Relaxation properties of porphyrin, diprotonated porphyrin, and isoelectronic tetraoxaporphyrin dication in the S2 state

The fluorescence spectra of unsubstituted porphyrin (H2P), diprotonated porphyrin (H4P2+), and isoelectronic tetraoxaporphyrin dication (TOxP2+) have been measured in solution at room temperature. The S2-->S0 fluorescence has been observed, much more intense for TOxP2+ than for H4P2+ and H2P. In the TOxP2+ case, the S2-->S0 fluorescence spectrum is remarkably sharp and shows an excellent mirror symmetry with respect to S0-->S2 absorption. On the contrary, the spectra of H4P2+ and H2P are shifted and more extended with respect to the absorption counterparts. The differences have been attributed primarily to the change of the equilibrium geometry upon excitation, larger in H2P and H4P2+ than in TOxP2+ and in the case of H4P2+ to the nonplanar conformation of the macrocycle. Also the S1-->S0 spectra of H2P, H4P2+, and TOxP2+ have been measured and more qualitatively discussed. The S1 and S2 fluorescence decays have been observed for H4P2+ and TOxP2+ exciting with ultrashort pulses. The S2 lifetime of TOxP2+ is of the order of the temporal resolution of our experimental apparatus, whereas that of H4P2+ is shorter. The S2-->S0 quantum yield of TOxP2+ has been estimated to be 0.035, approximately 3 orders of magnitude higher than that of H4P2+. It is proposed on the basis of ab initio model calculations that excited states of the H4P2+(CF3COO-)2 complex with charge-transfer character are responsible of the increased extension of the S2-->S0 spectrum with respect to that of H2P.     

Excited-state absorption and ultrafast relaxation dynamics of porphyrin, diprotonated porphyrin, and tetraoxaporphyrin dication

The relaxation dynamics of unsubstituted porphyrin (H2P), diprotonated porphyrin (H4P2+), and tetraoxaporphyrin dication (TOxP2+) has been investigated in the femtosecond-nanosecond time domain upon photoexcitation in the Soret band with pulses of femtosecond duration. By probing with spectrally broad femtosecond pulses, we have observed transient absorption spectra at delay times up to 1.5 ns. The kinetic profiles corresponding with the band maxima due to excited-state absorption have been determined for the three species. Four components of the relaxation process are distinguished for H2P: the unresolvably short B --> Qy internal conversion is followed by the Qy --> Qx process, vibrational relaxation, and thermalization in the Qx state with time constant approximately 150 fs, 1.8 ps, and 24.9 ps, respectively. Going from H2P to TOxP2+, two processes are resolved, i.e., B --> Q internal conversion and thermal equilibration in the Q state. The B --> Q time constant has been determined to be 25 ps. The large difference with respect to the B --> Qy time constant of H2P has been related to the increased energy gap between the coupled states, 9370 cm-1 in TOxP2+ vs 6100 cm-1 in H2P. The relaxation dynamics of H4P2+ has a first ultrafast component of approximately 300 fs assigned as internal conversion between the B (or Soret) state and charge-transfer (CT) states of the H4P2+ complex with two trifluoroacetate counterions. This process is followed by internal CT --> Q conversion (time constant 9 ps) and thermalization in the Q state (time constant 22 ps).     

Structural, electronic, and vibrational properties of amino-adamantane and rimantadine isomers

We performed a first principles total energy investigation on the structural, electronic, and vibrational properties of adamantane molecules, functionalized with amine and ethanamine groups. We computed the vibrational signatures of amantadine and rimantadine isomers with the functional groups bonded to different carbon sites. By comparing our results with recent infrared and Raman spectroscopic data, we discuss the possible presence of different isomers in experimental samples.     

