Interpreting DNA vibrational circular dichroism spectra using a coupling model from two-dimensional infrared spectroscopy

Two-dimensional infrared spectroscopy was recently used to measure the vibrational couplings between carbonyl bonds located on DNA nucleobases (Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem. B 2003, 107, 9165 and Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B 2006, 110, 13991). Here, we extend the coupling model derived from these 2D IR experiments to simulate the vibrational absorption and vibrational circular dichroism (VCD) spectra of three double-stranded DNA oligomers: poly(dG)-poly(dC), poly(dG-dC), and dGGCC. Using this model, we determine that the VCD spectrum of A-form poly(dG)-poly(dC) is dominated by interactions between stacked bases, whereas the coupling between base pairs and stacked bases carries equal importance in the VCD spectrum of B-form poly(dG-dC). We also simulate the absorption and VCD spectra of dGGCC, which is a combination of A- and B-form configurations. These simulations give insight into the structural interpretation of VCD and absorption spectroscopies that have long been used to monitor DNA secondary structure and kinetics.     

DNA vibrational coupling revealed with two-dimensional infrared spectroscopy: insight into why vibrational spectroscopy is sensitive to DNA structure

Two-dimensional infrared (2D IR) spectroscopy was used to study the carbonyl vibrational modes of guanine and cytosine bases in A- and B-form DNA. Located between 1600 and 1700 cm(-1), these modes are often used to monitor DNA secondary structure with traditional infrared spectroscopies such as FTIR, but traditional spectroscopies lack the necessary observables to unravel the coupling mechanisms that make these modes sensitive to secondary structure. By using 2D IR spectroscopy and electronic structure calculations on d(G(5)C(5)) and d(GC)(8) model nucleic acids, we find that hydrogen-bonded guanine/cytosine base pairs are primarily electrostatically coupled and that the coupling between these modes can be modeled with a transition dipole density approach. In comparison, electrostatics is insufficient to model stacked bases because of cooperative charge-sharing effects, but the coupling can be accurately calculated using a finite difference method. We find that the coupling is very strong for both hydrogen-bonded and stacked base geometries, creating vibrational modes that extend both across the base pairs and along the lengths of the helices. Our results provide a physical basis for understanding how strong coupling gives rise to the empirically established relationship between infrared spectroscopy and DNA/RNA secondary structure.     

Evidence for diffusional coupling in electrochemical thin layers: implications for surface coverage calibration via electrochemical infrared spectroscopy

The time dependence of the concentration of CO₂ in an electrochemical thin layer cavity is studied with Fourier transform infrared spectroscopy (FTIR) in order to evaluate the extent to which the thin layer cavity is diffusionally decoupled from the surrounding bulk electrolyte. For the model system of CO on Pt(111) in 0.1 M HClO₄, it is found that the concentration of CO₂, formed by electro-oxidation of CO, equilibrates rapidly with the surrounding bulk electrolyte. This rapid equilibration indicates that there is diffusion out of the thin layer, even on the short time scales of typical infrared experiments (1–3 min). However, since the measured CO₂ absorbance intensity as a function of time is reproducible to within 10%, a new time-dependent method for surface coverage calibration using solution-phase species is proposed. Dedicated to Prof. Dr. Teresa Iwasita on the occasion of her 65th birthday in recognition of her numerous contributions to interfacial electrochemistry.     

Systematization method for distinguishing plastic groups by using NIR spectroscopy.

A systematic classification method for polymers is not yet available in case of using near infrared spectra (NIR). That is why we have been searching for a systematic method. Because raw NIR spectra usually have few obvious peaks, NIR spectra have been pretreated by 2nd derivation for taking well modulated spectra. After the pretreatment, we applied classification and regression trees (CART) to the discrimination between the spectra and the species of polymers. As a result, we obtained a relatively simple classification tree. Judging from the obtained splitting conditions and the classified polymers, we concluded that obtained knowledge on the chemical function groups estimated by the important wavelength regions is not always applicable to this classification tree. However, we clarified the splitting rules for polymer species from the NIR spectral point of view.     

