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1.
J Am Chem Soc ; 146(26): 18019-18031, 2024 Jul 03.
Artículo en Inglés | MEDLINE | ID: mdl-38888987

RESUMEN

The membrane-bound hydrogenase (Mbh) from Pyrococcus furiosus is an archaeal member of the Complex I superfamily. It catalyzes the reduction of protons to H2 gas powered by a [NiFe] active site and transduces the free energy into proton pumping and Na+/H+ exchange across the membrane. Despite recent structural advances, the mechanistic principles of H2 catalysis and ion transport in Mbh remain elusive. Here, we probe how the redox chemistry drives the reduction of the proton to H2 and how the catalysis couples to conformational dynamics in the membrane domain of Mbh. By combining large-scale quantum chemical density functional theory (DFT) and correlated ab initio wave function methods with atomistic molecular dynamics simulations, we show that the proton transfer reactions required for the catalysis are gated by electric field effects that direct the protons by water-mediated reactions from Glu21L toward the [NiFe] site, or alternatively along the nearby His75L pathway that also becomes energetically feasible in certain reaction steps. These local proton-coupled electron transfer (PCET) reactions induce conformational changes around the active site that provide a key coupling element via conserved loop structures to the ion transport activity. We find that H2 forms in a heterolytic proton reduction step, with spin crossovers tuning the energetics along key reaction steps. On a general level, our work showcases the role of electric fields in enzyme catalysis and how these effects are employed by the [NiFe] active site of Mbh to drive PCET reactions and ion transport.


Asunto(s)
Hidrógeno , Hidrogenasas , Simulación de Dinámica Molecular , Pyrococcus furiosus , Hidrogenasas/química , Hidrogenasas/metabolismo , Hidrógeno/química , Hidrógeno/metabolismo , Pyrococcus furiosus/enzimología , Protones , Teoría Funcional de la Densidad , Dominio Catalítico , Oxidación-Reducción
2.
Acc Chem Res ; 56(21): 2921-2932, 2023 11 07.
Artículo en Inglés | MEDLINE | ID: mdl-37844298

RESUMEN

Oxygenic photosynthesis is the fundamental energy-converting process that utilizes sunlight to generate molecular oxygen and the organic compounds that sustain life. Protein-pigment complexes harvest light and transfer excitation energy to specialized pigment assemblies, reaction centers (RC), where electron transfer cascades are initiated. A molecular-level understanding of the primary events is indispensable for elucidating the principles of natural photosynthesis and enabling development of bioinspired technologies. The primary enzyme in oxygenic photosynthesis is Photosystem II (PSII), a membrane-embedded multisubunit complex, that catalyzes the light-driven oxidation of water. The RC of PSII consists of four chlorophyll a and two pheophytin a pigments symmetrically arranged along two core polypeptides; only one branch participates in electron transfer. Despite decades of research, fundamental questions remain, including the origin of this functional asymmetry, the nature of primary charge-transfer states and the identity of the initial electron donor, the origin of the capability of PSII to enact charge separation with far-red photons, i.e., beyond the "red limit" where individual chlorophylls absorb, and the role of protein conformational dynamics in modulating charge-separation pathways.In this Account, we highlight developments in quantum-chemistry based excited-state computations for multipigment assemblies and the refinement of protocols for computing protein-induced electrochromic shifts and charge-transfer excitations calibrated with modern local correlation coupled cluster methods. We emphasize the importance of multiscale atomistic quantum-mechanics/molecular-mechanics and large-scale molecular dynamics simulations, which enabled direct and accurate modeling of primary processes in RC excitation at the quantum mechanical level.Our findings show how differential protein electrostatics enable spectral tuning of RC pigments and generate functional asymmetry in PSII. A chlorophyll pigment on the active branch (ChlD1) has the lowest site energy in PSII and is the primary electron donor. The complete absence of low-lying charge-transfer states within the central pair of chlorophylls excludes a long-held assumption about the initial charge separation. Instead, we identify two primary charge separation pathways, both with the same pheophytin acceptor (PheoD1): a fast pathway with ChlD1 as the primary electron donor (short-range charge-separation) and a slow pathway with PD1PD2 as the initial donor (long-range charge separation). The low-energy spectrum is dominated by two states with significant charge-transfer character, ChlD1δ+PheoD1δ- and PD1δ+PheoD1δ-. The conformational dynamics of PSII allows these charge-transfer states to span wide energy ranges, pushing oxygenic photosynthesis beyond the "red limit". These results provide a quantum mechanical picture of the primary events in the RC of oxygenic photosynthesis, forming a solid basis for interpreting experimental observations and for extending photosynthesis research in new directions.


