Nano- and Microsecond Time-Resolved FTIR Spectroscopy of the Halorhodopsin Photocycle

Abstract— Step-scan Fourier transform infrared spectroscopy with 50 ns time resolution was applied to the early stages of the photocycle of halorhodopsin (hR) for the temperature range 3-42° C. Kinetic data analysis with global fitting revealed two distinct kinetic processes associated with relaxations of the early red-shifted photoproduct hK; these processes have time constants T₁? 280 ns and T₂? 360 μs at 20°C. Spectral features demonstrate that the T₁ process corresponds to a transition between two distinct bathointermediates, hK_E and hK_L. The vibrational difference bands associated with both T₁ and T₂ transitions are spread throughout the whole 1800-900 cm^?1 range. However, the largest bands correspond to ethylenic C=C stretches, fingerprint C-C stretches and hydrogen out-of-plane (HOOP) wags of the retinal chromophore. The time evolution of these difference bands indicate that both the T₁ and T₂ decay processes involve principally a relaxation of the chromophore and its immediate environment. The decay of the intense HOOP vibrations is nearly equally divided between the T₁ and T₂ processes, indicating a complex chromophore relaxation from a twisted nonrelaxed conformation in the primary (hK_E) bathointermediate, to a less-twisted structure in hK_L, and finally to a roughly planar structure in the hypsochromically shifted hL intermediate. This conclusion is also supported by the unexpectedly large positive entropy of activation observed for the T₁ process. The two relaxations from hK_E to hL are largely analogous to corresponding relaxations (K_E→ K_L→ L) in the bacterior-hodopsin photocycle, except that the second step is slowed down by over 200-fold in hR.     

Primary Reaction Dynamics of Proteorhodopsin Mutant D97N Observed by Femtosecond Infrared and Visible Spectroscopy†

Femtosecond time‐resolved spectroscopy in the visible and IR range was utilized to study the primary reaction dynamics of the proteorhodopsin (PR) D97N mutant in comparison with wild type PR at different pH values. The analysis of the data obtained in the mid‐IR closely resembles the results for wild type PR. The observation of the first ground state intermediate K is initially obscured by a complex reaction scheme of vibrational relaxation and heating effects, but its spectral signature clearly emerges at long delay times. In the visible range, a biexponential decay of the excited state within 30 ps and the formation of the K photoproduct is observed. The decay time constants derived for the D97N mutant in D₂O are slightly larger than in H₂O due to H/D exchange. This kinetic isotope effect is even less pronounced than for wild type PR at pH 6. These results support the current notion of a pH dependent hydrogen bonding network in the retinal binding pocket of PR and a weaker interaction between the retinal Schiff base and the counter ion complex compared to bacteriorhodopsin.     

Light‐induced Modulation of Protein Dynamics During the Photocycle of Bacteriorhodopsin†

Knowledge about the dynamical properties of a protein is of essential importance for understanding the structure–dynamics–function relationship at the atomic level. So far, however, the correlation between internal protein dynamics and functionality has only been studied indirectly in steady‐state experiments by variation of external parameters like temperature and hydration. In the present study we describe a novel type of (laser‐neutron) pump‐probe experiment, which combines in situ optical activation of the biological function of a membrane protein with a time‐dependent monitoring of the protein dynamics using quasielastic neutron scattering. As a first successful application we present data obtained selectively in the ground state and in the M‐intermediate of bacteriorhodopsin (BR). Temporary alterations in both localized reorientational protein motions and harmonic vibrational dynamics have been observed during the photocycle of BR. This observation is a direct proof for the functional significance of protein structural flexibility, which is correlated with the large‐scale structural changes in the protein structure occurring during the M‐intermediate. We anticipate that functionally important modulations of protein dynamics as observed here are of relevance for most other proteins exhibiting conformational transitions in the time course of functional operation.     

Retinal Conformation and Dynamics in Activation of Rhodopsin Illuminated by Solid‐state 2H NMR Spectroscopy†

Solid‐state NMR spectroscopy gives a powerful avenue for investigating G protein‐coupled receptors and other integral membrane proteins in a native‐like environment. This article reviews the use of solid‐state ²H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site‐specific ²H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability ²H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three‐fold (C₃) axes with an order parameter for the off‐axial motion of For the dark state, the ²H NMR structure of 11‐cis‐retinal manifests torsional twisting of both the polyene chain and the β‐ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11‐cis to trans isomerization. In addition, ²H NMR has been applied to study the retinylidene dynamics in the dark and light‐activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the β‐ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the β‐ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid‐state ²H NMR thus provides information about the flow of energy that triggers changes in hydrogen‐bonding networks and helix movements in the activation mechanism of the photoreceptor.     