Interaction of ester functional groups with aluminum oxide surfaces studied using infrared reflection absorption spectroscopy

The bonding of two types of ester group-containing molecules with a set of different oxide layers on aluminum has been investigated using infrared reflection absorption spectroscopy. The different oxide layers were made by giving typical surface treatments to the aluminum substrate. The purpose of the investigation was to find out what type of ester-oxide bond is formed and whether this is influenced by changes in the composition and chemistry of the oxide. The extent by which these bonded ester molecules resisted disbondment in water or substitution by molecules capable of chemisorption was also investigated. The ester groups were found to show hydrogen bonding with hydroxyls on the oxide surfaces through their carbonyl oxygens. For all oxides, the ester groups showed the same nu(C = O) carbonyl stretching vibration after adsorption, indicating very similar bonding occurs. However, the oxides showed differences in the amount of molecules bonded to the oxide surface, and a clear relation was observed with the hydroxyl concentration present on the oxide surface, which was determined from XPS measurements. The two compounds showed differences in the free to bonded nu(C = O) infrared peak shift, indicating differences in bonding strength with the oxide surface between the two types of molecules. The bonding of the ester groups with the oxide surfaces was found to be not stable in the presence of water and also not in the presence of a compound capable of chemisorption with the aluminum oxide surface.     

A new method for picosecond time-resolved infrared spectroscopy: applications to CO photodissociation from iron porphyrins

A new method for obtaining picosecond infrared spectra and kinetics is presented. It incorporates a tunable infrared diode laser in conjunction with two cavity-dumped dye lasers synchronously pumped by a mode-locked and Q-switched Nd:YAG laser. New results are obtained for the photodissociation of hemin and myoglobin carbonyls and for their geometric structures by means of IR-optical polarization measurements.     

Transient infrared spectroscopy: a new approach to investigate valence tautomerism

In this work we present, to our knowledge for the first time, the results of a transient infrared spectroscopic study of the photoinduced valence tautomerism process in cobalt-dioxolene complexes with sub-picosecond time resolution. The molecular systems investigated were [Co(tpa)(diox)]PF(6) (1) and [Co(Me(3)tpa)(diox)]PF(6) (2), where diox = 3,5-di-tert-butyl-1,2-dioxolene; tpa = tris(2-pyridylmethyl)amine and Me(3)tpa its 6-methylated analogue. Complex (1) is present in solution as ls-Co(III)(catecholate) (1-CAT), while (2) as hs-Co(II)(semiquinonate) (2-SQ). DFT calculation of the harmonic frequencies for (1) and (2) allowed us to identify the vibrational markers of catecholate and semiquinonate redox isomers. Irradiation with 405 and 810 nm pulses (~35 fs) of (1-CAT) induces the formation of an intermediate excited species from which the ground state population is recovered with a time constant of 1.5 ± 0.3 ns. Comparing the 1 ns transient infrared spectrum with the experimental difference spectrum FTIR(2-SQ)-FTIR(1-CAT) and with the calculated difference spectrum IR(c)(1-SQ)-IR(c)(1-CAT) we are able to unequivocally identify the long lived species as the semiquinonate redox isomer of (1). On the other hand, no evidence of photoconversion is observed upon irradiation of (2) with 405 nm. Temporal evolution of transient spectra was analyzed with the combined approach consisting of singular values decomposition and global fitting (global analysis). After 405 and 810 nm excitation of (1-CAT), the semiquinonate excited species is formed on an ultrafast time scale (<200 fs) and cools down within the first 50 ps. Excitation of (2-SQ) with 405 nm wavelength produces a short lived excited state in which the semiquinonate nature of dioxolene is preserved and the ground state recovery is completed within 30 ps.     

