Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

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To catalyze or not to catalyze: elucidation of the subtle differences between the hexameric capsules of pyrogallolarene and resorcinarene

The closely related, self-assembled resorcinarene and pyrogallolarene capsules display contrasting and puzzling encapsulation behaviors. Herein, we elucidate the reasons for these differences by combining experimental studies and DFT calculations. Furthermore, we report that, in contrast to the resorcinarene capsule, the pyrogallolarene derivative is not capable of catalyzing reactions with cationic transition states. The molecular mechanisms responsible for these observations are probed in detail

Benchmarking the performance of time-dependent density functional theory methods on biochromophores

Quantum chemical calculations are important for elucidating light-capturing mechanisms in photobiological systems. The time-dependent density functional theory (TDDFT) has become a popular methodology because of its balance between accuracy and computational scaling, despite its problems in describing, for example, charge transfer states. As a step toward systematically understanding the performance of TDDFT calculations on biomolecular systems, we study here 17 commonly used density functionals, including seven long-range separated functionals, and compare the obtained results with excitation energies calculated at the approximate second order coupled-cluster theory level (CC2). The benchmarking set includes the first five singlet excited states of 11 chemical analogues of biochromophores from the green fluorescent protein, rhodopsin/bacteriorhodopsin (Rh/bR), and the photoactive yellow protein. We find that commonly used pure density functionals such as BP86, PBE, M11-L, and hybrid functionals with 20-25% of Hartree-Fock (HF) exchange (B3LYP, PBE0) have a tendency to consistently underestimate vertical excitation energies (VEEs) relative to the CC2 values, whereas hybrid density functionals with around 50% HF exchange such as BHLYP, PBE50, and M06-2X and long-range corrected functionals such as CAM-B3LYP, omega PBE, omega PBEh, omega B97X, omega B97XD, BNL, and M11 overestimate the VEEs. We observe that calculations using the CAM-B3LYP and omega PBEh functionals with 65% and 100% long-range HF exchange, respectively, lead to an overestimation of the VEEs by 0.2-0.3 eV for the benchmarking set. To reduce the systematic error, we introduce here two new empirical functionals, CAMh-B3LYP and omega hPBE0, for which we adjusted the long-range HF exchange to 50%. The introduced parameterization reduces the mean signed average (MSA) deviation to 0.07 eV and the root mean square (rms) deviation to 0.17 eV as compared to the CC2 values. In the present study, TDDFT calculations using the aug-def2-TZVP basis sets, the best performing functionals relative to CC2 are omega hPBE0 (rms = 0.17, MSA = 0.06 eV); CAMh-B3LYP (rms = 0.16, MSA = 0.07 eV); and PBE0 (rms = 0.23, MSA = 0.14 eV). For the popular range-separated CAM-B3LYP functional, we obtain an rms value of 0.31 eV and an MSA value of 0.25 eV, which can be compared with the rms and MSA values of 0.37 and -0.31 eV, respectively, as obtained at the B3LYP level.Peer reviewe

High-latitude artificial aurora using the EISCAT high-gain HF facility

The EISCAT high-frequency (HF) transmitter facility at Ramfjord, Norway, has been used to accelerate F-region electrons sufficiently to excite the oxygen atoms and nitrogen molecules, resulting in optical emissions at 630, 557.7 and 427.8 nm. During O-mode transmissions at 5.423 MHz, using 630 MW effective radiated power, in the hours after sunset on 12 November 2001 several new observations were made, including: (1) The first high-latitude observation of an HF induced optical emission at 427.8 nm and (2) Optical rings being formed at HF on followed by their collapse into a central blob. Both discoveries remain unexplained with current theories

Fe-chitosan complexes for oxidative degradation of emerging contaminants in water: Structure, activity, and reaction mechanism

Versatile and ecofriendly methods to perform oxidations at near-neutral pH are of crucial importance for processes aimed at purifying water. Chitosan, a deacetylated form of chitin, is a promising starting material owing to its biocompatibility and ability to form stable films and complexes with metals. Here, we report a novel chitosan-based organometallic complex that was tested both as homogeneous and heterogeneous catalyst in the degradation of contaminants of emerging concern in water. The stoichiometry of the complex was experimentally verified with different metals, namely, Cu(II), Fe(III), Fe(II), Co(II), Pd(II), and Mn(II), and we identified the chitosan-Fe(III) complex as the most efficient catalyst. This complex effectively degraded phenol, triclosan, and 3-chlorophenol in the presence of hydrogen peroxide. A putative ferryl-mediated reaction mechanism is proposed based on experimental data, density functional theory calculations, and kinetic modeling. Finally, a film of the chitosan-Fe(III) complex was synthesized and proven a promising supported heterogeneous catalyst for water purification

Periconception endogenous and exogenous maternal sex steroid hormones and risk of asthma and allergy in offspring : protocol for a systematic review and meta-analysis

