Vibrational dynamics of DNA. I. Vibrational basis modes and couplings

Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm(-1). These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.     

Total Synthesis of (+)-Sch 725680: Inhibitor of Mammalian A-, B-, and Y-Family DNA Polymerases

The total synthesis of (+)-Sch 725680, a member of the hydrogenated azaphilone family, has been accomplished. The synthesis confirmed the absolute configuration and biological activities of the natural product. A key reaction to construct a hydrogenated azaphilone core skeleton is a Ti-mediated aldol reaction.     

Vibrational spectroscopic study of o-, m- and p-hydroxybenzylideneaminoantipyrines

Three structurally similar antipyrine derivatives of o-hydroxybenzylideneaminoantipyrine (o-HBAP), m-hydroxybenzylideneaminoantipyrine (m-HBAP) and p-hydroxybenzylideneaminoantipyrine (p-HBAP) were characterized by FT-IR, FT-Raman experimental techniques and density functional theoretical (DFT) calculations. The comparisons between the calculated and experimental results covering molecular structures, assignments of fundamental vibrational modes and thermodynamic properties were investigated. The optimized molecular geometries agree well with the corresponding experimental values by comparing with the XRD data. The comparisons and assignments of the vibrational frequencies indicate that the experimental spectra also coincide satisfactorily with those of theoretically simulated spectrograms except the hydrogen-bond coupling infrared vibrations, and compounds can be distinguished by the IR and Raman spectra due to the differences of the hydroxyl-substituted positions and molecular packing, and the strong Raman scattering activities of the compounds are tightly relative to the molecular conjugative moieties linked through the Schiff base imines. The thermodynamic functions and their correlations with temperatures were also obtained from the theoretical harmonic frequencies.     

Synthesis of combretastatins A-1 and B-1

Combretastatins A-1 and B-1 have been synthesized by coupling MOM-protected p-iodomethoxycatechol with 3,4,5-trimethoxyphenylacetylene in a Sonogashira reaction.     

Vibrational dynamics of DNA. II. Deuterium exchange effects and simulated IR absorption spectra

In Paper I, we studied vibrational properties of normal bases, base derivatives, Watson-Crick base pairs, and multiple layer base pair stacks in the frequency range of 1400-1800 cm(-1). However, typical IR absorption spectra of single- and double-stranded DNA have been measured in D(2)O solution. Consequently, the more relevant bases and base pairs are those with deuterium atoms in replacement with labile amino hydrogen atoms. Thus, we have carried out density functional theory vibrational analyses of properly deuterated bases, base pairs, and stacked base pair systems. In the frequency range of interest, both aromatic ring deformation modes and carbonyl stretching modes appear to be strongly IR active. Basis mode frequencies and vibrational coupling constants are newly determined and used to numerically simulate IR absorption spectra. It turns out that the hydration effects on vibrational spectra are important. The numerically simulated vibrational spectra are directly compared with experiments. Also, the (18)O-isotope exchange effect on the poly(dG):poly(dC) spectrum is quantitatively described. The present calculation results will be used to further simulate two-dimensional IR photon echo spectra of DNA oligomers in the companion Paper III.     

Vibrational spectroscopic identification of isoprene,pinenes and their mixture

Here we show a study of vibrational spectroscopic identification of a few typical organic compounds which are known as the main sources of organic aerosols(OAs) particle matter in air pollution. Raman and IR spectra of isoprene, terpenoids, pinenes and their mixture are meticulously examined, showing distinguishable intrinsic vibrational spectroscopic fingerprints for these chemicals, respectively. As a reference, first-principles calculations of Raman and infrared activities are also conducted. It is interestingly found that, the experimental spectra are peak-to-peak consistent with the DFT(Density Functional Theory)-calculated vibrational activities. Also found is that, in a certain case such as for bpinene, a dimer model, rather than an isolated single molecular model, reproduces the experimental results, indicating unneglected intermolecular interactions. Starting with this study, we are endeavoring to advocate a database of Raman/IR fingerprint spectra for OA haze identification.     

Organophosphorus chemistry: Part IV. Vibrational spectroscopic study of the PO,PS and PSe bonds in triarylphosphorous chalcogenides

The infrared and Raman spectra of the series (4-XC₆H₄)_3-n(C₆H₅)_nPY, (3-XC₆H₄)_3-n (C₆H₅)_nPY (X = Cl or F, n = 0,1,2) and (4-FC₆H₄)_3-n (3-FC₆H₄)_nPY (n = 1,2) (Y = O, S and Se) compounds have been studied and assignments for the v(P=O), v(P=S) and v(P=Se) stretching frequencies are proposed. The results indicate that the frequency shifts caused by the substituents bonded to phosphorus are more important in the PS and PSe bond than in the PO bond. Mechanisms for the changes in PY bond order as a result of changing the aromatic substituent are discussed.     