Structural,magnetic, and vibrational properties of stoichiometric clusters of CrN

We performed density‐functional‐theoretic calculations to investigate the structural, magnetic and vibrational properties of the stoichiometric clusters (CrN)_n ( ). We show that the building block of the ground‐state structures of these clusters is a square CrNCrN unit; the only exception with n > 2 occurs for (CrN)₃, but this cluster has an isomer not very far in energy from the ground state consisting of a pair of CrNCrN squares sharing a CrN bond. In the smaller CrN, (CrN)₂, and (CrN)₃ clusters the magnetic moments of the N atoms are non‐negligible and antiparallel to those of the Cr atoms, but for the larger species (CrN)₄, (CrN)₅, (CrN)₆, and (CrN)₉ the cluster magnetic moments are almost entirely due to the Cr atoms. Lack of imaginary vibrational frequencies in the predicted ground‐state structures of (CrN)_n ( ) confirms that they are mechanically stable equilibrium states. © 2015 Wiley Periodicals, Inc.     

Structural characterization, thermal, dielectric, vibrational properties and molecular motions in

[C₃N₂H₅]₆[Bi₄Br₁₈] has been synthesized and characterized by the X-ray (at 293 and 110 K), calorimetric, dilatometric and dielectric measurements. At room temperature it crystallizes in the monoclinic space group, C2/m. A crystal structure consists of disordered imidazolium cations and ordered discrete tetramers of [Bi₄Br₁₈]^6-. This compound reveals a rich polymorphism in a solid state. It undergoes three solid–solid phase transitions: from phase I to II at 426/423 K (heating–cooling), II→III at 227 K and III→IV at 219.5/219 K. A clear dielectric relaxation process is found in the room temperature phase II. Infrared studies of the polycrystalline [C₃N₂H₅]₆[Bi₄Br₁₈] showed that the ν(N–H), δ(ring) and δ(C–H) modes of the imidazolium cations appeared to be very sensitive to the IV→III phase transition. ¹H NMR measurements confirmed a key role of the imidazolium cations in the phase transitions mechanisms at low temperatures.     

Structural, vibrational, and thermal properties of densified silicates: Insights from molecular dynamics

Structural, vibrational, and thermal properties of densified sodium silicate (close to NS2) are investigated with classical molecular dynamics simulations of the glass and the liquid state. A systematic investigation of the glass structure with respect to density was performed. We observe a repolymerization of the network manifested by a transition from a tetrahedral to an octahedral silicon environment, the decrease of the amount of non-bridging oxygen atoms and the appearance of threefold coordinated oxygen atoms (triclusters). Anomalous changes in the medium range order are observed, the first sharp diffraction peak showing a minimum of its full-width at half maximum according to density. Generic vibrational trends are observed, such as the shift of the Boson peak intensity to higher frequencies and the decrease of its intensity. Finally, we show that the thermal behavior of the liquid can be reproduced by the Birch-Murnaghan equation of states, thus allowing us to compute the isothermal compressibility.     

Structural, elastic constant, and vibrational properties of wurtzite gallium nitride: a first-principles approach

Perdew-Wang proposed generalized gradient approximation (GGA) is used in conjunction with ultrasoft pseudopotential to investigate the structural, elastic constant, and vibrational properties of wurtzite GaN. The equilibrium lattice parameters, axial ratio, internal parameter, bulk modulus, and its pressure derivative are calculated. The effect of pressure on equilibrium lattice parameters, axial ratio, internal parameter (u), relative volume, and bond lengths parallel and perpendicular to the c-axis are discussed. At 52 GPa, the relative volume change is observed to be 17.8%, with an abrupt change in bond length. The calculated elastic constants are used to calculate the shear wave speeds in the [100] and [001] planes. The finite displacement method is employed to calculate phonon frequencies and the phonon density of states. The first- and second-order pressure derivative and volume dependent Gruneisen parameter (γ(j)) of zone-center phonon frequencies are discussed. These phonon calculations calculated at theoretical lattice constants agree well with existing literature.     

