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Real-space self-interaction corrected (time-dependent) density functional theory has been used to investigate the ground-state electronic structure and optical absorption profiles of a series of linear oligomers inspired by the natural product telomestatin. Length-dependent development of plasmonic excitations in the UV region is seen in the neutral species which is augmented by polaron-type absorption in the IR when the chains are doped with an additional electron/hole. Combined with a lack of absorption in the visible region this suggests these oligomers as good candidates for applications such as transparent antennae in dye-sensitised solar energy collection materials.

Cyclodextrins (Cds) are versatile carbohydrate hosts for developing multifunctional nanostructures of pharmaceutical interest. Factors affecting the thermodynamic signatures and stability of β- and γ-Cd complexes are detailed at the atomic level. The MD/PMF-based method is combined with the description of the nature and strength of the inter-partner affinity. Naphthalene, adamantane and lycorine derivatives are used as models of drug-leading structures. Guest size affects Cd-guest contact and the inclusion degree, inducing Cd deformation, which opposes inclusion. Complexation depends on the available Cd cavity volume, as guest fitting variations and the enthalpy penalty from Cd deformation impact on the binding constants (promoting a reduction of up to 104). The often neglected Cd deformation plays, thus, an important role in the interaction behavior of larger cavity Cd-based systems, being crucial in carbohydrate-mediated recognition phenomena. It corresponds to an increase in energy of ca. 90 kJ mol−1 in the simpler analyzed model system.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are structurally complex naturally occurring metabolites across all three domains of life. Despite the structural diversity of RiPPs that stems from the extensive post-translational modifications, only α-amino acid residues have been found in known RiPPs. Here we report discovery of a new 27-mer peptide, kintamdin, using comprehensive MS and NMR structural elucidation and genomic analysis together with computational modelling. The peptide features a β-amino acid residue and a new thioether macrocyclic ring. Heterologous expression and gene inactivation allowed the identification of the minimal biosynthetic gene cluster (BGC). The gene products in kin BGC share low homologues compared to other known RiPP pathways, further rendering the novelty of kintamdin. Biochemical analysis indicated that KinO mediate di-methylation reaction to yield kintamidn. Finally, the occurrence of the kin-like BGCs in Gram-positive bacteria suggested the biological importance of this new group of RiPPs.

Vibrational and electronic absorption spectra calculated at the (time-dependent) density functional theory level for the bismuth carbide clusters Bi n C 2 n + ( 3 ⩽ n ⩽ 9 ) indicate significant differences in types of bonding that depend on cluster geometry. Analysis of the electronic charge densities of these clusters highlighted bonding trends in these complex open-shell systems consistent with the spectroscopic information. The data indicate that larger clusters ( n > 5 ) have significant non-covalent bonding character and are likely to be kinetically unstable, in agreement with the cluster mass distribution obtained in gas-aggregation source experiments. The spectral fingerprints of the different clusters obtained from our calculations also suggest that identification of specific Bi n C 2 n + structural isomers should be possible based on infra-red and optical absorption spectroscopy.

As opposed to small molecules, macrocyclic peptides possess a large surface area and are recognised as promising candidates to selectively treat diseases by disrupting specific protein&ndash, protein interactions (PPIs). Due to the difficulty in predicting cyclopeptide conformations in solution, the de novo design of bioactive cyclopeptides remains significantly challenging. In this study, we used the combination of conformational analyses and molecular docking studies to design a new cyclopeptide inhibitor of the interaction between the human tumour necrosis factor alpha (TNF&alpha, ) and its receptor TNFR-1. This interaction is a key in mediating the inflammatory response to tissue injury and infection in humans, and it is also an important causative factor of rheumatoid arthritis, psoriasis and inflammatory bowel disease. The solution state NMR structure of the cyclopeptide was determined, which helped to deduce its mode of interaction with TNF&alpha, TNF&alpha, sensor cells were used to evaluate the biological activity of the peptide.

Kidney failure is frequently observed during and after COVID-19, but it remains elusive whether this is a direct effect of the virus. Here, we report that SARS-CoV-2 directly infects kidney cells and is associated with increased tubule-interstitial kidney fibrosis in patient autopsy samples. To study direct effects of the virus on the kidney independent of systemic effects of COVID-19, we infected human induced pluripotent stem cell-derived kidney organoids with SARS-CoV-2. Single cell RNA-sequencing indicated injury and dedifferentiation of infected cells with activation of pro-fibrotic signaling pathways. Importantly, SARS-CoV-2 infection also led to increased collagen 1 protein expression in organoids. A SARS-CoV-2 protease inhibitor was able to ameliorate the infection of kidney cells by SARS-CoV-2. Our results suggest that SARS-CoV-2 can directly infect kidney cells and induce cell injury with subsequent fibrosis. These data could explain both acute kidney injury in COVID-19 patients and the development of chronic kidney disease in Long-COVID., Graphical Abstract, Jansen, Reimer, Nagai et al report that SARS-CoV-2 infects kidney cells and is associated with kidney fibrosis in patients. Using single cell transcriptomics of infected kidney organoids, they show that SARS-CoV-2 causes kidney injury and stimulates pro-fibrotic signaling. Viral infection in organoids was inhibited by a recently developed protease blocker.

