Py Molecule Research Articles

Van der Waals interactions on semiconducting single-walled carbon nanotubes filled with porphyrin molecules: structure optimisation and Raman analysis

This study investigates the Raman analysis of the free base porphyrin (Py) molecule and its encapsulation within a carbon nanotube (CNT) framework using computational simulations.

Molecular insights into the HLA-B35 molecules' classification associated with HIV control.

Human leukocyte antigen (HLA) class I molecules have been shown to influence the immune response to HIV infection and acquired immunodeficiency syndrome progression. Polymorphisms within the HLA-B35 molecules divide the family into two groups, namely, Px and PY. The Px group is associated with deleterious effects and accelerated disease progression in HIV+ patients, whereas the PY group is not. The classification is based on the preferential binding of a tyrosine at the C-terminal part of the peptide in the PY group, and a nontyrosine residue in the Px group. However, there is a lack of knowledge on the molecular differences between the two groups. Here, we have investigated three HLA-B35 molecules, namely, HLA-B*35:01 (PY), HLA-B*35:03 (Px) and HLA-B*35:05 (unclassified). We selected an HIV-derived peptide, NY9, and demonstrated that it can trigger a polyfunctional CD8+ T-cell response in HLA-B*35:01+ /HIV+ patients. We determined that in the complex with the NY9 peptide, the PY molecule was more stable than the Px molecule. We solved the crystal structures of the three HLA molecules in complex with the NY9 peptide, and structural similarities with HLA-B*35:01 would classify the HLA-B*35:05 within the PY group. Interestingly, we found that HLA-B*35:05 can also bind a small molecule in its cleft, suggesting that small drugs could bind as well.

Short bandgap of porphyrin molecules (Py) filled in a semiconducting single-walled carbon nanotube (Py@NT17) for highly efficient organic photovoltaic cells

In this paper, the porphyrin (Py) molecule, which is filled in the semiconducting single-walled carbon nanotube (SWNT) known as CNT17, is investigated. We have calculated the optoelectronic characteristics of two configurations of the hybrid system with a single Py molecule filled into CNT17 (Py@CNT17 and Py2@CNT17) using density functional theory (DFT). According to the investigation’s findings, a charge transfer occurred between the Py molecules and the CNT17 nanotube, confirming the stability of the structure. As determined by the electronic calculation, we discovered that the rise in the fermi energy position of CNT17 after encapsulation, suggests a CT connection between Py and CNT17.

Opposite Raman Shift of Ring Stretching Dependent on the Coordinated Silver Volume in Surface-Enhanced Raman Spectroscopy of Polypyrrole.

Surface-enhanced Raman spectroscopy (SERS) can sense some molecules in a nondestructive manner. Using SERS, we investigate the shifts in the Raman peaks of polypyrrole (PPy) with two different coordinated silver (Ag) structures, Ag nanoparticles (NPs) and Ag dendrite film. The SERS spectrum of PPy with Ag NPs presents a ring-stretching peak that is red-shifted compared to the ring-stretching peak in the Raman spectrum of PPy. In contrast, the spectrum of the PPy with the Ag dendrite film exhibits a blue-shifted ring stretching peak. The various coordinated Ag nanostructures result in opposite Raman shifts of the ring stretching peak; this phenomenon has been investigated and confirmed by density functional theory (DFT) calculations of the Raman shift of the pyrrole (Py) molecule with a Ag layer (SERS of PPy with Ag NPs) and that of a charge-transferred Py molecule (SERS of PPy with Ag dendrite films). This result demonstrates that DFT calculations can be an effective tool to scrutinize Raman shifts in SERS.

