Switch the click: Ultrafast photochemistry of photoDIBO-OH tracked by time-resolved IR spectroscopy.

Click chemistry refers to selective reactions developed for grafting of bio(macro)molecules in their biological media. Caged click compounds have been employed to spatiotemporally control click reactions. Here, we survey the uncaging of photo-dibenzocyclooctyne-OH (photoDIBO-OH) to its click-chemistry active form DIBO-OH, with particular attention to its conversion timescale and efficiency. Ultraviolet pump-infrared probe experiments reveal a stepwise decarbonylation: first, carbon monoxide (C≡O) is released within 1.8 ps, and then, it converts, within 10 ps, to DIBO-OH. Completion of uncaging is achieved with an efficiency of ∼50%. A successful demonstration of two-photon uncaging of photoDIBO-OH at long wavelength (700 nm) confers enhanced in vivo compatibility and proceeds on the same timescale.

SH-It happens: S-H bonds as intrinsic 2D-IR labels in proteins.

Cysteine S-H bonds have a spectroscopically convenient stretching frequency of ∼2550 cm-1. However, their cross section is low, and the band can be strongly broadened in heterogeneous environments, making detection very challenging. With two-dimensional infrared (2D-IR) setups achieving ever higher sensitivities in recent years, systematic use of the weak cysteine sulfhydryls (Cys-SHs) absorption band is now within reach, even at low millimolar protein concentrations. Here, we demonstrate the capabilities of Cys-SH as an intrinsic 2D-IR label in pyruvate oxidase from E. coli, an enzyme with ten cysteines in its native sequence. 1D-IR measurements on the wild-type and individual cysteine knock-out variants show that two such residues have especially narrow SH signatures, caused by their intrahelical hydrogen bonding. 2D-IR analysis of these bands reveals an extraordinarily high anharmonicity (∼110 cm-1) and a long vibrational lifetime (∼4 ps). This allows monitoring spectral diffusion via center line slope analysis for up to 10 ps-separately for both the ground and excited states. The unique spectroscopic features and its ease of introduction make Cys-SH a useful IR spectroscopic label.

High-precision background correction and artifact suppression for ultrafast spectroscopy by quasi-simultaneous measurements in a split-sample cell.

Alternating acquisition of background and sample spectra is often employed in conventional Fourier-transform infrared spectroscopy or ultraviolet-visible spectroscopy for accurate background subtraction. For example, for solvent background correction, typically a spectrum of a cuvette with solvent is measured and subtracted from a spectrum of a cuvette with solvent and solute. Ultrafast spectroscopies, though, come with many peculiarities that make the collection of well-matched, subtractable background and sample spectra challenging. Here, we present a demountable split-sample cell in combination with a modified Lissajous scanner to overcome these challenges. It allows for quasi-simultaneous measurements of background and sample spectra, mitigating the effects of drifts of the setup and maintaining the beam and sample geometry when swapping between background and sample measurements. The cell is moving between subsequent laser shots to refresh the excited sample volume. With less than 45 µl of solution for 150 µm optical thickness, sample usage is economical. Cell assembly is a key step and covered in an illustrated protocol.

Photochemical mechanism of DEACM uncaging: a combined time-resolved spectroscopic and computational study.

The elementary steps of photocleavage in (coumarin-4-yl)methyl photoremovable protecting groups (PPGs) are elucidated by a combined electronic structure and time-resolved visible pump infrared probe (VIS-pump IR-probe) spectroscopic study. We specifically focus on the [7-(diethylamino)coumarin-4-yl]methyl (DEACM) PPG which has found increasing interest in biological applications over recent years. A series of leaving groups (LGs) are investigated, including azide (DEACM-N3), thiocyanate (DEACM-SCN), carbonate (DEACM-Carb), and a thymine nucleobase (DEACM-T) representing a model system for caged DNA. These systems are found to exhibit vastly different photocleavage time scales, ranging from the subpicosecond scale in the case of DEACM-SCN to ∼35 picoseconds in the case of DEACM-N3 and ∼540 picoseconds in the case of DEACM-Carb. In the case of DEACM-SCN, the appearance of the product is biphasic, with a fast (

Note: An automatic liquid nitrogen refilling system for small (detector) Dewar vessels.

Many infrared spectroscopy setups are in principle stable enough to run overnight or longer, but the detector's Dewar vessel must be refilled manually with liquid nitrogen (LN2) every couple of hours. Commercial automatic LN2 refilling systems work reliably only for large Dewars. Here, we present a refilling system which can non-invasively be applied to already installed small Dewars. The system reliably refills LN2 once it has dropped below an adjustable level, with quick refilling (<3 min) for a 0.6 l Dewar. Our design protects the setup and the detector from overflowing or running without LN2.

