Theory of electronic structure and nuclear quadrupole interactions in the BF3–NH3 complex and methyl derivatives

Magnetic Hyperfine and Nuclear Quadrupole Interactions (HFI and NQI) are now important tools for characterization of systems of interest in materials research and industry. Boron-Trifluoride is an inorganic compound that is very important in this respect as a catalyst in chemical physics research and industry, forming complexes in the process with compounds like ammonia, water and methyl alcohol. The present paper deals with the BF₃–NH₃ complex and methyl derivatives BF₃NH_x(CH₃)_3?x for which we have studied the electronic structures, binding energies, and ¹⁹F* (I?=?5/2) nuclear quadrupole interactions using the first-principles Hartree–Fock–Roothaan procedure combined with electron correlation effects. Our results for the ¹⁹F* nuclear quadrupole coupling constant (e ² qQ/h) in units of MHz compare well with experiment. Trends in the binding energies and NQI parameters between the complexes are discussed.     

HCCCH Experiment for Through-Bond Correlation of Thymine Resonances inC-Labeled DNA Oligonucleotides

Application of heteronuclear magnetic resonance pulse methods to¹³C,¹⁵N-labeled nucleic acids is important for the accurate structure determination of larger RNA and DNA oligonucleotides and protein–nucleic acid complexes. These methods have been applied primarily to RNA, due to the availability of labeled samples. The two major differences between DNA and RNA are at the C2′ of the ribose and deoxyribose and the additional methyl group on thymine versus uracil. We have enzymatically synthesized a¹³C,¹⁵N-labeled 32 base DNA oligonucleotide that folds to form an intramolecular triplex. We present two- and three-dimensional versions of a new HCCCH–TOCSY experiment that provides intraresidue correlation between the thymine H6 and methyl resonances via the intervening carbons (H6–C6–C5–Cme–Hme).     

Nuclear quadrupole interaction at133Ba (EC)133Cs in Eu1Ba2Cu3O7−°

We studied the nuclear quadrupole interaction (NQI) at¹³³Ba(EC)¹³³Cs in Eu₁Ba₂Cu₃O_7–6 by time differential perturbed angular correlation between 11 K and 300 K. No anomalies in the NQI parameters around T_c were detected. All Ba sites appear to be identical and the precession frequency is ω=80(2) Mrad/s (assuming axial symmetry), independent of temperature.     

The equilibrium and kinetics of intermolecular hydrogen bonding in nitroarene anion radical–alcohol system: 1,3‐dinitro‐benzene anion radical – R–OH (R═CH3–, C2H5–, (CH3)2 CH–)

To explore the possibility of hydrogen bonding of a stable anion radical with DNA – component sugar, hormones, steroid, and so on (through hydroxyl group), as a first step, the possibility of hydrogen bonding of 1,3‐dinitrobenzene anion radical (1,3‐DNB^??) with aliphatic alcohols was studied. It was found that 1,3‐DNB^?? anion radical undergoes hydrogen bonding with alcohols: methanol, ethanol, and 2‐proponal. The hydrogen‐bonding equilibrium constant K_eq and the (hydrogen‐bonding) rate constants k₂ were evaluated through the use of linear scan and cyclic voltammetry theory and techniques. The K_eq was found to be in the range of 1.4–6.0 m ^?1, whereas the rate constants k₂ were found to be in the range of 1.5–3.6 m ^?1 s^?1, depending upon the hydrogen‐bonding agent and the equation used for the calculation of the rate constants. The hydrogen‐bonding number n was found to be around 0.5 or 1.0. The implication of this study in, for example, the replication of DNA, the prevention of the formation of super oxide, and so on is discussed. Copyright © 2012 John Wiley & Sons, Ltd.     

