Pyrazine Molecules Research Articles

Adsorption structure of pyrazine on Si(100): Density-functional calculations

We have studied the adsorption structure of pyrazine $({\text{C}}_{4}{\text{H}}_{4}{\text{N}}_{2})$ on the Si(100) surface by using density-functional theory calculations within a slab representation. We found that the adsorption energetics strongly depends on the ${\text{C}}_{4}{\text{H}}_{4}{\text{N}}_{2}$ coverage. At 0.25 monolayer (one monolayer is defined as one pyrazine molecule per Si dimer), two different molecular configurations are equally favored in energy: the end-on model where ${\text{C}}_{4}{\text{H}}_{4}{\text{N}}_{2}$ adsorbs on the down atom of a Si dimer and the cross-row model where ${\text{C}}_{4}{\text{H}}_{4}{\text{N}}_{2}$ connects two dimer rows. At 0.5 monolayer, the interactions between adsorbed molecules results in a far stabilized cross-row configuration in which molecules arrange in series along the row-perpendicular direction. This cross-row chain configuration is in good accordance with the images of a recent scanning tunneling microscopy experiment. When including the van der Waals interactions in our calculations, the cross-row structures were found to have larger energy gains, thus being more favored in energy than the end-on structures. The adsorption picture of the present slab-model calculations differs from previous cluster-model calculations, which questions the accuracy of the cluster representation of this adsorbed system.

Theoretical investigation of the electronic spectrum of pyrazine

The description of Rydberg states by the complete active space self-consistent field (CASSCF) electronic structure method is known to be a difficult topic. In particular, two problems are frequently encountered: (a) the simultaneous presence of valence and Rydberg excited states in the same energy region can potentially lead to artificial valence–Rydberg mixing in the electronic wave functions. (b) Rydberg states have a tendency to be difficult to converge. We have implemented an approach for the consistent description of both valence and Rydberg excited states within the CASSCF electronic structure model. By employing the multiconfigurational second- and third-order perturbation theory (CASPT2/3) methods based on CASSCF reference wave functions, the procedure is verified by comparison with spectroscopic results for the example molecule pyrazine. Vertical excitation energies and other properties have been calculated for various electronic states. Basis sets and active spaces were selected to provide accurate results. Two combinations of aug-cc-pVTZ level basis sets complemented by Rydberg functions have been employed to calculate estimates for the properties of 19 singlet excited states of pyrazine. While many of the assignments made in previous studies could be confirmed, there are also several new aspects emerging from the present investigation.

Low temperature structural transformation in T[Ni(CN) 4]· xpyz with x=1,2; T=Mn,Co,Ni,Zn,Cd; pyz=pyrazine

The materials under study are pillared solids T[Ni(CN) 4]· xpyz with one and two ( x=1,2) pyrazine (pyz) molecules and where T=Mn, Co, Ni, Zn, Cd. Stimulated by their structural features and potential role as prototype of porous solids for hydrogen storage, the structural stability under cryogenic conditions for this series of pillared solids was studied. At low temperature, in the 100–200 K range, the occurrence of a reversible structural transformation was found. For T=Mn, Co, Zn, Cd, with x=2, the structural transformation was observed to occur around 185 K, and the low temperature phase crystallizes with a monoclinic unit cell (space group Pc). This structure change results from certain charge redistribution on cooling within the involved ligands. For T=Ni with x=1, both the low and high temperature phases crystallize with unit cells of tetragonal symmetry, within the same space group but with a different unit cell volume. In this case the structure change is observed around 120 K. Above that temperature the rotational states for the pyrazine molecule are thermally excited and all the pyrazine molecules in the structure become equivalent. Under this condition the material structure is described using a smaller structural unit. The structural study using X-ray powder diffraction data was complemented with calorimetric and Raman spectroscopy measurements. For the low temperature phases the crystal structures were solved from Patterson methods and then refined using the Rietveld method.