Asunto(s)
Fotosíntesis , Complejo de Proteína del Fotosistema II , Complejo de Proteína del Fotosistema II/química , Clorofila A , Transporte de Electrón , Clorofila/química , Clorofila/metabolismo
3.
Angew Chem Int Ed Engl ; 62(16): e202216276, 2023 04 11.
Artículo en Inglés | MEDLINE | ID: mdl-36791234

RESUMEN

Photosystem-II (PSII) is a multi-subunit protein complex that harvests sunlight to perform oxygenic photosynthesis. Initial light-activated charge separation takes place at a reaction centre consisting of four chlorophylls and two pheophytins. Understanding the processes following light excitation remains elusive due to spectral congestion, the ultrafast nature, and multi-component behaviour of the charge-separation process. Here, using advanced computational multiscale approaches which take into account the large-scale configurational flexibility of the system, we identify two possible primary pathways to radical-pair formation that differ by three orders of magnitude in their kinetics. The fast (short-range) pathway is dominant, but the existence of an alternative slow (long-range) charge-separation pathway hints at the evolution of redundancy that may serve other purposes, adaptive or protective, related to formation of the unique oxidative species that drives water oxidation in PSII.


Asunto(s)
Fotosíntesis , Complejo de Proteína del Fotosistema II , Complejo de Proteína del Fotosistema II/metabolismo , Clorofila/metabolismo , Oxidación-Reducción
4.
J Am Chem Soc ; 144(48): 22035-22050, 2022 12 07.
Artículo en Inglés | MEDLINE | ID: mdl-36413491

RESUMEN

Water channels and networks within photosystem II (PSII) of oxygenic photosynthesis are critical for enzyme structure and function. They control substrate delivery to the oxygen-evolving center and mediate proton transfer at both the oxidative and reductive endpoints. Current views on PSII hydration are derived from protein crystallography, but structural information may be compromised by sample dehydration and technical limitations. Here, we simulate the physiological hydration structure of a cyanobacterial PSII model following a thorough hydration procedure and large-scale unconstrained all-atom molecular dynamics enabled by massively parallel simulations. We show that crystallographic models of PSII are moderately to severely dehydrated and that this problem is particularly acute for models derived from X-ray free electron laser (XFEL) serial femtosecond crystallography. We present a fully hydrated representation of cyanobacterial PSII and map all water channels, both static and dynamic, associated with the electron donor and acceptor sides. Among them, we describe a series of transient channels and the attendant conformational gating role of protein components. On the acceptor side, we characterize a channel system that is absent from existing crystallographic models but is likely functionally important for the reduction of the terminal electron acceptor plastoquinone QB. The results of the present work build a foundation for properly (re)evaluating crystallographic models and for eliciting new insights into PSII structure and function.


Asunto(s)
Acuaporinas , Complejo de Proteína del Fotosistema II , Agua , Cristalografía
5.
Angew Chem Int Ed Engl ; 61(16): e202200356, 2022 04 11.
Artículo en Inglés | MEDLINE | ID: mdl-35142017

RESUMEN

Photosystem-II uses sunlight to trigger charge separation and catalyze water oxidation. Intrinsic properties of chlorophyll a pigments define a natural "red limit" of photosynthesis at ≈680 nm. Nevertheless, charge separation can be triggered with far-red photons up to 800 nm, without altering the nature of light-harvesting pigments. Here we identify the electronic origin of this remarkable phenomenon using quantum chemical and multiscale simulations on a native Photosystem-II model. We find that the reaction center is preorganized for charge separation in the far-red region by specific chlorophyll-pheophytin pairs, potentially bypassing the light-harvesting apparatus. Charge transfer can occur along two distinct pathways with one and the same pheophytin acceptor (PheoD1 ). The identity of the donor chlorophyll (ChlD1 or PD1 ) is wavelength-dependent and conformational dynamics broaden the sampling of the far-red region by the two charge-transfer states. The two pathways rationalize spectroscopic observations and underpin designed extensions of the photosynthetically active radiation limit.


