Tuning Fe-Se Tetrahedral Frameworks by a Combination of [Fe(en)[subscript 3]][superscript 2+] Cations and Cl[superscript -] Anions
Abstract not provided
Gamage, Eranga H.↗
SEARCH · Engineering Papers
Results for “backbone”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Influence of the Cubic Sublattice on Magnetic Coupling between the Tetrahedral Sites of Garnet
Here, we present a study on the nuclear and magnetic structures of two iron-based garnets with magnetic cations isolated on tetrahedral sites. Ca 2 YZr 2 Fe 3 O 12 and Ca 2 LaZr 2 Fe 3 O 12 offer an interesting comparison for examining the effect of increasing cation size within the diamagnetic backbone of the garnet crystal structure, and how such changes affect the magnetic order. Despite both systems exhibiting well-pronounced magnetic transitions at low temperatures, we also find evidence for diffuse magnetic scattering due to a competition between the nearest-neighbor, next nearest-neighbor, and so on, within the tetrahedral sites. This competition results in a complex noncollinear magnetic structure on the tetrahedral sublattice creating a mixture of ferro- and antiferromagnetic interactions above the long-range ordering temperature near 20 K and suggests that the cubic site of the garnet plays a significant role in mediating the superexchange interactions between tetrahedral cations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Chelating Rare-Earth Metals (Ln 3+ ) and 225 Ac 3+ with the Dual-Size-Selective Macrocyclic Ligand Py 2 -Macrodipa
Radioisotopes of metallic elements, or radiometals, are widely employed in both therapeutic and diagnostic nuclear medicine. For this application, chelators that efficiently bind the radiometal of interest and form a stable metal–ligand complex with it are required. Toward the development of new chelators for nuclear medicine, we recently reported a novel class of 18-membered macrocyclic chelators that is characterized by their ability to form stable complexes with both large and small rare-earth metals (Ln 3+ ), a property referred to as dual size selectivity. A specific chelator in this class called py-macrodipa, which contains one pyridyl group within its macrocyclic core, was established as a promising candidate for 135 La 3+ , 213 Bi 3+ , and 44 Sc 3+ chelation. Building upon this prior work, here we report the synthesis and characterization of a new chelator called py 2 -macrodipa with two pyridyl units fused into the macrocyclic backbone. Its coordination chemistry with the Ln 3+ series was investigated by NMR spectroscopy, X-ray crystallography, density functional theory (DFT) calculations, analytical titrations, and transchelation assays. These studies reveal that py 2 -macrodipa retains the expected dual size selectivity and possesses an enhanced thermodynamic affinity for all Ln 3+ compared to py-macrodipa. By contrast, the kinetic stability of Ln 3+ complexes with py 2 -macrodipa is only improved for the light, large Ln 3+ ions. Based upon these observations, we further assessed the suitability of py 2 -macrodipa for use with 225 Ac 3+ , a large radiometal with valuable properties for targeted α therapy. Radiolabeling and stability studies revealed py 2 -macrodipa to efficiently incorporate 225 Ac 3+ and to form a complex that is inert in human serum over 3 weeks. Although py 2 -macrodipa does not surpass the state-of-the-art chelator macropa for 225 Ac 3+ chelation, it does provide another effective 225 Ac 3+ chelator. Furthermore, these studies shed light on the fundamental coordination chemistry of the Ln 3+ series and may inspire future chelator design efforts.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Sulfur-Ligated [2Fe-2C] Clusters as Synthetic Model Systems for Nitrogenase
Metal clusters featuring carbon and sulfur donors have coordination environments comparable to the active site of nitrogenase enzymes. Here, we report a series of di-iron clusters supported by the dianionic yldiide ligands, in which the Fe sites are bridged by two μ 2 -C atoms and four pendant S donors. The [L 2 Fe 2 ] (L = {[Ph 2 P(S)] 2 C} 2– ) cluster is isolable in two oxidation levels, all-ferrous Fe 2 II and mixed-valence Fe II Fe III . The mixed-valence cluster displays two peaks in the Mössbauer spectra, indicating slow electron transfer between the two sites. The addition of the Lewis base 4-dimethylaminopyridine to the Fe2 II cluster results in coordination with only one of the two Fe sites, even in the presence of an excess base. Conversely, the cluster reacts with 8 equiv of isocyanide t BuNC to give a monometallic complex featuring a new C–C bond between the ligand backbone and the isocyanide. The electronic structure descriptions of these complexes are further supported by X-ray absorption and resonant X-ray emission spectroscopies.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Lewis Acids and Electron-Withdrawing Ligands Accelerate CO Coordination to Dinuclear Cu I Compounds
