Photochemistry of tobacco mosaic virus RNA. Effect of HCN

Abstract— In attempting to sort out possible mechanisms of photoreactivation of tobacco mosaic virus RNA (TMV-RNA) inactivated by ultraviolet radiation (u.v.) in buffer of ionic strength 0.25, we have investigated the effect of HCN on the quantum yield for u.v. inactivation of TMV-RNA and on the percent photoreactivation of inactivated TMV-RNA. Some photo-products produced by irradiation of model substances, polyuridylic acid (poly U) and polycytidylic acid (poly C), in the presence of HCN have also been studied. The ratio of the quantum yield for inactivation of TMV-RNA in the presence of HCN to that in the absence of HCN is 1.5, under non-photoreactivating conditions. By comparison, the ratio of the initial rates of loss of uracil residues in poly U under comparable conditions is 1.6; by contrast, the rate of loss of cytosine residues in poly C is unaffected by HCN. This similarity of ratios between poly U and TMV-RNA suggests that two of the mechanisms of u.v. inactivation of TMV-RNA at high ionic strength are akin to known reactions of uracil residues in poly U, i.e. hydrate and dimer formation. The photohydration reaction in poly U, as measured by the heat reversal of hydrated residues to uracil residues, is almost abolished by HCN, and the rate of dimerization, as measured by the appearance of dimer containing oligonucleotides following enzymatic hydrolysis of irradiated poly U, is reduced to half by HCN. HCN does not affect the rate of hydration of cytosine residues in poly C. Since photoreactivation of RNA inactivated in presence of HCN is only 60 per cent of that in absence of HCN it is suggested that uracil dimers are somehow involved in photoreactivation of TMV-RNA inactivated at high ionic strength.     

Raman and DFT study of static,dynamic interactions and isotope effect in pyridazine + H2O/D2O systems

Polarized Raman and density functional theory (DFT) approach have been applied to study the static and dynamic properties of pyridazine (PRD) in H₂O(W) and D₂O(D) environment. The possible hydrogen bonded (HB) complexes of PRD with H₂O in gas phase and in the water solvation (using IEF-PCM and Onsager models) have been calculated using a B3LYP functional and 6-31+G(d,p)/6-311++G(d,p) basis sets. The static interaction in the PRD + H₂O complex leads to a blue shift in all the Raman modes of PRD and red shift in the O–H modes of water. The IEF-PCM solvation model gives the Raman wavenumbers closest to the experimental values. Raman spectra of ～962 and 1061 cm^?1 mode of PRD in the mixture of PRD + H₂O and PRD + D₂O at different mole fractions of PRD (x) have been measured. A difference in the wavenumber shift of the two modes of PRD is observed experimentally when PRD is diluted with H₂O and D₂O. The wavenumber shift at maximum dilution (x = 0.1), however, takes the same value in both H₂O and D₂O. In view of the similar chemical properties of H₂O and D₂O, the difference in the trend of the wavenumber shift is not trivial. It has been explained on the basis of relative values of dipole moments of H₂O, D₂O, and conjugated molecules of PRD with H₂O/D₂O calculated theoretically and the role of larger diffusive property of H₂O compared to D₂O. The dynamical process in the mixture of PRD+ H₂O/D₂O is discussed by studying the variation of the linewidth with concentration. A theoretical model, which is based on the fact that the concentration in microscopic volume fluctuates, fits the experimental results nicely.     

Ultraviolet irradiation of tobacco leaves: inhibition of tobacco mosaic virus-ribonucleic acid photoreactivation

Abstract— Short-wave (254-nm) ultraviolet irradiation of the leaves of Nicotiana tabacum var. Xanthi, n.c. inhibits their ability to photoreactivate ultraviolet-inactivated tobacco mosaic virus ribonucleic acid (TMV-RNA). The inhibition is stable in the dark; however, subsequent illumination of the leaves relaxes the inhibition. The spectral region most effective in relaxing the inhibition is the same one effective in photoreactivation. These results are consistent with the hypothesis that ultraviolet-induced lesions in cellular nucleic acids in the dark form stable complexes with agents responsible for the photoreactivation of TMV-RNA (effectively isolating the agents from the TMV-RNA) and that upon illumination these complexes dissociate (presumably with repair of the lesions). We therefore suggest that the system which photoreactivates ultraviolet-damaged TMV-RNA also photorepairs ultraviolet damage in cellular nucleic acids.     

