Hydrogen bonding and proton transfer between nitro-phenols and lecithin in apolar solvents

The interaction of p-nitrophenol (p-NP), 2,4-dinitrophenol (DNP) (II) and 2,4,6-trinitrophenol (TNP)(III) with dipalmitoyllecithin in apolar solvents has been examined by IR and UV spectroscopy. Addition of any nitrophenol to the solution of lecithin in CCl₄ causes disappearance of broad absorption band of water bound with lecithin phosphate grops (3150–3600 cm^?1), which was accompanied by an insignificant increase of absorption near 3040 and 2800 cm^?1. Association of phenolic groups of (I) with the lecithin was observed by disappearance of the free OH absorption band. In UV spectra of (I), complex formation with lecithin results in a 30 nm red shift of phenol long-wave absorption band and in the appearance of an isosbestic point at 303 nm. In the case of III, addition of the lecithin causes a red shift and strong hyperchromic effect, which is accompanied by the appearance of a new absorption band near 420 nm. It was concluded, that nitrophenols displace a part of water from the polar groups of lipids and form hydrogen bonded complexes or ion-pair structures, depending upon acidic properties of the proton donor.     

A new approach to the characterization of the B and A forms of DNA by I.R. spectroscopy

The RNA conformational changes of B, A and C forms are reflected in the infrared absorption spectra in the region of 800 cm^?1 to 900 cm^?1 and allow one to investigate unoriented samples. The transition to the A form is characterized by the appearence of bands at about 870 cm^?1 and at 813 cm^?1 whereas the B and the C forms exhibit a band at 837 cm^?1, these bands undoubtedly arise from phosphate diester stretching vibrations and yield information about backbone conformation. The presence of these infrared bands provides a criterion for testing the simultaneous presence of two coexisting forms of DNA. It represents a useful method for structural studies of nucleic acid complexes such as protein-DNA for which it is difficult to obtain orientation.     

The structural analysis of three‐dimensional fibrous collagen hydrogels by raman microspectroscopy

To investigate molecular effects of 1‐Ethyl‐3‐(3‐dimethylaminopropyl) carbodiimide (EDC), EDC/N‐hydroxysuccinimide (NHS), glyceraldehyde cross‐linking as well as polymerization temperature and concentration on the three‐dimensional (3D) collagen hydrogels, we analyzed the structures in situ by Raman microspectroscopy. The increased intensity of the 814 and 936 cm^?1 Raman bands corresponding to the C—C stretch of a protein backbone and a shift in the amide III bands from 1241 cm^?1/1268 cm^?1 in controls to 1247 cm^?1/1283 cm^?1 in glyceraldehyde‐treated gels indicated changes to the alignment of the collagen molecules, fibrils/fibers and/or changes to the secondary structure on glyceraldehyde treatment. The increased intensity of 1450 cm^?1 band and the appearance of a strong peak at 1468 cm^?1 reflected a change in the motion of lysine/arginine CH₂ groups. For the EDC‐treated collagen hydrogels, the increased intensity of 823 cm^?1 peak corresponding to the C—C stretch of the protein backbone indicated that EDC also changed the packing of collagen molecules. The 23% decrease in the ratio of 1238 cm^?1 to 1271 cm^?1 amide III band intensities in the EDC‐modified samples compared with the controls indicated changes to the alignment of the collagen molecules/fibrils and/or the secondary structure. A change in the motion of lysine/arginine CH₂ groups was detected as well. The addition of NHS did not induce additional Raman shifts compared to the effect of EDC alone with the exception of a 1416 cm^?1 band corresponding to a COO^? stretch. Overall, the Raman spectra suggest that glyceraldehyde affects the collagen states within 3D hydrogels to a greater extent compared to EDC and the effects of temperature and concentration are minimal and/or not detectable. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 349–356, 2013.     

