Global phylogeny and taxonomic reassessment of the lichen genus Dendriscosticta (Ascomycota: Peltigerales)

peer reviewedThe genus Dendriscosticta (Ascomycota: Peltigerales) encompasses several distinctive lichen-forming fungal species restricted to the Northern Hemisphere. Most are flagship species of old-growth forests with good air quality. A global phylogeny of the genus based on multilocus sequence data (ITS, RPB1, EF-1α, MCM7), model-based phylogenetic methods, and morphological and chemical assessments, reveals a high level of cryptic speciation often associated with restricted geographical distribution and/or chemical characters. Using sequence-based species delimitation approaches, we circumscribe two main clades referred to as the D. wrightii clade, with five unequivocal species, including D. gelida sp. nov., and the D. praetextata clade, with eight putative species, including D. phyllidiata sp. nov. The absence of recently collected material of D. hookeri comb. nov. from the type locality unfortunately prevents assignment of this epithet to one of the five supported lineages sharing this morphotype. Three new combinations are proposed: D. hookeri, D. insinuans comb. nov. and D. yatabeana comb. nov. Epitypes are designated for D. wrightii and D. yatabeana. Species diversity within the genus increased from four to nine. Our morphological assessment confirmed that Sticta and Dendriscosticta can be readily distinguished by the presence of excipular algae whereas the structure of the lower surface pores is not a reliable diagnostic feature

Three new species of Parmeliaceae (Ascomycota) from Siberia

Cetrelia sayanensis, Myelochroa sibirica and M. sayanensis from Russia (West Sayan Mountains, southern Siberia) are described as new to science. All three species are characterized by the presence of capitate-pustulate or subpustulate soralia, as well a

Anharmonic Vibrational Analysis of the Gas-Phase Infrared Spectrum of 1,1-Difluoroethylene Using the Operator Van Vleck Canonical Perturbation Theory

Anharmonic vibration frequencies of 1,1-difluoroethylene (11DFE) in the gas phase are predicted by means of the numerical-analytic operator version of the canonical van Vleck perturbation theory in the second and fourth orders (CVPT2 and CVPT4). The full quartic and “semi-diagonal” sextic rectilinear normal coordinate potential energy surfaces, needed for CVPT2 and CVPT4, respectively, were obtained with the MP2/cc-pVTZ quantum-mechanical model. CVPT2 is superior to the traditional second-order vibrational perturbation theory approach (VPT2) because of the uniform general treatment of the Fermi and second-order Darling–Dennison resonances. The fourth-order version, CVPT4, provides a more refined solution and proves convergence of the perturbative treatment. Labeling of the basis functions by polyad numbers breaks down the infinite Hamiltonian matrix into a block-diagonal form. The polyad expression for 11DFE has been determined as P = 14(ν1 + ν7) + 8ν2 + 6(ν3 + ν8) + 4(ν4 + ν9) + 3(ν6 + ν11 + ν12) + 2(ν5 + ν10), where the νi are quantum numbers. The theoretical prediction of anharmonic infrared absorption intensities corroborated an assignment of the majority of observed gas-phase bands up to 3500 cm–1. The solution was refined by iteratively fitting harmonic frequencies, until predicted fundamental anharmonic frequencies matched the observed values. The average error for about 90 observed frequencies after fitting only fundamental frequencies is ∼1.05 cm–1. The fitted “semi-experimental” harmonic frequencies agree very well the quantum-mechanical predictions based on the CCSD(T)/cc-pVTZ and CCSD(T)/cc-pVQZ models

Nonempirical Anharmonic Vibrational Perturbation Theory Applied to Biomolecules: Free-Base Porphin

Anharmonic vibrational frequencies and intensities (infrared and Raman) of an isolated free-base porphin molecule are predicted from the quantum mechanical (QM) geometry, the “semi-diagonal” quartic force field, and dipole moment and polarizability surfaces. The second-order vibrational perturbation theory plus the numerical diagonalization of the Hamiltonian matrix containing off-diagonal Fermi and Darling–Dennison resonance couplings (VPT2+<i>WK</i>) was used. The QM calculations were carried out with the Becke–Lee–Yang–Parr composite exchange–correlation functional (B3LYP) and with the 6-31+G­(d,p) basis set. The harmonic force field for the equilibrium configuration was transformed into nonredundant local symmetry internal coordinates, and normal coordinates were defined. The semi-diagonal quartic rectilinear normal coordinate potential energy surface (PES), as well as the cubic surfaces of dipole moment (<i>p</i>) and polarizability (α) components, needed for the VPT2+<i>WK</i> calculation, were constructed by a five-point finite differentiation of Hessians (for PES) and of the values and first derivatives of <i>p</i> and α. They were obtained at the point of equilibrium and for 432 displaced configurations. This theoretical approach provides very good agreement between the predicted and experimental frequencies and intensities. However, the favorable result can be partly attributed to error cancellation within the B3LYP/6-31+G­(d,p) QM model, as observed in earlier studies. Reassignments of some observed bands are proposed