Analytic evaluation of the nonadiabatic coupling vector between excited states using equation-of-motion coupled-cluster theory

Theory and implementation for evaluation of the nonadiabatic coupling vector between excited electronic states described by equation-of-motion excitation energy coupled-cluster singles and doubles (EOMEE-CCSD) method is presented. Problems arising from the non-Hermitian nature of the theory are discussed in detail. The performance of the new approach is demonstrated by the nice agreement of the nonadiabatic coupling curves for LiH obtained at the EOMEE-CCSD and MR-CISD levels. Using the tools developed we also present a computational procedure to evaluate the interstate coupling constants used in vibronic coupling theories. As an application of this part of the implementation we present simulation of the electronic absorption spectrum of the pyrazine molecule within the linear vibronic coupling model.

Pyrazine control of the solid-state supramolecular chemistry of zinc phthalocyanine

Crystals of monoaxially coordinated T-shaped and H-shaped supramolecular zinc(II) phthalocyaninato complexes with pyrazine are obtained. In both types of molecules the central Zn atom of ZnPc complexes with pyrazine exhibits 4 + 1 coordination. The Zn atom is equatorially coordinated by four isoindole N atoms of Pc macrocycle and axially by N atom of pyrazine molecule. The interaction of the central Zn atom of ZnPc with the axial N atom of pyrazine leads to a deviation of Zn from the centre of cavity by 0.371(2) Å in the T-shaped complex and by 0.296(2) Å in the H-shaped complex. Thermogravimetric analysis of the crystals exhibits three slopes down, corresponding to the loss in succession of solvated pyrazine molecules, than the loss of ligated pyrazine molecules from the T-shaped complex and the finally the loss of the bridged pyrazine molecule from the H-shaped complex. Finally the thermal processing leads to the β-ZnPc as residue. The UV–Vis spectrum taken in solution shows the batochromic shift in the polar solvent like α-chloronaphthalene in relation to the spectrum in non-polar solvent like benzene.

Crystal structure of a two-dimensional Co(II) coordination polymer: [Co(μ-PP)2(SCN)2] n [PP = 2-(pyridine-3-yloxy)pyrazine

Solvothermal reaction (water/methanol) of cobalt perchlorate hexahydrate, sodium thiocyanate and 2-(pyridine-3-yloxy)pyrazine (PP) resulted in the formation of a two-dimensional coordination polymer [Co(μ-PP)2(SCN)2]n. The solid complex has been characterized by elemental analysis and IR spectroscopy; its crystal structure was determined by X-ray crystallography. The complex crystallizes in the monoclinic system, space group P21/n, a = 7.4643(19) A, b = 9.237(2) A, c = 15.540(4) A, β = 94.995(5)°, V = 1067.4(5) A3, Z = 1. In the crystal structure each 2-(pyridine-3-yloxy)pyrazine molecule acts as a bidentate bridging ligand coordinating to two adjacent Co(II) ions with Co...Co separation of 9.5176(18) A to yield a two-dimensional sheet structure in the plane (−1 0 1).

Diphenic Acid‐Based Cobalt(II) Complexes: Trinuclear and Double‐Helical Structures

AbstractThe linear trinuclear complex [Co3(dpa)2(Hdpa)2(1‐MeIm)2(H2O)2] (1) and the two‐dimensional coordination polymer [Co2(dpa)2(pyz)]n (2; H2dpa = diphenic acid, 1‐MeIm = 1‐methylimidazole, pyz = pyrazine) exemplify the versatile coordination chemistry of diphenic acid in conjunction with N‐donor ligands. Complex 1 consists of a discrete arrangement of three CoII atoms bridged by four diphenate ligands, whereas complex 2 contains a network of dinuclear CoII units bridged by two diphenate ligands to form double‐helical chains, which are further connected via pyrazine molecules into two‐dimensional sheets. A magnetochemical analysis of these complexes reveals both strong ligand field effects on the CoII 4F free ion ground state and ferro‐ and antiferromagnetic exchange contributions mediated by the dpa ligands. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