四氯苯醌与嘧啶类核酸碱基的光化学氢抽取和电子转移反应

采用纳秒时间分辨的激光闪光光解实验技术,研究了四氯苯醌(TCBQ)分子与两种嘧啶核酸碱基(胸腺嘧啶和尿嘧啶)分子在355nm激发下的光化学反应动力学. 355 nm将TCBQ分子布居到激发三重态³TCBQ^*,高反应活性的³TCBQ^*与碱基分子发生两个平行的反应,氢抽取反应和电子转移反应,分别对应生成瞬态光谱上观测到的两个光反应产物TCBQH·和TCBQ·^-. 这两个反应同时生成的碱基自由基和碱基阳     

Spectroscopic Study on the Interaction of Pyronine Y with Nucleic Acids and Its Analytical Application

ABSTRACT

The interaction of pyronine Y (PY) with nucleic acids was studied by resonance Rayleigh scattering (RRS) for nucleic acid detection. The enhanced RRS intensity of nucleic acids reacted with PY was proportional to the concentration of nucleic acids in the ranges of 27.0–625 ng ml^?1 for fish sperm DNA, 39.0–500 ng ml^?1 for calf thymus DNA, and 59.0–375 ng ml^?1 for yeast RNA. The limits of determination were 0.2 ng ml^?1 for fish sperm DNA, 0.6 ng ml^?1 for calf thymus DNA, and 0.7 ng ml^?1 for yeast RNA. The method had been successfully applied to the quick determination of nucleic acids in synthetic and natural samples.     

Determination of Nucleic Acids Sensitized by Emulsifier OP‐micelle Using Ethyl Rhodamine B as a Resonance Light‐Scattering Probe

Abstract

The resonance light scattering (RLS) spectra of ethyl rhodamine B with nucleic acid (calf thymus DNA and herring sperm DNA) have been studied. The effective factors and the optimum conditions have been studied, and the enhanced intensity of RLS is in proportion to the concentration of nucleic acids in the range 0～5.00 µg mL^?1 for calf thymus DNA (ctDNA) and 0～3.50 µg mL^?1 for herring sperm DNA (hsDNA). The limits of detection are 3.42 and 3.14 ng mL^?1, respectively. Based on this, a RLS method for the determination of nucleic acids sensitized by emulsifier OP‐micelle was accordingly established. The binding mode concerning the interactions of ethyl rhodamine B with nucleic acids was also studied, and this method has good selectivity and high sensitivity and it has been applied to the determination of DNA in synthetic samples and real samples with satisfactory results.     

Electrochemical methods for determination of thymine in medical pipefish samples based on HPMαFP/Ppy/GCE-modified electrode

A sensitive electrochemical method was developed for the voltammetric determination of thymine at a composite film-modified electrode 1-phenyl-3-methyl-4-(2-furoyl)-5-pyrazolone (HPMαFP)/polypyrrole (Ppy)/glassy carbon electrode (GCE). The electrochemical parameters of thymine were investigated by cyclic voltammetry and differential pulse voltammetry. In pH?=?7.4, one sensitive oxidation peak of thymine with E _pa?=?0.968 V was observed on the HPMαFP/PPy-modified electrode. The difference of peak potential (?E _pa) was 188 mV lower than that for bare GCE. Compared to the bare GCE and Ppy/GCE, the HPMαFP/Ppy/GCE-modified electrode showed an excellent electrocatalytic effect on the oxidation of thymine and displayed a shift of the oxidation potential in the negative direction with significant increase in the peak current. Under the optimum condition, the concentration calibration range and detection limit are 2?×?10^?6–1?×?10^?4 and 4.85?×?10^?7?M for thymine. This developed method had been applied to the direct determination of thymine in medical pipefish samples with satisfactory results.     

银岛膜表面胸腺嘧啶吸附行为的表面增强拉曼光谱和表面增强红外光谱研究

利用激光刻蚀法制备了具有化学纯净表面的银岛膜,该岛膜有很好的表面增强特性。利用表面增强拉曼光谱和表面增强红外光谱对胸腺嘧啶分子在银岛膜表面的吸附状态进行了对比研究。表面增强拉曼光谱中CN和C—O伸缩振动模式的出现表明胸腺嘧啶分子由原来的酮式结构变成了烯醇式结构;C(4)O伸缩振动谱带明显增强和N(3)的去质子化异构体特征峰的存在证明胸腺嘧啶分子是通过O(8)和N(3)的共同作用倾斜地吸附在银岛膜表面。对10-5 mol.L-1胸腺嘧啶在银岛膜表面上的红外光谱利用欧米采样器进行了反射法测量,发现其红外吸收增强了200倍。红外信号分析的结果支持了胸腺嘧啶分子通过O(8)与银表面发生相互作用的论断,同时也可得出胸腺嘧啶倾斜地吸附在银岛膜表面的结论。     

