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The increased interest in sequencing cyanobacterial genomes has allowed the identification of new homologs to both the N-terminal domain (NTD) and C-terminal domain (CTD) of the Orange Carotenoid Protein (OCP). The N-terminal domain homologs are known as Helical Carotenoid Proteins (HCPs). Although some of these paralogs have been reported to act as singlet oxygen quenchers, their distinct functional roles remain unclear. One of these paralogs (HCP2) exclusively binds canthaxanthin (CAN) and its crystal structure has been recently characterized. Its absorption spectrum is significantly red-shifted, in comparison to the protein in solution, due to a dimerization where the two carotenoids are closely placed, favoring an electronic coupling interaction. Both the crystal and solution spectra are red-shifted by more than 50 nm when compared to canthaxanthin in solution. Using molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) studies of HCP2, we aim to simulate these shifts as well as obtain insight into the environmental and coupling effects of carotenoid–protein interactions.

Multichromophoric interactions control the initial events of energy capture and transfer in the light harvesting peridinin-chlorophyll a protein (PCP) from marine algae dinoflagellates. Due to the van der Waals association of the carotenoid peridinin (Per) with chlorophyll a in a unique 4:1 stoichiometric ratio, supramolecular quantum mechanical/molecular mechanical (QM/MM) calculations are essential to accurately describe structure, spectroscopy, and electronic coupling. We show that, by enabling inter-chromophore electronic coupling, substantial effects arise in the nature of the transition dipole moment and the absorption spectrum. We further hypothesize that inter-protein domain Per-Per interactions are not negligible, and are needed to explain the experimental reconstruction features of the spectrum in wild-type PCP.

Chiral nanomaterials have recently stimulated significant interest in both fundamental research and practical applications (e.g., nanoprobes for biomolecular recognition). However, achieving chiral nanoclusters is still a major challenge. Herein, we report an effective strategy that affords achiral diphosphine ligand‐protected, chiral Au11 nanoclusters. Synchrotron radiation X‐ray diffraction solves the chiral structure of Au11(dppp)5Cl3 (dppp = 1,3‐bis(diphenylphosphino)propane) and further reveals that the critical feature of bidentate binding of diphosphine induces the unique ansa‐metallamacrocycle pattern (i.e., the “Au─P─CH2CH2CH2─P─Au” staple). All the possible ansa‐metallamacrocycle patterns are transferred to the most robust pattern by “ligand confinement,” giving rise to the chiral enantiomers. Using Density Functional Theory (DFT), we show that the chirality can emerge due to the low energy barriers facilitating the transformation of the symmetric Au11 core into the corresponding asymmetric chiral cluster, driven by a favorable fit of ligand bridges. This new type of chiral nanomaterial holds promise in chiral sensing/recognition and enantioselective applications. In this work, we prepare a chiral Au11 nanocluster ligated by diphosphine ligand, Au11(dppp)5Cl3, which is induced by the unique ansa‐metallamacrocycle stain (the “Au─P─CH2CH2CH2─P─Au” staple).

We report the development and implementation of hybrid methods that combine quantum mechanics (QM) with molecular mechanics (MM) to theoretically characterize thiolated gold clusters. We use, as training systems, structures such as Au 25 (SCH 2 –R) 18 and Au 38 (SCH 2 –R) 24 , which can be readily compared with recent crystallographic data. We envision that such an approach will lead to an accurate description of key structural and electronic signatures at a fraction of the cost of a full quantum chemical treatment. As an example, we demonstrate that calculations of the 1 H and 13 C NMR shielding constants with our proposed QM/MM model maintain the qualitative features of a full DFT calculation, with an order-of-magnitude increase in computational efficiency.

This paper reports computational studies of substrate water binding to the oxygen-evolving centre (OEC) of photosystem II (PSII), completely ligated by amino acid residues, water, hydroxide and chloride. The calculations are based on quantum mechanics/molecular mechanics hybrid models of the OEC of PSII, recently developed in conjunction with the X-ray crystal structure of PSII from the cyanobacterium Thermosynechococcus elongatus. The model OEC involves a cuboidal Mn3CaO4Mn metal cluster with three closely associated manganese ions linked to a single μ4-oxo-ligated Mn ion, often called the 'dangling manganese'. Two water molecules bound to calcium and the dangling manganese are postulated to be substrate molecules, responsible for dioxygen formation. It is found that the energy barriers for the Mn(4)-bound water agree nicely with those of model complexes. However, the barriers for Ca-bound waters are substantially larger. Water binding is not simply correlated to the formal oxidation states of the metal centres but rather to their corresponding electrostatic potential atomic charges as modulated by charge-transfer interactions. The calculations of structural rearrangements during water exchange provide support for the experimental finding that the exchange rates with bulk 18O-labelled water should be smaller for water molecules coordinated to calcium than for water molecules attached to the dangling manganese. The models also predict that the S1→S2 transition should produce opposite effects on the two water-exchange rates.

Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and structural refinement of macrobiomolecules (e.g., proteins and nucleic acids). These methods are highly efficient, since they implement quantum chemistry techniques for modeling only the small part of the system (QM layer) that undergoes chemical modifications, charge transfer, etc., under the influence of the surrounding environment. The rest of the system (MM layer) is described in terms of molecular mechanics force fields, assuming that its influence on the QM layer can be roughly decomposed in terms of electrostatic interactions and steric hindrance. Common limitations of QM/MM methods include inaccuracies in the MM force fields, when polarization effects are not explicitly considered, and the approximate treatment of electrostatic interactions at the boundaries between QM and MM layers. This article reviews recent advances in the development of computational protocols that allow for rigorous modeling of electrostatic interactions in extended systems beyond the common limitations of QM/MM hybrid methods. We focus on the moving-domain QM/MM (MoD-QM/MM) methodology that partitions the system into many molecular domains and obtains the electrostatic and structural properties of the whole system from an iterative self-consistent treatment of the constituent molecular fragments. We illustrate the MoD-QM/MM method as applied to the description of photosystem II as well as in conjunction with the application of spectroscopically constrained QM/MM optimization methods, based on high-resolution spectroscopic data (extended X-ray absorption fine structure spectra, and exchange coupling constants).

This work presents new developments of the moving-domain QM/MM (MoD-QM/MM) method for modeling protein electrostatic potentials. The underlying goal of the method is to map the electronic density of a specific protein configuration into a point-charge distribution. Important modifications of the general strategy of the MoD-QM/MM method involve new partitioning and fitting schemes and the incorporation of dynamic effects via a single-step free energy perturbation approach (FEP). Selection of moderately sized QM domains partitioned between and C (from C=O), with incorporation of delocalization of electrons over neighboring domains, results in a marked improvement of the calculated molecular electrostatic potential (MEP). More importantly, we show that the evaluation of the electrostatic potential can be carried out on a dynamic framework by evaluating the free energy difference between a non-polarized MEP and a polarized MEP. A simplified form of the potassium ion channel protein Gramicidin-A from Bacillus brevis is used as the model system for the calculation of MEP. Figure Schematic representation of the Moving Domain QM/MM method

Mechanistic investigations of the water-splitting reaction of the oxygen-evolving complex (OEC) of photosystem II (PSII) are fundamentally informed by structural studies. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy, and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the exact configuration of the catalytic metal cluster and its ligation scheme. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein, have proposed chemically satisfactory models of the fully ligated OEC within PSII that are maximally consistent with experimental results. The inorganic core of these models is similar to the crystallographic model upon which they were based, but comprises important modifications due to structural refinement, hydration, and proteinaceous ligation which improve agreement with a wide range of experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting in PSII as described by the intermediate oxidation states of the OEC. This review summarizes these recent advances in QM/MM modeling of PSII within the context of recent experimental studies.

Chiral nanomaterials have recently stimulated significant interest in both fundamental research and practical applications (e.g., nanoprobes for biomolecular recognition). However, achieving chiral nanoclusters is still a major challenge. Herein, we report an effective strategy that affords achiral diphosphine ligand‐protected, chiral Au 11 nanoclusters. Synchrotron radiation X‐ray diffraction solves the chiral structure of Au 11 (dppp) 5 Cl 3 (dppp = 1,3‐bis(diphenylphosphino)propane) and further reveals that the critical feature of bidentate binding of diphosphine induces the unique ansa‐metallamacrocycle pattern (i.e., the “Au─P─CH 2 CH 2 CH 2 ─P─Au” staple). All the possible ansa‐metallamacrocycle patterns are transferred to the most robust pattern by “ligand confinement,” giving rise to the chiral enantiomers. Using Density Functional Theory (DFT), we show that the chirality can emerge due to the low energy barriers facilitating the transformation of the symmetric Au 11 core into the corresponding asymmetric chiral cluster, driven by a favorable fit of ligand bridges. This new type of chiral nanomaterial holds promise in chiral sensing/recognition and enantioselective applications.

Understanding how chemical modifications alter the atomic‐scale organization of materials is of fundamental importance in materials engineering and the target of considerable efforts in computational prediction. Incorporating covalent and noncovalent interactions in designing crystals while “piggybacking” on the driving force of molecular self‐assembly has augmented efforts to understand the emergence of complex structures using directed synthesis. In this work, microcrystalline powders of the silver 2‐, 3‐, and 4‐fluorobenzenethiolates are prepared and their structures are resolved by small‐molecule serial femtosecond X‐ray crystallography. These three compounds enable the emergence and role of supramolecular synthons in the crystal structures of 3D metal‐organic chalcogenolates to be examined. The unique divergence in their optoelectronic, morphological, and structural behaviors is assessed. The extent of CHF interactions and their influence on the structure and the observed trends in the thermal stability of the crystals are quantified through theoretical calculations and thermogravimetric analysis. Exploiting noncovalent interactions in designing functional hybrid material systems is an attractive and efficient process for gaining atomic‐level organization. Modifying the nature, steric factors, and electronegativity of functional groups used in building supramolecular architectures serves as a frontier to understanding material properties and how to arrange them into remarkable functional materials.