A series of dinuclear molecular copper complexes were prepared and used to model the binding and Lewis acid stabilization of CO in heterogeneous copper CO 2 reduction electrocatalysts. Experimental studies (including measurement of rate and equilibrium constants) and electronic structure calculations suggest that the key kinetic barrier for CO binding may be a σ-interaction between CuI and the incoming CO ligand. The rate of CO coordination can be increased upon the addition of Lewis acids or electron-withdrawing substituents on the ligand backbone. Conversely, K eq for CO coordination can be increased by adding electron density to the metal centers of the compound, consistent with stronger π-backbonding. Lastly, the electrochemically measured kinetic results were mapped onto an electrochemical zone diagram to illustrate how these system changes enabled access to each zone.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ligand Noninnocence in β-Diketiminate and β-Diketimine Copper Complexes
Metal–ligand cooperative systems have a long precedent in catalysis, with the classification depending on the site of substrate bond cleavage and formation and on redox state changes. Recently, our group reported the participation of a β-diketiminate ligand in chemical bonding to heterocumulenes such as CO 2 and CS 2 by tricopper complexes, leading to cooperative catalysis. Herein, we report the reactivity of these copper clusters, [Cu 3 EL] – (E = S, Se; L = tris(β-diketiminate) cyclophane ligand), toward other electrophiles, viz. alkyl halides and Brønsted acids. We identified a family of ligand-functionalized complexes, Cu 3 EL (R) (R = primary alkyls), and a series of disubstituted products, Cu 3 EL (R) 2 , through single-crystal X-ray diffraction, mass spectrometry, and infrared and UV–visible spectroscopy. Furthermore, as part of mechanistic studies on these alkylation reactions, we evaluated the acid–base reactivity of these complexes and the influence of the backbone substitution on the reduction potential. Implications of these findings for ligand noninnocence and the relevance of the metal core as a cofactor for the ligand’s reactivity are discussed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure
Coarse-grained modeling can be used to explore general theories that are independent of specific chemical detail. In this paper, we present cg_openmm, a Python-based simulation framework for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics of cooperative secondary structures. cg_openmm facilitates the building of coarse-grained topology and random starting configurations, setup of GPU-accelerated replica exchange molecular dynamics simulations with the OpenMM software package, and features a suite of postprocessing thermodynamic and structural analysis tools. In particular, native contact analysis, heat capacity calculations, and free energy of folding calculations are used to identify and characterize cooperative folding transitions and stable secondary structures. In this work, we demonstrate the capabilities of cg_openmm on a simple 1–1 Lennard-Jones coarse-grained model, in which each residue contains 1 backbone and 1 side-chain bead. By scanning both nonbonded and bonded force-field parameter spaces at the coarse-grained level, we identify and characterize sets of parameters which result in the formation of stable helices through cooperative folding transitions. Furthermore, we show that the geometries and stabilities of these helices can be tuned by manipulating the force-field parameters.
36 MATERIALS SCIENCE↗
Low-Lying Excited States of Linear All- Trans Polyenes: Insights from Analytic Gradient and Nonadiabatic Coupling Calculations Based on Multireference Configuration Interaction
Polyenes serve as a rigorous test for theoretical models and electronic structure methods, playing a key role in advancing computational and theoretical chemistry. Here, we present a high-level theoretical investigation of linear, all-trans polyenes using energy gradients and nonadiabatic coupling vectors based on an MR-CISD wave function to describe electronic transitions involving the ground state (1 1 A g – ) and three low-lying excited states (2 1 A g – , 1 1 B u + , and 2 1 B u – ) of hexatriene, octatetraene, and decapentaene. This approach enables accurate evaluation of both adiabatic and vertical excitation and emission energies, yielding results in excellent agreement with experiment, as well as locating minima on the crossing seam between adiabatic states. Our results show that vertical excitation energies to the 1 1 B u + state are blue-shifted by 0.2–0.3 eV relative to the experimental absorption maximum, whereas the vertical emission energy from the 2 1 A g – state is red-shifted by ∼0.2 eV relative to the experimental emission maximum. Upon relaxation from the Franck–Condon geometry, the 2 1 A g – state stabilizes by around 1 eV, compared to 0.2–0.3 eV for the 1 1 B u + state. An analysis of the S 1 /S 0 crossing seam in hexatriene shows that its minimum involves asymmetric backbone deformations and provides an efficient channel for ultrafast internal conversion to the ground state, consistent with the absence of detectable fluorescence in this molecule. These results demonstrate the power of analytic gradients and nonadiabatic coupling vectors based on an MR-CISD wave function for accurately characterizing the electronic structure and photophysics of polyenes.