Single Crystals of NaPrTe2 with LiTiO2‐Type Structure

During attempts to synthesize rare‐earth nitride tellurides black and bead‐shaped single crystals of the title compound sodium praseodymium(III) ditelluride (NaPrTe₂) were obtained as a by‐product by reacting a mixture of praseodymium, sodium azide (NaN₃) and tellurium at 900 °C for seven days in evacuated torch‐sealed silica vessels. NaPrTe₂ crystallizes cubic (space group: Fd3¯m, Z = 16; a = 1285.51(9) pm, V_m = 79.96(1) cm³/mol, R₁ = 0.028 for 146 unique reflections) and exhibits the Na⁺ and Pr³⁺ cations in slightly distorted octahedra of six telluride anions (d(Na—Te) = 325 pm, d(Pr—Te) = 317 pm) each. The main characteristics of this new structure type for alkali‐metal rare‐earth(III) dichalcogenides can be derived from the rock‐salt type structure (NaCl, cubic closest‐packed Te^2— arrangement, all octahedral voids occupied with Na⁺ and Pr³⁺) with alternating layers consisting of Na⁺ and Pr³⁺ cations in a ratio of 3:1 and 1:3, respectively, piled along the [111] direction.     

Characterizing the rovibrational distribution of CD2CD2OH radicals produced via the photodissociation of 2-bromoethanol-d4

This work characterizes the internal energy distribution of the CD(2)CD(2)OH radical formed via photodissociation of 2-bromoethanol-d(4). The CD(2)CD(2)OH radical is the first radical adduct in the addition of the hydroxyl radical to C(2)D(4) and the product branching of the OH + C(2)D(4) reaction is dependent on the total internal energy of this adduct and how that energy is partitioned between rotation and vibration. Using a combination of a velocity map imaging apparatus and a crossed laser-molecular beam scattering apparatus, we photodissociate the BrCD(2)CD(2)OH precursor at 193 nm and measure the velocity distributions of the Br atoms, resolving the Br((2)P(1/2)) and Br((2)P(3/2)) states with [2 + 1] resonance enhanced multiphoton ionization (REMPI) on the imaging apparatus. We also detect the velocity distribution of the subset of the nascent momentum-matched CD(2)CD(2)OH cofragments that are formed stable to subsequent dissociation. Invoking conservation of momentum and conservation of energy and a recently developed impulsive model, we determine the vibrational energy distribution of the nascent CD(2)CD(2)OH radicals from the measured velocity distributions.     

Application of dynamic 2D FTIR to cellulose

Cellulose, the dominant polymer in the biosphere, is a homopolysaccharide composed of (1,4)-β-d-glucopyranose. Interactions between and within the cellulose polymer chains are mainly determined by inter- and intramolecular hydrogen bonds, which are therefore mainly responsible for mechanical properties of cellulosic materials. The coupling of dynamic mechanical analysis (DMA) and 2D step-scan Fourier transform infrared (FTIR) spectroscopy, is shown to be a very promising way of investigating these submolecular interactions in cellulosic materials. The broad and unstructured band in the OH-stretching vibration region (3100 and 3700 cm⁻¹) of the cellulose vibrational spectra, which contains information about the intra- and intermolecular hydrogen bonds, can be unraveled by this new technique. In the experiments reported here, cellulose sheets have been stretched sinusoidally at low strains while being irradiated with polarized infrared light. For the obtained dynamic IR signals (the in-phase and the out-of-phase responses of the sample), the dynamic IR cross-correlation was defined. It consists of two terms which are referred to as the synchronous and the asynchronous 2D infrared correlation intensities. In the 2D spectra, obtained by DMA–FTIR, several distinct peaks are observed in the OH-range between 3700 and 3100 cm⁻¹ which may be related to specific interactions.     

Analysis of the Rotational Structure of CO2 by FTIR Spectroscopy

A physical chemistry experiment is described that involves the determination of some spectroscopic parameters of carbon dioxide, a molecule that obeys Bose-Einstein statistics. The main advantage of this experiment is that the spectra are easily recorded, not requiring a gas cell, because the sensitivity and resolution of conventional FTIR spectrometers is good enough to record spectra with a high signal-to-noise ratio and good resolution of the fine rotational structure. From the rotational lines of the antisymmetric stretching band, the moments of inertia and the bond lengths of CO₂ in the fundamental and the first-excited state can be accurately obtained. The particular case that carbon dioxide represents helps students understand the restrictions that symmetry and statistics impose on some molecules and the consequences that they have on the absorption of radiation.     