Asunto(s)
Oxígeno , Fotosíntesis , Clorofila/química , Clorofila A , Electrónica , Complejo de Proteína del Fotosistema II/química
6.
Phys Chem Chem Phys ; 23(43): 24677-24684, 2021 Nov 10.
Artículo en Inglés | MEDLINE | ID: mdl-34708851

RESUMEN

Photosynthetic pigment-protein complexes harvest solar energy with a high quantum efficiency. Protein scaffolds are known to tune the spectral properties of embedded pigments principally through structured electrostatic environments. Although the physical nature of electrostatic tuning is straightforward, the precise spatial principles of electrostatic preorganization remain poorly explored for different protein matrices and incompletely characterized with respect to the intrinsic properties of different photosynthetic pigments. In this work, we study the electronic structure features associated with the lowest excited state of a series of eight naturally occurring (bacterio)chlorophylls and pheophytins to describe the precise topological differences in electrostatic potentials and hence determine intrinsic differences in the expected mode and impact of electrostatic tuning. The difference electrostatic potentials between the ground and first excited states are used as fingerprints. Both the spatial profile and the propensity for spectral tuning are found to be unique for each pigment, indicating spatially and directionally distinct modes of electrostatic tuning. The results define a specific partitioning of the protein matrix around each pigment as an aid to identify regions with a maximal impact on spectral tuning and have direct implications for dimensionality reduction in protein design and engineering. Thus, a quantum mechanical basis is provided for understanding, predicting, and ultimately designing sequence-modified or pigment-exchanged biological systems, as suggested for selected examples of pigment-reconstituted proteins.


Asunto(s)
Bacterioclorofilas/química , Feofitinas/química , Teoría Funcional de la Densidad , Conformación Molecular , Procesos Fotoquímicos , Electricidad Estática
7.
J Am Chem Soc ; 142(42): 18174-18190, 2020 10 21.
Artículo en Inglés | MEDLINE | ID: mdl-33034453

RESUMEN

Photosystem II (PSII) is a multisubunit pigment-protein complex that uses light-induced charge separation to power oxygenic photosynthesis. Its reaction center chromophores, where the charge transfer cascade is initiated, are arranged symmetrically along the D1 and D2 core polypeptides and comprise four chlorophyll (PD1, PD2, ChlD1, ChlD2) and two pheophytin molecules (PheoD1 and PheoD2). Evolution favored productive electron transfer only via the D1 branch, with the precise nature of primary excitation and the factors that control asymmetric charge transfer remaining under investigation. Here we present a detailed atomistic description for both. We combine large-scale simulations of membrane-embedded PSII with high-level quantum-mechanics/molecular-mechanics (QM/MM) calculations of individual and coupled reaction center chromophores to describe reaction center excited states. We employ both range-separated time-dependent density functional theory and the recently developed domain based local pair natural orbital (DLPNO) implementation of the similarity transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD), the first coupled cluster QM/MM calculations of the reaction center. We find that the protein matrix is exclusively responsible for both transverse (chlorophylls versus pheophytins) and lateral (D1 versus D2 branch) excitation asymmetry, making ChlD1 the chromophore with the lowest site energy. Multipigment calculations show that the protein matrix renders the ChlD1 → PheoD1 charge-transfer the lowest energy excitation globally within the reaction center, lower than any pigment-centered local excitation. Remarkably, no low-energy charge transfer states are located within the "special pair" PD1-PD2, which is therefore excluded as the site of initial charge separation in PSII. Finally, molecular dynamics simulations suggest that modulation of the electrostatic environment due to protein conformational flexibility enables direct excitation of low-lying charge transfer states by far-red light.