Supramolecular Polymeric Chemosensor for Biomedical Applications: Design and Synthesis of a Luminescent Zinc Metallopolymer as a Chemosensor for Adenine Detection

Adenine is an important bio-molecule that plays many crucial roles in food safety and biomedical diagnostics. Differentiating adenine from a mixture of adenosine and other nucleic bases (guanine, thymine, cytosine, and uracil) is particularly important for both biological and clinical applications. A neutral Zn^II metallosupramolecular polymer based on acyl hydrazone derived coordination centres (P1) were generated through self-assembly polymerization. It is a linear coordination polymer that behaves like self-standing film. The synthesis, ¹H-NMR characterization, and spectroscopic properties of this supramolecular material are reported. P1 was found to be a chemosensor specific to adenine, with a luminescent enhancement. The binding properties of P1 with common nucleic bases and nucleosides reveal that this supramolecular polymer is very selective to adenine molecules (~20 to 420 times more selectivity than other nucleic bases). The formation constant (K) of P1 to adenine was found to be log K?=?4.10?±?0.02. This polymeric chemosensor produces a specific response to adenine down to 90?ppb. Spectrofluorimetric and ¹H-NMR titration studies showed that the P1 polymer allows each Zn^II coordination centre to bind to two adenine molecules through hydrogen bonding with their imine and hydrazone protons.     

In-vivo study of the nuclear quadrupole interaction of99Mo (β- 99)Tc in nitrogenase of Klebsiella pneumoniaein nitrogenase of Klebsiella pneumoniae

We report on the first TDPAC-measurements of the nuclear quadrupole interaction (NQI) of (NQI) of⁹⁹Mo(β^-)⁹⁹Tc in the nitrogenase of the bacteria Klebsiella pneumoniae. Because nitrogenase is the only Mo-containing enzyme in Klebsiella pneumoniae under the chosen conditions, no further isolation of this enzyme was necessary. The majority of the incorporated⁹⁹Mo is subjected to a well defined NQI with ω=365(7) Mrad/s, η=1 and a reorientational correlation time of τ_coττ≈10nsec and is attributed to the active site of the FeMo cofactor. During sample preparation we noted a pronounced affinity of the bacteria to^99mTc.     

Formation of positive and negative ions of thymine molecules under the action of slow electrons

The formation of positive and negative molecules of thymine—a base of nucleic acids—under the action of slow electrons is investigated by the method of crossed electron and molecular beams. The method developed makes it possible to measure the molecular beam intensity and determine the energy dependences and absolute values of total cross sections for the formation of positive and negative ions of thymine molecules. It is found that the maximal cross section for the formation of positive ions is reached at an energy of 95 eV and its absolute value is, accordingly, 1.4 × 10^?15 cm². The total cross section for the formation of negative ions is 8.2 × 10^–18 cm² at an energy of 1.1 eV. The mass spectra of thymine molecules are measured and the cross sections of dissociative ionization are determined.     

Racah and Judd-Ofelt parameters for Pr3+, Nd3+, and Er3+ ions in a laser liquid

The values of the Slater-Condon (F₂, F₄, F₆), Racah (E¹, E², E³) and Lande ξ₄f coefficients the nephelauxetic ratio (β), the bonding parameter (σ), and the Judd-Ofelt intensity (T_λ) parameters have been calculated from the reported absorption spectra of Pr³⁺, Nd³⁺, and Er³⁺ ions in an aprotic solvent SeOCl₂ acidified with antimony pentachloride. The nature of the bonding is suggested to be covalent for praseodymium, neodymium and erbium ions in the laser liquid in view of the magnitude of the respective bonding parameters.     

