Density functional theory studies on the Raman and IR spectra of meso-tetraphenylporphyrin diacid

The vibrational spectra of meso-tetraphenylporphyrin diacid (H4TPP2+) have been studied with the density functional theory. Raman and IR spectra of H4TPP2+ and its N-deuterated analogue (D4TPP2+) are measured and compared with the computational results. Complete assignments of observed IR and Raman bands were proposed on the bases of calculation results. The DFT calculations reproduce 140 observed fundamentals with the RMS 8.6 cm-1. The computational as well as the experimental results reveal that the saddle-distortion of porphyrin macrocycle for the diacid leads to a significant effect on its vibrational spectra. Especially, several out-of-plane skeletal modes, which were either unobserved or very weak in the Raman spectra of CuTPP and H2TPP, are activated in the Raman spectra of the diacids. In addition, enhancement for the Raman bands of phenyl CC stretching modes were observed and attributed to the conjugation effect of pi-systems of the phenyl and the porphyrinato macrocycles.     

Trinuclear copper(II) complex showing high selectivity for the hydrolysis of 2'-5' over 3'-5' for UpU and 3'-5' over 2'-5' for ApA ribonucleotides

The cooperative action of multiple Cu(II) nuclear centers is shown to be effective and selective in the hydrolysis of 2'-5' and 3'-5' ribonucleotides. Reported herein is the specific catalysis by two trinuclear Cu(II) complexes of L3A and L3B. Pseudo first-order kinetic studies reveal that the L3A trinuclear Cu(II) complex effects hydrolysis of Up(2'-5')U with a rate constant of 28 x 10(-)(4) min(-)(1) and Up(3'-5')U with a rate constant of 0.5 x 10(-)(4) min(-)(1). The hydrolyses of Ap(3'-5')A and Ap(2'-5')A proceed with rate constants of 24 x 10(-)(4) min(-)(1) and 0.5 x 10(-)(4) min(-)(1) respectively. The L3A trinuclear Cu(II) complex demonstrates high specificity for Up(2'-5')U and Ap(3'-5')A. Similar studies with the more rigid L3B trinuclear Cu(II) complex shows no selectivity and yields lower rate constants for hydrolysis. The selectivity observed with the L3A ligand is attributed to the geometry of the ligand-bound diribonucleotide which ultimately dictates the proximity of the attacking hydroxyl and the phosphoester to a Cu(II) center for activation and subsequent hydrolysis.     

Relevance of the electric-dipole--electric-quadrupole contribution to Raman optical activity spectra

We examine the importance of the electric-dipole--electric-quadrupole polarizability tensor in the intensity theory of Raman optical activity (ROA) spectra. Using density functional theory, ROA spectra of organic cyclic compounds, alanine, oligoalanines, and examples from the literature are analyzed in detail, and a statistical investigation is performed. It is found that the contribution of the electric-dipole--electric-quadrupole tensor is often small, except for some special cases that involve C-H stretching vibrations.     

Effect of post-annealing in air on optical and XPS spectra of Y2O3 ceramics doped with CeO2

1. Download high-res image (147KB)
2. Download full-size image

     

Glucose-derived 3'-(carboxymethyl)-3'-deoxyribonucleosides and 2', 3'-lactones as synthetic precursors for amide-linked oligonucleotide analogues

Treatment of a 1,2-O-isopropylidene-3-ketopentofuranose derivative (obtained from D-glucose) with [(ethoxycarbonyl)methylene]triphenylphosphorane and catalytic hydrogenation of the resulting alkene gave stereodefined access to 3-(carboxymethyl)-3-deoxy-D-ribofuranose derivatives. Esters of 5-O-acetyl- or 5-azido-5-deoxy-3-(carboxymethyl)-D-ribofuranose were coupled with nucleobases to give branched-chain nucleoside derivatives. Ester saponification and protecting group manipulation provided 2'-O-(tert-butyldimethylsilyl) ethers of 5'-azido-5'-deoxy- or 5'-O-(dimethoxytrityl) derivatives of 3'-(carboxymethyl)-3'-deoxyribonucleosides that are effective precursors for synthesis of amide-linked oligoribonucleosides.     