Accessibility and strength of H-acceptor hydroxyls of ordered mesoporous silicas probed by pyridine donor

Ordered mesoporous silica (OMS) is an important and useful material for a variety of applications, including catalysis, adsorption, sensing and controlled drug delivery. The surface chemistry and the silanol groups on OMS pores are key properties for the potential modification and application of this material. This research aimed to synthesize (using standard protocols) and differentiate the accessibility and strength of the H-acceptor Si–OH from FDU-12, SBA-16, MCM-41 and SBA-15 by pyridine (Py) donor, where the first two have cubic pore structures and the last two have hexagonal pore structures. Donor–acceptor properties were assessed by calculation of the surface Si–OH densities by thermogravimetry (TG), H2O-TPD/MS, and 29Si MAS and CP/MAS NMR. The nature of the Si–OH groups on these materials was determined to be hydrogen-bonding sites using FT-IR spectroscopy of Py adsorption. The reactivity of these silanol groups was probed by Py-TG and slurry microcalorimetry of Py adsorption in cyclohexane. Differences in accessibility and reactivity were discussed considering the total potential sites on the surface (nOH) versus the actual sites that can react with the Py molecule (nPy). By using microcalorimetry, it was possible to quantitatively distinguish the strength of the sites: The acidity order was approximately the same as the relative amount of silanol groups (Si–OH) and Py on the surface of the OMS materials (αPy): FDU-12 > MCM-41 ≥ SBA-16 > SBA-15.

Synthesis and Crystal and Molecular Structure of the Solvated Complex [MoO2(L) · C5H5N], Where L2– Is the 2-[N-(2-Hydroxynaphthalidene)amino]propane-1,2,3-Triol Anion

A new dioxomolybdenum(VI) compound [MoO2(L) · C5H5N], where L2– is 2-[N-(2-hydroxynaphthalidene)amino]propane-1,2,3-triol, was synthesized and its structure was determined by IR spectroscopy and X-ray diffraction. The Mo atom is in an octahedral coordination environment formed by two oxo ligands in cis positions to each other, two O atoms and the N(2) atom of the tridentate bis(chelate) ligand L, and the N(1) atom of the pyridine (Py) molecule. The N(2)(L) and N(1)(Py) atoms are in trans positions to the O(oxo) ligands at distances that are elongated due to the structural trans effect of the multiply bonded oxo ligands (Mo–N(1), 2.476 A; Mo–N(2), 2.272 A).

Thermal induced spin transition in a series of iron(II) layered inorganic-organic solids. Role of the intermolecular interactions in the interlayer region

The understanding of the factors that determine the spin crossover phenomenon in transition metal-containing solids is a relevant subject in order to design new materials with tunable physical and functional properties based on such spin transition. This is a process that has been studied for decades but even not fully understood in terms of the electronic and structural features that could determine its control and tuning for a given potential application. In this contribution, we shed light in that sense, through an evaluation of the iron atom coordination environment from Raman, Mössbauer, XPS, and structural data for a series formed by the intercalation of the pyridine (Py) molecule (L) and its halogen-substituted derivatives (3X-py) between neighboring layers of iron(II) tetracyanonickellate, Fe(L)2[Ni(CN)4]. In their structure, the organic molecule (L) is found occupying the axial coordination sites for the iron atom. The halogen atom determines both, the relative orientation of neighboring molecules in the interlayer region and the dominant intermolecular forces, through dispersive interactions. When such interaction generates a local distortion for the iron atom coordination environment, the thermal induced spin transition is inhibited. This is properly supported by the herein discussed experimental data.

Chemical bonding mechanism in SERS effect of pyridine by CuO nanoparticles

AbstractThis article reports the theoretical and experimental study of nonresonant mechanisms (CHEM) of surface‐enhanced Raman spectroscopy (SERS) of pyridine (Py). An improvement in the Raman dispersion intensity of Py is determined after the chemical absorption on CuO nanoparticles synthesized in NaCl. The density functional theory predicts the formation of new electronic states as result of the chemical bond (CB) established between the Py molecule and the (CuO)n clusters. This study is focused on the study of the most intense vibrational modes of Py before and after chemical adsorption. The CHEM by CB mechanisms is found as responsible for the SERS effect in Py.