Vibrational spectroscopic studies of mesna and dimesna

Raman, and infrared spectra of mesna and dimesna have been collected in the present spectroscopic studies. Based on the group frequencies, relative intensities and Raman depolarization measurements, some vibrational assignments have been suggested. For both mesna and dimesna, at least two rotational conformers have been identified. Adsorption behavior was investigated from the recorded surface-enhanced Raman scattering (SERS) spectra. It was found that both mesna and dimesna adsorbed as thiolate on silver sol particles with the cleavage of the S-H bond in mesna and the S-S bond in dimesna. For the adsorbed thiolate, two conformers existed in the adsorption state.     

Vibrational spectroscopic study of hydrated uranyl oxide: Curite

Raman and infrared spectra of the uranyl oxyhydroxide hydrate: curite is reported. Observed bands are attributed to the (UO₂)²⁺ stretching and bending vibrations, U–OH bending vibrations, H₂O and (OH)⁻ stretching, bending and librational modes. U–O bond lengths in uranyls and O–H…O bond lengths are calculated from the wavenumbers assigned to the stretching vibrations. These bond lengths are close to the values inferred and/or predicted from the X-ray single crystal structure. The complex hydrogen-bonding network arrangement was proved in the structures of the curite minerals. This hydrogen bonding contributes to the stability of these uranyl minerals.     

Vibrational spectroscopic,conductivity, and calorimetric studies on tripotassium hydrogen diselenate

Infrared spectra of K₃H(SeO₄)₂ obtained at 300 and 77 K, conform to the pattern expected for a very strong O-H O hydrogen bond. Differential scanning calorimetry (DSC) and electrical conductivity measurements indicate the presence of a phase transition at 388 K to a state having high protonic conductivity.A. W. A. is a recipient of a La Trobe University Postgraduate Research Scholarship.     

Vibrational structure of titanium silicate catalysts. A spectroscopic and theoretical study.

A thorough analysis of the vibrational features of the titanium silicalite-1 (TS-1) catalyst is presented, based on quantitative IR measurements, Raman and resonant Raman experiments, quantitative XANES, and quantum chemical calculations on cluster and periodic models. The linear correlation of the intensity of the IR and Raman bands located at 960 and 1125 cm(-1) and the XANES peak at 4967 eV with the amount of tetrahedral Ti are quantitatively demonstrated. Raman and resonant Raman spectra of silicalite and TS-1 with variable Ti content are presented, showing main features at 960 and 1125 cm(-1) associated with titanium insertion into the zeolite framework. The enhancement of the intensity of the 1125 cm(-1) feature and the invariance of the 960 cm(-1) feature in UV-Raman experiments, are discussed in terms of resonant Raman selection rules. Quantum chemical calculations on cluster models Si[OSi(OH)(3)](4) and Ti[OSi(OH)(3)](4) at the B3LYP/6-31G(d) level of theory provide the basis for the assignment of the main vibrational contributions and for the understanding of Raman enhancement. The resonance-enhanced 1125 cm(-1) mode is unambiguously associated with a totally symmetric vibration of the TiO(4) tetrahedron, achieved through in-phase antisymmetric stretching of the four connected Ti-O-Si bridges. This vibration can also be described as a totally symmetric stretching of the four Si-O bonds pointing toward Ti. The resonance enhancement of this feature is explained in terms of the electronic structure of the Ti-containing moiety. Asymmetric stretching modes of TO(4) units show distinct behavior when (i) T is occupied by Si as in perfect silicalite, (ii) T is occupied by Ti as in TS-1, or (iii) the oxygen atom belongs to an OH group, such as in terminal tetrahedra of cluster models and in real defective zeolites. Asymmetric SiO(4) and TiO(4) stretching modes appear above and below 1000 cm(-1), respectively, when they are achieved through antisymmetric stretching of the T-O-Si bridges, and around 800 cm(-1) (in both SiO(4) and TiO(4)) when they involve symmetric stretching of the T-O-Si units. In purely siliceous models, the transparency gap between the main peaks at 800 and 1100 cm(-1) contains only vibrational features associated with terminal Si-OH groups, while in Ti-containing models it contains also the above-mentioned asymmetric TiO(4) modes, which in turn are strongly coupled with Si-OH stretching modes. Calculations on periodic models of silicalite and TS-1 free of OH groups using the QMPOT embedding method correctly reproduce the transparency gap of silicalite and the appearance of asymmetric TiO(4) vibrations at 960 cm(-1) in TS-1. Finally, we demonstrate, for the first time, that the distortion of the tetrahedral symmetry around Ti caused by water adsorption quenches the UV-Raman enhancement of the 1125 cm(-1) band.     