Theoretical vibrational spectra compared to the experiment and the anomeric effect in 2-chloro-1,3,2-dioxaphosphorinane-2-oxide, -sulfide,and -selenide. II. Vibrational spectra and assignments

2-Chloro-1,3,2-dioxaphosphorinane-2-oxide, -sulfide, and -selenide are studied with the help of DFT/B3LYP and several ab initio methods using a 6-311G** basis set. However, due to rather large relative energies of higher conformers in all three cases, the conformational equili-brium mixture contains more than 95% (see the preceding paper in this Journal) of the lowest chair-equatorial conformer (this indicates that the P=X bond is in the equatorial position), so we do not find any conformer bands in the experimental spectra and calculate our theoretical ones for the assignment only from the chair-equatorial conformer. The vibrational infrared and Raman spectra were calculated and are in fair agreement with their experimental counterparts. Potential energy distribution calculations are performed, and the theoretical modes where an experimental counterpart could be found to symmetry coordinates are assigned.     

Interpreting the optical spectra of trace Fe2+ in layer silicates

Estimates have been made of Fe²⁺ term splittings in axial crystalline fields. It is found that all three long-wave bands in the optical spectrum are due to Fe²⁺ Fe³⁺ charge transfer, while the splitting of ⁵T_2g and ⁵E_g occurs in low-symmetry fields. Experimental evidence is presented for these calculations.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 23, No. 4, pp. 464–468, July–August 1987.     

Investigations of the optical spectra and EPR g factors for the tetragonal Cu2+ centers in trigonal ZnCO3 crystal

Two distinctive theoretical methods, the complete diagonalization (of energy matrix) method (CDM) and the perturbation theory method (PTM), are employed to calculate the optical band positions and EPR g factors g_//, g_⊥ for the tetragonal Cu²⁺ centers in trigonal ZnCO₃ crystal. The results from the two methods coincide and are also in good agreement with the experimental values. So both the CDM and PTM are adequate for the investigations of optical and EPR data for d⁹ ions in crystals. The tetragonal distortion due to the static Jahn–Teller effect for the tetragonal Cu²⁺ centers in trigonal Zn²⁺ site of ZnCO₃ is also acquired from the calculations. The results are discussed.     

In vitro evolution of an RNA-cleaving DNA enzyme into an RNA ligase switches the selectivity from 3'-5' to 2'-5'

Deoxyribozymes that ligate RNA expand the scope of nucleic acid catalysis and allow preparation of site-specifically modified RNAs. Previously, deoxyribozymes that join a 5'-hydroxyl and a 2',3'-cyclic phosphate were identified by in vitro selection from random DNA pools. Here, the alternative strategy of in vitro evolution was used to transform the 8-17 deoxyribozyme that cleaves RNA into a family of DNA enzymes that ligate RNA. The parent 8-17 DNA enzyme cleaves native 3'-5' phosphodiester linkages but not 2'-5' bonds. Surprisingly, the new deoxyribozymes evolved from 8-17 create only 2'-5' linkages. Thus, reversing the direction of the DNA-mediated process from ligation to cleavage also switches the selectivity in forming the new phosphodiester bond. The same change in selectivity was observed upon evolution of the 10-23 RNA-cleaving deoxyribozyme into an RNA ligase. The DNA enzymes previously isolated from random pools also create 2'-5' linkages. Therefore, deoxyribozyme-mediated formation of a non-native 2'-5' phosphodiester linkage from a 5'-hydroxyl and a 2',3'-cyclic phosphate is strongly favored in many different contexts.     