Probing Deuterium Isotope Effect on Structure and Solvation Dynamics of Human Serum Albumin

The deuterium isotopic effect on the structure and solvation dynamics of the protein, human serum albumin (HSA), has been studied by using circular dichroism (CD), femtosecond up‐conversion, FRET, and single‐molecule spectroscopy. The CD spectra suggest that D₂O affects the structure of HSA, leading to a 20 % decrease in the helical structure. The FRET study indicates that the distance of C153 from the lone tryptophan residue of HSA is quite similar (≈21 Å) in H₂O and D₂O, and hence, the location of the probe in the protein remains the same in the two solvents. The single‐molecule study suggests that coumarin 153 (C153) binds almost exclusively (>96 %) to one site of HSA. Solvation dynamics of C153 in HSA is found to be markedly retarded in D₂O compared with H₂O. In H₂O, the solvation of C153 bound to HSA is found to be biexponential with one component of 7 ps (30 %) and a long component of 350 ps (70 %). In D₂O, we detected a short component of 4 ps (41 %) and a long component of 950 ps (59 %). Thus, the ultraslow component of the solvation dynamics of C153 bound to HSA in D₂O (950 ps) is 2.5‐fold slower than that in H₂O (350 ps). The marked deuterium isotope effect has been ascribed to water molecules confined in the protein environment and to a lesser extent to the structural modification of protein by D₂O.     

Hindered rotation of water molecule in van der Waals complex

The influence of water molecule symmetry on hindered rotation has been investigated for H₂O-He,H₂O(D₂O)-CO₂ systems, where CO₂ molecule is treated as an atom. A strong coupling model has been used for calculating the energy spectra. The eigenfunctions of Morse oscillator and asymmetric top have been used as a basis set. The results show that experimentally observed effect of spin-selective water vapour codensation may be explained by the differences between binding energies of para- and orthomodifications for H₂O(D₂O) molecules.     

An isotopic effect in the dielectric spectra of Ark. 9/water systems

Dielectric spectra of H₂O and D₂O molecules in the L_α liquid crystalline phase of nonylphenoxy-poly(ethylenoxy)ethanol(Ark. 9)/water lyotropic systems have been investigated by dielectric time domain spectroscopy in the frequency range from 10 MHz to 10 GHz. By fitting the Cole-Cole formula to the dielectric spectra, obtained at different temperatures the dielectric increments, the relaxation times and the distribution parameters have been calculated. A strong retardation of water molecules has been found for the lamellar phase with low water content, i.e. 10 water molecules (H₂O or D₂O) per one Ark. 9 molecule. The relaxation times obtained at room temperature for the light and heavy water are 63 and 93 ps, respectively. It means that the retardation factor for D₂O molecules in the L_α phase is close to 1.5 and higher than that found for pure heavy water (1.25). Any decomposition of the dielectric spectra obtained seems to be unsubstantiated. The temperature dependences of the relaxation times acquired for both kinds of water obey the Arrhenius behaviour.     

A Facile Strategy for the Construction of Purely Organic Optical Sensors Capable of Distinguishing D2O from H2O

Owing to the quite similar chemical properties of H₂O and D₂O, rational molecular design of D₂O optical sensors has not been realized so far. Now purely organic chromophores bearing OH groups with appropriate pK_a values are shown to display distinctly different optical responding properties toward D₂O and H₂O owing to the slight difference in acidity between D₂O and H₂O. This discovery is a new and facile strategy for the construction of D₂O optical sensors. Through this strategy, ratiometric colorimetric D₂O sensor of NIM‐2F and colorimetric/fluorescent dual‐channel D₂O sensor of AF were acquired successfully. Both NIM‐2F and AF can not only qualitatively distinguish D₂O from H₂O by the naked eye, but also quantitatively detect the H₂O content in D₂O.     

Thermodynamic properties of aqueous-organic systems with low water contents. 2. Limiting partial molar volumes of D2O and H2O intert-butyl alcohol and 1,4-dioxane at 288.15–318.15 K

The densities of dilute solutions of H₂O and D₂O in 1,4-dioxane and tert-BuOD have been measured in the interval 288.15–318.15 K with an error of 2·10^–6 g/cm³. The limiting partial molar volumes of D₂O and H₂O in 1,4-dioxane andtert-butanol have been determined by using an original procedure; the changes in the partial molar volume of water due to H-D substitution in the water molecules have been calculated. The analysis of the temperature dependence of the partial volumes of the components of the binary mixtures H₂O (D₂O) + 1,4-dioxane and H₂O (D₂O) +tert-BuOH (tert-BuOD) showed on the basis of Maxwell's crossing equations that the addition of small amounts of water significantly alters the structure of the unary organic solvent. In the presence of trace amounts of water the expansibility of 1,4-dioxane increases and that oftert-butanol decreases.For previous communication, see [1].Institute of the Chemistry of Nonaqueous Solutions, Russian Academy of Sciences, Ivanovo 153018. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 3, pp. 568–571, March, 1992.     