A Heterotetranuclear Zinc(II)-Cerium(IV) Salamo Complex Possessing Deca- and Dodeca-Coordinated Cerium(IV) Atoms: Synthesis, Structure, and Photophysical Properties

A heterotetranuclear zinc(II)-cerium(IV) complex [(ZnL)2Ce(OAc)2][Ce(NO3)6] · Py (H2L = 6,6′-methoxy-2,2′-[1,2-ethylenedioxybis(nitrilomethylidyne)]diphenol and Py = pyridine) is successfully prepared by a one-pot reaction of a Salamo-type ligand H2L with Zn(OAc)2·2H2O, Ce(NO3)3-6H2O, and an auxiliary ligand Py. The Znn-CeIV complex consists of one dicationic [(ZnL)2Ce(OAc)2]2+ unit with a deca-coordinated CeIV atom, one [Ce(NO3)6]2− dianionic unit with a dodeca-coordinated CeIV atom, and one uncoordinated Py molecule. Interestingly, the two CeIV atoms are positive tetravalent, which may probably be due to the oxidation of trivalent Cem atoms during the reaction. Moreover, the photophysical properties of the Znn-CeIV complex are studied.

A heterotetranuclear zinc(II)—cerium(IV) salamo complex possessing deca- and dodeca-coordinated cerium(IV) atoms: Synthesis, structure, and photophysical properties

A heterotetranuclear zinc(II)—cerium(IV) complex [(ZnL)2Ce(OAc)2][Ce(NO3)6]⋅Py (H2L = 6,6'-methoxy-2,2'-[1,2-ethylenedioxybis(nitrilomethylidyne)]diphenol and Py = pyri­dine) is successfully prepared by a one-pot reaction of a Salamo-type ligand H2L with Zn(OAc)2⋅2H2O, Ce(NO3)3⋅6H2O, and an auxiliary ligand Py. The ZnII—CeIV complex consists of one dicationic [(ZnL)2Ce(OAc)2]2+ unit with a deca-coordinated CeIV atom, one [Ce(NO3)6]2– dianionic unit with a dodeca-coordinated CeIV atom, and one uncoordinated Py molecule. Interestingly, the two CeIV atoms are positive tetravalent, which may probably be due to the oxidation of trivalent CeIII atoms during the reaction. Moreover, the photophysical properties of the ZnII—CeIV complex are studied.

Pyridine aided progression from amorphous to crystalline bis([5-(aryl)-1-diazenyl]quinolin-8-olato)zinc(II) compounds − Solution and solid-state structural characterization, nanoparticle formation and antibacterial activity

Ten new zinc(II) compounds, viz. [Zn(LQ)2(4-MePy)2]·H2O (1), [Zn(LMeAQ)2(Py)2]·C6H6 (2a), [Zn(LMeAQ)2(H2O)2] (2b), [Zn(LOMeAQ)2(H2O)2] (3), [Zn(LEtAQ)2(3-MePy)2] (4), [Zn(LOEtAQ)2(4-MePy)2]·0.5C6H7N (5a), [Zn(LOEtAQ)2(H2O)2] (5b), [Zn(LNMe2AQ)2(Py)2]·1.5C6H6·H2O (6), [Zn(LCAQ)2(Py)] (7) and [Zn(LBAQ)2(Py)] (8) (primary ligands: LQ = quinolin-8-olate and LXAQ = 4-substituted 5-[(E)-2-(aryl)-1-diazenyl]quinolin-8-olate; secondary ligands: Py = pyridine, 3-MePy = 3-methylpyridine, 4-MePy = 4-methylpyridine) have been synthesized and characterized by elemental analysis, IR, NMR, UV-vis and fluorescence spectroscopy and single-crystal X-ray diffraction analysis. The structural characterization revealed distorted octahedral geometries for 1–6, in which trans-disposed 8-quinolate ligands occupy the equatorial and the secondary ligands the axial positions. Compounds 7–8 comprise five-coordinate molecular structures with square-pyramidal coordination polyhedra based on trans-oriented quinolate ligands and a Py molecule in the apical position. In the crystal structures of 1–8, the molecules are assembled by π–stacking interactions and for the aquo-compounds additionally by OH⋅⋅⋅O hydrogen bonds. As representative example, compound 2a was used as starting material for the synthesis of ZnO nanoparticles in an average size range of 70–120 nm, as illustrated by PXRD analysis and TEM images. The antimicrobial activity of the pro-ligands and zinc(II) compounds studied herein was assessed by inhibition zone test in agar cultures against five indicator bacterial strains, i.e. Escherichia coli MTCC 730, Streptococcus pyogenes MTCC 1925, Klebsiella pneumoniae MTCC 109, Bacillus cereus MTCC 430 and Salmonella enterica MTCC 735.