Solid-phase synthesis and on-column deprotection of RNA from 2'- (and 3'-) O-levulinated (Lv) ribonucleoside monomers

[reaction: see text] The solid-phase synthesis of oligoribonucleotides derived from ribonucleosides esterified at the 2'- (or 3'-) position with the levulinyl (Lv) group is described. The oligomers can be released from the solid support as 2'-O-Lv ester derivatives or fully deprotected while still attached to the solid support.     

Experimental and theoretical study of the CD spectra and conformational properties of axially chiral 2,2'-, 3,3'-, and 4,4'-biphenol ethers

New chiral biphenol ethers (Biph22, Biph33, and Biph44), carrying (R)-methylpropyloxy groups at 2,2'-, 3,3'-, and 4,4'-positions of biphenyl, were prepared. The introduced peripheral chiral groups in these biphenol ethers induce an (averaged) axial chirality to give predominant aR- or aS-rotamers. The chiroptical properties of these axially chiral biphenol ethers in polar and nonpolar solvents were determined experimentally and were compared with the corresponding theoretical values to determine their conformational behavior in solution. Geometry optimization at the DFT-D/TZV2P level and subsequent time-dependent density functional theory (TD-DFT) at the BH-LYP/TZV2P level treatments to obtain rotatory strengths revealed that 6 out of 18 conformers (aR-Tg-, aR-Tg+, aR-G+t, aS-Tg-, aS-Tg+, and aS-G+t) are crucial to reproduce the experimental circular dichroism (CD) spectra and optical rotations. Although biphenyl molecules are in conformational equilibrium with varying interplanar angles in solution, our static approach to the prediction of the experimental CD spectra is simply based on pairs of thermally populated, local-minimum structures, that is, the dynamic behavior of the systems or the vibrational wave functions are not considered. The relative energies computed at the SCS-MP2/TZVPP level in the gas phase or in acetonitrile solution using the conductor-like screening model (COSMO) were found to be accurate enough to calculate the thermal population of the relevant conformers. Although most of the CD signals mutually cancel out each other between a pair of aR- and aS-rotamers, the remaining Cotton effects due to a small preference for a single rotamer produce characteristic CD spectra. In general (and somewhat unexpectedly), the delicate cancellation effects in the CD spectra are accurately described by the theoretical approach, and the simulated CD spectra are in excellent agreement with the experimental ones though observed rotatory strengths being always smaller (by 5-20 times) than the theoretical data. Accordingly, slight preferences for the P (or aR)-configuration for Biph22 and M-configuration for Biph33 and Biph44 are determined. The preference for the opposite isomer in the case of Biph22 is due to larger attractive intramolecular interactions between the chiral alkyl groups. This is also consistent with the lower oxidation potential found for Biph22 (DeltaE approximately 0.1 V), as compared with those for Biph33 and Biph44. The CT complex formation of Biph22-44 with various acceptors was also studied by UV-vis and CD spectroscopic methods.     

Molecular dynamics as studied by Fourier transforms of optical absorption spectra. Theoretical method and application to benzene

We have obtained the autocorrelation function of the transition dipole moment by a Fourier transform of the optical absorption spectrum of benzene in solution. From this, we have evaluated some parameters related to the molecular dynamics in the excited state, the Brownian motion of the solution and the HT and BO couplings.     

Investigations of the optical and EPR spectra for VO2+ in LiKSO4 crystals

The optical spectra and EPR spectra (characterized by the spin-Hamiltonian parameters g(//), g(perpendicular), A(//) and A(perpendicular)) for the molecular ion VO2+ in LiKSO4 crystals are calculated from two microscopic theory methods, one of which is the complete diagonalization (of energy matrix) method (CDM) and the other is the perturbation theory method (PTM). The calculated three optical absorption bands and four spin-Hamiltonian parameters from the two methods are not only close to each other, but also in reasonable agreement with the experimental values. It appears that both theoretical methods are effective in the explanation of optical and EPR spectra for 3d1 ions in crystals. The negative signs of hyperfine structure constants A(//) and A(perpendicular) for VO2+ in LiKSO4 crystals are also suggested from the calculations.     