A library of new chiral thiazolidines was prepared starting from l -cysteine and d -penicillamine in a simple, one-step procedure. 2-Arylthiazolidines were obtained, as diastereoisomeric mixtures, with good yields and in short reaction times, through a new and greener procedure, using microwave irradiation. Their use as chiral ligands in the enantioselective ethylation of aromatic aldehydes was studied and optimized, originating good to excellent conversions and ee up to 94% in 6 h. A series of heteroaromatic and aliphatic substrates were also enantioselectively ethylated with success, with ee up to 77%. The distinct opposite chirality in l -cysteine and d -penicillamine makes the use of these ligands an interesting approach for obtaining both the (S) and (R) enantiomers of the chiral alcohols, compounds with potential applications in the area of fine chemistry. NMR studies were carried out using a diastereoisomeric mixture of thiazolidines, allowing the identification of the most stable structure. Computational studies confirmed this result and also gave important insight into the species involved in the catalytic cycle of the enantioselective alkylation.

The critical roles of solvent, enthalpic, and entropic contributions in complexes between different hyaluronic acid derivatives bearing monomeric β-cyclodextrin and adamantene moieties are assessed combining our previously designed free energy oriented method and a recently proposed density-based noncovalent interaction analysis. This establishes the relevant thermodynamics signatures and identifies the stabilizing/destabilizing noncovalent interactions within the complexes used as models for the junction points. It is observed that structural variations promote major changes in the thermodynamic variables. The presence of the amphiphilic chains emphasizes inclusion and drastically increases the binding constant (to ca. 1028). A comprehensive thermodynamic scheme is thus provided, in which host–guest interactions, host conformation, and solvation play the leading roles. These results have direct implications for the rational design of supramolecular materials with specific properties based on these host–g...

The title compounds show different conformations in the solid state., The crystal structures of (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-benzyl­oxime, C12H12N4O3, (I), (E)-1-methyl-5-nitro-1H-imidazole-2-carb­alde­hyde O-(4-fluoro­benz­yl) oxime, C12H11FN4O3, (II), and (E)-1-methyl-5-nitro-1H-imidazole-2-carbaldehyde O-(4-bromo­benz­yl) oxime, C12H11BrN4O3, (III), are described. The dihedral angle between the ring systems in (I) is 49.66 (5)° and the linking Nm—C—C=N (m = methyl­ated) bond shows an anti conformation [torsion angle = 175.00 (15)°]. Compounds (II) and (III) are isostructural [dihedral angle between the aromatic rings = 8.31 (5)° in (II) and 5.34 (15)° in (III)] and differ from (I) in showing a near-syn conformation for the Nm—C—C=N linker [torsion angles for (II) and (III) = 17.64 (18) and 8.7 (5)°, respectively], which allows for the occurrence of a short intra­molecular C—H⋯N contact. In the crystal of (I), C—H⋯N hydrogen bonds link the mol­ecules into [010] chains, which are cross-linked by very weak C—H⋯O bonds into (100) sheets. Weak aromatic π–π stacking inter­actions occur between the sheets. The extended structures of (II) and (III) feature several C—H⋯N and C—H⋯O hydrogen bonds, which link the mol­ecules into three-dimensional networks, which are consolidated by aromatic π–π stacking inter­actions. Conformational energy calculations and Hirshfeld fingerprint analyses for (I), (II) and (III) are presented and discussed.

A necessary first step in the development of technologies such as artificial photosynthesis is understanding the photoexcitation process within the basic building blocks of naturally occurring light harvesting complexes (LHCs). The most important of these building blocks in biological LHCs such as LHC II from green plants are the chlorophyll a (Chl a) and chlorophyll b (Chl b) chromophores dispersed throughout the protein matrix. However, efforts to describe such systems are still hampered by the lack of computationally efficient and accurate methods that are able to describe optical absorption in large biomolecules. In this work, we employ a highly efficient linear combination of atomic orbitals (LCAOs) to represent the Kohn–Sham (KS) wave functions at the density functional theory (DFT) level and perform time-dependent density functional theory (TDDFT) calculations in either the reciprocal space and frequency domain (LCAO-TDDFT-k-ω) or real space and time domain (LCAO-TDDFT-r-t) of the optical absorption spectra of Chl a and b monomers and dimers. We find that our LCAO-TDDFT-k-ω and LCAO-TDDFT-r-t calculations reproduce results obtained with a plane-wave (PW) representation of the KS wave functions (PW-TDDFT-k-ω) but with a significant reduction in computational effort. Moreover, by applying the Gritsenko, van Leeuwen, van Lenthe, and Baerends solid and correlation derivative discontinuity correction Δx to the KS eigenenergies, with both LCAO-TDDFT-k-ω and LCAO-TDDFT-r-t methods, we are able to semiquantitatively reproduce the experimentally measured photoinduced dissociation results. This work opens the path to first principles calculations of optical excitations in macromolecular systems.

