Resonance‐Enhanced Multiphoton Ionisation of Purine

State‐of‐the‐art molecular‐beam techniques reveal that the lowest lying electronic excited state in purine is the nπ* state. Using multiphoton ionization spectroscopy, the origin is found to occur at 31 309 cm^?1, and a vibrational structure is visible that is assigned to the skeletal motion of the ring (see figure).

     

13C NMR of indazoles

The carbon-13 chemical shifts and some selected coupling constants of 183 indazoles are reported. The main conclusions of the original references are briefly summarized.Published in Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1159–1179, September, 1995.     

Solvent-Dependent Stabilization of a Charge Transfer State is the Key to Ultrafast Triplet State Formation in an Epigenetic DNA Nucleoside

2’-Deoxy-5-formylcytidine (5fdCyd), a naturally occurring nucleoside found in mammalian DNA and mitochondrial RNA, exhibits important epigenetic functionality in biological processes. Because it efficiently generates triplet excited states, it is an endogenous photosensitizer capable of damaging DNA, but the intersystem crossing (ISC) mechanism responsible for ultrafast triplet state generation is poorly understood. In this study, time-resolved mid-IR spectroscopy and quantum mechanical calculations reveal the distinct ultrafast ISC mechanisms of 5fdCyd in water versus acetonitrile. Our experiment indicates that in water, ISC to triplet states occurs within 1 ps after 285 nm excitation. PCM-TD-DFT computations suggest that this ultrafast ISC is mediated by a singlet state with significant cytosine-to-formyl charge-transfer (CT) character. In contrast, ISC in acetonitrile proceeds via a dark ¹nπ* state with a lifetime of ∼3 ps. CT-induced ISC is not favored in acetonitrile because reaching the minimum of the gateway CT state is hampered by intramolecular hydrogen bonding, which enforces planarity between the aldehyde group and the aromatic group. Our study provides a comprehensive picture of the non-radiative decay of 5fdCyd in solution and new insights into the factors governing ISC in biomolecules. We propose that the intramolecular CT state observed here is a key to the excited-state dynamics of epigenetic nucleosides with modified exocyclic functional groups, paving the way to study their effects in DNA strands.     

Glucomannan from Narcissus poeticus Studied by PMR and 13C NMR Spectroscopy

Native acetylated glucomannan of molecular weight (MW) 32000 with a glucose:mannose ratio 1:30 was isolated from bulbs of Narcissus poeticus. Glucomannan was depolymerized to a fragment of MW 15000 with an unchanged primary structure and was studied using PMR and ¹³C NMR spectroscopy. It was found that the linear chain of the biopolymer consists of 1-4-bound D-gluco- and D-mannopyranose units and the O-Ac groups are localized on C-2, C-3, and C-6 hydroxyls in certain anhydromannose units.     

Ultrafast excited state dynamics of a bithiophene-isoindigo copolymer obtained by direct arylation polycondensation and its application in indium tin oxide-free solar cells

A low band gap copolymer, P2TI (E_g = 1.6.eV), with bithiophene as donor and isoindigo as acceptor units is designed and synthesized by the direct arylation polycondensation (DAP) method. Absorbance of the polymer spans from 300 to 780 nm. It exhibits an absorption coefficient (ε) of 96 L/g cm in solution at its maxima. A HOMO level of −5.42 eV and LUMO level of −3.72 eV is measured by square wave voltammetry. ITO-free solar cells fabricated using a P2TI :PCBM71 bulk heterojunction shows a moderate efficiency of 1.02% with a high open circuit voltage of 0.81 V. An intramolecular charge transfer state is found in the relaxation of P2TI in solution, which is generated with a time constant of 2 ps as measured by femtosecond-transient absorption spectroscopy. Charge carriers were generated in <250 fs in P2TI: PCBM71 films. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 1475–1483     

<Superscript>13</Superscript>C NMR and mass spectrometry of soil organic matter

Liquid state, high resolution ¹³C NMR spectroscopy and mass spectrometry were used to study the composition and structure of soil organic matter (SOM) using soil extracts from two long-term experiments at the Rothamsted Experimental Station. Both one- and two-dimensional NMR techniques were applied. ¹³C NMR sub-spectra of the CH _n (n=0...3) groups, obtained by the Distortionless Enhancement by Polarisation Transfer (DEPT) technique, were used for the elucidation of the qualitative and quantitative composition of humic and fulvic acids in the soils. The chemical structure of SOM was further analysed at the molecular level through Fast Atom Bombardment Mass Spectrometry (FABMS) and Gas Chromatography-Mass Spectrometry (GC/MS). Humic and fulvic extract results were not only compared to each other, but also to the solid state ¹³C NMR results for the complete soil sample.     