Resonance Raman scattering and optical absorption of adrenodoxin and selena-adrenodoxin

Raman spectra have been recorded for native and selenium substituted adrenodoxin in dilute solution. Adrenodoxin shows three bands at 397, 350 and 297 cm^?1, all polarized, which can be associated with the iron-sulfur core. Selenium substitution leaves the 350 cm^?1 band essentially unshifted, but the other two bands disappear and are replaced by new bands at 355 and 263 cm^?1. The 350 cm^?1 band is assigned to stretching of iron-sulfur (cysteine) bonds, while the 397 and 297 cm^?1 bands are associated with vibrations of the labile sulfur atoms. The iron-selenium charge transfer bands were observed at 438 and 480 nm for the oxidized form and at 580 nm for the reduced form. The reduced selena-adrenodoxin displayed absorption maxima at 4, 450 and 5, 550 cm^?1, which can be assigned to the d-d transitions of high-spin ferrous ion. From this data and the reported g-values of electron paramagnetic resonance signals, the spin-orbit coupling constants were calculated to be 170 and 210 cm^?1 for the respective d-d transitions.     

Biochemical Studies on “Bakanae” Fungus. Part 55 Synthesis of Gibberellins

In order to clarify the structure of ring A of gibberellins, thirteen lactones of cyclohexan series, of which eight were new, were prepared to examine their infrared spectra. So far; the experiment is concerned, γ-lactones show the characteristic absorption band in the rang 1775~1782 cm^?1 in dioxane, while 5-ones in the range 1730/~1762 cm^?1. Since the absorptio band due to lactone carbonyl of gibberellins occurs at the range 1777~1786 cm^?1 in dioxane, the lactone ring of gibberellins seems to be γ.     

An FT-IR Study of DNA and RNA Conformational Transitions at Low Temperatures

Abstract

Fourier Transform Infrared (FT-IR) spectra of solid samples of DNA and RNA obtained from freeze-drying at solid CO₂ and liquid nitrogen temperatures, have been recorded and correlation between the conformational transitions and spectral changes is proposed. It is concluded that an equilibrium exists between A, B and Z conformations at low temperatures for the DNA molecule, which is temperature dependent, whereas the RNA molecule exhibits only the A conformation. The results have been compared with the metal-adducts of DNA and RNA, where one of the conformations is predominant.

Marker infrared bands for the B conformer have been found to be the strong band at 825 cm^?1 (sugar conformer mode) and a band with medium intensity at 690 cm^?1 (guanine breathing mode). The A conformation showed characteristic bands at 810 and 675 cm^?1. The B to Z conformational transition was characterized by the strong absorption bands near 820-810 cm^?1 and at 665-600 cm^?1.     

Ultraviolet circular dichroism of polyproline and oriented collagen

The ultraviolet absorption, linear dichroism, circular dichroism, and oriented circular dichroism of collagen are reported and the spectra are resolved into a self-consistent set of bands in accord with exciton theory. The parallel band at 200 nm has 40% of the π → π* intensity; the perpendicular band is placed at 189 nm yielding a splitting of 2700 cm^?1. The circular dichroism is resolved into two Gaussians at λ_∥ and λ_τ (rotational strengths +14 × 10^?40 and ?32 × 10^?40 esu². cm²) plus a large non-Gaussian (“helix”) band with ampplitude ?25,000° at 201 nm. These data appear to be in reasonably good accord with recent calculations. Measurements of the absorption, linear dichroism and circular dichroism of polyproline I and II are also reported and are resolved into their component bands. Polyproline I is in good accord with exciton theory, whereas polyproline II remains unsatisfactory.     

Resonance coherent anti-Stokes Raman scattering (CARS) spectra of flavin adenine dinucleotide,riboflavin binding protein and glucose oxidase

Coherent anti-Stokes Raman scattering spectra, in resonance with the isoalloxazine visible electronic transition, have been obtained down to 300 cm^?1 for flavin adenine dinucleotide, riboflavin binding protein and glucose oxidase, in H₂O and D₂O. Several isoalloxazine vibrational modes can be identified by analogy with those of uracil. Of particular interest is a band at ～1255 cm^?1 in H₂O, which is replaced by another at ～1295 cm^?1, in D₂O. The H₂O band appears to be a sensitive monitor of H-bonding of the N3 isoalloxazine proton to a protein acceptor group. It shifts down by 10 cm^?1 in riboflavin binding protein, and disappears altogether in glucose oxidase. Other band shifts, of 3–5 cm^?1, are similar for the two flavoproteins, and may reflect environmental changes between aqueous solution and the protein binding pockets.     