The Photocycle of Channelrhodopsin‐2: Ultrafast Reaction Dynamics and Subsequent Reaction Steps

The photocycle of channelrhodopsin‐2 is investigated in a comprehensive study by ultrafast absorption and fluorescence spectroscopy as well as flash photolysis in the visible spectral range. The ultrafast techniques reveal an excited‐state decay mechanism analogous to that of the archaeal bacteriorhodopsin and sensory rhodopsin II from Natronomonas pharaonis. After a fast vibrational relaxation of the excited‐state population with 150 fs its decay with mainly 400 fs is observed. Hereby, both the initial all‐trans retinal ground state and the 13‐cis‐retinal K photoproduct are populated. The reaction proceeds with a 2.7 ps component assigned to cooling processes. Small spectral shifts are observed on a 200 ps timescale. They are attributed to conformational rearrangements in the retinal binding pocket. The subsequent dynamics progresses with the formation of an M‐like intermediate (7 and 120 μs), which decays into red‐shifted states within 3 ms. Ground‐state recovery including channel closing and reisomerization of the retinal chromophore occurs in a triexponential manner (6 ms, 33 ms, 3.4 s). To learn more about the energy barriers between the different photocycle intermediates, temperature‐dependent flash photolysis measurements are performed between 10 and 30 °C. The first five time constants decrease with increasing temperature. The calculated thermodynamic parameters indicate that the closing mechanism is controlled by large negative entropy changes. The last time constant is temperature independent, which demonstrates that the photocycle is most likely completed by a series of individual steps recovering the initial structure.     

Rational Construction of 2D and 3D Borromean Arrayed Organic Crystals by Hydrogen‐Bond‐Directed Self‐Assembly

Borromean organic networks: The rigid and trigonal pyramidal molecule, 1,3,5‐tris(4‐carboxyphenyl)adamantane (TCA), self‐assembles into a 2D Borromean linked network by hydrogen bonds. Different linkers (methanol, phenazine, 4,4′‐bipyridine, and 4,4′‐azopyridine) result in more complex Borromean networks or a 3D polycatenation network.

     

Characterizing the Intramolecular H-bond and Secondary Structure in Methylated GlyGlyH<Superscript>+</Superscript> with H<Subscript>2</Subscript> Predissociation Spectroscopy

We report vibrational predissociation spectra of the four protonated dipeptides derived from glycine and sarcosine, GlyGlyH⁺•(H₂)_1,2, GlySarH⁺•(D₂)₂, SarGlyH⁺•(H₂)₂, and SarSarH⁺•(D₂)₂, generated in a cryogenic ion trap. Sharp bands were recovered by monitoring photoevaporation of the weakly bound H₂ (D₂) molecules in a linear action regime throughout the 700–4200 cm^–1 range using a table-top laser system. The spectral patterns were analyzed in the context of the low energy structures obtained from electronic structure calculations. These results indicate that all four species are protonated on the N-terminus, and feature an intramolecular H-bond involving the amino group. The large blue-shift in the H-bonded N–H fundamental upon incorporation of a methyl group at the N-terminus indicates that this modification significantly lowers the strength of the intramolecular H-bond. Methylation at the amide nitrogen, on the other hand, induces a significant rotation (~110^o) about the peptide backbone.     

Dimension Engineering of Stimuli-Responsive 1D Molecular Crystals into Unusual 2D and 3D Zigzag Waveguides

We demonstrate an innovative technique to achieve organic 2D and 3D waveguides with peculiar shapes from an acicular, stimuli-responsive molecular crystal, (2Z,2′Z)-3,3′-(anthracene-9,10-diyl)bis(2-(3,5-bis(trifluoromethyl)phenylacrylonitrile), Ant-CF₃. The greenish-yellow fluorescent (FL) Ant-CF₃ molecular crystals exhibit laser power-dependent permanent mechanical bending in 2D and 3D. Investigation of a single-crystal using spatially-resolved Raman/FL/electron microscopy, and theoretical calculations revealed photothermal (Z,E)/(E,E) isomerization-assisted transition from crystalline to amorphous phase at the laser-exposed regions. This phenomenon facilitates the dimension engineering of a 1D crystal waveguide into 2D waveguide on a substrate or a 3D waveguide in free space. The bends can be used as interconnection points to couple different optical elements. The presented technique has broader implications in organic photonics and other crystal-related photonic technologies.     