Modifications Induced by UV-Vis Irradiation on DNA Extract of Kiwifruit Investigated by Spectroscopic and Statistic Methods

ABSTRACT

Revealing molecular alterations induced on kiwifruit under UV-Vis irradiation requires a discussion of biochemical-cell infrared (IR) fingerprint (900 cm^?1–1800 cm^?1) bands characteristic of nucleic acids. FTIR-ATR spectroscopy and statistics and nondestructive methods for screening exposure effects induced by irradiation were used. There the irradiation influence on the main molecular bonds (i.e., ν(C-C), ν_s(PO₂?) and ν_as(PO₂?)) can be observed. Regression methods were used for statistical investigations. Two categories of variables were used: the absorbance measured at fixed wavenumber variables and the exposure dose. The bivariate correlations, partial correlations, and polynomial regression methods from SPSS were used for statistical investigations. The obtained results show that FTIR-ATR, in correlation with statistics techniques, might be useful to assess immediate radiation and oxidative-induced damage to nucleic acids. In this case IR spectroscopy can be used successfully to study conformational changes during DNA reversible denaturation especially on the sugar-phosphate vibrations domain.     

Interaction of ethidium bromide and caffeine with DNA in aqueous solution

Two component (ethidium bromide–caffeine, ethidium bromide–DNA) and three component (ethidium bromide–caffeine–DNA) systems in aqueous saline (0.01 M NaCl) phosphate buffer solutions (pH 6.86, T = 298 K) are studied spectrophotometrically. The equilibrium constants for dimerization of caffeine, K _D  = 1.22 ± 2 M⁻¹, and for heteroassociation of ethidium bromide with caffeine, K = 71 ± 8 M⁻¹, in ethidium bromide–caffeine systems are determined. When the concentration of caffeine is increased, the dynamic equilibrium of the solution shifts toward formation of heterocomplexes which are, presumably, stabilized by dispersive and hydrophobic interactions of chromophores. The equilibrium parameters for ethidium bromide complex formation with DNA are calculated: the coupling constant for the dye with the biopolymer, K ₁ = (232 ± 16)⋅103 M⁻¹, and the number of base pairs of the biopolymer participating in bonding with the ligand, n ₁ = 3.6 ± 0.2, are calculated. Given these values, it is suggested that under these experimental conditions there are two types of bonding between ethidium bromide and the nucleic acid — intercalation and “external” bonds. A McGhee–von Hippel model for a three component system and the numerical values of the parameters for molecular complex formation in two component systems are used to calculate the bonding constant for caffeine with DNA, K ₂ = 127 ± 30 M⁻¹, and the number of base pairs of DNA which bond with caffeine, n ₂ = 1.7 ± 0.2. The concentrations of ethidium bromide and caffeine in the composition of two and three component complexes are calculated as functions of the nucleic acid content in the solution. An analysis of the concentration dependences shows that heteroassociation of ligands has a significant effect on the reduction in the concentration of ethidium bromide–DNA complexes in a three component system for low DNA concentrations, while at high DNA concentrations the bonding of caffeine with the biopolymer has this effect. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 76, No. 1, pp. 143–151, January–February 2009.     

ESR and optical absorption spectra of Cu2+ in LiKSO4

ESR spectra of Cu²⁺ in LiKSO₄ have been studied at different temperatures. The measured g-values suggest a rhombic field for Cu²⁺ ion in the lattice. Optical absorption spectra of the crystal have been studied at room and liquid nitrogen temperatures. From the nature and position of the observed bands, they have been attributed to Cu²⁺ ions in D_2h symmetry. The orbital reduction parameters obtained indicate a substantial degree of covalency in the bonding of the copper ion.     