Theoretical Study of Internal Conversion Decay Rates Associated with the Three Lowest Singlet Electronic States in Pyrazine

The general expressions we recently derived for calculating internal conversion decay rate constants between two adiabatic and between two diabatic displaced-distorted-rotated harmonic potential energy surfaces (including all vibrational modes) are now applied to determine the decay rate constants of 1B(2u)(pi pi*)-->1B(3u)(n pi*), 1B(2u)(pi pi*)-->1A(g), and 1B(3u)(n pi*)-->1A(g) internal conversions in pyrazine molecule. The minimal models with respect to the number and the types of vibrational modes are investigated for these processes. An exact expression for the adiabatic vibrational frequencies of the coupling modes in terms of interstate coupling constants and the parameters determining the diabatic potential energy surfaces are also derived.

Substituent Effect on the Mechanical Properties of Au−N Nanojunctions

We report on the calculated binding energies and rupture forces of a series of ortho-substituted pyrazines bonded to gold nanoclusters. This system is proposed as a model for the 4,4-bipyridine−gold nanojunction to assess the effect of the substituent on the mechanical stability and the rupture modes of such nanojunction. The present results show that although there is a definite trend to a reduced rupture force for a more electron withdrawing substituent on the pyrazine molecule, this dependence is small, allowing for the construction of nanojunctions with different transport properties but similar mechanical stabilities. A clear-cut correlation is found between the rupture force of the nanojunction and the pKa value of the structurally related pyridines, providing with a simple empirical way of predicting the stability of the system. The possibility of attaching the molecule to the cluster through a monatomic gold chain is also explored, with the finding that the Au−Au rupture at the chain is a possible...

Unique coordination of pyrazine in T[Ni(CN) 4]·2pyz with T=Mn, Zn, Cd

The materials under study, T[Ni(CN) 4]·2pyz with T=Mn, Zn, Cd, were prepared by separation of T[Ni(CN) 4] layers in citrate aqueous solution to allow the intercalation of the pyrazine molecules. The obtained solids were characterized from chemical analyses, X-ray diffraction, infrared, Raman, thermogravimetry, UV–Vis, magnetic and adsorption data. Their crystal structure was solved from ab initio using direct methods and then refined by the Rietveld method. A unique coordination for pyrazine to metal centers at neighboring layers was observed. The pyrazine molecule is found forming a bridge between Ni and T atoms, quite different from the proposed structures for T=Fe, Ni where it remains coordinated to two T atoms to form a vertical pillar between neighboring layers. The coordination of pyrazine to both Ni and T atoms minimizes the material free volume and leads to form a hydrophobic framework. On heating the solids remain stable up to 140 °C. No CO 2 and H 2 adsorption was observed in the small free spaces of their frameworks.

Multimode quantum dynamics using Gaussian wavepackets: The Gaussian-based multiconfiguration time-dependent Hartree (G-MCTDH) method applied to the absorption spectrum of pyrazine

The Gaussian-based multiconfiguration time-dependent Hartree (G-MCTDH) method is applied to calculate the S(2)(pipi( *)) absorption spectrum of the pyrazine molecule, whose diffuse structure results from the ultrafast nonadiabatic dynamics at the S(2)-S(1) conical intersection. The 24-mode second-order vibronic-coupling model of Raab et al. [J. Chem. Phys. 110, 936 (1999)] is employed, along with 4-mode and 10-mode reduced-dimensional variants of this model. G-MCTDH can be used either as an all-Gaussian approach or else as a hybrid method using a partitioning into primary modes, treated by conventional MCTDH basis functions, and secondary modes described by Gaussian particles. Comparison with standard MCTDH calculations shows that the method converges to the exact result. The variational, nonclassical evolution of the moving Gaussian basis is a key element in obtaining convergence. For high-dimensional systems, convergence is significantly accelerated if the method is employed as a hybrid scheme.