Oxygen binding to hemocyanin: a resonance Raman spectroscopic study

Oxygenation of hemocyanin gives rise to resonance Raman peaks at 742 and 282 cm^?1. The 742 cm^?1 peak which is in resonance with the 575 nm charge transfer band shifts to 704 cm^?1 when ¹⁸O₂ is substituted for ¹⁶O₂. Our results establish that the bound oxygen is in the form of peroxide (O₂^2?). The 282 cm^?1 peak which is in resonance with the 340 nm optical transition is insensitive to isotopic substitution, suggesting that the 282 cm^?1 peak corresponds to a vibration involving the magnetically-coupled Cu(II)··Cu(II) centers.     

Interaction of Calf-Thymus DNA With Trivalent La,Eu, and Tb Ions. Metal Ion Binding,DNA Condensation and Structural Features

Abstract

The interaction of calf-thymus DNA with La³⁺, Eu³⁺ and Tb³⁺ has been investigated in aqueous solution at pH 6.5, using metal/DNA(P) molar ratios (r) 1/80, 1/40, 1/20, 1/10, 1/4 and 1/2. Correlations between FTIR spectral changes and DNA structural properties have been established. At low metal/DNA(P) (r) 1/80, the metal ions bind mainly to the PO^? ₂ groups of the backbone, resulting in increased base-stacking interaction and duplex stability. At (r) 1/40 and 1/20, metal ion binding to the PO^? ₂ and the guanine N-7 site (chelation) predominates with minor perturbations of the A-T base pairs. Evidence for this comes from the displacement of the band at 1712 cm^?1 (T,G) towards a lower frequency and the PO^? ₂ antisymmetric band at 1222 cm^?1 towards a higher frequency. At higher metal/DNA(P) ratio, r> 1/20, DNA begins to condensate and drastic structural changes occur, which are accompanied by the shift and intensity changes of several G-C and A-T absorption bands. No major departure from B-DNA conformation was observed before and after DNA condensation eventhough some local structural modifications were observed. A comparison with the Cu-DNA complexes (denaturated DNA) shows some degree of helical destabilizition of the biopolymer in the presence of lanthanide ions.     

Ultrasmall Nanoplatelets: The Ultimate Tuning of Optoelectronic Properties

2D semiconducting nanoplatelets (NPLs) are an emerging class of photoactive materials. They can be used as building blocks in optoelectronic devices thanks to their large absorption coefficient, high carrier mobility, and unique thickness‐dependent optical transitions. The main drawback of NPLs is their large lateral size, which results in unfavorable band energy levels and low quantum yield (QY). Here, ultrasmall lead chalcogenide PbSe_1–x S_x NPLs are prepared, which exhibit an unprecedented QY of ≈60%, the highest ever reported for this structure. The NPLs are applied as light absorber in a photoelectrochemical system, leading to a saturated photocurrent density of ≈5.0 mA cm^?2 (44 mL cm^?2 d^?1), which is a record for NPL‐based photoelectrodes in solar‐driven hydrogen generation. Ultrasmall NPLs hold the potential for breakthrough developments in the field of optically active nanomaterials.     

Infrared spectrum of a DNA-RNA hybrid

The infrared absorption spectrum in the 4000–400 cm^? region of an oriented film of a DNA–RNA hybrid in its undeuterated and deuterated states was observed with the polarized radiation. Most of the stronger bands found in the double-helical DNA's and double-helical RNA's are identified in the spectrum of the hybrid. The absorption band at 1225 cm^?1 shows a perpendicular dichroism and that at 1085 cm^?1 shows almost no dichroism. These facts indicate that the orientation of the group with respect to the helix axis in the hybrid structure is not entirely the same as that in the double-helical Na DNA at, 75% RH., although the x-ray diffraction pattern of the hybrid is quite similar to that of the DNA A form. The PO₂^? orientation is not the same as that in the double-helical RNA either. The observed dichroism is explained, however, by considering that the PO₂^? group in the RNA moiety takes nearly the same orientation as that in the double-helical RNA, and the PO₂^? group in the DNA moiety takes nearly the same as that in the double-helical DNA.     

Relation of certain infrared bands to conformational changes of cellulose and cellulose oligosaccharides

The i.r. spectra of D-glucose and cellulose oligosaccharides up to cellopentaose have been compared with those of cellulose at various temperatures between that of liquid nitrogen and ～250°. Significant changes in frequency and intensity of the bands at ～3400 cm^?1 were observed. The a_1372cm^?1/a_2900cm^?1 ratio for each carbohydrate studied decreased gradually as the temperature was increased above ambient. The change of the band intensifies at 1429 and 893 cm^?1 with temperature was also investigated. The observed spectral changes are assumed to be associated with changes of hydrogen bonding.     