In order to accelerate the isolation and characterization of structurally new or novel secondary metabolites, it is crucial to develop efficient strategies that prioritize samples with greatest promise early in the workflow so that resources can be utilized in a more efficient and cost-effective manner. We have developed a metrics-based prioritization approach using exact LC-HRMS, which uses data for 24 618 marine natural products held in the PharmaSea database. Each sample was evaluated and allocated a metric score by a software algorithm based on the ratio of new masses over the total (sample novelty), ratio of known masses over the total (chemical novelty), number of peaks above a defined peak area threshold (sample complexity), and peak area (sample diversity). Samples were then ranked and prioritized based on these metric scores. To validate the approach, eight marine sponges and six tunicate samples collected from the Fiji Islands were analyzed, metric scores calculated, and samples targeted for isolation and characterization of new compounds. Structures of new compounds were elucidated by spectroscopic techniques, including 1D and 2D NMR, MS, and MS/MS. Structures were confirmed by computer-assisted structure elucidation methods (CASE) using the ACD/Structure Elucidator Suite.

Exciton coupling between two or more chlorophyll (Chl) pigments is a key mechanism associated with the color tuning of photosynthetic proteins but it is difficult to disentangle this effect from shifts that are due to the protein microenvironment. Herein, we report the formation of the simplest coupled system, the Chl a dimer, tagged with a quaternary ammonium ion by electrospray ionization. Based on action spectroscopic studies in vacuo, the dimer complexes were found to absorb 50–70 meV to the red of the monomers under the same conditions. First-principles calculations predict shifts that somewhat depend on the relative orientation of the two Chl units, namely 50 and 30 meV for structures where the Chl rings are stacked and unstacked, respectively. Our work demonstrates that Chl association alone can produce a large portion of the color shift observed in photosynthetic macromolecular assemblies., B.F.M. acknowledges funding from the Portuguese Foundation for Science and Technology (CONT_DOUT/11/UC/405/10150/18/2008) and thanks the DIPC and CFM (UPV/EHU) and the Laboratory for Advanced Computation (University of Coimbra) for support. S.B.N. acknowledges support from the Danish Council for Independent Research (4181-00048B) and the Villum Foundation. A.R. acknowledges financial support from the European Research Council (ERC-2010-AdG-267374), a Spanish grant (FIS2013-46159-C3-1-P), Grupos Consolidados (IT578-13), AFOSR (FA2386-15-1-0006), AOARD (144088), the H2020-NMP-2014 project MOSTOPHOS (SEP-210187476), and COST Action (MP1306, “EUSpec”).

A new 1D complex has been prepared and characterized. X-ray single crystal structure confirms that the Cu(II) ions assemble in alternating chains with Cu … Cu distances of 2.5685(4) and 3.1760(4) A. The temperature dependence of the magnetic susceptibility reveals an antiferromagnetic interaction between the paddle-wheel copper centers with an exchange of −300 cm−1. The exchange integral was also determined by quantum chemical ab-initio calculations, using polarised and unpolarised basis sets reproducing well the experimental value. The second harmonic generation efficiency of a concomitantly crystallized material was evaluated and was found to be comparable to urea.

The physics of surface plasmons has a long tradition in condensed matter theory but as the dimension of the systems reaches the nano scale, new effects appear. In this work, by calculating the absorption spectra of a single wall carbon nanotube, using time dependent density functional theory, the effect of adding/removing electrons on the surface plasmon energy is studied. It is shown that removing electrons from the single wall carbon nanotube does not affect the surface plasmon energy peak. In contrast, adding electrons to the single wall carbon nanotube will redshift the plasmonic peak energy, an effect that is explained by an increase of the electron effective mass.

First-principles calculations have been used to investigate the potential use of circular dichroism (CD) spectroscopy in single-molecule sensing. Using a real-space implementation of time-dependent density functional theory (TDDFT), several systems involving single-walled carbon nanotubes (SWCNT) and small molecules have been studied to evaluate their CD response. Large induced CD (ICD) effects, differing for each test molecule, were observed in all SWCNT–molecule complexes. As the SWCNT used in this study shows no intrinsic CD response, the ICD spectra are the result of interaction with the small molecules. This finding is general and independent of the (a)chiral nature of the adsorbed molecule. Our results indicate that it is possible to design a system that uses SWCNT for detection of molecules using the change in CD spectrum of the system induced by adsorption of the molecule onto the SWCNT surface.

A novel erbium(III) complex with acetylacetone (Hacac) and bathophenanthroline (4,7-diphenyl-1,10-phenanthroline, bath) ligands, formulated as [Er(acac)3(bath)], has been characterized by elemental analysis, X-ray diffraction, thermogravimetric analysis, Fourier transform infrared spectroscopy, Raman spectroscopy, absorption and emission spectroscopies. In the theoretical part of this study, semi-empirical quantum chemistry methods using AM1, PM3, PM6 and PM7 models have been employed to predict the structure of the complex, calculate the geometric and crystallographic parameters, and make comparisons with spectroscopic data using INDO/S-CI calculations. Real-time time-dependent density-functional theory (TDDFT) has also been used to calculate the optical absorption spectrum of the complex in the gas phase.

