generally higher than those in ionization from bonding orbitals. These features are interpreted in terms of the Coulomb phase and photoelectron angular distribution in the molecular frame.

Fragmentation Dynamics of Size-Selected Pyrrole Clusters Prepared by Electron Impact Ionization: Forming a Solvated Dimer Ion Core

Structure and dynamics of size-selected charged pyrrole clusters have been studied by means of molecular beam scattering experiments and ab initio calculations. Small neutral Pyn clusters were produced in Py/He mixture expansions, and the scattering experiment with a secondary beam of He-atoms was exploited to select the neutral clusters of different sizes. The complete size-selected fragmentation patterns for the neutral dimer to the tetramer after an electron impact ionization at 70 eV were obtained from the measurements of the angular and velocity distributions at different fragment masses. All the investigated cluster sizes decay mainly to the monomer ions Py+1 (from 60 to 80% of the corresponding neutral size) and to the dimer ion Py+2 (20-30%). The trimer ions Py+3 are generated to less than 10% from the neutral trimer and tetramer. To explain the observed results, we have calculated the structures and energetics of pyrrole clusters up to the trimer for the neutral and the ionic state using DFT and PMP2 methods. The ab initio calculations show that ionized pyrrole clusters are formed with a dimeric core that is solvated by neutral pyrrole molecules. In addition, the ground and ionic state of Py-Ar complexes were calculated at CCSD(T) level with extended basis in relevance to the mixed clusters produced in supersonic expansions of Py seeded in Ar. The calculated dissociation energies of the Py-Ar and (Py-Ar)+ complexes indicate that Ar atoms are able to rapidly evaporate after ionization. The combined analysis of the fragmentation probabilities, and calculations allowed us to estimate the distribution of energy deposited in the clusters after the electron impact, which peaks above 1 eV and has a tail up to 5 eV.

Excited state dynamics in pyrrole–water clusters: First-principles simulation

The excited state dynamics in pyrrole–water clusters is investigated using restricted open-shell Kohn–Sham theory. While the isolated pyrrole molecule dissociates in the excited state, no dissociation is observed in the presence of water molecules. Instead an electron is transferred to water and moves as solvated electron between the water molecules. The results are compared to data obtained from other first-principles and ab initio calculations.

Experimental and theoretical study of the pyrrole cluster photochemistry: Closing the πσ* dissociation pathway by complexation

Photolysis of size selected pyrrole clusters has been investigated and compared to the photolysis of an isolated pyrrole molecule. Experimentally, size distributions of different mean cluster sizes (n=3 and n>>5) have been prepared in supersonic expansions and the clusters were photolyzed at 243 and 193 nm. The kinetic energy distributions of the H photofragments have been measured. The distributions exhibit a bimodal character with fast and slow H-fragment peaks similar to the spectra of the bare molecule. However, with increasing cluster size the slow component gains intensity with respect to the fast one. A similar effect is observed with increasing the excitation energy from 243 to 193 nm. Theoretical calculations at the CASSCF/CASPT2 level have been performed for bare and complexed pyrroles (pyrrole is complexed with an argon atom and with another pyrrole unit). Combination of theoretical and experimental approaches leads to the conclusion that the direct dissociative pathway along the pisigma* potential energy surface in the N-H stretch coordinate is closed by the presence of the solvent molecule. This pathway is an important channel leading to the fast H atoms in the dissociation of the bare molecule. The solvent molecule influences significantly the electronic structure in the Rydberg-type pisigma* state while it has little influence on the valence states. The slow channel is mostly populated by the out-of-plane deformation mode which is also not influenced by solvation. We have also studied other possible reaction channels in pyrrole clusters (hydrogen transfer, dimerization). The present study shows that more insight into the bulk behavior of biologically relevant molecules can be gained from cluster studies.