Asunto(s)
Complejo de Proteína del Fotosistema II/metabolismo , Simulación de Dinámica Molecular , Complejo de Proteína del Fotosistema II/química , Conformación Proteica , Teoría Cuántica , Thermosynechococcus/enzimología
8.
J Am Chem Soc ; 141(7): 3217-3231, 2019 02 20.
Artículo en Inglés | MEDLINE | ID: mdl-30666866

RESUMEN

Photosystem II (PSII) of oxygenic photosynthesis captures sunlight to drive the catalytic oxidation of water and the reduction of plastoquinone. Among the several redox-active cofactors that participate in intricate electron transfer pathways there are two tyrosine residues, YZ and YD. They are situated in symmetry-related electron transfer branches but have different environments and play distinct roles. YZ is the immediate oxidant of the oxygen-evolving Mn4CaO5 cluster, whereas YD serves regulatory and protective functions. The protonation states and hydrogen-bond network in the environment of YD remain debated, while the role of microsolvation in stabilizing different redox states of YD and facilitating oxidation or mediating deprotonation, as well the fate of the phenolic proton, is unclear. Here we present detailed structural models of YD and its environment using large-scale quantum mechanical models and all-atom molecular dynamics of a complete PSII monomer. The energetics of water distribution within a hydrophobic cavity adjacent to YD are shown to correlate directly with electron paramagnetic resonance (EPR) parameters such as the tyrosyl g-tensor, allowing us to map the correspondence between specific structural models and available experimental observations. EPR spectra obtained under different conditions are explained with respect to the mode of interaction of the proximal water with the tyrosyl radical and the position of the phenolic proton within the cavity. Our results revise previous models of the energetics and build a detailed view of the role of confined water in the oxidation and deprotonation of YD. Finally, the model of microsolvation developed in the present work rationalizes in a straightforward way the biphasic oxidation kinetics of YD, offering new structural insights regarding the function of the radical in biological photosynthesis.


Asunto(s)
Complejo de Proteína del Fotosistema II/química , Protones , Tirosina/química , Cianobacterias/enzimología , Espectroscopía de Resonancia por Spin del Electrón , Enlace de Hidrógeno , Simulación de Dinámica Molecular , Oxidación-Reducción , Conformación Proteica , Teoría Cuántica , Solventes/química , Termodinámica , Thermosynechococcus , Agua/química
9.
Chemphyschem ; 18(20): 2859-2863, 2017 Oct 19.
Artículo en Inglés | MEDLINE | ID: mdl-28766864

RESUMEN

This Communication presents the crystal structure of the organometallic complexes (η4 -1,3-cyclohexadiene) iron tricarbonyl (I) and (methyl cyclopentadienyl) manganese tricarbonyl (II) which are both liquid at room temperature. The crystal structures were determined using a state-of-the-art in situ cryocrystallization technique. The bonding features were elucidated using topological analysis of charge density in the framework of quantum theory of atoms in molecules (QTAIM) and theoretical charge density analysis (multipolar refinement), to decipher the metal-carbonyl, metal-olefin and metal-carbocyclic ligand interactions in these complexes. Complex I displayed a simultaneous interplay of a "synergic effect" (σ-donation and π-back-bonding in the metal and an end-on coordinated carbonyl interaction) as well as consistency with the Dewar-Chatt-Duncanson (DCD) model (metal and side-on coordinated π-ligand interactions).

10.
Chem Sci ; 15(20): 7767-7780, 2024 May 22.
Artículo en Inglés | MEDLINE | ID: mdl-38784751

RESUMEN

The Light-Dependent Protochlorophyllide Oxidoreductase (LPOR) catalyzes a crucial step in chlorophyll biosynthesis: the rare biological photocatalytic reduction of the double C[double bond, length as m-dash]C bond in the precursor, protochlorophyllide (Pchlide). Despite its fundamental significance, limited structural insights into the active complex have hindered understanding of its reaction mechanism. Recently, a high-resolution cryo-EM structure of LPOR in its active conformation challenged our view of pigment binding, residue interactions, and the catalytic process. Surprisingly, this structure contrasts markedly with previous assumptions, particularly regarding the orientation of the bound Pchlide. To gain insights into the substrate binding puzzle, we conducted molecular dynamics simulations, quantum-mechanics/molecular-mechanics (QM/MM) calculations, and site-directed mutagenesis. Two Pchlide binding modes were considered, one aligning with historical proposals (mode A) and another consistent with the recent experimental data (mode B). Binding energy calculations revealed that in contrast to the non-specific interactions found for mode A, mode B exhibits distinct stabilizing interactions that support more thermodynamically favorable binding. A comprehensive analysis incorporating QM/MM-based local energy decomposition unraveled a complex interaction network involving Y177, H319, and the C131 carboxy group, influencing the pigment's excited state energy and potentially contributing to substrate specificity. Importantly, our results uniformly favor mode B, challenging established interpretations and emphasizing the need for a comprehensive re-evaluation of the LPOR reaction mechanism in a way that incorporates accurate structural information on pigment interactions and substrate-cofactor positioning in the binding pocket. The results shed light on the intricacies of LPOR's catalytic mechanism and provide a solid foundation for further elucidating the secrets of chlorophyll biosynthesis.