Proton Dynamics and Room-Temperature Ferroelectricity in Anilate Salts with a Proton Sponge

Ferroelectricity as well as characteristic proton-transfer dynamics are achieved by combining a 2,3,5,6-tetra(2'-pyridyl)pyrazine (TPPZ) molecule with anilic acids (H2xa). Dielectric measurements revealed phase transitions at T(c) = 334 and 172 K for bromanilate (Hba(-)) and chloranilate (Hca(-)) salts, respectively. The room-temperature ferroelectricity of the (H2-TPPZ)(Hba)2 crystal is evidenced by the slow polarization reversal with modest pyroelectricity. In accord with the observed large deuteration effect, synchrotron X-ray diffraction studies disclosed proton dynamics in an intramolecular N...H(+)...N bond of the H2-TPPZ(2+) dication and in an O-H...O(-) hydrogen-bonded cyclic dimer of the ortho-quinoid Hxa(-) anions. The disordered (Hxa(-))2 dimer in two-fold orientation manifests its double-proton transfer process above T(c), whereas these protons are ordered in the ferroelectric phase. The H2-TPPZ(2+) dication acts as a proton sponge by forming two intramolecular N...H(+)...N hydrogen bridges between the pyridyl units with a very short N...N distance. The dication in the paraelectric state adopts a nonpolar geometry due to the delocalization of the protons over two sites in the respective N...H(+)...N bonds. Below T(c), only one of the two protons gets localized, and the resultant acentric H2-TPPZ(2+) ion generates the dipole moment responsible for the ferroelectricity.

VUV photoionisation of free azabenzenes: Pyridine, pyrazine, pyrimidine, pyridazine and s-triazine

Photoionisation mass spectrometry was used to obtain the fragmentation pathways of pyridine, pyridazine, pyrimidine, pyrazine and s-triazine molecules upon absorption of 23.0, 15.7 and 13.8 eV synchrotron photons. The ionic fragments observed vary from molecule to molecule, however C 2H 2 +, HCN +and HCNH + are common to all five molecules at the three photon energies. Furthermore, the presence of C 2H 2N 2 +, C 3H 3N + and C 4H 4 + in the spectra of some of the molecules suggests dissociation pathways via loss of HCN moieties. The respective parent cations, m / q = 79 , 80 and 81 have a greater yield at low photon energies when compared to the most intense fragment peak in each spectra. We recorded two of the fragment cation yields, as well as the parent photoion yield curves of pyridine, pyridazine, and pyrimidine in the 8–30 eV range. The formation of abundant cation fragments show a strong propensity of the molecules for dissociation after the absorption of VUV photons higher than 14 eV. The differences in relative fragment yields from molecule to molecule, and when changing the excitation energy, suggest significant bond rearrangements and nuclear motion during the dissociation time. Thus, bond cleavage is dependent on the photon energy deposited in the molecule and on intramolecular reactivity. With the aid of photoion yield curves and energy estimations we have assigned major peaks in the spectra and discussed their fragmentation pathways.

Rectangular two-dimensional antiferromagnetic systems: Analysis of copper(II) pyrazine dibromide and dichloride

The structure of copper pyrazine dibromide (or dichloride) consists of dihalide-bridged copper chains parallel to the c-axis with the copper sites linked in a perpendicular direction by bridging pyrazine molecules parallel to the b-axis. Superexchange interactions are propagated through both halides and pyrazine so the magnetic structure is a rectangular layer with two exchange strengths, J and J′ ( J′ = αJ), where 0 < α < 1. The susceptibility of a rectangular antiferromagnetic Heisenberg lattice with S = 1/2 has been simulated using Quantum Monte Carlo techniques and the results compared to the experimental data. Best fits of the magnetic susceptibility data to the simulated data yield: for Cu(pz)Br 2, α = 0.20(5), C = 0.430(1) emu K/mol, 2 J = −46(1) K, and 2 J′ = −9(2) K and for Cu(pz)Cl 2, α = 0.30(5), C = 0.426(1) emu K/mol, 2 J = −28(1) K, and 2 J′ = −8(2)) K. The values are in good agreement with the literature and thus demonstrate the effectiveness of the technique for rectangular lattices.