Ultrafast dynamics in a nanocage of enzymes: solvation and fluorescence resonance energy transfer in reverse micelles

In this contribution we report studies of the nature of solvation and resonance energy transfer processes in a reverse micelle (RM) upon encapsulation of a digestive enzyme, alpha-chymotrypsin (CHT). We have used one donor, Coumarin 500 (C500), and three acceptors Rhodamine 123 (R123, cationic), ethidium bromide (EtBr, cationic), and Merocyanine 540 (MC540, anionic). By selectively exciting the donor at the surface of the RM with a proper excitation wavelength we have examined solvation dynamics in the microenvironment. The solvation correlation function in the RM without CHT exhibits single-exponential decay with time constant approximately 660 ps, which is similar to that of the CHT-included RM. However, in the case of CHT-included RM (w(0)=10), the time-resolved anisotropy and spectral linewidth analysis of the surface-bound donor reveal the existence of an annular aqueous channel of thickness approximately 2.5 A between the enzyme surface and the inner surface of the RM. The aqueous channel is a potential host for the water-soluble substrate and also is involved in maintaining the proper functionality of RM encapsulated CHT. The studies use both steady-state and time-resolved fluorescence resonance energy transfer (FRET) techniques to measure donor-acceptor distances in the RM and also emphasize the danger of using steady-state fluorescence quenching as a method in careful estimation of the distances. The local geometrical restriction on the donor and acceptor molecules was estimated from time-resolved polarization (anisotropy) measurements. The time-resolved anisotropy of the donor and acceptor molecules also revealed significant randomization of the relative orientation of transition dipoles of the donor and acceptor, justifying the use of 2/3 as the value of the orientation factor kappa2. These studies attempt to elucidate the excellence of the RM as a nanohost of biological macromolecules.     

Effect of DNA and bivalent metal ions on the interaction of thermostable DNA polymerase <Emphasis Type="Italic">Tte</Emphasis> with dNTPs

The interaction of DNA polymerase Tte from Thermus thermophilus B35 with dUTP analog containing a fluorescein residue bound to C(5) of the base (Flu-dUTP) was studied by fluorescence titration. The dissociation constants of the enzyme—substrate complexes in the absence and in the presence of a DNA duplex containing an extended template and bivalent metal ions and the kinetic parameters of polymerization by DNA polymerase Tte in the presence of Flu-dUTP were determined. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1268–1272, May, 2005.     

Polysaccharides and sterols from green algae Caulerpa lentillifera and C. sertularioides

Sterols and polysaccharides of green alga Caulerpa lentillifera grown under laboratory conditions and in mariculture and polysaccharides of green alga C. sertularioides grown under natural conditions were studied. The sterol fraction consisted of C₂₇-C₂₉ steroidal alcohols with Δ⁵-unsaturation in the steroid core regardless of the growth conditions. The dominant (79.9%) steroid component of the sterol fraction was clionasterol. The water-soluble fraction of C. lentillifera grown under laboratory conditions was a mixture of 1,4-α- and 1,3-β-D-glucans and protein. The same fraction isolated from C. lentillifera grown in mariculture contained only protein. The water-soluble fraction of C. sertularioides grown under natural conditions contained 1,3;1,6-β-D-galactan sulfated at C2. The principal components of the base-soluble polysaccharide fractions from all algae samples were 1,4-α-D-glucans. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 5-8, January-February, 2009.     

Evaluation of <Superscript>13</Superscript>C NMR spectra of cyclopropenyl and cyclopropyl acetylenes by theoretical calculations

A convenient methodology was developed for a very accurate calculation of ¹³C NMR chemical shifts of the title compounds. GIAO calculations with density functional methods (B3LYP, B3PW91, PBE1PBE) and 6-311+G(2d,p) basis set predict experimental chemical shifts of 3-ethynylcyclopropene (1), 1-ethynylcyclopropane (2) and 1,1-diethynylcyclopropane (3) with high accuracy of 1–2 ppm. The present article describes in detail the effect of geometry choice, density functional method, basis set and effect of solvent on the accuracy of GIAO calculations of ¹³C NMR chemical shifts. In addition, the particular dependencies of ¹³C chemical shifts on the geometry of cyclopropane ring were investigated.     