Water network-mediated, electron-induced proton transfer in [C5H5N ⋅ (H2O)n](-) clusters.

The role of proton-assisted charge accommodation in electron capture by a heterocyclic electron scavenger is investigated through theoretical analysis of the vibrational spectra of cold, gas phase [Py ⋅ (H2O)n=3-5](-) clusters. These radical anions are formed when an excess electron is attached to water clusters containing a single pyridine (Py) molecule in a supersonic jet ion source. Under these conditions, the cluster ion distribution starts promptly at n = 3, and the photoelectron spectra, combined with vibrational predissociation spectra of the Ar-tagged anions, establish that for n > 3, these species are best described as hydrated hydroxide ions with the neutral pyridinium radical, PyH((0)), occupying one of the primary solvation sites of the OH(-). The n = 3 cluster appears to be a special case where charge localization on Py and hydroxide is nearly isoenergetic, and the nature of this species is explored with ab initio molecular dynamics calculations of the trajectories that start from metastable arrangements of the anion based on a diffuse, essentially dipole-bound electron. These calculations indicate that the reaction proceeds via a relatively slow rearrangement of the water network to create a favorable hydration configuration around the water molecule that eventually donates a proton to the Py nitrogen atom to yield the product hydroxide ion. The correlation between the degree of excess charge localization and the evolving shape of the water network revealed by this approach thus provides a microscopic picture of the "solvent coordinate" at the heart of a prototypical proton-coupled electron transfer reaction.

Unique effects of the chain lengths and anions of tetra-alkylammonium salts on quenching pyrene excimer.

Pyrene (Py) excimer, through its unique fluorescence quenching, exhibits high sensitivity and high selectivity in detecting specific electron-deficient molecules, providing a potential platform for sensing technology, optical switch, and probing hydrophobicity of molecular environment. In solution state, its quenching mechanism has been well-studied. However, there remain many unknown properties regarding the quenching mechanism of the solid-state Py excimer. In this paper, the effects of a series of tetra-alkylammonium salts (with a variety of chain lengths and anions) on Py excimer quenching are investigated to identify the controlling parameters of the fluorescence quenching in the binary system. Several experimental approaches including steady-state fluorescence spectroscopy, UV absorption, (13)C-nuclear magnetic resonance (NMR) spectra, X-ray diffraction, scanning electron microscopy, and time-dependent fluorescence decay are employed to seek for the fundamental understanding of the quenching mechanism. The result indicates a unique quenching effect of tetrabutylammonium cation on the pyrene excimer, and which is not observed in the other cations with different chain lengths (the same associated hexafluorophosphate anions). Meanwhile, hexafluorophosphate anion (in the presence of tetrabutylammonium) is able to effectively retain Py excimer fluorescence when the system is prepared by evaporating solvent at high temperature. It is also confirmed that dynamic quenching is involved in the process. Hydrophobic environment around Py molecules shows strong correlation with the formation of Py excimer. The knowledge obtained in this study provides the insights to how the interaction between salt and Py molecule affects the excimer fluorescence.

Precise Analysis of Small Wavenumber Shift of Pyridine on Dilution with H2O and D2O Using RDS Technique

Abstract The wavenumber difference (Δν) of the ring breathing mode (ν 1), ring deformation mode (ν 12) and C–H stretching mode (ν 3) of pyridine (Py) dissolved in both H2O and D2O at equal mole fractions of the solute (Py) and the solvent (H2O/D2O) has been determined precisely by using the technique of Raman difference spectroscopy (RDS) in order to analyze the relative shift caused by these two solvents. The spectra of the two systems, for which the difference spectrum is to be generated, were recorded simultaneously and the wavenumber shifts up to almost one hundredth part of the linewidth of a band could be determined precisely. The values of Δν for the three modes as a function of mole fraction are compared with the Δν obtained by the solvation of Py molecule in the media of dielectric constants equal to that of the mixture of Py and H2O/D2O at the experimental mole fractions using DFT and MP2 methods. The variation in Δν with mole fraction seems to be the result of difference of dielectric constants of Py+H2O and Py+D2O at equal mole fraction. The absolute peak position and linewidth of the three modes as a function of mole fraction have been discussed in terms of relevant models, which show the effective role of diffusion and concentration fluctuation in the mixture.

