Raman spectroscopic studies on the conformational changes of calf thymus DNA induced by Cd~(2+) ions

We used Raman spectroscopy to study the conforniational changes of DNA induced by Cd2+ ions in different Cd2+ concentrations solution. The experimental results show that when the Cd2+/PO2- ratio R increased from 0 to 3.0, the band 835.0 cm-1 shifted about 8 cm-1, and the overlapping spectra of 1446.0 and 1461.0 cm-1 separated and moved to 1441.0 and 1458.0 cm-1, respectively. This indicates that the conformation of DNA has changed from a "normal" B-form to a "modified" B'-form. At the same time,     

Methylene blue as a DNA probe for a comparative study of Cd, Pb and Cr ions binding to calf thymus DNA

Methylene blue (MB) was developed as a sensitive DNA probe for a comparative study of Cd²⁺, Pb²⁺ and Cr³⁺ ions binding with calf thymus DNA (ctDNA). The fluorescence intensity of the MB-ctDNA system increased dramatically when heavy metal ions (Cd²⁺, Pb²⁺ and Cr³⁺ ions) were added, which indicated that some of the bound MB molecules were released from the ctDNA base pairs. To compare the binding affinity of these three different heavy metal ions with ctDNA, the relationships between the fluorescence intensity of the MB-ctDNA-M (Metal ions) system and the concentration ratio of [M]/[DNA(p)] were investigated. The results showed that the order of the binding affinity of heavy metal ions with ctDNA had the following sequence: Cr³⁺> Cd²⁺>Pb²⁺. This order was further proved by the effects of heavy metal ions on the number of MB bound to ctDNA, the measurements of binding constants of these heavy metal ions to ctDNA, and the effects of heavy metal ions on the absorption of the MB-ctDNA system. In addition, the interaction mechanisms of Cd²⁺, Pb²⁺ and Cr³⁺ ions with ctDNA were also discussed in detail. These results indicated that their interaction mechanisms are related to the concentration ratios of heavy metal ions to DNA.     

Raman spectroscopic study of calf thymus DNA: an effect of proton‐ and γ‐irradiation

Raman spectroscopy was applied to analyse structural changes in calf thymus double‐stranded deoxyribonucleic acid (dsDNA) after proton‐ and γ‐irradiation (0.5, 5 and 50 Gy). Characteristic Raman bands of phosphodiester linkages, nucleic bases and deoxyribose moieties were sensitive to irradiation. A significant damage of the macromolecules was observed only at the highest dose (50 Gy) of both types of radiations. Spectral changes confirmed a radiation‐induced alteration of the native structure of dsDNA. Nucleic bases, especially pyrimidines, were the most sensitive to radiation, while some alterations in the sugar–phosphate backbone were also detected. The differences in the dose‐dependent effects of proton vs γ‐irradiation on studied biomolecule are discussed. Copyright © 2007 John Wiley & Sons, Ltd.     

ATR-FTIR spectroscopic studies on density changes of fused silica induced by localized CO2 laser treatment

The surface density changes of the central region of the sites treated by using the CO_2 laser-based non-evaporative damage mitigation for fused silica are investigated by attenuated total reflectance-Fourier transform infrared spectroscopy(ATR-FTIR).The ATR-FTIR peak shifts of the treated sites of fused silica are monitored to determine the changes of the corresponding density.For the quenching treated sites,the surface density is increased by(0.24±0.01)%compared with the initial density but the laser annealing by the exposure of a power ramp down after damage mitigation effectively suppresses the structural changes of treated sites,which could reduce the increase of the corresponding density to(0.08±0.01)%.The results provide sufficient evidence that the laser annealing by a power ramp down after damage mitigation has a positive effect on the control of the structural change induced by CO_2 laser-based damage mitigation.     