Donor‐unsupported Phosphanylmethanides Li[CH2PR2] (R = tBu,Ph) – Crystal Structure of Li[CH2PtBu2] Solved by XRPD and DFT‐D Calculations

The solvent‐free methyllithium derivatives Li[CH₂PR₂] (R = tBu, Ph) were prepared via the reaction of CH₃PR₂ with Li[tBu]. It should be noted that the deprotonation of CH₃PtBu₂ with Li[tBu] occurred at 60 °C, whereas Li[CH₂PPh₂] was already formed from CH₃PPh₂ with Li[tBu] at ambient temperature. The structure determination of di‐tert‐butylphosphanylmethyllithium was performed by high resolution X‐ray powder diffraction analysis at different temperatures. This led to two possible structure solutions with similar quality criteria (space groups Iba2 and I2/a). Therefore CASTEP DFT‐D calculations were applied to verify the correct crystal structure. The solid‐state structure of di‐tert‐butylphosphanylmethyllithium consists of alternating edge‐sharing six‐ and four‐membered rings, which form a polymeric, infinite double‐chain along the crystallographic c axis in the monoclinic space group I2/a. Two Li[CH₂PtBu₂] units connected via an inversion center form a six‐membered Li₂C₂P₂ ring in the chair conformation. The nearly flat four‐membered Li₂C₂ ring, is oriented perpendicularly to the twofold axis.     

Solution-State 2D NMR Spectroscopy of Mixtures HyperpolarizedUsing Optically Polarized Crystals

The HYPNOESYS method (Hyperpolarized NOE System), which relies on the dissolution of optically polarized crystals, has recently emerged as a promising approach to enhance the sensitivity of NMR spectroscopy in the solution state. However, HYPNOESYS is a single-shot method that is not generally compatible with multidimensional NMR. Here we show that 2D NMR spectra can be obtained from HYPNOESYS-polarized samples, using single-scan acquisition methods. The approach is illustrated with a mixture of terpene molecules and a benchtop NMR spectrometer, paving the way to a sensitive, information-rich and affordable analytical method.     

Conformation and Interaction of a D,L-alternating peptide with a bilayer membrane: x-ray reflectivity, CD, and FTIR spectroscopy.

Peptides with alternating amino acid configuration provide helical secondary structures that are especially known from the membrane channel and pore-forming gramicidin A. In analogy to this natural D,L-alternating pentadecapeptide, the potential of D,L-alternating peptides for membrane insertion is investigated using the model dodecamer peptide H-(Phe-Tyr)(5)-Trp-Trp-OH. This aromatic peptide is introduced as a novel pore-forming synthetic analogue of gramicidin A. It forms a well-organized homodimer similar to one of the gramicidin A transmembrane motifs. X-ray reflectivity measurements are performed on solid-supported peptide-lipid complexes to obtain information about the influence of the artificial dodecamer peptide on the bilayer parameters. In addition, Fourier-transform infrared (FTIR) and circular dichroism (CD) spectroscopic studies determine the conformational state of H-(Phe-Tyr)(5)-Trp-Trp-OH within the model membrane. Site-specific iodine labeling assists in determining the topology of the membrane-embedded peptide by pinpointing the position of the iodine label within the bilayers.     

Stitching 2D Polymeric Layers into Flexible Interpenetrated Metal–Organic Frameworks within Single Crystals

A 2D coordination polymer prepared with bulky diethylformamide solvates exhibits channels which allow dipyridyl bridging ligands to diffuse into the crystal lattice. The absorbed dipyridyls thread through the pores of one layer and substitute the surface diethylformamide molecules on the neighboring layers to stitch alternate layers to form flexible interpenetrated metal–orgaic frameworks. The threading process also results in exchange of the bulky diethylformamide solvates for aqua to minimize congestion and, more strikingly, forces the slippage of two‐dimensional layers, while still maintaining crystallinity.     

Growth and Structure of Lanthanum Polysulfide Crystals

Single crystals of lanthanum polysulfide were grown under nearly equilibrium conditions according to the P _S ndash;T–x diagram of the LaS_1.5–LaS₂ system described in the literature, and quenched from a temperature of 820°C. The structure of these crystals was determined. Their compositions are LaS_1.96(2) and LaS_2.00(2). The crystals of both compositions belong to the rhombic Pnma space group with a slight variation in lattice parameters in the ranges a = 8.133–8.124, b = 16.345–16.334, and c = 4.128–4.131. The nonstoichiometric polysulfide LaS_1.96 is treated as a spatially averaged, disordered individual phase. Arguments are given that these polysulfide phases have compositions intermediate between LaS_1.5 and LaS₂.