11.
J Phys Chem A ; 117(41): 10772-82, 2013 Oct 17.
Artículo en Inglés | MEDLINE | ID: mdl-24032346

RESUMEN

The existence of rare-gas-containing hydride ions of boron (HRgBF(+)) has been predicted by using ab initio quantum chemical methods. The HRgBF(+) ions are obtained by inserting a rare gas (Rg) atom in between the H and B atoms of a HBF(+) ion, and the geometries are optimized for minima as well as transition states using second-order Møller-Plesset perturbation theory (MP2), density functional theory (DFT), and coupled-cluster theory (CCSD(T)) based techniques. The predicted HRgBF(+) ions are found to be metastable, and they exhibit a linear structure at the minima and a nonlinear planar structure at the transition state, corresponding to C∞v and Cs symmetries, respectively. All of the predicted HRgBF(+) ions show negative binding energies with respect to the two-body dissociation channel, leading to global minima (HBF(+) + Rg) on the singlet potential energy surface. In contrast, the dissociation energies corresponding to another two-body dissociation channel leading to HRg(+) + BF and two three-body dissociation channels corresponding to the dissociation into H + Rg + BF(+) and H(+) + Rg + BF show very high positive energies. Apart from positive dissociation energies, the predicted ions show finite barrier heights corresponding to the transition states involving a H-Rg-B bending mode, leading to the global minima products (HBF(+) + Rg). The finite barrier heights in turn would prevent the metastable HRgBF(+) species from transforming to global minima products. Structure, harmonic vibrational frequencies, stability, and Mulliken and natural bonding orbital (NBO) charge distribution values for all of the species are reported using the MP2 and DFT methods. Furthermore, the intrinsic reaction coordinate analysis confirms that the metastable minimum-energy structure and the global minimum products are connected through the corresponding transition state for each of the species on the respective singlet potential energy surface. Atoms-in-molecules (AIM) analysis indicates that the HRgBF(+) ions are best described as HRg(+)BF and are analogous to the isoelectronic HRgCO(+) and HRgN2(+) ions. The energetic along with charge redistribution and spectroscopic data strongly support the possible existence of HRgBF(+) ions. Hence, it might be possible to generate HRgBF(+) ions in the DC discharge plasma of a BF3/H2/Rg mixture at low temperature, and the predicted ions may be characterized using the magnetic field modulated infrared laser spectroscopic technique, which has been used earlier to characterize HBF(+) ions.

12.
Science ; 382(6666): 109-113, 2023 10 06.
Artículo en Inglés | MEDLINE | ID: mdl-37797025

RESUMEN

Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). We present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O-O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.


Asunto(s)
Proteínas Bacterianas , Entomoplasmataceae , Ribonucleótido Reductasas , Transporte de Electrón , Protones , Ribonucleótido Reductasas/química , Cristalografía por Rayos X/métodos , Entomoplasmataceae/enzimología , Dominio Catalítico , Proteínas Bacterianas/química
13.
Chem Sci ; 12(12): 4463-4476, 2021 Feb 12.
Artículo en Inglés | MEDLINE | ID: mdl-34163712