A pyridine adduct of bis(di-iso-butyldithiocarbamato-S,S′)cadmium(II): Multinuclear (13C, 15N, 113Cd) CP/MAS NMR spectroscopy, crystal and molecular structure, and thermal behaviour

Crystalline bis(N,N-di-iso-butyldithiocarbamato-S,S′)(pyridine)cadmium(II) – adduct 1 was prepared and studied by means of multinuclear 13C, 15N, 113Cd CP/MAS NMR spectroscopy, single-crystal X-ray diffraction and simultaneous thermal analysis (STA). In molecular structure 1, the cadmium atom coordinates with four sulphur atoms and one nitrogen atom of pyridine, forming a coordination polyhedron [CdS4N], whose geometry is an almost ideal tetragonal pyramidal (C4v). The coordinated py molecule is in the apical position, while two structurally non-equivalent di-iso-butyldithiocarbamate ligands, playing the same terminal S,S′-chelating function, define the basal plane. To characterise additionally the structural state of the cadmium atom in this fivefold coordination, 113Cd chemical shift anisotropy (CSA) parameters, δaniso and η, were calculated from experimental MAS NMR spectra that revealed an almost axially symmetric 113Cd chemical shift tensor. From a combination of TG and DSC measurements taken under an argon atmosphere, we found that the mass of adduct 1 is lost in two steps involving initial desorption of coordinated py molecules with subsequent thermal destruction of liberated cadmium(II) di-iso-butyldithiocarbamate, with yellow-orange, fine-powdered solid CdS as the final product.

Hydrolysis of coordinated aminoacetonitrile in a platinum(IV) complex. Crystal structure of [PtPy(NH2CH2COO)Cl3

Heating of a hydrochloric acid solution of trans-PtPy(NH2CH2CN)Cl4 results in the hydrolysis of coordinated aminoacetonitrile to aminoacetic acid with the formation of a five-membered chelate ring attached to platinum through the nitrogen atom of the amino group and the oxygen atom of the carboxy group. X-ray diffraction analysis of [PtPy(NH2CH2COO)Cl3] is carried out. The crystals are monoclinic: space group C2/c, a = 21.704(2), b = 8.7027(7), c = 15.576(1) A, β = 126.606(1)o, V = 2361.8(3) A3, Z = 8; Rhkl = 0.057, wR = 0.141. In the neutral complex, the Pt atom has a distorted octahedral coordination. The equatorial plane is formed by a Cl atom (Pt-Cl, 2.284(3) A), the N atom of the Py molecule (Pt-N, 2.062(8) A), and the N and O atoms of the bidentate-chelating ligand (Pt-N, 2.039(8); Pt-O, 2.026(7) A); two Cl atoms are arranged in the apical positions (Pt-Cl, 2.301(3) and 2.312(3) A). The five-membered chelate ring has a flattened gauche conformation with an NCCO torsion angle of 19(1)°.

The thermodynamic characteristics of step complex formation in the (5,10,15,20-tetraphenylporphyrinato)(chloro)indium(III)-pyridine-toluene system

The thermodynamic characteristics, step mechanism, and spectral manifestations of step reactions between (5,10,15,20-tetraphenylporphyrinato)(chloro)indium(III) ((Cl)InTPP) and organic base pyridine (Py) in inert toluene were studied using spectrophotometric titration and physicochemical analysis of intermediate forms. The coordination of Py molecule (K 1 = 9.45 × 102 l/mol at 298 K) with the formation of (Cl)(Py)InTPP, the substitution of Cl− in (Cl)(Py)InTPP with the second Py molecule (K 2 = 2.3 × 102 l/mol), and the coordination of the third Py molecule to produce [(Py)3 InTPP]+ · Cl− (K 3 = 8.7 l/mol) were observed at the first, second, and third steps, respectively. The fourth reaction stage most likely corresponds to π−π complex formation equilibrium between the aromatic complex and pyridine with a 1: 2 stoichiometry. The thermodynamic parameters of step reactions ΔH ∘ and ΔS ∘ well correspond to the stoichiometric mechanism of the reaction. Prospects for the use of the metalloporphyrin as a receptor of organic N-bases are considered.