Excited states↗
Substituent Effects on the Electronic Spectroscopy of Four-Carbon Criegee Intermediates
Atmospheric ozonolysis of biogenic and anthropogenic alkenes generates zwitterionic carbonyl oxide intermediates (R 1 R 2 C=O + O – ), known as Criegee intermediates, with different structural motifs and conformations. This study reports a systematic laboratory study of substituent effects on the electronic spectroscopy of four-carbon Criegee intermediates (CIs) with methyl–ethyl (MECI) and isopropyl (IPCI) groups, which are isomers produced in ozonolysis of asymmetric branched alkenes. The four-carbon CIs are separately generated by an alternative synthetic route, and spectroscopically characterized on the strong π* ← π transition associated with the carbonyl oxide group in a pulsed supersonic expansion with VUV photoionization at 118 nm and UV-induced depletion of the m/z 88 signal. The resultant broad and unstructured UV spectral features for MECI and IPCI are peaked at ca. 320 and 330 nm, respectively, with large absorption cross-sections of ca. 10 –17 cm 2 . Comparisons are made with the four-carbon CIs formed in isoprene ozonolysis, methyl vinyl ketone oxide (MVK-oxide) and methacrolein oxide (MACR-oxide), which have the same backbone connectivity as MECI and IPCI but have extended conjugation across the vinyl and carbonyl groups. A remarkable 50 nm shift of the peak absorption to longer wavelength is observed for MVK-oxide and MACR-oxide compared to MECI and IPCI, respectively. Furthermore, vertical excitation energies computed theoretically agree well with the experimental findings, confirming that the spectral shifts are caused by the extended π conjugation in the isoprene-derived Criegee intermediates.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
High-Accuracy Heats of Formation for Alkane Oxidation: From Small to Large via the Automated CBH-ANL Method
It is generally challenging to obtain high-accuracy predictions for the heat of formation for species with more than a handful of heavy atoms, such as those of importance in standard combustion mechanisms. To this end, we construct the CBH-ANL approach and illustrate that, for a set of 194 alkane oxidation species, it can be used to produce ΔH f (o K) values with 2σ uncertainties of 0.2-0.5 kcal mol -1 . This set includes the alkanes, hydroperoxides, and alkyl, peroxy, and hydroperoxyalkyl radicals for 17 representative hydrocarbon fuels containing up to 10 heavy atoms with various degrees of branching in the alkane backbone. The CBH-ANL approach, automated in the QTC and AutoMech software suites, builds balanced chemical equations for the calculation of ΔH f (o K), in which the reference species may be up to five heavy atoms. The high-level ANLo and ANL1 reference ΔH f (o K) values are further refined for even the largest of these reference species with a novel laddering approach. We perform a comprehensive quantification of the uncertainties for both the individual reference species (the largest of which is 0.15 kcal mol -1 ) and the propagation of those uncertainties when used in the calculation of ΔH f (o K) for the 194 target species. Here we examine the sensitivity of the predicted ΔH f (o K) values to (i) electronic energies from various methods, including ωB97X-D/cc-pVTZ, B2PLYP-D3/cc-pVTZ, CCSD(T)-F12b/cc-pVDZ-F12//B2PLYP-D3/cc-pVTZ, and CCSD(T)-F12b/cc-pVTZ-F12//B2PLYP-D3/cc-pVTZ; (ii) the zero-point vibrational energies (ZPVEs), where we consider harmonic ZPVEs as well as two scaling-based estimates of the anharmonic ZPVEs, all implemented for both ωB97X-D/cc-pVTZ and B2PLYP-D3/cc-pVTZ calculations; (iii) the particular CBH-ANL scheme employed; and (iv) the procedure for choosing the reference conformer for the analyses. The discussion concludes with a summary of the estimated overall uncertainty in the predictions and a validation of the predictions for the alkane subset.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Formation of 1 H -Phenalene (C 13 H 10 ) in the Taurus Molecular Cloud via Methylidyne Addition-Cyclization-Aromatization (MACA)
The formation of 1H-phenalene (C 13 H 10 ) in cold molecular clouds, such as the Taurus Molecular Cloud-1 (TMC-1), presents a significant challenge to traditional astrochemical models, which predominantly suggest high-temperature pathways for polycyclic aromatic hydrocarbon (PAH) formation. In this study, we explore computationally the Methylidyne Addition-Cyclization-Aromatization (MACA) mechanism as a viable, barrierless pathway for phenalene synthesis under low-temperature conditions. Through electronic structure calculations and Rice–Ramsperger–Kassel–Marcus (RRKM) statistical methods, we demonstrate that the reaction of 1-vinylnaphthalene (C 10 H 7 C 2 H 3 ) with the methylidyne radical (CH) leads to the formation of 1H-phenalene via a bimolecular reaction, a process that is exoergic and without entrance