Synthesis and spectroscopic properties of the elusive 3a,9a-diazaperylenium dication

The 3a,9a-diazaperylenium dication (1) was synthesized for the first time in two steps from p-phenylene diamine. Ab initio calculations show a twisted ground state with a 6.4 degrees tilt between the two quinolizinium building blocks. Dication 1 is photoluminescent in fluid solutions of H(2)O, CH(3)CN, and CH(3)NO(2), but not in rigid matrices of the same solvents. This phenomenon has been attributed to a geometric relaxation of the tilted ground state into an emitting planar lowest singlet excited state. [structure: see text]     

Perturbation of local solvent structure by a small dication: a theoretical study on structural, vibrational, and reactive properties of beryllium ion in water

A molecular based understanding of beryllium chemistry in the context of biomolecules is necessary for gaining progress in prevention and treatment of chronic beryllium disease. One aspect that has hindered the theoretical progress has been the lack of a simple classical two-body potential for the aqueous beryllium ion (Be2+) to be used with biomolecular simulations. We provide new parameters for Be2+ that capture the structural and reactive properties of this small dication. Using classical molecular dynamics simulations, we show that these parameters reproduce the correct radial distribution function and coordination numbers for this cation in explicit aqueous solution when compared to published diffraction and NMR measurements. The geometrical parameters obtained using classical simulations are also in agreement with ab initio calculations. We successfully predict the vibrational modes of the tetra aqua Be2+ dication from ab initio calculations on solvated structures obtained from the simulations. The calculated vibrational modes show better agreement with experiments compared to any published work. This new potential also produces a well-established hydrogen bonding between the first and second solvation shells. More importantly, when the molecular dynamics (MD) and ab initio results are interpreted in concert, the dynamics and nature of interactions between the first and second shells capture the pivotal role they play on the reactivity of aqua-Be complexes.     

Structural,vibrational and thermodynamics propertiesof Zn-based semiconductors

We have preformed first-principle calculations for the structural, vibrational and thermodynamic properties of the IIB–VIA Zn-based semiconductor compounds ZnX (X = O, S, Se, Te). The phonon dispersion curves along several high-symmetry lines at the Brillouin zone together with the corresponding phonon density of states are calculated using density-functional perturbation theory. The calculated phonon frequencies at the Γ, X, and L points of the Brillouin zone show good agreement with the experimental values and other calculations. The thermodynamics properties including the phonon contribution to the Helmholtz free energy ΔF, the phonon contribution to the internal energy ΔE, the entropy S, and the constant-volume specific heat C_V are determined within the harmonic approximation based on the calculated phonon dispersion relations. If 298 K is taken as a reference temperature, the difference values of H ? H₂₉₈ have been also calculated and compared with the available experimental data.     

Synthesis,properties and reduction of 1,8-naphthylenebis(diphenylcyclopropenium) dication

Synthesis, properties, and the result of one-electron reduction are described for the title compound, which is the first example of the stable dication containing two cationic rings in a close face-to-face arrangement.     

Structural, vibrational and DSC investigations of the tetraethylammonium hydrogenselenate crystal

The X-ray structure of tetraethylammonium hydrogenselenate, [N(C₂H₅)₄]HSeO₄, was determined at room temperature. The crystal belongs to the P space group of triclinic system, Z=2, a=8.290(2), b=9.073(2), c=9.517(2) Å, =76.75(3), β=74.31(3) and γ=63.92(3)°. The hydrogenselenate anions are joined into cyclic dimers by two identical (equivalent by C_i) strong hydrogen bonds O(2)–H(02)O(1^a); the O(2)O(1^a) distance equals 2.611(5) Å. Powder IR and Raman spectra are discussed with respect to the crystal structure. The DSC reveals two phase transitions at 328 and 358 K.     