Theoretical and Experimental Study of Changes in the Structure of the Intermediate Layer during Friction between Contacting Bodies

Friction is often accompanied by local fracture at the boundary of contacting bodies. The space between contacting bodies usually contains moving particles of a different nature, and a change in the effective friction conditions can be associated with a change in the structure of the contact area. This paper presents a new series of experiments where balls simulated the particles of the intermediate layer interacting with an elastic layer of different thickness. The effects of regularization when the balls approached each other were investigated considering different initial configurations (line and spatial structure). The balls simulated the particles of the intermediate layer interacting with the elastic layer of different thickness. The opposite effects of convergence and separation of the balls were observed in different experiments. A model of mutual effect during the contact of two balls with a two-layered elastic half-space was developed. An analysis of tangential forces due to the mutual effect was performed for different layer thicknesses, its relative compliance, and different distances between the balls. It was found that the input parameters defined the sign of the tangential force, which led to the convergence or the separation of the balls. The results can be used to create structures controlling the motion in the intermediate layer

Ab Initio Anharmonic Analysis of Vibrational Spectra of Uracil Using the Numerical-Analytic Implementation of Operator Van Vleck Perturbation Theory

The numerical-analytic implementation of the operator version of the canonical Van Vleck second-order vibrational perturbation theory (CVPT2) is employed for a purely <i>ab initio</i> prediction and interpretation of the infrared (IR) and Raman anharmonic spectra of a medium-size molecule of the diketo tautomer of uracil (2,4­(1<i>H</i>,3<i>H</i>)-pyrimidinedione), which has high biological importance as one of the four RNA nucleobases. A nonempirical, semidiagonal quartic potential energy surface (PES) expressed in normal coordinates was evaluated at the MP2/cc-pVTZ level of theory. The quality of the PES was improved by replacing the harmonic frequencies with the “best” estimated CCSD­(T)-based values taken from the literature. The theoretical method is enhanced by an accurate treatment of multiple Fermi and Darling–Dennison resonances with evaluation of the corresponding resonance constants <i>W</i> and <i>K</i> (CVPT2+<i>WK</i> method). A prediction of the anharmonic frequencies as well as IR and Raman intensities was used for a detailed interpretation of the experimental spectra of uracil. Very good agreement between predicted and observed vibrational frequencies has been achieved (RMSD ∼4.5 cm^–1). The model employed gave a theoretically robust treatment of the multiple resonances in the 1680–1790 cm^–1 region. Our new analysis gives the most reliable reassignments of IR and Raman spectra of uracil available to date

Anharmonic Vibrational Analysis of the Infrared and Raman Gas-Phase Spectra of s-trans - and s-gauche -1,3-Butadiene

A quantum-mechanical (hybrid MP2/cc-pVTZ and CCSD(T)/cc-pVTZ) full quartic potential energy surface (PES) in rectilinear normal coordinates and the second-order operator canonical Van Vleck perturbation theory (CVPT2) are employed to predict the anharmonic vibrational spectra of s-trans- and s-gauche-butadiene (BDE). These predictions are used to interpret their infrared and Raman scattering spectra. New high-temperature Raman spectra in the gas phase are presented in support of assignments for the gauche conformer. The CVPT2 solution is based on a PES and electro-optical properties (EOP; dipole moment and polarizability) expanded in Taylor series. Higher terms than those routinely available from Gaussian09 software were calculated by numerical differentiation of quadratic force fields and EOP using the MP2/cc-pVTZ model. The integer coefficients of the polyad quantum numbers were derived for both conformers of BDE. Replacement of harmonic frequencies by their counterparts from the CCSD(T)/cc-pVTZ model significantly improved the agreement with experimental data for s-trans-BDE (root-mean-square deviation approximate to 5.5 cm(-1)). The accuracy in predicting the rather well-studied spectrum of fundamentals of s-trans-BDE assures good predictions of the spectrum of s-gauche-BDE. A nearly complete assignment of fundamentals was obtained for the gauche conformer. Many nonfundamental transitions of the BDE conformers were interpreted as well. The predictions of multiple Fermi resonances in the complex CH-stretching region correlate well with experiment. It is shown that solving a vibrational anharmonic problem through a numerical-analytic implementation of CVPT2 is a straightforward and computationally advantageous approach for medium-size molecules in comparison with the standard second-order vibrational perturbation theory (VPT2) based on analytic expressions