Cyano-tryptophans as dual infrared and fluorescence spectroscopic labels to assess structural dynamics in proteins.

The steady state and time-resolved fluorescence and infrared (IR) properties of 4- and 5-cyanotryptophan (CNTrp) are investigated and compared, and the tryptophan (Trp) analogs are found to be very attractive to study structural and dynamic properties of proteins. The position of the nitrile substitution as well as the solvent environment influences the spectroscopic properties (solvatochromism). Similar to native Trp, electronic (nanosecond) lifetime and emission spectra are modulated by the environment, making CNTrps attractive fluorescent probes to study the structural dynamics of proteins in complex media. The nitrile absorption in the IR region can provide local structural information as it responds sensitively to changes in electrostatics and hydrogen bond (HB) interactions. Importantly, we find that 4CNTrp exhibits a single absorption in the nitrile stretch region, while the model compound 4CN-indole (4CNI) shows two. Even though the spectrum of the model compound is perturbed by a Fermi resonance, we find that 4CNTrp itself is a useful IR label. Moreover, if the nitrile group is substituted at the 5 position, the Trp analog predominantly reports on its HB status. Because the current literature on similar compounds is too limited for a detailed solvatochromic analysis, we extend the available data significantly. Only now are microscopic details such as the mentioned sensitivity to electrostatics coming to light. The vibrational lifetime of the CN moiety (acting on a picosecond time scale in contrast to the nanosecond time scale for fluorescent emission) allows for its application in 2D-IR spectroscopy in the low picosecond range. Taken together, the benefits of CNTrps are that they absorb and emit separately from the naturally occurring Trp and that in these dual fluorescence/vibrational labels, observables of IR and fluorescence spectroscopy are modulated differently by their surroundings. Because IR absorption and fluorescence operate on different time and length scales, they thus provide complementary structural information.

Picosecond activation of the DEACM photocage unravelled by VIS-pump-IR-probe spectroscopy.

The light-induced ultrafast uncaging process of the [7-(diethylamino)coumarin-4-yl]methyl (DEACM) cage is measured by time-resolved visible-pump-infrared-probe spectroscopy, and supported by steady-state absorption spectroscopy in the visible and infrared spectral regions. Understanding the uncaging process is important because its favorable properties make DEACM an interesting case for chemical and biological applications. It has a convenient absorption in the visible spectral range, and is relatively easily modified to carry leaving groups (LGs) such as nucleotides, substrates or inhibitors, which are inactive when bound and active when released. Previous work suggested a lower limit for the uncaging rate, which places it among the fastest available cages. Here, we determine the photodissociation directly to occur on the picosecond time scale by monitoring the appearance of the released LG in the infrared spectral region. In the present study, azide (N3) is chosen as an LG to monitor photodissociation because its vibrational mode is spectrally isolated (hence easy to follow) and its absorption wavenumber is sensitive to local structural rearrangements. The uncaging process is recorded up to 3 nanoseconds and compared to the collected steady-state spectra. The free LG appears on a picosecond time scale, rendering this one of the fastest known cages. No evidence is found for a tight-ion pair (TIP) preceding the free LG. The uncaging mechanism is found to be slowed down upon the addition of water to acetonitrile.

Exploring photochemistry of p-bromophenylsulfonyl, p-tolylsulfonyl and methylsulfonyl azides by ultrafast UV-pump-IR-probe spectroscopy and computations.

The photochemistry of p-bromophenylsulfonyl azide (BsN3), p-tolylsulfonyl azide (TsN3) and methylsulfonyl azide (MsN3) was studied by femtosecond time-resolved infrared spectroscopy with CH2Cl2 and CCl4 as solvents along with quantum chemical calculations. The photolysis of these azides after 267 nm light excitation leads to the population of each respective azide S1 excited state. Decay of the S1 excited state gives rise to singlet nitrene formation. In the case of BsN3, the decay was found to correlate with the formation of a pseudo-Curtius photoproduct (PCP) BrC6H4NSO2. Transient electronic ground states of the three azides on their way to singlet nitrenes and PCPs were shown by locating the corresponding transition states on the potential energy surfaces. The lifetime of singlet (1)(BsN) and (1)(TsN) nitrenes is τ(S) = ∼20 ps in CH2Cl2 and ∼700 ps in CCl4. Singlet (1)(MsN) was not detected. Due to fast intersystem crossing (ISC), singlet nitrenes are converted into the triplet spin isomers lying lower in energy, the formation time constants being equal to the corresponding singlet nitrene lifetime. The formation of (3)(MsN) was shown and the formation time constant in CH2Cl2 was found to be τ(ISC) = 34 ± 3 ps. Internal conversion of the S1 excited state to the ground state of the azide was low (Φ ≈ 0.15) for BsN3 and TsN3 and was not found in the case of MsN3.