Balancing Light Absorption and Charge Transport in Vertical SnS2 Nanoflake Photoanodes with Stepped Layers and Large Intrinsic Mobility

Significant optical absorption in the blue–green spectral range, high intralayer carrier mobility, and band alignment suitable for water splitting suggest tin disulfide (SnS₂) as a candidate material for photo‐electrochemical applications. In this work, vertically aligned SnS₂ nanoflakes are synthesized directly on transparent conductive substrates using a scalable close space sublimation (CSS) method. Detailed characterization by time‐resolved terahertz and time‐resolved photoluminescence spectroscopies reveals a high intrinsic carrier mobility of 330 cm² V^?1 s^?1 and photoexcited carrier lifetimes of 1.3 ns in these nanoflakes, resulting in a long vertical diffusion length of ≈1 µm. The highest photo‐electrochemical performance is achieved by growing SnS₂ nanoflakes with heights that are between this diffusion length and the optical absorption depth of ≈2 µm, which balances the competing requirements of charge transport and light absorption. Moreover, the unique stepped morphology of these CSS‐grown nanoflakes improves photocurrent by exposing multiple edge sites in every nanoflake. The optimized vertical SnS₂ nanoflake photoanodes produce record photocurrents of 4.5 mA cm^?2 for oxidation of a sulfite hole scavenger and 2.6 mA cm^?2 for water oxidation without any hole scavenger, both at 1.23 V_RHE in neutral electrolyte under simulated AM1.5G sunlight, and stable photocurrents for iodide oxidation in acidic electrolyte.     

Raman studies of conformational changes in model membrane systems

Laser Raman spectra of concentrated samples of phosphatidyl choline and phosphatidyl ethanolamine were taken at approximately 10° intervals over a temperature range of 90°–19°C. The spectral region from 30 to 3300 cm^?1 was investigated. Several new spectral features were discovered which are correlated to phospholipid liquid crystalline structure. It is shown that 1) frequency shifts occur in the $\text{PO}{}_2{}^{\mathrm{?}}$ symmetric stretch band which suggest a change in exposure of the PO₂ group to the solvent upon melting, 2) the frequency of the translational hydrocarbon mode around 150 cm^?1 appears to indicate the degree to which the hydrocarbon chain is extended, 3) the methyl and methylene stretch bands at 2890 and 2850 cm^?1 very clearly demonstrate hydrocarbon chain melting, and 4) the 720 cm^?1 band, previously assigned to the symmetric OPO diester stretch, appears to be due instead to the symmetric CN stretch of choline.     

Flexibility of DNA and RNA upon Binding to Different Metal Cations. An Investigation of the B to A to Z Conformational Transition by Fourier Transform Infrared Spectroscopy

Abstract

The interaction of DNA and RNA with Cu(II), Mg(II), [Co(NH₃)₆]³⁺ [Co(NH₃)₅Cl]²⁺ chlorides and, cis- and trans-Pt(NH₃)₂Cl₂ (CIS-DDP, trans-DDP) has been studied by Fourier Transform Infrared (FT-IR) spectroscopy and a correlation between metal-base binding and conformational transitions in the sugar pucker has been established. It has been found that RNA did not change from A-form on complexation with metals, whereas DNA exhibited a B to Z transition. The marker bands for the A-form (C′₃-endo-anti conformation) were found to be near 810–816 cm^?1, while the bands at 825 and 690 cm^?1 are marker bands for the B- conformation (C′₂-endo, anti), The B to Z (C₃′-endo, syn conformation) transition is characterized by the shift of the band at 825 cm^?1 to 810–816 cm^?1 and the shift of the guanine band at 690 cm^?1 to about 600–624 cm^?1.     