barrier. The MACA mechanism facilitates the growth of the aromatic carbon backbone via a [5 + 1] ring annulation, providing a new insight into PAH formation in cold molecular clouds. Notably, the MACA mechanism has previously been shown to form indene (C9H8), which was detected in TMC-1 as well, via a [4 + 1] annulation, demonstrating its potential to produce a variety of complex PAHs by addition of a five- and six-membered ring to a benzene moiety via [4 + 1] and [5 + 1] annulation, respectively. As a result, this work highlights the importance of barrierless, exoergic reactions involving MACA in the synthesis of complex aromatic molecules in space, expanding our physicochemical understanding of carbon-rich chemistry in cold molecular clouds.
Aromatic compounds↗
N-Terminal Decarboxylation as a Probe for Intramolecular Contact Formation in $γ$-Glu-(Pro) n -Met Peptides
The kinetics of intramolecular-contact formation between remote functional groups in peptides with restricted conformational flexibility were examined using designed peptides with variable-length proline bridges. As probes for this motion, free radicals were produced using the • OH-induced oxidation at the C-terminal methionine residue of γ-Glu-(Pro) n -Met peptides ( n = 0–3). The progress of the radicals’ motion along the proline bridges was monitored as the radicals underwent reactions along the peptides’ backbones. Of particular interest was the reaction between the sulfur atom located in the side chain of the oxidized Met residue and the unprotonated amino group of the glutamic acid moiety. Interactions between them were probed by the radiation-chemical yields (expressed as G values) of the formation of C-centered, α-aminoalkyl radicals (αN) on the Glu residue. These radicals were monitored directly or via their reaction with p -nitroacetophenone (PNAP) to generate the optically detected PNAP •– radical anions. The yields of these αN radicals were found to be linearly dependent on the number of Pro residues. A constant decrease by 0.09 μM J –1 per spacing Pro residue of the radiation-chemical yields of G (αN) was observed. Previous reports support the conclusion that the αN radicals in these cases would have to result from (S$\therefore$N) + -bonded cyclic radical cations that arose as a result from direct contact between the ends of the peptides. Furthermore, by analogy with the rate constants for the formation of intramolecularly (S$\therefore$S) + -bonded radical cations in Met-(Pro) n -Met peptides ( J. Phys. Chem. B 2016 , 120 , 9732), the rate constants for the formation of intramolecularly (S$\therefore$N) + -bonded radical cations are activated to the same extent for all of the γ-Glu-(Pro) n -Met peptides. Thus, the continuous decrease of G (αN) with the number of Pro residues (from 0 to 3) suggests that the formation of a contact between the S-atom in the C-terminal Met residue and the N-atom of a deprotonated N-terminal amino group of Glu is controlled in peptides with 0 to 3 Pro residues by the relative diffusion of the S •+ and unoxidized N-atom. The overall rate constants of cyclization to form the (S$\therefore$N)-bonded radical cations were estimated to be 3.8 × 10 6 , 1.8 × 10 6 , and 8.1 × 10 5 s –1 for peptides with n = 0, 1, and 2 Pro residues, respectively. If activation is the same for all of the peptides, then these rate constants are a direct indication for the end-to-end dynamics along the chain.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids
Peptoids (poly-N-substituted glycines) are a class of synthetic polymers that are regioisomers of peptides (poly-C-substituted glycines), in which the point of side-chain connectivity is shifted from the backbone C to the N atom. Peptoids have found diverse applications as peptidomimetic drugs, protein mimetic polymers, surfactants, and catalysts. Computational modeling is valuable in the understanding and design of peptoid-based nanomaterials. In this work, we report the bottom-up parameterization of coarse-grained peptoid force fields based on the MARTINI peptide force field against all-atom peptoid simulation data. Our parameterization pipeline iteratively refits coarse-grained bonded interactions using iterative Boltzmann inversion and nonbonded interactions by matching the potential of mean force for chain extension. We assure good sampling of the amide bond cis/trans isomerizations in the all-atom simulation data using parallel bias metadynamics. We develop coarse-grained models for two representative peptoids—polysarcosine (poly(N-methyl glycine)) and poly(N-((4-bromophenyl)ethyl)glycine)—and show their structural and thermodynamic properties to be in excellent accord with all-atom calculations but up to 25-fold more efficient and compatible with MARTINI force fields. Here, this work establishes a new rigorously parameterized coarse-grained peptoid force field for the understanding and design of peptoid nanomaterials at length and time scales inaccessible to all-atom calculations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Distinguishing Mesoscale Polar Order (Unidirectional vs Bidirectional) of Cellulose Microfibrils in Plant Cell Walls Using Sum Frequency Generation Spectroscopy