The first-order hyperpolarizability, β, has been calculated for a group of marine natural products, the makaluvamines. These compounds possess a common cationic pyrroloiminoquinone structure that is substituted to varying degrees. Calculations at the MP2 level indicate that makaluvamines possessing phenolic side chains conjugated with the pyrroloiminoquinone moiety display large β values, while breaking this conjugation leads to a dramatic decrease in the calculated hyperpolarizability. This is consistent with a charge-transfer donor-π-acceptor (D-π-A) structure type, characteristic of nonlinear optical chromophores. Dynamic hyperpolarizabilities calculated using resonance-convergent time-dependent density functional theory coupled to polarizable continuum model (PCM) solvation suggest that significant resonance enhancement effects can be expected for incident radiation with wavelengths around 800 nm. The results of the current work suggest that the pyrroloiminoquinone moiety represents a potentially useful new chromophore subunit, in particular for the development of molecular probes for biological imaging. The introduction of solvent-solute interactions in the theory is conventionally made in a density matrix formalism, and the present work will provide detailed account of the approximations that need to be introduced in wave function theory and our program implementation. The program implementation as such is achieved by a mere combination of existing modules from previous developments, and it is here only briefly reviewed.

A new siderophore containing a 4,5-dihydroimidazole moiety was isolated from Pseudoalteromonas piscicida S2040 together with myxochelins A and B, alteramide A and its cycloaddition product, and bromo- and dibromoalterochromides. The structure of pseudochelin A was established by spectroscopic techniques including 2D NMR and MS/MS fragmentation data. In bioassays selected fractions of the crude extract of S2040 inhibited the opportunistic pathogen Pseudomonas aeruginosa. Pseudochelin A displayed siderophore activity in the chrome azurol S assay at concentrations higher than 50 mu M, and showed weak activity against the fungus Aspergillus fumigatus, but did not display antibacterial, anti-inflammatory or anticonvulsant activity. (C) 2017 Elsevier Ltd. All rights reserved.

The oxyluciferin molecule in its anionic form is responsible for light emission from fireflies and some railroad worms and click beetles. Here we have studied the breakdown of the ions after photoexcitation by 550-nm light, and identified the atom composition of eight fragment ions based on mass spectrometric experiments on isotope-labeled compounds. A sector instrument with an electrospray ion source and a pulsed laser system was used for the experiments. After photoexcitation the time for dissociation was up to about 15 μs, which is much shorter than the 100-μs time constant for dissociation after one-photon absorption. The laser power was therefore kept high to allow the oxyluciferin anions to absorb two photons to produce enough fragment ions on the instrumental relevant time scale. The reaction energies leading to these ions were obtained from density functional theory calculations. The dominant fragment ion was deprotonated 2-cyano-6-hydroxybenzothiazole. Interestingly this behavior mirrors that of oxyluciferin both in vivo in insects, where the same nitrile is an intermediate in the postulated regeneration of d -luciferin from oxyluciferin or in vitro in near-neutral aqueous buffer. Dissociation of the oxyluciferin anion into this fragment ion was calculated to require 1.86 eV, which is less than the energy of one photon (2.25 eV). Experiments done on 5,5-dimethyloxyluciferin revealed a similar fragmentation pattern.

Time-dependent density functional theory has been used to investigate the effects of group 15/16 element substitution on the optical response of firefly oxyluciferin. A range of analogues containing symmetrical substitutions at the N and S atom positions of the naturally-occurring oxyluciferin have been found to have red-shifted electronic excitation energies with the heaviest derivative investigated (As/Se) displaying a shift of −0.69 eV. Fluorescence emission wavelengths for all P- and As-containing derivatives in DMSO are estimated to lie in the 710–930 nm region making them interesting for bio-imaging applications., The author thanks the Donostia International Physics Centre and the Centre for Materials Physics, University of the Basque Country (UPV/EUH) for financial support and the Laboratory for Advanced Computation of the University of Coimbra for the provision of computer resources, technical support and assistance.

In certain materials, and for certain voltage ranges, electrical current flowing through the material decreases when the voltage across the sample is increased. This negative differential conductance (NDC) is important for oscillators, amplifiers, and fast switching devices. In this work, using real time quantum simulations, we show that this phenomenon occurs in isolated finite armchair single wall carbon nanotubes (SWCNT) without end contacts. For metallic SWCNT, like the armchair SWCNT, electron transfer to secondary valleys-the most common cause of NDC-is not expected to be observed, as there are two quantum channels at the Fermi energy available for conduction. The NDC is due to the finite nature of the SWCNT and the existence of excited states that are blocked, similarly to a Coulomb blockade system, thus preventing any further current flow. We also show that the SWCNT conductivity depends on its length and that the current flowing on the SWCNT behaves like a Bloch oscillation that is disrupted in the presence of a molecule, decreasing the conductivity, and thus providing a rationalisation for the behaviour of SWCNT organic gas sensors.