Supramolecular Architecture from a Sodium Coordination Polymer with a 3D Net Containing 3‐Aminopyrazine‐2‐carboxylic acid (APZC):Synthesis, Characterization and Crystal Structure of [Na2(APZC)2(μ‐H2O)2(μ3‐H2O)]n

AbstractThe synthesis and spectroscopic properties of a Na+ complex with ligand 3‐aminopyrazine‐2‐carboxylic acid were described. The resulting complex was characterized by elemental analysis, IR, UV‐Vis, NMR spectroscopy and single crystal X‐ray diffraction method. The title compound crystallizes in the triclinic system with space group . The crystalline structure of this compound consists of supramolecular architectures involving strong intramolecular N–H···O in pyrazine molecules and intermolecular O–H···N, O–H···O, and N–H···N hydrogen bonds between substituted pyrazine and water molecules.

Competition between Photochemistry and Energy Transfer in UV-Excited Diazabenzenes. 4. UV Photodissociation of 2,3-, 2,5-, and 2,6-Dimethylpyrazine

The quantum yield for HCN formation via 248 nm photodissociation of 2,3-, 2,5-, and 2,6-dimethylpyrazine (DMP, C6N2H8) was measured using diode laser probing of the HCN photoproduct. The total quantum yield is phi = 0.039 +/- 0.07, 0.14 +/- 0.02, and 0.30 +/- 0.06 for 248 nm excitation of 2,3-, 2,5- and 2,6-DMP, respectively. Analysis of the quenching data within the context of a gas kinetic, strong collision model allows an estimate of the rate constant for HCN production via DMP photodissociation, ks = 4.1 x 10(3), 1.0 x 10(3), and 1.3 x 10(4) s(-1) for 2,3-, 2,5- and 2,6-DMP, respectively. Unlike HCN produced from the photodissociation of pyrazine and methylpyrazine, the amount of HCN produced via a prompt, unquenched dissociation channel was essentially zero, suggesting little multiphoton UV absorption. The rate constants for HCN formation together with previously measured rate constants for HCN production from photodissociation of pyrazine and methylpyrazine have been used to investigate possible reaction mechanisms. The position of the methyl group affects the HCN rate constant, suggesting that the mechanism for pyrazine dissociation involves an initial step that is hindered by the addition of the methyl groups. The proposed initial molecular motion of the mechanism, an out-of-plane H atom migration across a N atom, is consistent with (1) the position of the methyl groups, (2) the dissociation lifetime of the various pyrazine molecules studied, and (3) the observed large energy transfer magnitudes from pyrazine near dissociation. These so-called "supercollisions" have been linked to low-frequency, out-of-plane motion, suggesting that the molecular motions leading to efficient energy transfer are the same motions involved in dissociation. In addition, the pyrazine (C4N2H4) 248 nm photoproduct (C3H3N) was identified as acrylonitrile using IR spectroscopy, an observation that aids in understanding the dissociation mechanism.

Self-Assembled Metallacycles with Pyrazine Edges: A New Example in Which the Unexpected Molecular Triangle Prevails over the Expected Molecular Square