Cellulose in plant cell walls are synthesized as crystalline microfibrils with diameters of 3–4 nm and lengths of around 1–10 μm. These microfibrils are known to be the backbone of cell walls, and their multiscale three-dimensional organization plays a critical role in cell wall functions including plant growth and recalcitrance to degradation. The mesoscale organization of microfibrils over a 1–100 nm range in cell walls is challenging to resolve because most characterization techniques investigating this length scale suffer from low spatial resolution, sample preparation artifacts, or inaccessibility of specific cell types. Here, we report a sum frequency generation (SFG) study determining the mesoscale polarity of cellulose microfibrils in intact plant cell walls. SFG is a nonlinear optical spectroscopy technique sensitive to the molecular-to-mesoscale order of noncentrosymmetric domains in amorphous matrices. However, the quantitative theoretical model to unravel the effect of polarity in packing of noncentrosymmetric domains on SFG spectral features has remained unresolved. In this work, we show how the phase synchronization principle of the SFG process is used to predict the relative intensities of vibrational modes with different polar angles from the noncentrosymmetric domain axis. Applying this model calculation for the first time and employing SFG microscopy, we found that cellulose microfibrils in certain xylem cell walls are deposited unidirectionally (or biased in one direction) instead of the bidirectional polarity which was believed to be dominant in plant cell walls from volume-averaged characterizations of macroscopic samples. Here, with this advancement in SFG analysis, one can now determine the relative polarity of noncentrosymmetric domains such as crystalline biopolymers interspersed in amorphous polymer matrices, which will open opportunities to study new questions that have not been conceived in the past.
36 MATERIALS SCIENCE↗
Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N -1-Phenylethyl Sidechains
N-substituted glycines (polypeptoids) containing chiral hydrophobic sidechains are known to fold into biomimetic alpha helices. These helix formers often produce conformationally heterogeneous structures and are difficult to characterize at a sub-nanometer resolution. Previously, peptoid N-1-phenylethyl (S)-enantiomer sidechains (Nspe) were inferred from various experiments to form right-handed helices and (R)-enantiomers (Nrpe), left-handed helices. Prior computational work for N(s/r)pe oligomers has struggled to reproduce this trend. Herein, quantum mechanics calculations and molecular dynamics simulations are used to understand the origins of this discrepancy. Results from DFT and molecular mechanics calculations on a variety of Nspe and Nrpe oligomers as a function of chain length are in agreement, showing that Nspe and Nrpe prefer left- and right-handed helices, respectively. Additional metadynamics simulations are used to study Nrpe and Nspe oligomers folding in water. These results show that the free-energy driving forces for assembly into a helical backbone configuration are very small (within ~k B T). Lastly, we compare DFT calculations for other experimentally characterized peptoid sidechains, N(r/s)sb, N(r/s)tbe, and N(r/s)npe. In this analysis, we show that peptoid sidechains determined to be more robust experimentally (tbe and npe) have helical preferences opposite the trend seen in less robust assemblies formed by N(r/s)pe and N(r/s)sb chemistries. Furthermore, the more robust tbe and nnpe favor the (S)-enantiomer to right-handed and the (R)-enantiomers to left-handed helices.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA
Performing spectroscopic measurements on biomolecules labeled with fluorescent probes is a powerful approach to locating the molecular behavior and dynamics of large systems at specific sites within their local environments. The indocarbocyanine dye Cy3 has emerged as one of the most commonly used chromophores. The incorporation of Cy3 dimers into DNA enhances experimental resolution owing to the spectral characteristics influenced by the geometric orientation of excitonically coupled monomeric units. Various theoretical models and simulations have been utilized to aid in the interpretation of the experimental spectra. In this study, we employ all-atom molecular dynamics simulations to study the structural dynamics of Cy3 dimers internally linked to the dsDNA backbone. We used quantum mechanical calculations to derive insights from both the linear absorption spectra and the circular dichroism data. Furthermore, we explore potential limitations within a commonly used force field for cyanine dyes. The molecular dynamics simulations suggest the presence of four possible Cy3 dimeric populations. The spectral simulations on the four populations show one of them to agree better with the experimental signatures, suggesting it to be the dominant population. Furthermore, the relative orientation of Cy3 in this population compares very well with previous predictions from the Holstein–Frenkel Hamiltonian model.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Photoactivation Transition State and Dynamical Response of the Orange Carotenoid Protein