Crystallography reveals the rotomer in the salt isolated from EtOH solution has an anti disposition of the OH and imine-NH hydrogen atoms while that from EtOCH2CH2OH solution has a syn disposition. Both molecules have an E configuration about the C=N bond and are essentially planar (dihedral angles between aromatic groups = 2.4 (3)° and 6.42 (9)°, respectively). The anti-rotomer crystallizes in the monoclinic space group P21/n with a = 10.8795 (10) A, b = 10.7730 (11) A, c = 13.1257 (7) A, λ = 104.806 (5)°, and Z = 4. The syn-rotomer crystallizes in the monoclinic space group C2/c with a = 14.4610 (5) A, b = 11.3073 (5) A, c = 17.8849 (7) A, β = 91.904 (2)°, and Z = 8. Planar anti- and syn-rotomers of the title compound feature intramolecular O–H···N or intermolecular O–H···Cl hydrogen bonds, respectively, and two- and three-dimensional supramolecular architectures, respectively.

The excited-state physics of the firefly luciferin anion depends on its chemical environment, and it is therefore important to establish the intrinsic behavior of the bare ion. Here we report electronic absorption spectra of the anion isolated in vacuo obtained at an electrostatic ion storage ring and an accelerator mass spectrometer where ionic dissociation is monitored on a long time scale (from 33 μs and up to 3 ms) and on a short time scale (0-3 μs), respectively. In the ring experiment the yield of all neutrals (mainly CO(2)) as a function of wavelength was measured whereas in the single pass experiment, the abundance of daughter ions formed after loss of CO(2) was recorded to provide action spectra. We find maxima at 535 and 265 nm, and that the band shape is largely determined by the sampling time interval, which is due to the kinetics of the dissociation process. Calculations at the TD-B3LYP/TZVPP++ level predict maximum absorption at 533 and 275 nm for the carboxylate isomer in excellent agreement with the experimental findings. The phenolate isomer lies higher in energy by 0.22 eV, and also its absorption maximum is calculated to be at 463 nm, which is far away from the experimental value. Our data serve to benchmark future theoretical models for bioluminescence from fireflies.

In this work we present results of density functional theory (DFT) calculations on dicopper patellamides and their affinity for molecular oxygen and carbonate. Patellamides are cyclic octapeptides that are produced by a cyanobacterium, and may show promise as therapeutics. Thus, carbonate binding to a dicopper patellamide center gives a stable cyclic octapeptide with a twist of almost 90°. The system exists in close-lying open-shell singlet and triplet spin states with two unpaired electrons in orthogonal σ ∗ orbitals on each metal center. Subsequently, we replaced carbonate with dioxygen and found a stable Cu 2 (μ-O) 2 diamond shaped patellamide core. In this structure the original dioxygen bond is significantly weakened to essentially a single bond, which should enable the system to transfer these oxygen atoms to substrates. We predicted the IR and Raman spectra of the Cu 2 (μ-O) 2 diamond shaped patellamide structure using density functional theory and found a considerable isotope effect on the O–O stretch vibration for 16 O 2 versus 18 O 2 bound structures. Our studies reveal that carbonate forms an extremely stable complex with dicopper patellamide, but that additional molecular oxygen to this system does not give a potential oxidant. Therefore, it is more likely that carbonate prepares the system for dioxygen binding by folding it into the correct configuration followed in the proposed catalytic cycle by a protonation event preceding dioxygen binding to enable the system to reorganize to form a stable Cu 2 (μ-O) 2 -patellamide cluster. Alternatively, carbonate may act as an inhibitor that blocks the catalytic activity of the system. It is anticipated that the Cu 2 (μ-O) 2 -patellamide structure is a potential active oxidant of the dicopper patellamide complex.

Action spectroscopy provides key insights into the nature of electronic transitions of coordination complexes such as porhyrin-containing biochromophores like chlorophyll or transition metal complexes such as tris(bipyridine)ruthenium.

The exact color of light absorbed by chlorophyll (Chl) pigments, the light-harvesters in photosynthesis, is tuned by the protein microenvironment, but without knowledge of the intrinsic color of Chl it remains unclear how large this effect is. Experimental first absorption energies of Chl a and b isolated in vacuo and tagged with quaternary ammonium cations are reported. The energies are largely insensitive to details of the tag structure, a finding supported by first-principles calculations using time-dependent density functional theory. Absorption is significantly blue-shifted compared to that of Chl-containing proteins (by 30–70 nm). A single red-shifting perturbation, such as axial ligation or the protein medium, is insufficient to account even for the smallest shift; the largest requires pigment–pigment interactions., B.F.M. thanks DIPC and CFM (UPV/EHU) and the Laboratory for Advanced Computation (University of Coimbra) for support. S.B.N. acknowledges support from Lundbeckfonden. A.R. acknowledges support from ERC Advanced Grant DYNamo (ERC-2010-AdG-267374), Spanish Grant (FIS2013-46159-C3-1-P), Grupos Consolidados UPV/EHU del Gobierno Vasco (IT578-13), and EC FP7 CRONOS (Grant 280879-2).