Tetracyanonickelate compounds as sorptive materials and the substitution of their H2O content by D2O

The compounds NiNi(CN)₄·3,5H₂O and Ni(NH₃)₂Ni(CN)₄·H₂O have been studied to examine the possibility of substituting their H₂O or NH₃ content by D₂O. Contact with D₂O was performed after heating the compounds to several temperatures. Depending on the degree of decomposition of the original compounds different ranges of substitution were possible. In such manner the compounds NiNi(CN)₄·3,5D₂O, NiNi(CN)₄·5D₂O, Ni(NH₃)₂Ni(CN)₄·D₂O, and Ni(D₂O)₂Ni(CN)₄·D₂O were prepared and thermally they were less stable than the original ones. The substitution by D₂O is in agreement with the sorptive properties of the original tetracyanonickelate against different organic compounds using GC, since these could substitute the guest component and sometimes also the ligands during their decomposition.     

Luminescence in near-thermal charge exchange. II. He+ + H2O and He+ + D2O

An ICR spectrometer fitted with synchronous photon counting equipment is used to study the emission produced by near-thermal (? 0.1 eV) collisions between He⁺ and H₂O (D₂). Within the investigated wavelength region, 185 to 500 nm, the only significant emission features are the A³Π (υ' ? 3) → X³Σ^? bands in OH⁺ and OD⁺, and the A²Σ⁺ → X²Π(0.0) band in OH and, possibly, in OD. The corresponding excitation rate constants represent only ? 2% of the total He⁺/H₂O (D₂O) charge transfer. The resonant electron-jump model for thermal-energy charge exchange is discussed in the light of recent information on the He⁺/H₂O reaction and on the excited states of H₂O⁺ and their excitation by electron and photon impact on H₂O (D₂O).     

D2O–H2O solvent isotope effects on the volumetric properties of aqueous 1,3-dimethyl-2-imidazolidinone between (278.15 and 318.15) K

Densities of dilute solutions of 1,3-dimethyl-2-imiazolidinone in H₂O and D₂O, with the solute mole-fractions ranging up to 0.01, have been measured with an error of 1.5 · 10⁻⁵ g · cm⁻³ at (278.15, 288.15, 298.15, 308.15, 313.15, and 318.15) K and atmospheric pressure using a vibrating-tube densimeter. The partial molar volumes of the dissolved DMI (down to the infinite dilution) and solvent (H₂O or D₂O) as well as the excess molar volumes of the isotopically distinguishable solutions have been calculated. The effects of the solvent isotope substitution, solute concentration and temperature on the volume changes caused by DMI hydration have been considered. The obvious relationship between the D₂O–H₂O solvent isotope effects on the partial molar volume and enthalpy of solution of DMI has been discovered.     

THE QUENCHING OF TYROSINE AND TRYPTOPHAN FLUORESCENCE BY H2O AND D2O*

Abstract— The quantum yields and lifetimes of the fluorescence of tyrosine and tryptophan were determined in D₂O-H₂O and glycerol-H₂O solvent mixtures of varying composition from 10 vol.% to 100% H₂O at 15°C. Forboth amino acids the ratio of the quantum yields in D₂O and H₂O (i.e., q_D/q_H) was smaller than the ratio of the corresponding lifetimes (_D/_H). For tyrosine the ratio of the quantum yields in glycerol and H₂O (q_G/q_H) was also smaller than the corresponding _G/_H ratio, but for tryptophan q_G/g_HG/_H. The proximity of the q vs. plots for tyrosine in the two solvent mixtures indicates that at 15°C neither D₂O nor glycerol, in the pure state or when diluted with H₂O, quench tyrosine significantly. However, H₂O quenches tyrosine by a dynamic process, which increases both the radiative and the nonradiative rate constant. The quenching action is attributed to a tyrosine-H₂O exciplex, whose formation is independent of bulk viscosity and dielectric constant. Unlike tyrosine, tryptophan is quenched weakly by D₂O by a static process at 15°C (i.e., involving no change in), but H₂O quenches tryptophan much more efficiently by a dynamic process, which involves the nonradiative rate constant, but not the radiative constant. These results are explained on the basis of electrostatic complexation of the ammonium group to the carbon atom adjacent to the ring nitrogen with a lifetime which is longer thanin D₂O but shorter thanin H₂O, with solvent reorientation possibly also being an important factor in the quenching. This explanation is consistent with the fact that concentrated (8 M) urea increases q andof aqueous tryptophan ? 15–20%, while guanidine hydrochloride (6.4 M) has the opposite effect, i.e., it decreases q and t of tryptophan ? 15–20%, and with the fact that neither 8 M urea nor 6.4 M guanidine hydrochloride affects any fluorescence parameter of tyrosine at all.     