IR spectra and structure of 2-aryl-3-hydroxypyridines

The IR spectra of methyl, chloro, and phenyl derivatives of 3-hydroxypyridines in CCl₄ solutions and in the crystalline state were studied. A comparison of the frequencies, half widths, and integral intensities of the bands of the stretching vibrations of the hydroxyl groups in the spectra of solutions of the 3-hydroxypyridine derivatives in CCl₄ with the characteristic OH bands in the spectra of phenols demonstrates that 3-hydroxypyridines exist practically completely in the hydroxy form in dilute CCl₄ solutions. The shift in the OH bands in the spectra of 2-phenyl-3-hydroxypyridine derivatives indicates that the OH group forms a -hydrogen bond with the phenyl ring. The presence also of a band of a free OH group is evidence for the existence of s-cis and s-trans conformers relative to the C-O bond.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 187–190, February, 1972.     

NIR to UV absorption spectra and the optical constants of phthalocyanines in glassy medium

Optical absorption studies of phthalocyanines (Pc-s) in borate glass matrix have been reported for the first time. Measurements have been done corresponding to photon energies between 1.1 and 6.2 eV for free base, manganese, iron, nickel, molybdenum, cobalt and copper phthalocyanines. Several new discrete transitions are observed in the UV-vis region of the spectra in addition to a strong continuum component of absorption in the IR region. Values of some of the important optical constants viz. absorption coefficient (alpha), molar extinction coefficient (epsilon), absorption cross-section (sigma(a)), band width (delta lambda), electric dipole strength (q2) and oscillator strength (f) for the relevant electronic transitions are also presented. All the data reported for Pc-s in the new matrix have been compared with those corresponding to solution, vapor and thin film media.     

Synthesis and characterization of the oxidized dGTP lesions spiroiminodihydantoin-2'-deoxynucleoside-5'- triphosphate and guanidinohydantoin-2'-deoxynucleoside-5'- triphosphate

Two convenient synthetic routes to the oxidized guanosine triphosphate lesions spiroiminodihydantoin-2'-deoxynucleoside-5'-triphosphate (dSpTP) and guanidinohydantoin-2'-deoxynucleoside-5'-triphosphate (dGhTP) are reported. Both two-electron oxidation of 2'-deoxy-7,8-dihydro-8-oxoguanosine-5'-triphosphate (dOGTP) using SO4*- generated photolytically from K2S2O8 or four-electron oxidation of 2'-deoxyguanosine-5'-triphosphate (dGTP) from singlet oxygen provide either dSpTP or dGhTP at pH 8.0 or 4.4, respectively. Highly purified triphosphates are obtained by ion pair reversed-phase HPLC.     

Theoretical study of the Raman optical activity spectra of 3(10)-helical polypeptides

Raman optical activity (ROA) spectroscopy is a promising analytical method for studying the structure and conformation of polypeptides and proteins in solution. However, the structural information obtained from such vibrational spectra is only indirect and theoretical studies are often necessary to identify how the structure determines the observed spectra. One particular target is the identification and discrimination of different helical secondary structure elements. Herein, a theoretical investigation of the ROA spectra of a series of 3(10)-helical polypeptides is presented. In particular, the effect of chain length, C(α)-substitution pattern, the introduction of larger aliphatic side chains, and the variation of their conformation on the ROA spectra is studied. To extract general principles from these calculations, the positions, intensities, and shapes of the ROA bands are analyzed in terms of localized modes, which makes it possible to identify possible ROA signatures of 3(10) -helical structures, but also provides fundamental insight into the generation of ROA signals in complex polypeptides. Finally, the calculated spectra can be compared to the previously reported ROA spectrum of a specifically designed 3(10) -helical heptapeptide. This allows most of the features in the experimental spectrum to be assigned.