Raman spectroscopic studies of pulsed laser‐induced defect evolution in graphene

Raman spectra were obtained for graphene after irradiating the samples by pulsed laser (λ = 248 nm). Changes in the spectra were observed as the pulse laser energy density (PLED) was varied from 0.1 to 0.25 J/cm². Changes in bilayer graphene were accompanied by the appearance of the D peak and the broadening of the G peak. Changes in multilayer graphene are more profound as the Raman spectra changes from a multilayer to bilayer and subsequently to monolayer graphene in response to a slow increase in the PLED. The threshold PLED was found to be dependent on the number of graphene layers. We also irradiate graphene with very high PLED (much above the threshold), and the Raman spectra were found to be significantly changed. The G‐band became broader, and red shifted, while the intensity of the 2D‐band was drastically reduced and an intense defect‐related D peak appeared at about 1350 cm⁻¹. The laser ablation of graphene, both with low‐ and high‐energy intensity, is consistent with the reported theoretical predictions. Copyright © 2013 John Wiley & Sons, Ltd.     

High-pressure Raman and infrared spectroscopic studies of ZrP2O7

High-pressure Raman and mid-infrared spectroscopic studies were carried out on ZrP₂O₇ to 23.2 and 13 GPa respectively. In the pressure range 0.7–4.3 GPa the lattice mode at 248 cm^?1 disappears, new modes appear around 380 and 1111 cm^?1 and the strong symmetric stretching mode at 476 cm^?1 softens, possibly indicating a subtle phase transition. Above 8 GPa all the modes broaden, and all of the Raman modes disappear beyond 18 GPa. On decompression from the highest pressure, 23.2, to 0 GPa all of the modes reappear but with larger full width at half maximum. Lattice dynamics of the high temperature phase of ZrP₂O₇ were studied using first principles method and compared with experimental values.     

Dissociation of 14N2+ ions induced by slow electrons

The cross sections and thermal rate coefficients for the dissociative recombination (DR) of the molecular nitrogen ions initially in the first four vibrational levels of the ground electronic state have been computed in the framework of the multichannel quantum defect theory. An energy range of 0.001–1 eV has been considered. The contribution of the indirect DR mechanism involving Rydberg states associated with the first excited ion core has also been investigated.     

Phase transitions of Decylammonium chloride by Raman and infrared spectroscopic studies

Raman scattering and infrared absorption were used to study phase transition between a non intercalated structure and an intercalated one in Decylammonium chloride C₁₀H₂₁NH₃Cl, in the temperature range from 79 to 370 K and to determine the transition temperature. The melting of the chains seems to be the cause of the transition. Unusual splitting of some vibration modes help us to characterize the intercalated structure. The entering of air into the structure seems to be at the origin of the discrepancy that appears in the experimental results.     

Dependence of surface-enhanced Raman scattering from Calf thymus DNA on anions

Dependence of surface-enhanced Raman scattering (SERS) from Calf thymus DNA on anions is investigated.With the silver colloid,the bands at 732,960 and 1333 cm-1 for adenine (A),1466 cm-1 for deoxyribose,and 1652 cm-1 for the C=O group of thymine (T) are observably enhanced.With the presence of the Cl- or SO42- anions,the bands at 732 and 1326/1329 cm-1 for the symmetric stretching and skeletal vibrational modes of adenine (A) are dramatically enhanced,and the enhancement effect with the SO24- ion is more than that with the Cl- ion.The experimental results show that the DNA molecule can be adsorbed on the silver colloid particles through the C6N and N7 of adenine (A),the C=O of thymine (T) and deoxyribose.Moreover,the formed hydrogen bonding of the Cl- or S2O4- ions to the C6NH2 group of adenine (A) can induce larger C6N electronegativity,which is favor for the C6N/N7 cooperative adsorption on the (Ag) n colloid particles.     

Raman spectroscopic study of the phase transitions induced by hydrostatic pressure in a Rb2KScF6 crystal

The Raman spectra of Rb₂KScF₆ elpasolite crystals are studied in the pressure range up to 7 GPa. A phase transition is revealed at a pressure of approximately 1 GPa. Analysis of the changes in the spectral parameters shows that the phase transition is accompanied by a doubling of the volume of the primitive cell in the initial cubic phase. Judging from the character of the variations in the pressure dependences of the frequency of the observed vibrations, there can exist another transition to the phase with a lower symmetry at a pressure of approximately 2.1 GPa.     