The orange carotenoid protein (OCP) regulates light harvesting in cyanobacteria by acting as a photoreceptor in its resting form, OCP O , and by effecting the quenching of bilin excitons upon binding to the core of the phycobilisome in its photoactivated red form, OCP R . We show herein using fluorescence anisotropy measurements and the action spectra for the rate constants of the two light-driven steps in the mechanism that the photoactivation of the OCP from Synechocystis sp. PCC 6803 is triggered by excited-state motions of the canthaxanthin chromophore that yield a twisted and bent conformation. Well-tempered metadynamics simulations reveal that a bicycle-pedal configuration, due to twisting of the two adjacent C=C bonds at the C13−C14 and C15−C15′ positions in the center of canthaxanthin’s π-conjugated isoprenoid backbone, can be accommodated by the binding site in the OCP, with the energy of a captured photon required to cross the local activation energy barriers from the dark equilibrium structure. The bicycle-pedal configuration breaks the conserved hydrogen-bonding interactions between the carbonyl substituent of the β-ionone end ring of canthaxanthin and the adjacent W288 and Y201 residues in the C-terminal domain. The action spectra are modulated by the vibronic excitation prepared by absorption transitions to the S 2 state, indicating that the photoactivation reactions are triggered by the canthaxanthin chromophore well prior to vibrational equilibration. These findings show that an ultrafast structural response of the OCP protein to the excited-state motions of the canthaxanthin chromophore controls the photoactivation yield and the sensing of blue light.
Fluorescence↗
Exploring Local Vibrational Structure in Protein-Bound Chlorophyll a: Isotope-Enrichment Experiments and Electrostatic Analysis
Local chlorophyll (Chl) vibrations play an essential role in biological photosynthesis by facilitating rapid energy transfer between pigments. In research studies, they also provide a useful spectroscopic probe of the local protein environment that surrounds each pigment. However, measuring the complete vibrational absorption spectrum of a protein-bound Chl molecule is much more difficult than, for example, Chl in neat solvent due to overlap with protein vibrations that typically drown out Chl vibrational features. Resonance Raman and fluorescence spectroscopies provide a way around this problem for Franck–Condon active vibrations, but these often rely on cryogenic measurement conditions and fail to capture vibrational signatures from, e.g., ester-group vibrations that lack coupling to a convenient electronic transition. In the present contribution, we use 13 C-enrichment of the protein backbone to shift protein background signals to lower frequency, providing a largely clean spectral window in which to study local Chl a C═O stretch modes. A room-temperature absorption spectrum for Chl a in the water-soluble chlorophyll protein (WSCP) of Lepidium virginicum is thus extracted as a difference between protein-plus-pigment and protein-only vibrational spectra. Excellent agreement in the molecular fingerprint region with the vibrational spectrum of Chl a in organic solvents confirms that the resulting spectrum represents the response of the protein-bound Chl a molecule. Furthermore, the ester group resonance is observed to shift in response to the S53P mutation that eliminates a 17 3 ester group hydrogen bond from the protein environment. Finally, we analyze these experimental results using MD-based electrostatic analysis, finding that electric-field mapping at the C atom of the ester group provides a satisfactory explanation for the observed frequency shifts between organic solvent and protein environment. MD analysis further suggests that a red-shifted ester peak observed experimentally for the S53P mutant results from solvation of the 17 3 Chl ester group due increase water penetration into the Chl-binding pocket relative to wild-type WSCP. Here, we anticipate that these results will prove useful both for benchmarking future simulation work and as a reference for interpreting Chl vibrational spectra as a probe of pigment–protein interactions.
14 SOLAR ENERGY↗