Anharmonic Vibrational Analysis of the Gas-Phase Infrared Spectrum of 1,1-Difluoroethylene Using the Operator Van Vleck Canonical Perturbation Theory

Anharmonic vibration frequencies of 1,1-difluoroethylene (11DFE) in the gas phase are predicted by means of the numerical-analytic operator version of the canonical van Vleck perturbation theory in the second and fourth orders (CVPT2 and CVPT4). The full quartic and “semi-diagonal” sextic rectilinear normal coordinate potential energy surfaces, needed for CVPT2 and CVPT4, respectively, were obtained with the MP2/cc-pVTZ quantum-mechanical model. CVPT2 is superior to the traditional second-order vibrational perturbation theory approach (VPT2) because of the uniform general treatment of the Fermi and second-order Darling–Dennison resonances. The fourth-order version, CVPT4, provides a more refined solution and proves convergence of the perturbative treatment. Labeling of the basis functions by polyad numbers breaks down the infinite Hamiltonian matrix into a block-diagonal form. The polyad expression for 11DFE has been determined as <i>P</i> = 14­(ν₁ + ν₇) + 8ν₂ + 6­(ν₃ + ν₈) + 4­(ν₄ + ν₉) + 3­(ν₆ + ν₁₁ + ν₁₂) + 2­(ν₅ + ν₁₀), where the ν_<i>i</i> are quantum numbers. The theoretical prediction of anharmonic infrared absorption intensities corroborated an assignment of the majority of observed gas-phase bands up to 3500 cm^–1. The solution was refined by iteratively fitting harmonic frequencies, until predicted fundamental anharmonic frequencies matched the observed values. The average error for about 90 observed frequencies after fitting only fundamental frequencies is ∼1.05 cm^–1. The fitted “semi-experimental” harmonic frequencies agree very well the quantum-mechanical predictions based on the CCSD­(T)/cc-pVTZ and CCSD­(T)/cc-pVQZ models

Anharmonic Vibrational Analysis of the Infrared and Raman Gas-Phase Spectra of <i>s‑trans</i>- and <i>s‑gauche</i>-1,3-Butadiene

A quantum-mechanical (hybrid MP2/cc-pVTZ and CCSD­(T)/cc-pVTZ) full quartic potential energy surface (PES) in rectilinear normal coordinates and the second-order operator canonical Van Vleck perturbation theory (CVPT2) are employed to predict the anharmonic vibrational spectra of <i>s-trans-</i> and <i>s-gauche-</i>butadiene (BDE). These predictions are used to interpret their infrared and Raman scattering spectra. New high-temperature Raman spectra in the gas phase are presented in support of assignments for the gauche conformer. The CVPT2 solution is based on a PES and electro-optical properties (EOP; dipole moment and polarizability) expanded in Taylor series. Higher terms than those routinely available from Gaussian09 software were calculated by numerical differentiation of quadratic force fields and EOP using the MP2/cc-pVTZ model. The integer coefficients of the polyad quantum numbers were derived for both conformers of BDE. Replacement of harmonic frequencies by their counterparts from the CCSD­(T)/cc-pVTZ model significantly improved the agreement with experimental data for <i>s-trans</i>-BDE (root-mean-square deviation ≈ 5.5 cm^–1). The accuracy in predicting the rather well-studied spectrum of fundamentals of <i>s-trans</i>-BDE assures good predictions of the spectrum of <i>s-gauche</i>-BDE. A nearly complete assignment of fundamentals was obtained for the gauche conformer. Many nonfundamental transitions of the BDE conformers were interpreted as well. The predictions of multiple Fermi resonances in the complex CH-stretching region correlate well with experiment. It is shown that solving a vibrational anharmonic problem through a numerical-analytic implementation of CVPT2 is a straightforward and computationally advantageous approach for medium-size molecules in comparison with the standard second-order vibrational perturbation theory (VPT2) based on analytic expressions