Development of a rapid process monitoring method for dry-coated tableting process by using near-infrared spectroscopy

A nondestructive transmittance near-infrared (NIR) method for detecting off-centered cores in dry-coated (DC) tablets was developed as a monitoring system in the DC tableting process. Caffeine anhydrate was used as a core active pharmaceutical ingredient (API), and DC tablets were made by the direct compression method. NIR spectra were obtained from these intact DC tablets using the transmittance method. The reference assay was performed with HPLC. Calibration models were generated by partial least squares (PLS) regression and principal component regression (PCR) utilizing external validations. Hierarchical cluster analysis (HCA) of the results confirmed that NIR spectroscopy correctly detected off-centered cores in DC tablets. We formulated and used the Centering Index (CI) to evaluate the precision of core alignment and generated an NIR calibration model that could correctly predict this index. The principal component (PC) 1 loading vector of the final calibration model indicated that it could specifically detect the misalignment of tablet cores. The model also had good linearity and accuracy. The CIs of unknown sample tablets predicted by the final calibration model and those calculated through the HPLC analysis were closely parallel with each other. These results demonstrate the validity of the final calibration model and the utility of the transmittance NIR spectroscopic method developed in this study as a monitoring system in DC tableting process.     

Rheo-attenuated total reflectance infrared spectroscopy: a new tool to study biopolymers

Whilst rheology is the reference technique to study the mechanical properties of unspun silk, we know little of the structure and the dynamics that generate them. By coupling infrared spectroscopy and shearing forces to study silk fibroin conversion, we are introducing a novel tool to address this gap in our knowledge. Here the silk conversion process has been studied dynamically using polarized attenuated total reflectance Fourier transform infrared spectroscopy whilst applying shear, thus revealing silk protein conformation and molecular orientation in situ. Our results show that the silk conversion process starts with a pre-alignment of the proteins followed by a rapid growth of the β-sheet formation and then a subsequent deceleration of the growth. We propose that this tool will provide further insight into not only silk but any biopolymer solution, opening a new window into biological materials.     

Reproducible discrimination between gram-positive and gram-negative bacteria using surface enhanced Raman spectroscopy with infrared excitation

The on time diagnostics of bacterial diseases is one of the essential steps in the foregoing treatment of such pathogens. Here we sought to present an easy to use and robust method for the discrimination between Gram-positive (Enterococcus faecalis and Streptococcus pyogenes) and Gram-negative (Acinetobacter baumannii and Klebsiella pneumoniae) bacterial genera based on surface enhanced Raman scattering (SERS) spectroscopy. The robustness of our approach lies in the novel method for the production of the SER substrate based on silver nanoparticles and their subsequent re-crystallization in solutions containing high concentrations of chloride ions. The method presented here could be an interesting alternative both to commonly used histochemical approaches and commercial SERS substrates.     

Calculations of the exciton coupling elements between the DNA bases using the transition density cube method

Excited states of the double-stranded DNA model (A)12.(T)12 were calculated in the framework of the Frenkel exciton theory. The off-diagonal elements of the exciton matrix were calculated using the transition densities and ideal dipole approximation associated with the lowest energy pipi* excitations of the individual nucleobases as obtained from time-dependent density functional theory calculations. The values of the coupling calculated with the transition density cubes (TDC) and ideal dipole approximation (IDA) methods were found to be significantly different for the small interchromophore distances. It was shown that the IDA overestimates the coupling significantly. The effects of structural fluctuations of the DNA chain on the magnitude of dipolar coupling were also found to be very significant. The difference between the maximum and minimum values was as large as 1000 and 300 cm(-1) for the IDA and TDC methods, respectively. To account for these effects, the properties of the excited states were averaged over a large number of conformations obtained from the molecular dynamics simulations. Our calculations using the TDC method indicate that the absorption of the UV light creates exciton states carrying the majority of the oscillator strength that are delocalized over at least six DNA bases. Upon relaxation, the excitation states localize over at least four contiguous bases.     

Detection of trace materials with Fourier transform infrared spectroscopy using a multi-channel detector