Vibrational Spectroscopic and Theoretical Studies of Urea Derivatives with Biochemical Interest: N,N′-Dimethylurea,N,N,N′,N′-Tetramethylurea,and N,N′-Dimethylpropyleneurea

Abstract

Mid-infrared, far-infrared, and Raman vibrational spectroscopic studies were combined with density functional theory (DFT) calculations and normal coordinate force field analyses for N,N′-dimethylurea (DMU), N,N,N′,N′-tetramethylurea (TMU), and N,N′-dimethylpropyleneurea (DMPU: IUPAC name 1,3-dimethyltetrahydropyrimidin-2(1H)-one). The equilibrium molecular geometry of DMU (all three conformers), TMU, and DMPU and the frequencies, intensities, and depolarization ratios of their fundamental infrared (IR) and Raman vibrational transitions were obtained by DFT calculations. The vibrational spectra were fully analyzed by normal coordinate methods as well. A starting force field for DMPU was obtained by adapting corresponding force constants for DMU and TMU, resulting after refinements in the stretching force constants C=O (7.69, 7.30, 7.68 N·cm^?1), C–N (5.16, 5.55, 5.05 N·cm^?1), and C-Me (5.93, 4.00, 4.22 N·cm^?1) for DMU, TMU, and DMPU, respectively. The dominating conformer of liquid DMU was identified as trans-trans, strong intermolecular hydrogen bonding was verified in solid DMU, and weak dipole–dipole association was found in liquid TMU and in DMPU. Special attention was paid to analyzing the methyl group frequencies, which revealed deviations from local C_3v symmetry. A linear correlation was found between the CH stretching force constants and the inverse of the CH bond lengths (1/r ²). The averaged NH stretching frequencies of gaseous, dissolved, and solid urea and of DMU, with variations for hydrogen bonding of different strength, are linearly correlated to the NH stretching force constants. Characteristic skeletal vibrations were assigned for a broad variety of urea derivatives and also for pyrimidine derivatives, which all contain the N₂C=O entity. The very strong IR bands of C=O stretching (1,676 ± 40 cm^?1) and asymmetric CN₂ stretching (1,478 ± 60 cm^?1), and the very intense Raman feature of symmetric CN₂ stretching or ring breathing (757 ± 80 cm^?1), can be recognized as fingerprint bands also for the pyrimidine derivatives cytosine, thymine, and uracil, which all are nucleobases in DNA and RNA nucleotides.     

EPR and optical absorption studies on VO ions in zinc lactate trihydrate

EPR and optical absorption studies of VO²⁺-doped zinc lactate trihydrate single crystals are done at room temperature. The EPR spectra of VO²⁺ are characteristic of tetragonally compressed octahedral site. The angular variation of the EPR spectra shows single site occupying interstitial position in the lattice. The spin Hamiltonian parameters are evaluated as g_x=1.9771, g_y=2.0229, g_z=1.9236 and A_x=76, A_y=104, A_z=197 (×10⁻⁴) cm⁻¹. Using these parameters and optical absorption data various bonding parameters are determined and the nature of bonding in the complex is discussed.     

Superposition model (SPM) analysis of zero-field splitting parameters of Mn doped ZnAl2S4 crystal

In this study, superposition model (SPM) is employed to investigate the local environment around the different Mn²⁺ centers in ZnAl₂S₄ spinel. Using SPM and crystallographic data, the zero-field splitting (ZFS) parameters b₂⁰, b₄⁰, and b₄³ are calculated for Mn²⁺ at the B-site (with local symmetry D_3d), whereas b₄⁰ and b₄⁴ for the A-site (T_d). The lattice relaxation due to Mn²⁺ impurities is analyzed in terms of the bonding lengths and the angles between the Mn-S bond and the crystallographic axis [1 1 1]. Our SPM analysis of ZFS parameters indicates that satisfactory agreement can be achieved between the theoretical and the experimental results. Additional structural information about Mn²⁺ impurity centers is also obtained.     

TDPAC studies of111mCd in calciproteins: Calmodulin and parvalbumin

TDPAC measurements of the 150–247 keV gamma-ray cascade in¹¹¹Cd have been performed at room temperature on Calmodulin (CaM) and Parvalbumin (Pa) labelled with radioactive^111mCd. The anisotropy of the coincidence counting rate shows a time-dependent behaviour, typical of two different nuclear quadrupole interactions (NQI) in CaM. The NQI parameters indicate the presence of two distinct metal-binding sites, presenting non-equivalent local electric charge structure. In Pa samples, only one NQI is observed and the measured electric field gradient (EFG) value agrees well with the large one obtained in CaM.