Ultrafast Vibrational Dynamics and Local Interactions of Hydrated DNA

Biochemical processes occur mainly in aqueous environments, where interactions with water molecules play a key role for both the structure and function of biomolecules. Deoxyribonucleic acid (DNA), the basic carrier of genetic information, is characterized by an equilibrium double helix structure which is held together by intermolecular hydrogen bonds between base pairs and hydrated by an environment of water molecules with fluctuating hydrogen bonds. Basic vibrational motions of hydrated DNA and the fastest changes in the DNA–water interactions and hydration geometries occur in less than 1 ps. These processes can be accessed by mapping the vibrational dynamics of DNA and water in a time‐resolved way by nonlinear ultrafast vibrational spectroscopy. Recent studies provide a detailed understanding of DNA vibrations and their dynamics, and give insight into nonequilibrium properties and structures of hydrated DNA.     

Theoretical study on the structures and electronic spectra of C120On (n=1,2)

ZINDO series calculations have been carried out to study the double‐cage oxides C₁₂₀O_n (n=1,2). The results show that the formation of a furan ring by the bridge‐bond between the two cages connected the two C₆₀ fullerene units and formed the C₁₂₀O with C_2v symmetry. C₁₂₀O₂ has two isomers with C_2v symmetry depending on either 6–6 or 6–5 connection between the two cages. Two furan rings and a pure four‐member ring form in this molecule. The formation of C₁₂₀O assuages the constraint of epoxide structure in C₆₀O, shortens the distance of the monomers, and produces some finite interaction between the two balls. More bonding in C₁₂₀O₂ shortens the distance of the two cages further and brings about stronger interaction. However, the two cages in C₁₂₀O_n (n=1,2) behave somehow independently that the electronic spectra of C₁₂₀O_n (n=1,2) are similar to those of C₆₀. The 6–6 connection isomer of C₁₂₀O₂ is more stable; its spectra are in good agreement with those of the experiment. The calculated electronic spectra of C₁₂₀O not only are in good agreement with the experiment in the ultraviolet region but also get some weak peaks in the visible region (>400 nm) not observed in experiment. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 291–307, 2000     

Controllable Electronic Structures and Photoinduced Processes of Bay‐Linked Perylenediimide Dimers and a Ferrocene‐Linked Triad

A series of perylene‐3,4,9,10‐bis(dicarboximide) (PDI) dimers linked through the bay regions was systematically synthesized to examine the electronic structures and photophysical properties in dependence on the distance and orientation between the two PDI units. The spectroscopic and electrochemical measurements suggested that the coupling value of a directly linked PDI dimer (PDI)₂ is much larger than those of para‐ and meta‐phenylene‐bridged PDI dimers p‐(PDI)₂ and m‐(PDI)₂. The width of Davydov splitting was quantitatively evaluated to compare the coupling values between the two PDI units in these dimers by absorption spectroscopy in frozen 2‐methyl‐THF. Excimer formation of PDI dimers induced the strong fluorescence quenching and large red‐shifts. Femtosecond transient absorption revealed a broad absorption derived from an excimer in the range from about 600 nm to the near‐IR region. The rate constants of formation and decay of the excimer are strongly dependent on the coupling values. Time‐resolved measurements on ferrocene‐linked p‐(PDI)₂ revealed a competition between the photoinduced processes of electron transfer and excimer formation in PhCN, which is in sharp contrast with the sole electron‐transfer process in toluene.     

Crystal and molecular structure of polyunsaturated macrobicyclic carbosilane C24H38Si6

The crystal and molecular structure of the polyunsaturated macrocyclic carbosilane 1,4,4,7,7,10,13, 13,16,16-decamethyl-1,4,7,10,13,16-hexasilabicyclo-[8.8.2]-eucosa-5,14-diene-2,8,11,17-tetrain containing SiC(sp), SiC(sp ²), and SiC(sp ₃) endocyclic bonds was studied by XRD. The two strained 12-membered rings of this molecule have different (trans-zigzag and staggered) conformations. The lengths of the endocyclic bonds SiC(sp) are 1.821–1.852 Å, SiC(sp ²) 1.855–1.874 Å, and SiC(sp ³) 1.847–1.853 Å. The structure of the rings was solved by direct methods and refined by the full-matrix least-squares method. Calculations were carried out with SHELXTL PLUS 5.1 software.     

Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases

We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2–3 bright states and all the close by dark states, for a total of 6–9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.     

