Dynamic NMR spectroscopy in studies of the kinetics of photoinduced chemical exchange in solutions

Modern NMR-based methods of studying the kinetics and mechanisms of reversible photochemical reactions in solutions are surveyed. Detailed consideration of peculiar features of the experimental techniques based on NMR lineshape analysis and double resonance NMR and used for the determination of the effective rate constants for and quantum yields of photoinduced chemical exchange processes is presented. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1631–1641, October, 2006.     

Sub-picosecond mid-infrared spectroscopy of phytochrome Agp1 from Agrobacterium tumefaciens.

The photoinduced primary reaction of the biliverdin binding phytochrome Agp1 (Agp1-BV) from Agrobacterium tumefaciens was investigated by sub-picosecond time-resolved Vis pump-IR probe spectroscopy. Three time constants of tau(1)=0.7+/-0.05 ps, tau(2)=3.3+/-0.2 ps and tau(3)=33.3+/-1.5 ps could be isolated from the dynamics of structurally specific marker bands of the BV chromophore. These results together with those of accompanying sub-picosecond Vis pump-Vis probe spectroscopy allow the extension of the reaction scheme for the primary process by a vibrationally excited electronic ground state. The isomerization at the C15=C16 bond occurs within the lifetime of the excited electronic state. A quantum yield of 0.094 for the primary reaction is determined, suggesting that the quantum yield of formation of the P(fr) far-red-absorbing form is already established in the primary photoreaction of the P(r) (red-absorbing) form.     

Far infrared fourier transform spectroscopy of semiconductors

Fourier transform spectroscopy (FTS) is one of the most important tools in the study of shallow level donors and acceptors in semiconductors. When combined with a two-step photothermal ionization process detected photoconductively, FTS allows measurement of optical transitions of donor-bound electrons (and acceptor-bound holes) in ultra-pure germanium samples with impurity concentrations <10⁹ cm^–3 (i.e. one electrically active impurity in 4×10¹³ host atoms). The experimental high resolution study of the hydrogen-like excited state series of shallow levels has yielded as many as 19 lines of width as small as 10eV for some centers. These results have stimulated theoretical work which has led to the unambiguous assignment of quantum states to many bound excited states. Extensive studies of ultra-pure Ge crystals grown under different well-controlled conditions have led to the discovery of a large number of novel shallow impurity complexes. Study of the multiplicities and symmetries of the associated electronic states has led to a detailed understanding of the unusual static and dynamic structures of these novel centers. The chemical composition has been deduced from correlations between the concentration of a particular center and the materials involved in crystal gowth. Isotopic substitution of hydrogen with deuterium has led to the unambiguous proof of the presence of hydrogen in several of the novel centers. In addition to the high resolution spectra of shallow electronic levels, vibrational spectra of bond-centered interstitial oxygen in ultra-pure Ge are noteworthy for their extraordinarily sharp lines.     

Two-dimensional infrared (2D IR) spectroscopy. A new tool for interpreting infrared spectra

Two-dimensional infrared (2D IR) spectroscopy is used to study atactic polystyrene. 2D IR is a technique based on time-resolved detection of IR signals in response to an external perturbation, such as mechanical strain. Since different chemical functional groups respond to the applied perturbation at unique and often different rates, characteristic time-dependent variations of the IR-band intensities are observed. Correlation analysis of the dynamic variation of the IR signals yields a new spectrum defined by two independent wave numbers. Peaks located on a 2D IR spectral plane imply interactions and connectivities among chemical functional groups. By spreading convoluted IR bands over two dimensions, the spectral resolution is also greatly enhanced.     

Oxidation states and CO ligand exchange kinetics in a self-assembled monolayer of a triruthenium cluster studied by in situ infrared spectroscopy

Oxidation states and CO ligand exchange kinetics in a self-assembled monolayer (SAM) of an oxo-centered triruthenium cluster [Ru(3)(mu3-O)(mu-CH3COO)6(CO)(L1)(L2)] (L1 = [(NC5H4)CH2NHC(O)(CH2)10S-]2, L2 = 4-methylpyridine) have been extensively investigated on the surface of a gold electrode in aqueous and nonaqueous solutions. The SAM exhibits three consecutive one-electron transfers and four oxidation states, which have been characterized by electrochemistry, in situ infrared spectroscopy, and in situ sum frequency generation (SFG) vibrational spectroscopy measurements. The original electron-localized state of the Ru cluster center was changed to electron delocalization states by oxidation or reduction of the central Ru ions. These changes are revealed by the IR absorptions of the CO ligand and the bridging acetate ligands of the triruthenium cluster in the SAM. The IR absorptions of the two kinds of ligands are strongly dependent on the oxidation state of the Ru cluster center. One-electron oxidation of the central Ru ion in the SAM triggers a CO ligand liberation process. Solvent molecules may then occupy the CO site to result in a CO-free SAM. One-electron reduction of this CO-free SAM in a CO-saturated solution leads to re-coordination of the CO ligand into the SAM. Both processes can be precisely controlled by tuning the electrode potential. The kinetics of the CO exchange cycle in the SAM, including liberation and coordination, has been investigated by in situ IR and SFG measurements for the first time. The CO exchange cycle is significantly dependent on the temperature. The reaction rate greatly decreases with decreasing solution temperature, which is an important factor in the CO ligand exchange process. The activation energies of both CO liberation and coordination have been evaluated from the reaction rate constants obtained at various temperatures.     