Spectra and structure of phosphorus-boron compounds : IV. Vibrational spectra of solid trifluorophosphineborane

The Raman spectra of F₃PBH₃ and F₃PBD₃ have been recorded (2500-10 cm⁻¹) of the liquids (−80°C) and solids (−196°C) as well as the infrared spectra (4000-33 cm⁻¹) of the solids. In the spectrum of the solid state many of the ¹⁰B and ¹¹B fundamentals were clearly defined and it was also possible to assign the BH₃ torsional frequency from the infrared and Raman spectra of the solids. A complete vibrational assignment is proposed and a normal coordinate calculation carried out. The force constant of 2.46 mdyn Å⁻¹ for the P-B stretching mode is consistent with the short P-B bond; this constant is compared to the similar quantity for several other phosphorus-boron compounds. All of the E modes for the “free” molecule are shown to be split by the site symmetry which indicates that the molecules occupy C_s or C₁ sites. The large number of observed lattice modes is consistent with two or more molecules per primitive cell. The torsional frequency was observed at 224 cm⁻¹ and 167 cm⁻¹ in hydrogen and deuterium compounds in the solid, respectively. These frequencies gave a periodic barrier of 4.15 kcal mole⁻¹ for F₃PBH₃ and 4.31 kcal mole⁻¹ for F₃PBD₃. CNDO/2 calculations have been carried out for F₃PBH₃ and the isoelectronic F₃SiCH₃ molecule in both the staggered and eclipsed forms and the dipole and barrier origins are discussed.     

Vibrational spectroscopic studies, conformations and ab initio calculations of 3,3,3-trifluoropropyltrichlorosilane

Infrared spectra of 3,3,3-trifluoropropyltrichlorosilane (CF3CH2CH2SiCl3) were obtained in the vapour, amorphous and crystalline solid phases in the range 4000-50 cm-1. Additional spectra in argon matrices at 5.0 K were recorded before and after annealing to 20-36 K. Raman spectra of the compound as a liquid were recorded at various temperatures between 298 and 210 K and spectra of the amorphous and crystalline solids were obtained. The spectra suggested the existence of two conformers (anti and gauche) in the fluid phases and in the matrix. When the vapour was shock-frozen on a cold finger at 80 K and subsequently annealed to 120-150 K, six weak or very weak Raman bands vanished in the crystal. Similar variations were observed in the corresponding infrared spectra after annealing and four very weak IR bands disappeared after crystallization. From intensity variations between 298 and 210 K of three Raman band pairs an average value Delta(conf)H degrees (gauche-anti)=6.1+/-0.5 kJmol-1 was obtained in the liquid. Annealing experiments indicate that the anti conformer also has a lower energy in the argon matrices. The conformational equilibrium is highly shifted towards anti in the liquid, and the low energy conformer also forms the crystal. The spectra of the abundant anti conformer and the few bands ascribed to the gauche conformer have been interpreted. Ab initio calculations at the HF/6-311G(**) and B3LYP/6-311G(**) gave optimized geometries, infrared and Raman intensities and vibrational frequencies for the anti and gauche conformers. The conformational energy differences derived were 11.8 and 9.2 kJmol-1 from the HF and the B3LYP calculations, respectively.     

Effect of glycation on the structure and dynamics of DNA: a critical spectroscopic approach

Glycated DNA is considered to be a pathogenic factor for diabetes mellitus. Here we present a novel and preliminary study on normal and glycated (with fructose and glucose-6-phosphate as reducing sugars) human placenta DNA using agarose gel electrophoresis and photon correlation spectroscopy. The former is used to find structural alterations, while the latter is exploited to observe differences in the dynamics between normal (i.e., pure) and glycated DNA molecules. For scattering angles up to 90 degrees , we obtained a quasi-single-exponential relaxation process for the pure DNA, whereas at higher scattering angles the relaxation of pure DNA becomes broader with a stretching parameter beta approximately 0.6 at 130 degrees. Interestingly, for both the glycated DNAs stretched relaxation profiles and higher relaxation rates (Omega) are observed for all scattering angles. Moreover, a separate and very fast relaxation (e.g., relaxation time tau approximately 2 micros at 90 degrees ) can be noticed for both the glycated DNAs at all the studied scattering angles. Thus, the dramatic changes in the relaxation parameters (Omega, tau, and beta) of the glycated DNA show at the molecular level, for the first time, that the structure and dynamics of DNA are strongly affected by glycation. Implications of the results are discussed.     