Structural and oxygen binding properties of dimeric horse myoglobin

Myoglobin (Mb) stores dioxygen in muscles, and is a fundamental model protein widely used in molecular design. The presence of dimeric Mb has been known for more than forty years, but its structural and oxygen binding properties remain unknown. From an X-ray crystallographic analysis at 1.05 ? resolution, we found that dimeric metMb exhibits a domain-swapped structure with two extended α-helices. Each new long α-helix is formed by the E and F helices and the EF-loop of the original monomer, and as a result the proximal and distal histidines of the heme originate from different protomers. The heme orientation in the dimer was in the normal mode as in the monomer, but regulated faster from the reverse to normal orientation. The dimer possessed the oxygen binding property, although it exhibited a slightly higher oxygen binding affinity (～1.4 fold) compared to the monomer and showed no cooperativity for oxygen binding. The oxygen binding rate constant (k(on)) of the dimer ((14.0 ± 0.7) × 10(6) M(-1) s(-1)) was similar to that of the monomer, whereas the oxygen dissociation rate constant (k(off)) of the dimer (8 ± 1 s(-1)) was smaller than that of the monomer (12 ± 1 s(-1)). We attribute the similar k(on) values to their active site structures being similar, whereas the faster regulation of the heme orientation and the smaller k(off) in the dimer are presumably due to the slight change in the active site structure and/or more rigid structure compared to the monomer. These results show that domain swapping may be a new tool for protein engineering.     

Structural flexibility of a helical peptide regulates vibrational energy transport properties

Applying ultrafast vibrational spectroscopy, we find that vibrational energy transport along a helical peptide changes from inefficient but mostly ballistic below approximately 270 K into diffusive and significantly more efficient above. On the basis of molecular dynamics simulations, we attribute this change to the increasing flexibility of the helix above this temperature, similar to the glass transition in proteins. Structural flexibility enhances intramolecular vibrational energy redistribution, thereby refeeding energy into the few vibrational modes that delocalize over large parts of the structure and therefore transport energy efficiently. The paper outlines concepts how one might regulate vibrational energy transport properties in ultrafast photobiological processes, as well as in molecular electronic devices, by engineering the flexibility of their components.     

Structural, electronic, and optical properties of oxygen defects in Zn3N2

The structural, electronic, and optical properties of oxygen-defective Zn(3)N(2) were studied by means of density functional theory. The geometry optimization result shows that pure Zn(3)N(2) is cubic in structure, which is in agreement with experiment. Our results indicate that Zn(3)N(2) with nitrogen replaced by oxygen is more stable than that with interstitial oxygen and the substitutional oxygen for nitrogen in defective Zn(3)N(2) is responsible for the n-type conduction character. The possible optical transition mechanisms are discussed.     

Structural, vibrational and ab initio studies of L-histidine oxalate

Single crystals of L-histidine oxalate were obtained by slow evaporation of an aqueous solution at room temperature. The grown crystals have been subjected to X-ray diffraction (XRD), Infrared, and Raman spectroscopy. The title compound crystallises in the non-centrosymmetric space group P2(1)2(1)2(1,) the crystal cohesion is achieved by relatively strong hydrogen bonds, so that the NH3 groups show significant distortion with respect to the tetrahedral symmetry. Raman and infrared spectra of the title compound were recorded in the frequency range 300-3200 and 400-4000 cm-1, respectively. To obtain a reliable assignment of the observed spectral lines, we have calculated the geometry and the frequencies of the vibrational modes of histidine cation and the oxalate anion using the semi empirical PM3 method.     

Diguanidinium hydrogenarsenate monohydrate and its deuterated analogue vibrational, DSC and X-ray investigations

The crystal structure of diguanidinium hydrogenarsenate monohydrate has been found to belong to the P42(1)/c space group of the tetragonal system, with Z = 8, a = 17.114(2) A, c = 7.3500(10) A. In this complex, a network of hydrogen bonds links water molecules and hydrogenarsenate ions. The hydrogenarsenate ions form hydrogen-bonded chains along the crystallographic c-axis. Detailed vibrational studies have been carried out (FTIR and FT-Raman on powder samples, polarized FTIR microscope on a small single crystal at room temperature). The vibrational spectra are discussed in relation to the crystal structure. Calorimetric (DSC) studies have been performed, but no phase transition was found in the temperature range 100-350 K.     

Structural characterisation of the first mononuclear bismuth porphyrin

A single carboxylate picket bismuth porphyrin has been characterised in the solid state as the first instance of a non-dimeric structure; the carboxylate picket, bent over the macrocycle, is coordinated to the bismuth, inducing a significant distortion of the porphyrin core.