Monitoring by Raman spectroscopy of the damage induced in the wake of energetic ions

This article reports micro‐Raman experiments performed on cross sections of 6H‐SiC crystals irradiated with heavy ions of different energies. The results demonstrate that this technique is very powerful to quantify the damage created in the wake of energetic ions from the surface of samples down to the ion resting position. For slow ions (900‐keV I), ballistic collisions lead to the amorphization of the surface region of samples. For swift ions (36‐MeV W), the surface region remains crystalline and amorphization occurs around the end of the ion path. Moreover, synergistic effects between electronic and nuclear slowing down processes are put forward. The methodology used in this work may be adapted to other materials where radiation effects need to be investigated, provided that the damage created by irradiation is detectable by Raman spectroscopy. Copyright © 2014 John Wiley & Sons, Ltd.     

Raman and surface‐enhanced Raman spectroscopic studies of the 15‐mer DNA thrombin‐binding aptamer

Aptamers are single‐stranded oligonucleotides that selectively bind to their target molecules owing to their ability to form secondary structures and shapes. The 15‐mer (5′‐GGTTGGTGTGGTTGG‐3′) DNA thrombin‐binding aptamer (TBA) binds to thrombin following the formation of a quadruplex structure via the Hoogsten‐type G–G interactions. In the present study, Raman and SERS spectra of TBA and thiolated TBA (used to facilitate covalent bonding to metal nanoparticle) in different conditions are investigated. The spectra of the two analogs exhibit vibrations, such as the C8N7 H2 deformation band at ∼1480 cm⁻¹ of the guanine tetrad, that are characteristic of the quadruplex structure in the presence of K⁺ ions or at low temperature. Interestingly, SERS spectra of the two analogs differ markedly from their respective normal Raman spectra, possibly due to changes in the conformation of the aptamer upon binding, as well as to the specific interaction of individual vibrational modes with the metal surface. In addition, the SERS spectra of the thiolated aptamer show significant changes with different concentrations, which may be due to different orientation of the molecule with respect to the metal surface. This study provides useful information for the development of label‐free aptamer‐based SERS sensors and assays. Copyright © 2009 John Wiley & Sons, Ltd.     

Raman and X‐ray investigations of the incorporation of Ca2+ and Cd2+ in the ZrO2 structure

The formation of solid solution and ZrO₂ phase stabilization were investigated by Raman spectroscopy and X‐ray diffraction (XRD) in calcium‐containing and cadmium‐containing zirconium oxide samples heated at 1073 K in air. The adopted preparation procedure led to the incorporation of calcium and cadmium in solid solution into the zirconia structure. The solid solution favored the tetragonal and cubic zirconia phases at the expense of the thermodynamically stable monoclinic modification. Combined macro‐ and micro‐Raman spectroscopy disclosed that instead of forming a homogeneous phase t″, intermediate between the tetragonal t′ and the cubic phase, the tetragonal and cubic phases coexisted in the range 9.49–13.89 mol% for Ca and 11.88–17.23 mol% for Cd. At higher dopant contents the cubic form stabilized. The impurity content necessary to stabilize the high‐symmetry phases was defined. Copyright © 2007 John Wiley & Sons, Ltd.     

MD studies on conformational behavior of a DNA photolyase enzyme

In this work, molecular dynamics (MD) simulations were performed on a DNA photolyase protein with two cofactors, FAD (flavin adenine dinucleotide) and MTHF (methenyltetrahydrofolate), inside the enzyme pocket. A DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane-pyrimidine dimer in damaged DNA. We were aimed to compare the conformational changes of the FAD cofactor and other constituent fragments of the molecular system under consideration. The conformational behavior of the FAD molecule is very important for understanding the functional and structural properties of the DNA repair protein photolyase. The photoactive FAD is an essential cofactor both for specificial binding to damaged DNA and for catalysis. The second chromophore (MTHF or 8-HDF) is not necessary for catalysis and has no effect on specific enzyme—substrate binding. The obtained results were discussed to gain insight into the light-driven mechanism of DNA repair by a DNA photolyase enzyme—based on the enzyme structure, the FAD mobility, and conformation shape.     