FTIR spectroscopy is one of the most powerful methods for material characterization. However, the sensitivity of this analytical tool is often very limited especially for materials with weak infrared absorption or when spectral bands of the targeted trace material overlap with the spectral bands of major components. Fortunately, for heterogeneous samples, there is an opportunity to improve the sensitivity of detection by using an imaging approach. This paper explores the opportunity of enhancing the sensitivity of FTIR spectroscopy to detect trace amounts of materials using the FTIR imaging approach based on a focal plane array (FPA) detector. Model sample tablets of ibuprofen in hydroxypropyl methylcellulose (HPMC) have been used to exemplify the detection limits of FTIR spectroscopy using: (a) a conventional mercury cadmium telluride (MCT) detector and (b) a FPA detector. The sensitivity level was compared and it has been found that for this particular set of samples, the lowest concentration of ibuprofen in HPMC that can be detected using attenuated total reflection (ATR) measuring mode with the single element MCT detector was 0.35 wt% while using the FPA detector, the presence of drug has been detected in a sample that contains as little as 0.075 wt% of drug. The application of using this enhanced sensitivity offered by the multi-channel detector to probe trace amounts of drug particles left on the surface of a finger after handling a small amount of the drug has also been demonstrated. These results have broad implications for forensic, biomedical and pharmaceutical research.     

Ruthenium-catalyzed coupling of aldimines with arylboronates: new synthetic method for aromatic ketones

Using the chelation strategy, the reaction of aldimines bearing the 3-picolin-2-yl group with various arylboronates in the presence of a ruthenium catalyst furnished the corresponding ketimines in high yields for a short reaction time; the resulting ketimines were readily converted to ketones by hydrolysis.     

Symmetry-based 29Si dipolar recoupling magic angle spinning NMR spectroscopy: a new method for investigating three-dimensional structures of zeolite frameworks

A new 29Si solid-state MAS NMR experiment is described for investigating the framework structures of pure silica zeolites. The symmetry-based homonuclear dipolar recoupling sequence SR26411 has been incorporated into a two-dimensional NMR experiment to probe the Si-O-Si bonding connectivities and long-range Si-Si distances in zeolite frameworks. This dipolar recoupling sequence is shown to have a number of advantages over the J-coupling-based INADEQUATE experiment. For the clathrasil Sigma-2, it is demonstrated that there is excellent agreement between experimental double-quantum build-up curves obtained from a series of two-dimensional double-quantum correlation spectra and simulated curves which consider all Si-Si distances out to 8 A. This result suggests that this experiment could be used to solve zeolite frameworks with unknown structures.     

A new method for synthesizing hyperbranched polymers with reductive groups using redox/RAFT/SCVP

The novel hyperbranced polymers containing reductive groups were successfully prepared and characterized using redox/reversible addition fragmentation chain transfer(RAFT)/self-condensing vinyl polymerization(SCVP) method. Several redox initiating chemicals such as Cu(III)/―CONH2, Ce(IV)/―CONH2 and Ce(IV)/―OH were chosen to increase the free radical generating rate, and the chain transfer agent(CTA) was used to reduce the molecular chain propagating rate, in order to obtain polymers with high degree of branching. Detailed analyses based on the molecular weight, ? value and the degree of branching of polymers(DB) obtained from 1H-NMR spectra and multi detector size exclusion chromatography(MDSEC) suggested the acquiring of hyperbranced polyacrylamides with Cu(III)/―CONH2 and Ce(IV)/―CONH2 as initiator in the presence of the CTA. Meanwhile, the as-prepared poly(N-hydroxymethyl acrylamide)(PNHAM) with higher DB value(0.48) proved that using Ce(IV)/―OH as the initiator could increase the free radical generating rate and diminish the gap between the propagating rate and the initiation rate during the reaction procedure. In addition, the effect of oxidant concentration on the Mark-Houwink index(?) value and the DB was also studied.     

A new experimental method for heteronuclear correlation spectroscopy with cross-polarization

A new experiment is proposed for two-dimensional heteronuclear correlation spectroscopy. It involves the rapid creation of pure heteronuclear ZQC under cross-polarization, followed by an evolution period during which ZQC is converted to DQC. A read pulse is used to detect the signal. No phase cycling is required to determine the sign of ω₁.     