Introduction Pregnancy is associated with several hormonal changes which influence the developing fetus. Variations in maternal endogenous hormones and prepregnancy use of hormonal preparations have been linked to asthma and allergy in the offspring, but findings are inconsistent. We plan to undertake a systematic review to synthesise the evidence on the association between endogenous and exogenous maternal sex hormones and the risk of asthma and allergy in the offspring. Methods and analysis We will search Medline, Embase, Cochrane Library, Institute of Scientific Information Web of Science, Cumulative Index of Nursing and Allied Health, Scopus, Google Scholar, Allied and Complementary Medicine Database, Global Health, Psychological Information (PsycINFO), Centre for Agriculture and Bioscience (CAB) International and WHO Global Health Library from inception until 2016 to identify relevant studies on the topic. Additional studies will be identified by searching databases of proceedings of international conferences, contacting international experts in the field and searching the references cited in identified studies. We will include analytical epidemiological studies. Two researchers will independently screen identified studies, undertake data extraction and assess risk of bias in eligible studies, while a third reviewer will arbitrate any disagreement. We will use the Effective Public Health Practice Project tool to assess the risk of bias in the studies. We will perform a random-effects meta-analysis to synthesise the evidence. We will use the Grading of Recommendations Assessment, Development and Evaluation approach to rate the strength and quality of the overall evidence with respect to each outcome. Ethics and dissemination Ethical approval is not required since the study is a systematic review of published literature. Our findings will be reported in a peer-reviewed scientific journal.Peer reviewe

Absorption shifts of diastereotopically ligated chlorophyll dimers of photosystem I

The light-harvesting chlorophyll (Chl) molecules of photosynthetic systems form the basis for light-driven energy conversion. In biological environments, the Chl chromophores occur in two distinct diastereotopic configurations, where the alpha and beta configurations have a magnesium-ligating histidine residue and a 17-propionic acid moiety on the opposite side or on the same side of the Chl ring, respectively. Although beta-ligated Chl dimers occupy conserved positions around the reaction center of photosystem I (PSI), the functional relevance of the alpha/beta configuration of the ligation is poorly understood. We employ here correlated ab initio calculations using the algebraic-diagrammatic construction through second order (ADC(2)) and the approximate second-order coupled cluster (CC2) methods in combination with the reduced virtual space (RVS) approach in studies of the intrinsic excited-state properties of alpha-ligated and beta-ligated Chl dimers of PSI. Our ab initio calculations suggest that the absorption of the alpha-ligated reaction-center Chl dimer of PSI is redshifted by 0.13-0.14 eV in comparison to the beta-ligated dimers due to combined excitonic coupling and strain effects. We also show that time-dependent density functional theory (TDDFT) calculations using range-separated density functionals underestimate the absorption shift between the alpha- and beta-ligated dimers. Our findings may provide a molecular starting point for understanding the energy flow in natural photosynthetic systems, as well as a blueprint for developing new molecules that convert sunlight into other forms of energy.Peer reviewe

Terminal Electron–Proton Transfer Dynamics in the Quinone Reduction of Respiratory Complex I

Complex I functions as a redox-driven proton pump in aerobic respiratory chains. By reducing quinone (Q), complex I employs the free energy released in the process to thermodynamically drive proton pumping across its membrane domain. The initial Q reduction step plays a central role in activating the proton pumping machinery. In order to probe the energetics, dynamics, and molecular mechanism for the proton-coupled electron transfer process linked to the Q reduction, we employ here multiscale quantum and classical molecular simulations. We identify that both ubiquinone (UQ) and menaquinone (MQ) can form stacking and hydrogen-bonded interactions with the conserved Q binding-site residue His-38 and that conformational changes between these binding modes modulate the Q redox potentials and the rate of electron transfer (eT) from the terminal N2 iron-sulfur center. We further observe that, while the transient formation of semiquinone is not proton-coupled, the second eT process couples semiconcerted proton uptake from conserved tyrosine (Tyr-87) and histidine (His-38) residues within the active site. Our calculations indicate that both UQ and MQ have low redox potentials around -260 and -230 mV, respectively, in the Q-binding site, respectively, suggesting that release of the Q toward the membrane is coupled to an energy transduction step that could thermodynamically drive proton pumping in complex I.Peer reviewe

Identifying Local and Centralized Mental Health ServicesThe Development of a New Categorizing Variable

The challenges of mental health and substance abuse services (MHS) require shifting of the balance of resources from institutional care to community care. In order to track progress, an instrument that can describe these attributes of MHS is needed. We created a coding variable in the European Service Mapping Schedule-Revised (ESMS-R) mapping tool using a modified Delphi panel that classified MHS into centralized, local services with gatekeeping and local services without gatekeeping. For feasibility and validity, we tested the variable on a dataset comprising MHS in Southern Finland, covering a population of 2.3 million people. There were differences in the characteristics of services between our study regions. In our data, 41% were classified as centralized, 37% as local without gatekeeping and 22% as local services with gatekeeping. The proportion of resources allocated to local services varied from 20% to 43%. Reclassifying ESMS-R is an easy way to compare the important local vs. centralized balance of MHS systems globally, where such data exists. Further international studies comparing systems and validating this approach are needed.Peer reviewe