Molecular magnetic properties of heteroporphyrins: a theoretical analysis

B3LYP/6-31G(d) optimization of porphyrin, tetraphenylporphyrin and their 21,23-diheteroatom substituted derivatives with O, S, and Se heteroatoms was performed. A planar macrocycle was found in all cases except 21,23-dioxatetraphenylporphyrin which presents only slight deviations from planarity. A Bader analysis uncovers the presence of S-S and Se-Se interactions in the four corresponding heteroporphyrins, which appreciably distort the original unsubstituted macrocycles. In the minimum energy structures of heterotetraphenylporphyrins the four meso phenyl groups slant alternatively to right or left so that the two pairs of opposite phenyls present a staggered conformation. The pi current induced by a perpendicular magnetic field in porphyrin bifurcates across both types of pyrrole subunits but the presence of O, S and Se heteroatoms in 21,23-diheteroporphyrins causes a diminution of the current density through the inner section of the two heterorings and, consequently, the current path goes then through the outer section of these rings. The NICS values at the ring critical points of the heterorings are much larger (in absolute value) than those at the pyrrole ring critical points but appreciably smaller than that at the ring critical point of a pyrrole molecule. In agreement with experimental data the (1)H NMR present appreciable downfield shifts for the beta H atoms of the heterorings in the 21,23-heterosubstituted molecules.

LONG-RANGE-CORRECTED TIME-DEPENDENT DENSITY FUNCTIONAL STUDY ON ELECTRONIC SPECTRA OF FIVE-MEMBERED RING COMPOUNDS AND FREE-BASE PORPHYRIN

Long-range-corrected time-dependent density functional theory (LC-TDDFT) was applied to five-membered ring compounds (cyclopentadiene, pyrrole, and furan molecules) and free-base porphyrin. The vertical π-π* and Rydberg excitation energies and corresponding oscillator strengths were calculated by LC-TDDFT. The LC scheme obviously improved the Rydberg excitation energies and oscillator strengths of these systems, which have been fairly underestimated by TDDFT with conventional pure and hybrid B3LYP functionals. On the whole, LC-TDDFT results were very close to the results of the ab initio symmetry-adapted cluster configuration interaction (SAC-CI) method for most excitations. However, LC-TDDFT is poor in describing doubly excited states such as the 1 1A1 state of five-membered ring compounds.

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.

Conductivity Measurements of Pyrrole Molecules Incorporated into Chemically Adsorbed Monolayer by Conducting Probe Technique in Atomic Force Microscope

A monomolecular layer containing pyrrolyl groups at the surface was prepared between two parallel Pt electrodes on a glass substrate by a chemical adsorption technique using N-[11-(trichlorosilyl)undecyl] pyrrole (PNN). Then, the pyrrolyl was polymerized with pure water by applying a DC voltage of 10 V between the two Pt electrodes. It was confirmed using an optical microscope that many electric paths were formed between the two Pt electrodes by a decoration technique using electrochemical polymerization in an aqueous medium containing pyrrole after the polymerization. Next, a conductive probe of an atomic force microscope (AFM) was used to examine an electrical polymerized path through the surface of the polypyrrolyl group in a chemically adsorbed monomolecular layer. The resistance of one electric path in the monomolecular layer was measured using an AFM with an attached Au-covered tip at room temperature. With a measurement volume of about 0.2 nm (the thickness of the electric path in the monomolecular layer) × 200 µm (the average width of the electric path) × 100 µm (the distance between the Pt electrode and the Au-covered AFM tip), the resistance at room temperature of one electric path was 4 k Ω under ambient conditions. From the results in the atmosphere, the conductivity of a super long conjugated polypyrrolyl group without any dopant in a lateral direction was ohmically estimated to be at least 6.0 ×105 S/m.

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.

Gas phase studies of metal dimer complexes, M 2L n+, where M = Zn and Mn, and L = pyrrole and furan, for n in the range 1–5

The combination of a pick-up technique and high resolution mass spectrometry have been used to prepare and study the fragmentation patterns of singly charged metal dimer complexes consisting of Zn 2 and Mn 2 in association with up to five molecules of either pyrrole or furan. The results of the fragmentation experiments are consistent with the picture that the metal dimers remain intact within the complexes, but that Zn 2 does not appear to carry a positive charge. Of the two molecules, furan appears to be less strongly bound than pyrrole to either metal dimer.