天然产物Combretastatin A-1和Combretastatin B-1的合成

基于Perkin反应策略合成了具有强效抗肿瘤、抗血管活性的天然产物Combretastatin A-1(CA1)和Combretastatin B-1(CB1).以2,3,4-三羟基苯甲醛(1)为起始物, 经单甲基化反应得到2,3-二羟基-4-甲氧基苯甲醛(2), 再经酚羟基保护得到2,3-二异丙基-4-甲氧基苯甲醛(3), 该化合物与3,4,5-三甲氧基苯乙酸(4)发生Perkin反应分离得到E-2-(3,4,5-三甲氧基苯基)-3-(2',3'-二异丙氧基-4'-甲氧基)丙烯酸(E-5), 经脱羧反应得到Z-3,4,4',5-四甲氧基-2',3'-二异丙氧基二苯乙烯(6), 最后经脱保护反应得到CA1.另外, 将E-2-(3,4,5-三甲氧基苯基)-3-(2',3'-二异丙氧基-4'-甲氧基)丙烯酸(E-5)脱去保护基得到E-2-(3,4,5-三甲氧基苯基)-3-(2',3'-二羟基-4'-甲氧基)丙烯酸(7), 该化合物经脱羧-异构化反应得到E-3,4,4',5-四甲氧基-2',3'-二羟基二苯乙烯(E-CA1), 最后经催化氢化得到CB1.     

Vibrational spectroscopic study of rotational isomerism in O,O-dimethylphosphorodithioic acid

In this paper, the IR and Raman spectra of (CH₃O)₂P(S)SH have been studied at room temperature and at lower temperature. It is found that the P = S stretching vibrational band consists of four sub-bands, which shows that there are four rotational isomers for (CH₃O)₂P(S)SH. With the aid of computer we have separated the P=S bands and measured the relative intensities of each sub-band at different temperatures, so the relation of interconversion between isomers was obtained. Moreover, there exists intermolecular hydrogen bond in this compound, which will impede the rotation of S-H about P-S bond. Therefore, the interconversion of isomers results only from the rotation of O-CH₃ about P-O bond.     

Vibrational raman spectroscopic study of scytonemin, the UV-protective cyanobacterial pigment

The Raman spectrum of the photoprotective pigment scytonemin found in cyanobacterial sheaths has been obtained for the first time. Its skeletal structure is extensively conjugated and unique in nature. Detailed molecular vibrational assignments are proposed and a distinctive group of four corroborative vibrational bands have been identified as unique indicators for the compound. These bands, especially a prominent feature at wavenumber 1590 cm(-1), are sufficiently conspicuous to be detectable in the mixed biomolecular pools of undisturbed natural microbial communities. This has been confirmed by demonstrating the Raman spectral bands for scytonemin in a sample of an intact intertidal cyanobacterial mat.     

Vibrational spectroscopic studies of vinyltriethoxysilane sol-gel and its coating

Infrared and Raman spectra of vinyltriethoxysilane (VTES), the VTES sol-gel, and the sol-gel coated aluminum have been collected. The assignments of the vibrational modes for the silane, the sol-gel, and the sol-gel films have been made based on the group frequencies and the spectral variation collected at different physical and chemical states of the sol-gel samples. Applying the sol-gels onto the metal grids allowed the drying and the high temperature treatment of the samples for the collection of infrared transmission spectra. From the variation of the sol-gel and the sol-gel coated aluminum IR spectra with temperature, it was noticed that the samples partially decomposed when the temperature was higher than 100 degrees C. Electrochemical experiments have demonstrated that the anticorrosion property of the coated aluminum has significantly increased. The water and the hexadecane contact angle measurements showed that the surface modified metal had a much higher hydrophobic property than the untreated metal.     

Vibrational spectroscopic characterization of wild growing mushrooms and toadstools

Recently, there has been increase of general interest in fungi because of the possible medical applications of their polysaccharide constituents called glucans, some of which are reported to have immunomodulatory properties. Since an extraction method can change the chemical composition of a substance, especially a delicate one such as fungal thallus, it is necessary and useful to know more about the studied matter in advance in order to choose the chemical procedure properly. We demonstrated the usefulness of vibrational spectroscopy in identifying different glucan types in various parts of intact fruiting bodies of Asco- and Basidiomycetes. Fourier transform-infrared (FT-IR) spectroscopy was used for obtaining vibrational spectra of spores and fruiting bodies of more than 70 species belonging to 37 different genera of wild growing mushrooms. The list of the bands in 750-950 cm(-1) interval, assigned to alpha- and beta-glucans, is provided for all species studied. Vibrational spectra in the interval 1000-1200 cm(-1) could serve as an indicator of mushroom genus, although particular species cannot be identified spectroscopically. Great similarities in spectra of spores of the same genus, but different species, e.g. Tricholoma album and Trichloma sulphureum, were observed. On the other hand, spectra of cap, stalk and spores of the same mushroom show great differences, indicating variety in the chemical composition of different parts of the same fruiting body.