RESUMEN

Natural photosynthesis relies on light harvesting and excitation energy transfer by specialized pigment-protein complexes. Their structure and the electronic properties of the embedded chromophores define the mechanisms of energy transfer. An important example of a pigment-protein complex is CP47, one of the integral antennae of the oxygen-evolving photosystem II (PSII) that is responsible for efficient excitation energy transfer to the PSII reaction center. The charge-transfer excitation induced among coupled reaction center chromophores resolves into charge separation that initiates the electron transfer cascade driving oxygenic photosynthesis. Mapping the distribution of site energies among the 16 chlorophyll molecules of CP47 is essential for understanding excitation energy transfer and overall antenna function. In this work, we demonstrate a multiscale quantum mechanics/molecular mechanics (QM/MM) approach utilizing full time-dependent density functional theory with modern range-separated functionals to compute for the first time the excitation energies of all CP47 chlorophylls in a complete membrane-embedded cyanobacterial PSII dimer. The results quantify the electrostatic effect of the protein on the site energies of CP47 chlorophylls, providing a high-level quantum chemical excitation profile of CP47 within a complete computational model of "near-native" cyanobacterial PSII. The ranking of site energies and the identity of the most red-shifted chlorophylls (B3, followed by B1) differ from previous hypotheses in the literature and provide an alternative basis for evaluating past approaches and semiempirically fitted sets. Given that a lot of experimental studies on CP47 and other light-harvesting complexes utilize extracted samples, we employ molecular dynamics simulations of isolated CP47 to identify which parts of the polypeptide are most destabilized and which pigments are most perturbed when the antenna complex is extracted from PSII. We demonstrate that large parts of the isolated complex rapidly refold to non-native conformations and that certain pigments (such as chlorophyll B1 and ß-carotene h1) are so destabilized that they are probably lost upon extraction of CP47 from PSII. The results suggest that the properties of isolated CP47 are not representative of the native complexed antenna. The insights obtained from CP47 are generalizable, with important implications for the information content of experimental studies on biological light-harvesting antenna systems.

14.
J Chem Theory Comput ; 17(3): 1858-1873, 2021 Mar 09.
Artículo en Inglés | MEDLINE | ID: mdl-33566610

RESUMEN

Protein-embedded chromophores are responsible for light harvesting, excitation energy transfer, and charge separation in photosynthesis. A critical part of the photosynthetic apparatus are reaction centers (RCs), which comprise groups of (bacterio)chlorophyll and (bacterio)pheophytin molecules that transform the excitation energy derived from light absorption into charge separation. The lowest excitation energies of individual pigments (site energies) are key for understanding photosynthetic systems, and form a prime target for quantum chemistry. A major theoretical challenge is to accurately describe the electrochromic (Stark) shifts in site energies produced by the inhomogeneous electric field of the protein matrix. Here, we present large-scale quantum mechanics/molecular mechanics calculations of electrochromic shifts for the RC chromophores of photosystem II (PSII) using various quantum chemical methods evaluated against the domain-based local pair natural orbital (DLPNO) implementation of the similarity-transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD). We show that certain range-separated density functionals (ωΒ97, ωΒ97X-V, ωΒ2PLYP, and LC-BLYP) correctly reproduce RC site energy shifts with time-dependent density functional theory (TD-DFT). The popular CAM-B3LYP functional underestimates the shifts and is not recommended. Global hybrid functionals are too insensitive to the environment and should be avoided, while nonhybrid functionals are strictly nonapplicable. Among the applicable approximate coupled cluster methods, the canonical versions of CC2 and ADC(2) were found to deviate significantly from the reference results both for the description of the lowest excited state and for the electrochromic shifts. By contrast, their spin-component-scaled (SCS) and particularly the scale-opposite-spin (SOS) variants compare well with the reference DLPNO-STEOM-CCSD and the best range-separated DFT methods. The emergence of RC excitation asymmetry is discussed in terms of intrinsic and protein electrostatic potentials. In addition, we evaluate a minimal structural scaffold of PSII, the D1-D2-CytB559 RC complex often employed in experimental studies, and show that it would have the same site energy distribution of RC chromophores as the full PSII supercomplex, but only under the unlikely conditions that the core protein organization and cofactor arrangement remain identical to those of the intact enzyme.


Asunto(s)
Clorofila/química , Teoría Funcional de la Densidad , Feofitinas/química , Complejo de Proteína del Fotosistema II/química , Clorofila/metabolismo , Feofitinas/metabolismo , Complejo de Proteína del Fotosistema II/metabolismo
15.
J Phys Chem B ; 124(40): 8761-8771, 2020 10 08.
Artículo en Inglés | MEDLINE | ID: mdl-32930590

RESUMEN

The ability to accurately compute low-energy excited states of chlorophylls is critically important for understanding the vital roles they play in light harvesting, energy transfer, and photosynthetic charge separation. The challenge for quantum chemical methods arises both from the intrinsic complexity of the electronic structure problem and, in the case of biological models, from the need to account for protein-pigment interactions. In this work, we report electronic structure calculations of unprecedented accuracy for the low-energy excited states in the Q and B bands of chlorophyll a. This is achieved by using the newly developed domain-based local pair natural orbital (DLPNO) implementation of the similarity transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD) in combination with sufficiently large and flexible basis sets. The results of our DLPNO-STEOM-CCSD calculations are compared with more approximate approaches. The results demonstrate that, in contrast to time-dependent density functional theory, the DLPNO-STEOM-CCSD method provides a balanced performance for both absorption bands. In addition to vertical excitation energies, we have calculated the vibronic spectrum for the Q and B bands through a combination of DLPNO-STEOM-CCSD and ground-state density functional theory frequency calculations. These results serve as a basis for comparison with gas-phase experiments.