Radiolysis in H2O/D2O mixtures. Hydrogen production under LOCA simulation

The hydrogen isotope radiolytic yields, G(H₂), G(HD) and G(D₂) were determined in H₂O/D₂O mixtures under chemical conditions close to a LOCA in a PHWR like Atucha I Nuclear Station, that is 2·10^–3 MH₃BO₃ and p(H+D)=8.5±0.2. The total hydrogen radiolytic yield G(H₂+HD+D₂) as a function of the deuterium atom fraction goes through a flat maximum at about 0.58. This result in dicates that the 4% flammability limit for hydrogen in the reactor's containment with be reached sooner than what is expected assuming a linear combination of pure H₂ and D₂ radiolytic yields. Hydrogen radiolytic production in 10^–3 M KBr in H₂O/D₂O mixtures gives the same results as in the boric solutions suggesting a bimolecular B(OH) ₄ ^– +OH reaction. Identical isotope concentration factors were calculated for both solutions.     

Isotopic substitution effects on the volumetric and viscosimetric properties of water-dimethylsulfoxide mixtures at 25°C

Densities and viscosities of binary mixtures (H₂O or D₂O) (1) + (DMSO or DMSO-D6)(2) have been measured over the entire mole fraction range; and the excess volumes, excess viscosities, and excess partial molar volumes Vf of the components have been obtained. All systems show negative excess volume V^e at all compositions, values for mixtures containing D₂O being more negative than those with H₂O byca. 0.03 cm³-mol^-1 at x₁, = 0.6, where a minimum is observed. The difference between DMSO and DMSO-D6 containing mixtures is negligible. The excess viscosity η^e is always positive and shows a maximum at x₁ = 0.65; at this composition, the substitution of H₂O with D₂O causes an excess viscosity increment ofca. 0.35 mPa-s, while deuteration of DMSO brings about a smaller increase,ca. 0.1 mPa-s. The trend of V ₂ ^E with concentration shows the characteristic features of moderately hydrophobic solutes in water (negative values and a minimum in the water-rich region), features that are slightly but significantly more marked in D₂O than in H₂O. The V ₂ ^E values in the water-diluted region and at x₁, =0 are more negative for D₂O than for H₂O.     

On the structure of the water dimer

The infrared spectrum of the mixed water dimer H₂O·D₂O has been observed at 20 K in a nitrogen matrix. The O-H(D) … O stretching vibrations are found to be slightly shifted compared to the corresponding vibrations in (H₂O)₂ and (D₂O)₂. The results are interpreted as evidence for the open dimer structure of Tursi and Nixon.     

Simultaneous Sensing of H2O,D2O and HOD through Peroxo Vibrations

Detection of HOD simultaneously in the presence of a mixture of H₂O and D₂O is still an experimental challenge. Till date, there is no literature report of simultaneous detection of H₂O, D₂O and HOD based on vibrational spectra. Herein we report simultaneous quantitative detection of H₂O, D₂O and HOD in the same reaction mixture with the help of bridged polynuclear peroxo complex in absence and presence of Au nanoparticles on the basis of a peroxide vibrational mode in resonance Raman and surface enhanced resonance Raman spectrum. We synthesize bridged polynuclear peroxo complex in different solvent mixture of H₂O and D₂O. Due to the formation of different nature of hydrogen bonding between peroxide and solvent molecules (H₂O, D₂O and HOD), vibrational frequency of peroxo bond is significantly affected. Mixtures of different H₂O and D₂O concentrations produce different HOD concentrations and that lead to different intensities of peaks positioned at 897, 823 and 867 cm⁻¹ indicating H₂O, D₂O and HOD, respectively. The lowest detection limits (LODs) were 0.028 mole fraction of D₂O in H₂O and 0.046 mole faction of H₂O in D₂O. In addition, for the first time the results revealed that the cis-peroxide forms two hydrogen bonds with solvent molecules.     