Step Complex Formation in the Dichloro(5,10,15,20-tetraphenylporphinate)hafnium(IV)—Pyridine—Toluene System

The thermodynamic characteristics and kinetics of step reactions between dichloro(5,10,15,20-tetraphenylporphinate)hafnium(IV) (Cl)2HfTPP and a “small” organic base, pyridine (Py), in toluene were studied. The coordination of the Py molecule (K1 = 1.50 × 104 l/mol) was determined. The slow irreversible displacement of Cl− in (Cl)2(Py)HfTPP into the second coordination sphere (k1 = 9.74 × 10si−4 s−1), the substitution of the second Py molecule for Cl− in (Cl)2(Py)HfTPP (K2 = 14.15 l/mol), subsequent irreversible displacement of the second Cl− ion into the outer sphere (k2 = 6.05 × 10−4 s−1), and the coordination of the third Py molecule as a result of the replacement of Cl− with the formation of [(Py)3HfTPP]2+ 2Cl− (K3 = 0.23 l/mol) at the first, second, and third stages, respectively, were observed. Prospects for the use of the metalloporphyrin as a receptor of organic N-bases were considered.

A Chiral Coordination Polymer of Silver(I) with Saccharinate and Pyridine: Synthesis, Spectral, Thermal, and Structural Characterization of [Ag(sac)(py)

The first silver(I) complex of saccharinate (sac) with pyridine (py), [Ag(sac)(py)] n has been synthesized and characterized by elemental analysis, IR spectroscopy and single crystal X-ray diffractometry. The complex crystallizes in chiral, trigonal space group P3121 (No. 152) with unit cell parameters of a = 11.2605(2) A, c = 17.3300(4) A, V = 1903.02(6) A3 and Z = 6. [Ag(sac)(py)] n contains monomeric [Ag(sac)(py)] units linked into infinite helices by way of Ag⋅sAg interactions [d(Ag⋅sAg) = 2.909(2) and 2.985(1) A]. The distorted square-planar environment of Ag is completed by an N-bonded sac [Ag—N = 2.084(2) A] and a py molecule [Ag—N = 2.116(2) A]. The Nsac—Ag—Npy angle is 173.85(10)∘. The one-dimensional chains are crosslinked by C—H⋅sO interactions involving the carbonyl and sulfonyl O atoms of sac and aromatic-ring hydrogen atoms of both sac and py. The thermal stability of the title complex was investigated using thermogravimetry and differential thermal analysis in a static atmosphere of air. The first decomposition stage between 90 and 160∘C corresponds to removal of the py molecule in a single stage, while the degradation of the sac moiety occurs at two stages in the temperature range 370–515∘C, giving an end product of metallic Ag.

Theoretical investigation of tetra-substituted pyrenes for organic light emitting diodes

Abstract Pyrene derivatives have been developed to blue fluorescent light emitting materials for organic light emitting diodes (OLEDs). Luminescence efficiency of pyrene molecule is very low, however pyrenes substituted with large group can give a bright blue fluorescence. Substituted pyrenes were investigated to increase luminescence efficiency and color purity. In this paper, we studied 1,3,6,8-tetra-substituted pyrenes theoretically. The investigation was studied by ab initio method. Density functional theory (DFT) utilizing the B3LYP functional with the 6-31G(d) basis set was used for energy calculation and geometry optimization of the ground electronic state of those compounds. The geometry optimization of the first excited electronic states was determined using configuration interaction with single excitations (CIS) method. Energies of vertical and adiabatic transition were calculated using time-dependent density functional theory (TD-DFT) with B3LYP/6-31G(d) calculation. The investigation on 1,3,6,8-tetra-substituted pyrenes with the effect of the aromatic substituents showed that the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) was decreased as the conjugation length was increased. This trend was also appeared when the nitrogen atom was substituted with carbon atom in the aromatic substituents. Also the substituted pyrenes with large moieties were slightly distorted from the planar structure. Thus, the luminescent efficiencies of tetra-substituted pyrenes were increased more than that of the pyrene molecule. In this paper, t(dpe)py molecule was proposed as a new efficient blue emitter for OLED from calculated result.