Bioreactor monitoring with spectroscopy and chemometrics: a review

Biotechnological processes are crucial to the development of any economy striving to ensure a relevant position in future markets. The cultivation of microorganisms in bioreactors is one of the most important unit operations of biotechnological processes, and real-time monitoring of bioreactors is essential for effective bioprocess control. In this review, published material on the potential application of different spectroscopic techniques for bioreactor monitoring is critically discussed, with particular emphasis on optical fiber technology, reported for in situ bioprocess monitoring. Application examples are presented by spectroscopy type, specifically focusing on ultraviolet-visible, near-infrared, mid-infrared, Raman, and fluorescence spectroscopy. The spectra acquisition devices available and the major advantages and disadvantages of each spectroscopy are discussed. The type of information contained in the spectra and the available chemometric methods for extracting that information are also addressed, including wavelength selection, spectra pre-processing, principal component analysis, and partial least-squares. Sample handling techniques (flow and sequential injection analysis) that include transport to spectroscopic sensors for ex-situ on-line monitoring are not covered in this review.     

Determination of equilibrium constants for the reaction between acetone and HO2 using infrared kinetic spectroscopy

The reaction between the hydroperoxy radical, HO(2), and acetone may play an important role in acetone removal and the budget of HO(x) radicals in the upper troposphere. We measured the equilibrium constants of this reaction over the temperature range of 215-272 K at an overall pressure of 100 Torr using a flow tube apparatus and laser flash photolysis to produce HO(2). The HO(2) concentration was monitored as a function of time by near-IR diode laser wavelength modulation spectroscopy. The resulting [HO(2)] decay curves in the presence of acetone are characterized by an immediate decrease in initial [HO(2)] followed by subsequent decay. These curves are interpreted as a rapid (<100 μs) equilibrium reaction between acetone and the HO(2) radical that occurs on time scales faster than the time resolution of the apparatus, followed by subsequent reactions. This separation of time scales between the initial equilibrium and ensuing reactions enabled the determination of the equilibrium constant with values ranging from 4.0 × 10(-16) to 7.7 × 10(-18) cm(3) molecule(-1) for T = 215-272 K. Thermodynamic parameters for the reaction determined from a second-law fit of our van't Hoff plot were Δ(r)H°(245) = -35.4 ± 2.0 kJ mol(-1) and Δ(r)S°(245) = -88.2 ± 8.5 J mol(-1) K(-1). Recent ab initio calculations predict that the reaction proceeds through a prereactive hydrogen-bonded molecular complex (HO(2)-acetone) with subsequent isomerization to a hydroxy-peroxy radical, 2-hydroxyisopropylperoxy (2-HIPP). The calculations differ greatly in the energetics of the complex and the peroxy radical, as well as the transition state for isomerization, leading to significant differences in their predictions of the extent of this reaction at tropospheric temperatures. The current results are consistent with equilibrium formation of the hydrogen-bonded molecular complex on a short time scale (100 μs). Formation of the hydrogen-bonded complex will have a negligible impact on the atmosphere. However, the complex could subsequently isomerize to form the 2-HIPP radical on longer time scales. Further experimental studies are needed to assess the ultimate impact of the reaction of HO(2) and acetone on the atmosphere.     

Discrimination between coupling networks of glucopyranosides varying at a single stereocenter using two-dimensional vibrational correlation spectroscopy

A combination of two-dimensional infrared (2DIR) correlation spectroscopy, linear absorption spectroscopy, and density functional theory quantum calculations was used to identify characteristic spectral features of two anomers of acetylated 2-azido-2-deoxy-D-glucopyranose. While the linear absorption spectra for the α and β anomers were distinctive, a substantial difference between them was observed only in the spectral region below 1200 cm(-1). The infrared correlation spectra of the two anomers differed significantly, even in regions where their linear absorption spectra were similar. Very substantial differences were found for the N≡N/C=O stretch mode region of the 2DIR correlation spectrum, indicating differences in the anharmonic coupling of the N≡N stretching mode of the equatorially oriented N(3) group with the CO modes when the C(1) ester was either in the axial (α anomer) or equatorial (β anomer) orientation. In addition, the energy transport patterns originating from the excited N≡N stretching mode were found to be different for the two anomers; up to a 1.8-fold difference in the energy transport times was observed for the probed modes of the same type in the two anomers. The results demonstrate the capability of 2DIR and relaxation-assisted 2DIR (RA 2DIR) spectroscopies to provide unique spectroscopic data specific to sugar anomers that vary at a single stereochemical center. These methods identify unique coupling networks within individual sugar stereochemical units and demonstrate the potential to identify a number of stereochemical differences among them.