Asunto(s)
Clorofila , Teoría Cuántica , Clorofila A , Transferencia de Energía , Fotosíntesis
16.
Acta Crystallogr E Crystallogr Commun ; 74(Pt 5): 607-612, 2018 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-29850076

RESUMEN

Crystals of the liquid compound 2,2,2-tri-fluoro-aceto-phenone (TFAP, C8H5F3O) were obtained using the state-of-art in situ cryocrystallization technique. TFAP crystallizes in the monoclinic space group C2/c, and its crystal structure is mainly stabilized by a set of C-H⋯F, C-H⋯O, F⋯F and F⋯O supra-molecular contacts. The overall mol-ecular arrangement shows the formation of mol-ecular sheets parallel to the bc plane, which are in turn stacked along the a-axis direction. The weak inter-actions have been studied thoroughly, performing both a Hirshfeld surface analysis and theoretical calculations, to obtain the inter-molecular inter-action energies. A structural comparison of this compound with the previously reported substituted analogs was also carried out, showing a qualitative difference in terms of packing behaviour.

17.
Acta Crystallogr B Struct Sci Cryst Eng Mater ; 73(Pt 2): 140-152, 2017 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-28362276

RESUMEN

In the current study, the crystal structure of 1-(3-nitrophenyl)-2,2,2-trifluoroethanone (A1) and (E)-4-((4-fluorophenyl) diazenyl)phenol (A2) has been analyzed for the characterization of the presence of a `unique' and `rare' intermolecular C(sp3/sp2)-F...O contact, which has been observed to play a significant role in the crystal packing. Theoretical charge-density calculations have been performed to study the nature and strength associated with the existence of this intermolecular F...O contact, wherein the F atom is attached to an sp3-hybridized C atom in the case of A1 and to an sp2 hybridized carbon in the case of A2. The crystal packing of the former contains two `electronically different' Csp3-F...O contacts which are present across and in between the layers of molecules. In the latter case, it is characterized by the presence of a very `short' (2.708 Å) and `highly directional' (168° at ∠C4-F1...O1 and 174° at ∠C10-O1...F1) Csp2-F...O contact. According to the Cambridge Structural Database (CSD) study, it is a rare example in molecular crystals. Topological features of F...O contacts in the solid state were compared with the gas-phase models. The two-dimensional and three-dimensional static deformation density obtained from theoretical multipole modeling confirm the presence of a charge depleted region on the F atoms. Minimization of the electrostatic repulsion between like charges are observed through subtle arrangements in the electronic environment in two of the short intermolecular F...O contacts. These contacts were investigated using inputs from pair energy decomposition analysis, Bader's quantum theory of atoms in molecules (QTAIM), Hirshfeld surface analysis, delocalization index, reduced density gradient (RDG) plot, electrostatic potential surface and distributed atomic polarizability. The intermolecular energy decomposition (PIXEL) and RDG-NCI (non-covalent interaction) analysis of the F...O contacts establish the interaction to be dispersive in nature. The mutual polarization of an O atom by fluorine and vice versa provides real physical insights into the role of atomic polarizability in interacting atoms in molecules in crystals.

18.
Chem Commun (Camb) ; 52(45): 7225-8, 2016 Jun 07.
Artículo en Inglés | MEDLINE | ID: mdl-27149236

RESUMEN

We report an unusual intramolecular C-FO[double bond, length as m-dash]C and C-HCl-C parallel dipole-dipole alignment which "locks" the molecular conformation of cryocrystallized liquids towards planarity where the diatropic ring current establishes the existence of aromaticity in the five-membered ring associated with FO contact. Topological analysis establishes the bonding interaction between [F, O] and [H, Cl].

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