In situ synthesis of DNA micro-arrays using typography technique

A novel typography technique was developed to in situ synthesize oligonucleotide arrays on glass slide, which has the celerity, high spatial resolution, lower cost, reliable operation, and high synthetic efficiency. The principle and process of the typography technique for fabricating gene-chips have been described in detail. A suit of poly(terafluoroethylene) devices for synthesizing oligonucleotide arrays were designed and prepared, and the fiber tubes with a number of nano-or micron-channels were employed. The oligonucleotide arrays of 16 and 160 features with four different probes were synthesized using the typography technique. The four specific oligonucleotide probes including the matched and the mismatched by the fluorescent target sequence gave obviously different hybridization fluorescent signals. It was indicated that the gene-chip fabricated by the typography method could be used to rapidly screen single-nucleotide polymorphisms (SNP) and to detect mutations. Supported by the National Natural Science Foundation of China (Grant Nos. 60571032, 60571001, 90606027 and 60121101), the National Hi-Tech Research and Development Program of China (Grant No. 2006AA03Z357), the Natural Science Foundation of Hunan Province (Grant Nos. 04jj40023 and 06JJ4012) and the Natural Science Foundation of Guangdong Province (Grant No. 04008782)     

Raman and infrared spectra of6Li2C2O4 and7Li2C2O4

Raman and infrared spectra of polycrystalline⁶Li₂C₂O₄ and⁷Li₂C₂O₄ have been investigated in the wavenumber region from 1,800 to 40 cm^–1. The internal C₂O₄ ^–2 vibrations have been studied on the basis of a D_2h molecular structure and the correlation field splittings have been found to be about 40 cm^–1 for the stretching modes and about 15 cm^–1 for the bending modes. The external vibrations of the Li⁺ and C₂O₄ ^–2 sites have been discussed by considering the results of the factor group analysis and the⁶Li/⁷Li isotope effect on the normal vibrations.

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Raman- und Infrarot-Spektren von⁶Li₂C₂O₄ und⁷Li₂C₂O₄

Zusammenfassung Es wurdenRaman- und IR-Spektren von polykristallinem⁶Li₂C₂O₄ und⁷Li₂C₂O₄ im Bereich der Wellenzahlen von 1800 bis 40 cm^–1 untersucht. Die internen Schwingungen wurden auf der Basis einer D_2h Molekülstruktur analysiert. Für die Streckschwingungen wurde eine Korrelationsaufspaltung von etwa 40 cm^–1 gefunden, für die Deformationsschwingungen etwa 15 cm^–1. Die Diskussion der externen Schwingungen von Li⁺ und C₂O₄ ^–2 erfolgte unter Berücksichtigung der Resultate der Faktorgruppenanalyse und des⁶Li/⁷Li Isotopeneffekts auf die Normalschwingungen.

     

Genomewide expression analysis in amino acid-producing bacteria using DNA microarrays

DNA microarray technology has become an important research tool for biotechnology and microbiology. It is now possible to characterize genetic diversity and gene expression in a genomewide manner. DNA microarrays have been applied extensively to study the biology of many bacteria including Escherichia coli, but only recently have they been developed for the Grampositive Corynebacterium glutamicum. Both bacteria are widely used for biotechnological amino acid production. In this article, in addition to the design and generation of microarrays as well as their use in hybridization experiments and subsequent data analysis, we describe recent applications of DNA microarray technology regarding amino acid production in C. glutamicum and E. coli. We also discuss the impact of functional genomics studies on fundamental as well as applied aspects of amino acid production with C. glutamicum and E. coli.     

Chromatographic Behavior of C60 and C70 Fullerenes at Subambient Temperature with n-Alkanes Mobile Phases

The influence of temperature on the retention and separation of C60 and C70 fullerenes was studied under HPLC conditions. Particularly, chromatographic experiments were conducted using moderate carbon loaded octadecylsilica stationary phase and homologous series of n-alkanes including n-pentane, n-hexane and n-heptane as the mobile phases. All studies were performed across wide range of subambient temperature from −80 to +20 °C. From practical point of view the best chromatographic conditions for baseline separation of the components of interest were selected. The retention of analytes was strongly affected by temperature and below minus 30 °C strong deviation from van't Hoff behavior was observed. To explore this phenomenon selected thermodynamic parameters including changes of enthalpy (ΔH^o) and changes of entropy (ΔS^o) were estimated. Positive values of the ΔH^o and ΔS^o at low temperature region may indicate the lack of the interaction with the stationary phase ligands. A possible retention mechanism at different temperatures for C60 and C70 molecules has been discussed.