Ion beam induced luminescence studies of LiAlO2 using negative ions

Lithium aluminate (LiAlO₂) is the candidate material for solid tritium breeder applied in the developing fusion reactors. The research of its defect behavior under ion irradiation was proceeded in the negative ions induced luminescence setup of the GIC4117 Tandem accelerator in Beijing Normal University. The ion beam induced luminescence (IBIL) measurement was performed by 20 keV H⁻ ions at room temperature. The luminescence spectra showed seven emission bands: the 4.55 eV may due to a self-trapped exciton (STE), the 4.06 eV and the 1.72 eV may due to impurity or intrinsic defect, the 3.54 eV due to F center, the 3.20 eV due to F⁺ center, the 2.93 eV due to F₂ center, the 2.30 eV due to F-center aggregates (F_n center), respectively. The intensity evolutions of each band with fluence were presented and the corresponding mechanisms were discussed.     

Na离子和Cl离子引起He原子直接多重电离过程的研究

利用2～8 MeV的Naq+、Clq+(q=2,3,4,5)轰击氦原子,对碰撞的直接多重电离过程进行研究.实验采用反冲离子-散射离子飞行时间符合技术,通过反冲离子飞行时间谱区分不同价态反冲离子;利用静电偏转和位置灵敏探测技术区分不同电荷态散射离子;结合CAMAC-PC多参数获取系统得到一定价态散射离子所对应的反冲离子电荷态分布谱;经分析该谱得到直接多重电离截面与直接单电离截面之比R21.讨论了R21随入射离子速度和电荷态的变化关系.     

EPR studies of Cu2+ and V4+ ions in phosphate glasses

Two lead-phosphate glass systems doped with both copper and vanadium ions in different ratios were studied by EPR (electron paramagnetic resonance) method. EPR spectra and parameters (g_‖ = 2.44, g_⊥ = 2.08 andA _‖ = 117.6 · 10⁻⁴ cm⁻¹) obtained for x(CuO · V₂O₅)(l−x)[2P₂O₅ · PbO] glasses withx ≤ 10 mol% suggest a tetrahedral (Td) coordination of Cu²⁺ ions and not a tetragonally elongated octahedron as has been assumed in previous works. The ground state of the paramagnetic electron is thed _xy copper orbital with a 4p_z contribution of 6%. For 20 ≤x ≤ 40 mol% a broad line (ΔB = 307 G) characteristic for clustered ions appears atg = 2.18. The V⁴⁺ ions are evidenced only in the spectra of x(CuO · 2V₂O₅)(1 −x)[2P₂O₅ · PbO] glasses and the resonance parameters suggest a pentacoordinated C_4v local symmetry for these ions. The hyperfine structures characteristic for Cu²⁺ and V⁴⁺ ions disappear for 10 ≤x ≤ 40 mol% due to the mixed exchange Cu²⁺−V⁴⁺ pair formation in these glasses.     

The substitution of Fe2+ ions by Ni2+ ions in green rust one compounds

The oxidation of Fe(OH)₂ in the presence of Cl^– or CO ₃ ^2– ions leads, in the first stage of the reaction, to chloride-containing green rust one (GR1), 3Fe(OH)₂· Fe(OH)₂Cl·nH₂O, or carbonate-containing GR1, 4Fe(OH)₂·Fe₂(OH)₄CO₃·nH₂O, respectively. These GR1 compounds give the ferric oxyhydroxides by further oxidation. If a hydroxide Ni _x Fe_1–x (OH)₂ is initially precipitated, the reaction leads to a nickelous-ferric compound isomorphous to the ferrous-ferric GR1, but stable with respect to the oxidizing action of air. Similarly, the oxidation of a nickelous-ferrous hydroxide, in the presence of excess OH^– ions, leads to a nickelous-ferric GR1, a layered hydroxide with anionic interlayers made of OH^– ions and water molecules. The Mössbauer spectra of these nickelousferric GR1 display two ferric doublets, D₀ withIS=0.34 mm/s andQS=0.45 mm/s and D₁ withIS=0.36 mm/s andQS=0.86 mm/s. The existence of a ferrous-ferric GR1 incorporating OH^– ions, a compound never observed so far, is strongly suspected.