Intensities of wagging and rocking bands of water in MnCl2 · 2H2O and CoCl2 · 2H2O

IR relative integrated intensities and half-widths of rocking (R) and wagging (W) bands of water in MnCl₂ · 2H₂O and CoCl₂ · 2H₂O are presented at 300 K and 120 K. Departure of observed intensity into D_W/D_R from those predicted by the fixed dipole model is attributed to anisotropic dynamic changes in dipole during these oscillations. A quantity representing the variation of this anisotropy between W and R oscillations is computed and its origin is discussed. An increase by 20% to 50% in both D_W and D_R on lowering the temperature has also been discussed.     

PHOTOREACTIVATION OF DNA-CONTAINING CAULIFLOWER MOSAIC VIRUS AND TOBACCO MOSAIC VIRUS RNA ON DATURA

Abstract— Datura stramonium L. is a local lesion host for TMV-RNA and DNA-containing cauliflower mosaic virus (CAMV). Datura can photorepair UV-damaged TMV-RNA and CAMV, giving photoreac-tivation sectors of 0.40 and 0. 33 , respectively. Dose response curves for photoreactivation of TMV-RNA and CAMV show that 4540 min of cool white light (15 W.m^-2) is required for maximum photoreactivation. Blue light and near UV are equally effective in photoreactivating UV-irradiated TMV-RNA, whereas near UV is initially more effective than blue light for the photorepair of UV-inactivated CAMV. Higher doses of near UV apparently inactivate the CAMV photorepair system. In the case of CAMV, photoreactivating light must be applied immediately after inoculation with the virus. Two to three hours of incubation in the dark after inoculation results in complete loss of response to photoreactivating irradiation. In contrast, limited photoreactivation of TMV-RNA occurs even after 4 h of dark incubation after inoculation, although photoreactivating irradiation is most effective when applied immediately after inoculation. Light is required for the maintenance of photoreactivation for both TMV-RNA and CAMV. Daturas placed in the dark for six days lose their ability to photoreacti-vate. Recovery of the TMV-RNA photorepair system is rapid; complete recovery attained with 90 or more min of white light (15 W m-'). Recovery of CAMV photorepair system is slow; 90% recovery attained after only 20 h of light. However, full recovery can be induced by as little as 6h of light when CAMV is inoculated 24 h after the onset of illumination. These results suggest two photorepair systems are present in Datura .     

Dissociation energies of O–H bonds in alkylseleno- and alkyltelluro-substituted phenols

The O?H bond dissociation energy (D _O?H) has been determined for eight alkylseleno-substituted phenols, one alkyltelluro-substituted phenol, and one alkyltelluro-substituted pyridinol. D _O?H has been estimated by the intersecting-parabolas method from kinetic data using five reference compounds: α-tocopherol (D _O?H = 330.0 kJ/mol), 3,5-di-tert-butyl-4-methoxyphenol (D _O?H = 347.6 kJ/mol), 4-methylphenol (D _O?H = 361.6 kJ/mol), 2,6-di-tert-butyl-4-methylthiophenol (D _O?H = 336.3 kJ/mol), and 2,6-di-ter-tbutyl-4-methylphenol (D _O?H = 338.0 kJ/mol). The following D _O?H values (kJ/mol) have been obtained: 335.9 for 2,5,7,8-tetramethyl-2-phytyl-6-hydroxy-3,4-dihydro-2H-1-benzoselenopyran, 342.6 for 2-methyl-5-hydroxy-2,3-dihydrobenzoselenophene, 333.5 for 2,4,6,7-tetramethyl-5-hydroxy-2,3-dihydrobenzoselenophene, 339.4 for 2-tert-butyl-4-methoxy-6-octylselenophenol, 357.9 for dodecyl 3-(4-hydroxyphenyl) propyl selenide, 348.5 for dodecyl 3-(3,5-dimethyl-4-hydroxyphenyl)propyl selenide, 350.9 for dodecyl 3-(3-tert-butyl-4-hydroxyphenyl)propyl selenide, 338.0 for dodecyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl) propyl selenide, 343.0 for 2,6-di-tert-butyl-4-(tellurobutyl-4′-phenoxy)phenol, and 338.8 for 6-octyltelluro-3-pyridinol. The stabilization energies of phenoxyl radicals containing R substituents (X = O, S, Se, Te) have been compared.     

Infrared spectrum of D2O vibrationally decoupled in H2O ice Ic

The study of D₂O isolated in amorphous H₂O (ice Iv) has been extended to the determination of the bending mode frequency (1230 cm^?1) and to the measurement of the vibrational spectrum of the cubic ice phase (ice Ic). The vibrationally decoupled stretching frequencies (ν₁ = 2367 cm^?1 and ν₃ = 2444 cm^?1) for D₂O in the H₂O (Ic) have been obtained and an estimate of the exchange activation energy is given.