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence., First-principles calculations within the framework of real-space time-dependent density functional theory have been performed for the complete chlorophyll (Chl) network of the light-harvesting complex from green plants, LHC-II. A local-dipole analysis method developed for this work has made possible the studies of the optical response of individual Chl molecules subjected to the influence of the remainder of the chromophore network. The spectra calculated using our real-space TDDFT method agree with previous suggestions that weak interaction with the protein microenvironment should produce only minor changes in the absorption spectrum of Chl chromophores in LHC-II. In addition, relative shifting of Chl absorption energies leads the stromal and lumenal sides of LHC-II to absorb in slightly different parts of the visible spectrum providing greater coverage of the available light frequencies. The site-specific alterations in Chl excitation energies support the existence of intrinsic energy transfer pathways within the LHC-II complex., The authors acknowledge financial support from the European Research Council Advanced Grant DYNamo (ERC-2010-AdG-267374), European Commission Project CRONOS (grant number 280879-2, CRONOS CP-7P7), Spanish Grant (FIS2013-46159-C3-1-P), Grupos Consolidados UPV/EHU del Gobierno Vasco (IT578-13 and IT395-10), UPV/EHU (grant UFI11/45), COST Actions CM1204 (XLIC) and MP1306 (EUSpec). JJS gratefully acknowledges the Comissionat per a Universitats i Recerca del Departament dInnovacio, Universitats i Empresa, de la Generalitat de Catalunya for financial support, and the Marie Curie Cofund Action (FP7) of the European Union for the Beatriu de Pinos (2010 BP-A2-00024) postdoctoral fellowship. JAR acknowledges the fellowship of the UPV/EHU. JJPS acknowledges financial support from the National Institute Of General Medical Sciences of the National Institutes of Health (Award Number 1R44GM108085-01A1). BFM acknowledges financial support from the Portuguese Foundation for Science and Technology (CONT_DOUT/11/UC/ 405/10150/18/2008), the Donostia International Physics centre and the Centro de Fisica de Materiales, UPV/EHU, for financial support.

We have performed gas-phase absorption spectroscopy in the Soret-band region of chlorophyll (Chl) a and b tagged by quaternary ammonium ions together with time-dependent density functional theory (TD-DFT) calculations. This band is the strongest in the visible region of metalloporphyrins and an important reporter on the microenvironment. The cationic charge tags were tetramethylammonium, tetrabutylammonium, and acetylcholine, and the dominant dissociation channel in all cases was breakage of the complex to give neutral Chl and the charge tag as determined by photoinduced dissociation mass spectroscopy. Two photons were required to induce fragmentation on the time scale of the experiment (microseconds). Action spectra were recorded where the yield of the tag as a function of excitation wavelength was sampled. These spectra are taken to represent the corresponding absorption spectra. In the case of Chl a we find that the tag hardly influences the band maximum which for all three tags is at 403 ± 5 nm. A smaller band with maximum at 365 ± 10 nm was also measured for all three complexes. The spectral quality is worse in the case of Chl b due to lower ion beam currents; however, there is clear evidence for the absorption being to the red of that of Chl a (most intense peak at 409 ± 5 nm) and also a more split band. Our results demonstrate that the change in the Soret-band spectrum when one peripheral substituent (CH3) is replaced by another (CHO) is an intrinsic effect. First principles TD-DFT calculations agree with our experiments, supporting the intrinsic nature of the difference between Chl a and b and also displaying minimal spectral changes when different charge tags are employed. The deviations between theory and experiment have allowed us to estimate that the Soret-band absorption maxima in vacuo for the neutral Chl a and Chl b should occur at 405 nm and 413 nm, respectively. Importantly, the Soret bands of the isolated species are significantly blueshifted compared to those of solvated Chl and Chl–proteins. The protein microenvironment is certainly not innocent of perturbing the electronic structure of Chls., SBN and MHS acknowledge Lundbeckfonden and Villumfonden for support. BFM thanks the Donostia International Physics centre and the Centre de Física de Materiales, University of the Basque Country for financial support. AR acknowledges financial support from the European Research Council Advanced Grant DYNamo (ERC-2010- AdG-267374), Spanish Grant (FIS2013-46159-C3-1-P), Grupos Consolidados UPV/EHU del Gobierno Vasco (IT578-13) and European Community FP7 project CRONOS (Grant number 280879-2) and COST Actions CM1204 (XLIC) and MP1306 (EUSpec). LM and YT acknowledge Cost Action CM1204 (XLIC) for support (ECOST-STSM-CM1204- 301114-047659).

The MeCOCH2CMe2 ligand in X3SnCMe2CH2COMe (2; X = halide) acts as a C,O-chelating group both in the solid state and in non-coordinating solutions. The intramolecular SnO bond lengths in trigonal bipyramidal 2 (X = Cl and I), as determined by X-ray crystallography, indicate that the stronger interaction occurs in 2 X = Cl. Comparisons with the SnO bond lengths in the estertin trihalides, X3SnCH2CH2CO2R (1; R = Me), suggest that the latter form stronger chelates than do 2. In chlorocarbon solution, 2 (X = Cl, I) undergoes exchange reactions, as shown by NMR spectra, to give all possible halide derivatives, ∑(ClnI3−nSnCMe2CH2COMe) (n = 0–3). Various ab initio calculations on 2 and X3SnCH2CH2COMe (3) have been carried out. Comparisons of the theoretical and experimental structures of 2 for X = Cl or I are reported. Copyright © 2005 John Wiley & Sons, Ltd.