A study of the spectral and luminescence manifestations of the aggregation of thymine chromophores in polythymidylic acid aqueous solutions at room temperature in the context of photochemical information recording using thymine

The luminescence and excitation spectra of polythymidylic acid aqueous solutions at room temperature were studied. In addition to the previously described band at 338 nm, two new bands at 320 and 350 nm were recorded at various excitation wavelengths. An examination of the excitation spectra that had not been studied previously, as well as their comparison with the differential absorption spectra previously recorded during photodimerization, allowed us to interpret the band at 320 nm as the band of noninteracting chromophores; the band at 338 nm as the band of the most photochemically active, densely packed stacking dimmers (exciton splitting of absorption band of ～4000 cm^?1); and the band at 350 nm as the band of photochemically inactive large stacking aggregates (n ≥ 10, exciton splitting of ～8000 cm^?1). The changes in the optical density of the polythymidylic acid aqueous solution at γ = 270 nm after successive irradiation of the solution with light at 279 + 302 and 248 nm were studied. The reasons for their incomplete reversibility are discussed.     

FT-IR and 1H NMR spectroscopic evidence of sugar ring conformational change in NH4GpG on complexation to form cis-[Pt(NH3)2(GpG)]+

The conformational change of the ribose ring in NH₄GpG and cis-[Pt(NH₃)₂(GpG)]⁺ was confirmed by FT-IR spectroscopic evidence as being C2′-endo, C3′-endo, anti, gg sugar ring pucker in the solid state. These results were compared with ¹H NMR spectral data in aqueous solution. The FT-IR spectrum of NH₄GpG shows marker bands at 802 cm^?1 and 797 cm^?1 which are assigned to the C3′-endo, anti, gg sugar-phosphate vibrations of ribose (?pG) and ribose (Gp?), respectively. The FT-IR spectrum of cis-[Pt(NH₃)₂(GpG)]⁺ (with N7N7 chelation in the GpG sequence) shows a marker band at 800 cm^?1 which is assigned to the C3′-endo, and a new shoulder band at 820 cm^?1 related to a C2′-endo ring pucker. The ribose conformation of (?pG) moiety in NH₄-GpG, C3′-endo, anti, gg changes into C2′-endo, anti, gg when a platinum atom is chelated to N7N7 in the GpG sequence.     

Ultrasonic absorption in aqueous solution of lysozyme.

The titration curve of ultrasonic absorption at 2.82 MHz in aqueous solutions of lysozyme measured by Zana and Lang [J. Phys. Chem., 74 , 2734 (1970)] is theoretically analyzed. The maxima at pH 3 and pH 11 are describable with proton-transfer reactions of dissociable carboxyl and amino groups by assuming that volume changes due to the reactions are 2.3 and 5.2 cm³/mole, respectively, which are appreciably smaller than those of simple amino acids. The remaining, pH-independent excess absorption over solvent is measured at frequencies ranging from 3 to 150 MHz. The absorption is ascribed to the internal loss of protein. The complex compressibility β′_p ? iβ″_p of lysozyme molecule is evaluated as β′_p = 7.2 × 10^?12 cm²/dyne and β″_P = 4.3 × 10^?14 cm²/dyne from the increments over solvent in absorption as well as in sound velocity.     

Wet Chemical Colorimetric Estimation of CO: An Update on the Reduced Silver Sol Spectral and Kinetic Transformations to Silver nanoparticle

Measurements of ppm (v/v) level CO_g concentration is conveniently performed by its preconcentration in alkaline absorber solution of Ag⁺-(4)- HCO₂-C₆H₄-SO₂NH₂ complex, followed by a spectral measurement of the reduced silver sol. In this study, the transitory nature of this latter species and its subsequent real-time transformation to silver nanoparticle are presented. These results were based on spectral measurements made under varying concentrations of alkali, (4)-HCO₂-C₆H₄-SO₂NH₂, and Ag⁺ in the absorber solution, and in the presence of a wide range of sampled CO_g concentration. The initially created light yellow colored sol with its broad absorption profile peaking at 380 nm and absorption coefficient 3500?±?300 cm^?1 M^?1 (related to the amount of sampled [CO_g] as standardized by gas chromatographic analysis) changed into the characteristic yellow orange nanoparticle with its plasmon band peak absorption at 425 nm and absorption coefficient 6350?±?300 cm^?1 M^?1. Under different sampling conditions, the respective first-order conversion rates varied between 0.03 and 0.15 h^?1, whereas simultaneous dynamic light scattering measurements revealed steady growth of the averaged particle size ranging from 60 to 300 nm.