The combination of cis-protected metal fragments with linear linkers is expected to yield molecular squares. We found instead that treatment of the 90 degrees angular precursor trans-[RuCl2(dmso-S)4] (1) with an equivalent amount of the linear and rigid pyrazine (pyz) linker unexpectedly yields, in a number of different experimental conditions, the molecular triangle [{trans,cis-RuCl2(dmso-S)2(mu-pyz)}3] (3), together with polymeric material. Very similar results were also obtained from the reaction between 1 and the preformed corner fragment trans,cis,cis-[RuCl2(dmso-S)2(pyz)2] (6). In both cases, the expected molecular square [{trans,cis-RuCl2(dmso-S)2(mu-pyz)}4] (4) was observed only as a transient species. These results suggest that 3, which is the first example of a neutral molecular triangle with octahedral metal corners and pyrazine edges, is both the thermodynamic and the kinetic product of the reactions described above. The X-ray structure of 3 shows that the main distortions from ideal coordination geometry concern the N-Ru-N angles, which are narrower than 90 degrees , and the coordination bonds of pyz. The pyrazine molecules, which are basically planar, are significantly tilted from linearity. Calculations performed on 6 indicated that the N-Ru-N angle is ca. six times more rigid than the tilt angle of pyrazine. The structural and theoretical findings on 3 and 6, together with the previous examples of molecular triangles and squares with cis-protected metal corners and linear pyz edges, suggest that the entropically favored molecular triangles might be preferred over the expected molecular squares with metal corner fragments that spontaneously favor Npyz-M-Npyz angles narrower than 90 degrees because of the presence of ancillary ligands with significant steric demand on the coordination plane. The rather-flexible coordination geometry of pyrazine can accommodate the moderate distortions from linearity required to close the small metallacycle with modest additional strain.

Mn(H2O)4(C4N2H4)][C6H4(COO)2] – Ein eindimensionales Koordinationspolymer mit kettenartigen [Mn(H2O)4(C4N2H4)]n2n+ Polykationen

Abstract[Mn(H2O)4(C4N2H4)][C6H4(COO)2] – An One‐Dimensional Coordination Polymer with Chain‐like [Mn(H2O)4(C4N2H4)]n2n+ PolycationsOrthorhombic single crystals of [Mn(H2O)4(C4N2H4)][C6H4(COO)2] have been prepared in aqueous solution at room temperature. Space group Imm2 (no. 44), a = 1039.00(6) pm, b = 954.46(13) pm, c = 737.86(5) pm, V = 0.73172(12) nm3, Z = 2. Mn2+ is coordinated in a octahedral manner by four water molecules and two nitrogen atoms stemming from the pyrazine molecules (Mn–O 215.02(11) pm; Mn–N 228.7(4), 230.7(4) pm). Mn2+ and pyrazine molecules form chain‐like polycations with [Mn(H2O)4(C4N2H4)]n2n+ composition. The positive charge of the polycationic chains is compensated for by phthalate anions, which are accomodated between the chains. The phthalate anions are linked by hydrogen bonds to the polycationic chains. Thermogravimetric analysis in air revealed that the loss of water of crystallisation and pyrazine occurs in two steps between 130 and 245 °C. The resulting sample was stable up to 360 °C. Further decomposition yielded Mn2O3.

Low-energy electron scattering by pyrazine

We report cross sections for low-energy elastic electron collisions with the diazabenzene molecule pyrazine, obtained from first-principles calculations. The integral elastic cross section exhibits three sharp peaks that are nominally shape resonances associated with trapping in the vacant ${\ensuremath{\pi}}^{*}$ molecular orbitals. Although the two lowest-energy resonances do in fact prove to be nearly pure single-channel shape resonances, the third contains a considerable admixture of core-excited character, and accounting for this channel coupling effect is essential to obtaining an accurate resonance energy. Such resonant channel coupling has implications for electron interactions with the DNA bases, especially the pyrimidine bases for which pyrazine is a close analog. In the absence of data on pyrazine itself, we compare our elastic differential cross section to measurements on benzene and find close agreement.

DFT Investigations About Pyrazine Molecules on Si(100)-2×1 Surface

It is important to understand the interface of aromatic molecules on semiconductor surfaces because of the rich functionality of such molecules on semiconductor surfaces. The chemisorption of pyrazine molecules on the Si(100)-2×1 surface has been investigated using the B3LYP density functional theory with Si 9 H 12 one-dimer and Si 15 H 16 two-dimer cluster models. The calculated results predict that N -dative bonded-state, C2 = C5 [4+2] and the tightbridge 1,2,5,6 products may coexist on the Si(100)-2×1 surface.