It is vital that methylated trivalent arsenicals [MA(III) and DMA(III)] are described and characterized unequivocally due to their high toxicity. Two different ways of generating the methylated trivalent arsenicals have been practiced-reduction of the methylated pentavalent arsenical either by the sodium-metabisulfite (Na(2)S(2)O(5))/sodium thiosulfate (Na(2)S(2)O(3)) reagent (method A) or by KI, H(2)SO(4), and SO(2) (method B). The shared identity between the products of the two synthetic methods has never been questioned or proven. Here, we characterize and identify the arsenic species formed when reducing DMA(V) by method A or B. Dimethylarsinous acid [DMA(III)] was formed when reducing DMA(V) by method B, but DMA(III) was not the main product of the reaction by method A. The product was revealed by HPLC-ICP-MS coupled simultaneously to HPLC-ES-MS and ES-Q-TOF-MS to have the molecular formula C(2)H(7)OSAs. The structure was further confirmed by (1)H NMR, and ab initio tautomeric energy calculations showed it to be present as Me(2)As(=S)OH (dimethylarsinothioic acid). Dimethylarsinothioic acid was also identified as a metabolite in urine and in wool extract from sheep naturally consuming large amounts of arsenosugars (35 mg of As daily) through their major food source, seaweed.

A theoretical study of tetrabutylammonium [bis(1,3-dithiole-2-thione-4,5-dithiolato)bismuthate], [NBu 4 ][Bi(dmit) 2 ] is reported. The vibrational spectrum and the molecular orbitals were calculated at the Hartree–Fock level of theory with the pseudo-potential SBKJC for Bi and a basis set of 6-31G or 6-31G(d,p) for the other atoms. The molecular geometry of the anion, [Bi(dmit) 2 ] − , was optimised with the same level of theory and basis sets, but utilising the polarisable continuum method, for simulation of acetone and benzene media. Molecular geometries of solvated and solid-state species are compared: solvation effects are discussed in terms of anisotropy or isotropy of the media. Analysis of the molecular orbitals allowed a qualitative description of the anion–anion intermolecular interactions.

Solvent dependent conformational change of the thiazole and oxazoline containing cyclic peptides, the patellamides, is examined by a combination of experimental and theoretical methods. A mechanism for the simultaneous formation of two type-II β-turns in the patellamides is proposed based on molecular dynamics and NOE restrained molecular dynamics studies as well as literature evidence. The effect of the solvent and desymmetrisation of the patellamides is crucial, with symmetrical patellamides in polar solvents giving the open type-I conformation, whereas symmetrical patellamides in non-polar solvents and asymmetrical patellamides in both polar and non-polar solvents give rise to the folded type-II conformation.

Studies on the Thz, Thn and Oxn containing cyclic peptides, lissoclinamides 9 ( 9 ) and 10 ( 10 ) isolated from the Indo-Pacific ascidian (seasquirt) Lissoclinum patella have delineated their metal binding selectivity. MS and CD competition studies show that lissoclinamide 10 ( 10 ) shows selectivity for Cu 2+ in the presence of an excess of Zn 2+ whereas lissoclinamide 9 ( 9 ) is less selective for Cu 2+ . Comparison of the solution state conformations derived from nOe restrained molecular dynamics and additional Monte–Carlo conformational searches suggested binding environments for the Cu 2+ which confirmed the MS measurements and suggested a reason for the selectivity in the case of lissoclinamides 9 and 10.

Single-crystal X-ray structures are presented for three forms of 5H,10H-dithiolo[2,3-b]-2,5-benzodithiocine-2-thione. The α (at 150 K) and α′ (at ambient) forms are very similar and differ only in the presence of crystallographic m symmetry in the molecules of α′, which is absent in the case of α. This pair is related by an order–disorder transition. The β phase (also determined at 150 K) has a different structure in terms of the molecular packing from either of the other two and therefore constitutes a true polymorph. Molecular mechanics calculations indicated that the most stable CHCl3-solvated conformations for the title compound were a pair of twisted U-shaped enantiomers, UR and UL , i.e. similar to the arrangements found in the α and β phases, with the low-lying saddle point between them corresponding to the situation in the α′ phase. These calculations also indicated that the most stable CHCl3-solvated conformation for the related dibromo-5H,10H-dithiolo[2,3-b]-2,5-benzodithiocine-2-thione was Z-shaped, in agreement with the crystal structure determined earlier for its DMSO solvate [Wang et al. (1998). Synthesis, pp. 1615–1618].

We have chemically characterized a preparation of halitoxins, (1,3 alkyl-pyridinium salts) isolated from the marine sponge Callyspongia ridleyi. At concentrations of 50 and 5 microg/ml the halitoxin preparation caused irreversible membrane potential depolarization, decreased input resistance and inhibited evoked action potentials when applied to cultured dorsal root ganglion neurones. Under whole cell voltage clamp the halitoxins produced an increase in cation conductance that was attenuated by replacing sodium with N-methyl-d-glucamine. Fura-2 fluorescence ratiometric calcium imaging was used to directly measure calcium flux into neurones after exposure to halitoxins. Calcium influx, evoked by the halitoxins, persisted when the neurones were bathed in medium containing the voltage-activated calcium channel antagonists cadmium and nickel. Experiments on undifferentiated F-11 cells showed little or no calcium influx in response to depolarizing concentrations of potassium and indicated that halitoxins evoked massive calcium influx in the absence of voltage-activated calcium channels. The halitoxins also produced transient increases in intracellular calcium when F-11 cells were bathed in calcium-free medium suggesting that the toxins could release calcium from intracellular stores. The pore-forming action of the halitoxins was identified when the toxins were applied to artificial lipid bilayers composed of phosphatidylcholine and cholesterol. Halitoxins evoked channel-like activity in the lipid bilayers, with estimated unitary conductances of between 145pS and 2280pS, possibly indicating that distinct channels could be produced by the different components in the preparation of halitoxins.