Real-time monitoring of chemical transformations by ultrafast 2D NMR spectroscopy

An approach enabling the acquisition of 2D nuclear magnetic resonance (NMR) spectra within a single scan has been recently proposed. A promising application opened up by this "ultrafast" data acquisition format concerns the monitoring of chemical transformations as they happen, in real time. The present paper illustrates some of this potential with two examples: (i) following an H/D exchange process that occurs upon dissolving a protonated protein in D2O, and (ii) real-time in situ tracking of a transient Meisenheimer complex that forms upon rapidly mixing two organic reactants inside the NMR observation tube. The first of these measurements involved acquiring a train of 2D 1H-15N HSQC NMR spectra separated by ca. 4 s; following an initial dead time, this allowed us to monitor the kinetics of hydrogen exchange in ubiquitin at a site-resolved level. The second approach enabled us to observe, within ca. 2 s after the triggering of the reaction, a competition between thermodynamic and kinetic controls via changes in a series of 2D TOCSY patterns. The real-time dynamic experiments hereby introduced thus add to an increasing family of fast characterization techniques based on 2D NMR; their potential and limitations are briefly discussed.     

New accessory for studies of isotopic 1H/2H exchange and biomolecular interactions using transmission infrared spectroscopy

We present here a new accessory for IR transmission measurements of ¹H/²H exchange, as an ancillary tool for monitoring structural features of biomolecules in aqueous solution. This new accessory results from the combination of two dialysis membranes and a conventional liquid cell having two cylinders containing ²H₂O buffer. When compared with conventional transmission measurements, carried out either after dissolving lyophilized biomolecules in ²H₂O or after dialyzing the aqueous solution considered against ²H₂O buffer, this accessory shows the following advantages: (1) controlled measurements over the initial steps of this isotopic exchange and absence of molecular aggregation, and (2) smaller sample amounts. This new Fourier transform IR cell can also be used to analyze ligand–biomolecule and drug–cell interactions.      

Ultrafast 2D-IR spectroscopy of transient species.

Multidimensional spectroscopic experiments offer fascinating insights into molecular structure and dynamics in the field of NMR spectroscopy. With the introduction of ultrafast two-dimensional infrared spectroscopy (2D-IR), multidimensional concepts have entered the optical domain, measuring couplings and correlations between molecular vibrations with femtosecond time resolution. In the transient 2D-IR (T2D-IR) experiments described in this minireview we exploit the high time resolution of 2D-IR to study transient species during fast nonequilibrium processes in real time. Information on molecular structure and dynamics is obtained that is not available from one-dimensional spectroscopy. We discuss examples from chemistry, physics and biophysics.     

Phosphorus-containing podands. 8. A study of metal-ligand interaction by fourier transform infrared spectroscopy in anhydrous acetonitrile

The interaction of phosphorus-containing monopodands with Li⁺, Na⁺, and K⁺ cations in anhydrous CH₃CN has been studied by FTIR spectroscopy. It has been shown that phosphoryl groups of the ligands take part in the formation of complexes with the alkali metal cation. The IR results obtained do not permit a clear conclusion as to whether or not the ether oxygen atoms of the ligand polyether chain participate in the complexation. It is suggested that in CH ₃ CN the formation of 1:1 complexes is not accompanied by conformational reorganization of the monopodand.Institute of Physiologically Active Substances, Russian Academy of Sciences, Chernogolovka 142432. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 884–889, April, 1992.     

Gas-phase infrared photodissociation spectroscopy of tetravanadiumoxo and oxo-methoxo cluster anions.

The infrared spectra of the binary vanadium oxide cluster anions V(4)O(9)(-) and V(4)O(10)(-) and of the related methoxo clusters V(4)O(9)(OCH(3))(-) and V(4)O(8)(OCH(3))(2)(-) are recorded in the gas phase by photodissociation of the mass-selected ions using an infrared laser. For the oxide clusters V(4)O(9)(-) and V(4)O(10)(-), the bands of the terminal vanadyl oxygen atoms, nu(V-O(t)), and of the bridging oxygen atoms, nu(V-O(b)-V), are identified clearly. The clusters in which one or two of the oxo groups are replaced by methoxo ligands show additional absorptions which are assigned to the C-O stretch, nu(C-O). Density functional calculations are used as a complement for the experimental studies and the interpretation of the infrared spectra. The results depend in an unusual way on the functional employed (BLYP versus B3LYP), which is due to the presence of both V-O(CH(3)) single and V=O double bonds as terminal bonds and to the strong multireference character of the latter.     