High resolution photofragment translational spectroscopy studies of the near ultraviolet photolysis of 2,5-dimethylpyrrole

The photodissociation dynamics of 2,5-dimethylpyrrole (2,5-DMP) has been investigated following excitation at 193.3 nm and at many near ultraviolet (UV) wavelengths in the range 244 < lambda(phot) < 282 nm using H Rydberg atom photofragment translational spectroscopy (PTS). Complementary UV absorption and, at the longest excitation wavelengths, one photon resonant multiphoton ionisation spectra of 2,5-DMP are reported also; analysis of the latter highlights the role of methyl torsional motions in promoting the parent absorption. The deduced fragmentation dynamics show parallels with that reported recently (B. Cronin, M. G. D. Nix, R. H. Qadiri and M. N. R. Ashfold, Phys. Chem. Chem. Phys., 2004, 6, 5031) for the bare pyrrole molecule. Excitation at the longer wavelengths leads to (vibronically induced) population of the 1(1)A(2)(pisigma*) excited state of 2,5-DMP, but once lambda(phot) decreases to approximately 250 nm stronger, dipole allowed transitions start to become apparent in the parent absorption. All total kinetic energy release (TKER) spectra of the H + 2,5-dimethylpyrrolyl (2,5-DMPyl) fragments measured at lambda(phot)> or=244 nm show a structured fast component, many of which are dominated by a peak with TKER approximately 5100 cm(-1); analysis of this structure reveals lambda(phot) dependent population of selected vibrational levels of 2,5-DMPyl, and enables determination of the N-H bond strength in 2,5-DMP: D(0) = 30 530 +/- 100 cm(-1). Two classes of behaviour are proposed to account for details of the observed energy partitioning. Both assume that N-H bond fission involves passage over (or tunnelling through) a small exit channel barrier on the 1(1)A(2) potential energy surface, but differ according to the vibrational energy content of the photo-prepared molecules. Specific parent out-of-plane skeletal modes that promote the 1(1)A(2)-X(1)A(1) absorption appear to evolve adiabatically into the corresponding vibrations of the 2,5-DMPyl products. Methyl torsions can also promote the 1(1)A(2)<-- X(1)A(1) absorption in 2,5-DMP, and provide a means of populating a much higher density of excited vibrational levels than in pyrrole. Such excited levels are deduced to dissociate by redistributing the minimum amount of internal energy necessary to overcome the exit channel barrier in the N-H dissociation coordinate. Coupling with the ground state surface via a conical intersection at extended N-H bond lengths is proposed as a further mechanism for modest translational --> vibrational energy transfer within the separating products. The parent absorption cross-section increases considerably at wavelengths approximately 250 nm, and PTS spectra recorded at lambda(phot)< or = 254 nm display a second, unstructured, peak at lower TKER. As in pyrrole, this slower component is attributed to H atoms from the unimolecular decay of highly vibrationally excited ground state molecules formed via radiationless decay from photo-excited states lying above the 1(1)A(2) state.

Organic field-effect transistors based on Langmuir-Blodgett films of an extended porphyrin analogue – Cyclo[6]pyrrole

Field-effect transistors using cyclo[6]pyrrole as active layers were prepared by Langmuir-Blodgett (LB) method. Cyclo[6]pyrrole is a porphyrin analogue with an extended π-system(22-π-electron). It could form a stable, reproducible monolayer at the air–water interface, which could be transferred onto a substrate with nearly unity transfer ratio and resulted in multilayer structure with the cyclo[6]pyrrole molecules stacking in a face-to-face configuration due to strong intermolecular π–π interactions. An un-optimized device based on this LB films displayed a mobility of 0.014 cm 2 V −1 s −1, which is higher than the highest value of the devices based on typical porphyrins reported.

High-Performance Field-Effect Transistors Based on Langmuir−Blodgett Films of Cyclo[8]pyrrole

We demonstrate the field-effect transistors (FETs) made of cyclo[8]pyrrole thin films prepared by the Langmuir-Blodgett (LB) method. The cyclo[8]pyrrole molecule possesses a 30-pi-electron system and narrower highest-occupied molecular orbital-lowest-unoccupied molecular orbital energy gap (0.63 eV), forms a stable, reproducible monolayer at the air-water interface, and transfers onto a substrate with a nearly unity transfer ratio and face-to-face configuration due to its strong pi-pi interaction. The LB films are uniform characterized by atomic force microscopy and in ordered form confirmed by X-ray diffraction. The FET exhibited high performances with one of the highest hole mobilities (0.68 cm2 V(-1) s(-1)) for thin-film transistors and a high on/off ratio, implying a promising material in the FET family.

Silica‐Assisted Reactions of Pyrroles with 1‐Acyl‐2‐bromoacetylenes.

AbstractFor Abstract see ChemInform Abstract in Full Text.