Sequestering sea squirts: Liquid chromatography with parallel inductively coupled plasma mass spectrometry/electrospray mass spectrometry was used to discover and identify novel lipophilic metal complexes in the solvent extract of the ascidian Eudistoma gilboviride. Using these tools it is now possible to examine whether such complexes play an integral part in an organism's physiology.

The optical absorption spectra and quadratic hyperpolarisabilities of 1,3,5,7-tetra-substituted cubane derivatives containing group 15 atoms have been investigated computationally using Coulomb-attenuated time-dependent density functional theory. The non-linear optical responses of these octupolar systems are shown to be highly dependent on the group 15 heteroatom with the bismuth-containing derivative displaying large enhancement of its quadratic hyperpolarisability, β, relative to 1,3,5,7-tetraazacubane in vacuo and with acetonitrile solvation. Spin–orbit coupling and scalar relativistic corrections play an important part in determining the value of β for compounds containing As, Sb and Bi.

Theoretical analysis using quadratic response theory within the time-dependent density functional theory (TDDFT) formalism shows that the dermacozines, a group of phenazine-based compounds isolated from cultures of Dermacoccus abyssi found in the Mariana Trench, possess large first hyperpolarisability (β) values at common incident laser wavelengths that are highly sensitive to the degree and type of substitution of the core structure. The phenazine moiety is a versatile and tunable chromophore for non-linear optics and this work serves to highlight the potential that (marine) natural products, even those found in the darkest places on the planet, may have for aiding developments in optical materials design.

A complete understanding of the physics underlying the varied colors of firefly bioluminescence remains elusive because it is difficult to disentangle different enzyme-lumophore interactions. Experiments on isolated ions are useful to establish a proper reference when there are no microenvironmental perturbations. Here, we use action spectroscopy to compare the absorption by the firefly oxyluciferin lumophore isolated in vacuo and complexed with a single water molecule. While the process relevant to bioluminescence within the luciferase cavity is light emission, the absorption data presented here provide a unique insight into how the electronic states of oxyluciferin are altered by microenvironmental perturbations. For the bare ion we observe broad absorption with a maximum at 548 ± 10 nm, and addition of a water molecule is found to blue-shift the absorption by approximately 50 nm (0.23 eV). Test calculations at various levels of theory uniformly predict a blue-shift in absorption caused by a single water molecule, but are only qualitatively in agreement with experiment highlighting limitations in what can be expected from methods commonly used in studies on oxyluciferin. Combined molecular dynamics simulations and time-dependent density functional theory calculations closely reproduce the broad experimental peaks and also indicate that the preferred binding site for the water molecule is the phenolate oxygen of the anion. Predicting the effects of microenvironmental interactions on the electronic structure of the oxyluciferin anion with high accuracy is a nontrivial task for theory, and our experimental results therefore serve as important benchmarks for future calculations.

Nitrogen is a common structural element in the acceptor moieties of organic donor-acceptor nonlinear optical (NLO) chromophores. In order to assess the effect of substitution with heavier group 15 elements, computational studies of the nonlinear optical properties of betaine derivatives, (CH(3))(3)X(+)CH(2)CO(2)(-) (X = N, P, As, Sb, Bi), have been performed. First hyperpolarisabilities, β(HRS)(-2ω; ω, ω), corresponding to hyper-Rayleigh scattering susceptibilities have been estimated for this series using TDDFT quadratic response calculations including polarisable-continuum method water solvation and show a five-fold increase on going from N to Bi. Differential frequency dispersion effects lead to a gradual increase in this ratio as the wavelength of the incident radiation is increased from 1907 nm to 800 nm. The depolarisation ratio of the NLO response indicates that the change in β is accompanied by a change in the type of chromophore from octupolar (X = N) to a linear donor-acceptor type (X = Bi). The observed increase of the NLO response correlates with the changing electronic configurations of the group 15 elements and alterations in the character of the frontier molecular orbitals. Relativistic effects are found to play an important part in enhancement of the NLO response in the Sb and Bi betaine derivatives. These results suggest that derivatisation of organic molecules that otherwise display small β values with heavy group 15 elements is a useful method for creating enhanced NLO chromophores.

Bioassay-guided fractionation of the sub-Arctic ascidian Synoicum pulmonaria collected off the Norwegian coast led to the isolation of a novel family of brominated guanidinium oxazolidinones named synoxazolidinones A and B (1 and 2). The backbone of the compounds contains a 4-oxazolidinone ring rarely seen in natural products. The structure of the compounds was determined by spectroscopic methods. The synoxazolidinones exhibited antibacterial and antifungal activities.