Calculation of two-dimensional infrared spectra of ultrafast chemical exchange with numerical Langevin simulations

We combine numerical Langevin simulations with numerical integration of the Schrodinger equation to calculate two-dimensional infrared spectra of ultrafast chemical exchange. This provides a tool to model and interpret such spectra of molecules undergoing chemical processes, such as isomerization and solvent exchange reactions. Two-dimensional infrared spectroscopy has already been used to extract reaction rates for ultrafast chemical reactions. We demonstrate that these spectra are not only sensitive to the rates, but also to the finite duration of the exchange. This is emphasised by comparing with the popular Kubo two-state jump models, which do not account for finite exchange times.     

Analysis of thin solid films and surfaces by infrared spectroscopy

Thin solid films and surfaces are characterized by IR spectroscopy, based on reflectance and transmittance measurements, in particular with polarized light at oblique incidence. Thus two independent data sets fors- andp-polarization are available. Atp-polarization additional absorption lines at the zeros of the dielectric function are observed (Berreman-mode). The interpretation of the measured spectra is carried out by a fit procedure to simulate the observed spectra. As a result the specimens are characterized in terms of vibronic resonances and their oscillator strengths or concentration, thicknesses of various films in a stack of layers, profiles of depth depending chemical composition, or concentration and mobility of conduction electrons.All examples are relevant for application in technology, as microelectronics, thin film technology, catalysis, e.g. The results of the IR analysis are compared with those of other analytical methods as SIMS, RBS, and AES. The agreement is very good. One important advantage of the IR analysis, however, is the fact that it is a non-destructive method.     

Characterization of fungal degraded lime wood by FT-IR and 2D IR correlation spectroscopy

The action of soft-rot fungus Chaetomium globosum has been studied. The decayed lime wood samples were observed for different periods of exposure. The degree of decay was determined by weight loss which was of 50.4% after 133 days. The samples were analyzed by FT-IR and 2D IR correlation spectroscopy.The intensity bands assigned to different vibrations from cellulose and hemicelluloses show a decrease, while the intensities of the bands assigned to C–O vibrations due to the formation of oxidized structures increase. At the same time, the intensity of the band assigned to C–O in metoxyl groups from lignin shows a decrease with increasing exposure time. The differences between reference and decayed wood spectra were examined in detail using 2D correlation spectroscopy and the second derivative analysis for two exposure time periods — of 0–70 days and 70–133 days. The formation of reactive species due to oxidation reactions induced by enzymes and the demethoxylation of the lignin structure was evidenced.     

Rapid discrimination of Eurycoma longifolia extracts by Fourier transform infrared spectroscopy and two dimensional correlation infrared spectroscopy

Eurycoma longifolia is a herbal medicinal plant of South-East Asian origin, popularly recognized as ‘Tongkat Ali’. The root extracts have been used in indigenous traditional medicines for its unique antimalarial, anti-pyretic, antiulcer, cytotoxic and aphrodisiac properties. It is an important task that fast and effective analysis methods monitor the inherent qualities of traditional herbal medicines and its corresponding extracts products as a complicated mixture system. Owing to the unique fingerprint character and extensive applicability to test sample, infrared spectral method have been used in many research fields. In this paper, we use FT-IR, second derivative infrared spectroscopy and two-dimensional correlation infrared spectroscopy (2D-IR) step by step to analyze E. longifolia and its different extracts (extracted by hexane, ethyl acetate, dichloromethane and methanol in turn). The findings indicated that FT-IR and 2D-IR can provide many holistic variation rules of chemical constituents. The structural information of the samples indicated that E. longifolia and its extracts contain a large amount of quassinoids, since some characteristic absorption peaks of quassinoids, such as ∼1700 cm⁻¹, ∼1670 cm⁻¹, ∼1600 cm⁻¹,∼1500 cm⁻¹, and ∼1270 cm⁻¹ can be detected. This method, having its high resolution and excellent macroscopic fingerprint features, can not only supply lots of structural information of main components in the complicated system, but also can differentiate the tiny differences between the similar systems according to the macro-fringerprint characters. This method is highly rapid, effective, accurate and well repetitive for pharmaceutical research.     

Stochastic simulation of chemical exchange in two dimensional infrared spectroscopy

The stochastic Liouville equations are employed to investigate the combined signatures of chemical exchange (two-state jump) and spectral diffusion (coupling to an overdamped Brownian oscillator) in the coherent response of an anharmonic vibration to three femtosecond infrared pulses. Simulations reproduce the main features recently observed in the OD stretch of phenol in benzene.