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Aims: The existence of insulin- or glucagon-expressing extra-islet endocrine cells scattered in the pancreas is well-known, but they have been sparsely characterized. The aim of this study was to examine their density, distribution, transcription-factor expression, and mitotic activity in young non-diabetic subjects. Methods: Multispectral imaging was used to examine PDX1, ARX, Ki67, insulin and glucagon in extra-islet endocrine cells in pancreatic tissue from organ donors aged 1–25 years. Results: Extra-islet insulin- or glucagon-positive cells were frequent in all donors (median 17.3 and 22.9 cells/mm2 respectively), with an insulin:glucagon cell ratio of 0.9. The density was similar regardless of age. PDX1 localized mainly to insulin-, and ARX mainly to glucagon-positive cells but, interestingly, many of the cells were negative for both transcription factors. Double-hormone-positive cells were rare but found in all age groups, as were insulin-positive cells expressing ARX and glucagon-positive cells expressing PDX1. Extra-islet endocrine cells with Ki67 expression were present but rare (0–2%) in all age groups. Conclusions: Extra-islet endocrine cells are more frequent than islets. The preserved extra-islet cell density during pancreas volume-expansion from childhood- to adulthood indicates that new cells are formed, possibly from replication as cells with mitotic activity were discovered. The lack of transcription-factor expression in many cells indicates that they are immature, newly formed or plastic. This, together with the mitotic activity, suggests that these cells could play an important role in the expansion of beta-cell mass in situations of increasing demand, or in the turnover of the endocrine cell population. [ABSTRACT FROM AUTHOR]

X-ray processes involve interactions with high-energy photons. For these short wavelengths, the perturbing field cannot be treated as constant, and there is a need to go beyond the electric-dipole approximation. The exact semi-classical light–matter interaction operator offers several advantages compared to the multipole expansion such as improved stability and ease of implementation. Here, the exact operator is used to model x-ray scattering in metal K pre-edges. This is a relativistic two-photon process where absorption is dominated by electric-dipole forbidden transitions. With the restricted active space state-interaction approach, spectra can be calculated even for the multiconfigurational wavefunctions including second-order perturbation. However, as the operator itself depends on the transition energy, the cost for evaluating integrals for hundreds of thousands unique transitions becomes a bottleneck. Here, this is solved by calculating the integrals in a molecular-orbital basis that only runs over the active space, combined with a grouping scheme where the operator is the same for close-lying transitions. This speeds up the calculations of single-photon processes and is critical for the modeling of two-photon scattering processes. The new scheme is used to model Kα resonant inelastic x-ray scattering of iron–porphyrin complexes with relevance to studies of heme enzymes, for which the total computational time is reduced by several orders of magnitude with an effect on transition intensities of 0.1% or less. [ABSTRACT FROM AUTHOR]

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree–Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions. [ABSTRACT FROM AUTHOR]

In the H2S molecule, the interplay between different core levels can be investigated in great detail in relation to x-ray spectroscopy, which requires a theory for interpretation. Hence, valence and core excitations into the two antibonding molecular orbitals of the H2S molecule have been calculated within a multi-configurational wave function framework. Scanning along the S–H stretching coordinates, we derive potential energy surfaces and transition dipole moments involving the ground state and core and valence excited states. Both valence excitations and the S1s−1 and S2p−1 core excitations show pairs of dissociative and bound electronic states. These pairs of states are nearly degenerate in H2S at the ground state geometry. The close degeneracy together with conical intersections makes H2S an interesting target for x-ray spectroscopy involving ultra-fast dissociation influenced by non-adiabatic transitions and interference. For future investigations with x-ray absorption spectroscopy (XAS) and resonant inelastic x-ray scattering (RIXS), it is valuable to compare H2S with the water molecule, which exhibits state-selective gating to different vibrational modes [R. C. Couto et al., Nat. Commun. 8, 14165 (2017)] in its well-separated O1s−1 core excited states. The dense manifolds of the S2p−1 core excited states will complicate the analysis of Kα edge RIXS, but dynamical effects could be evaluated through detuning and by comparing with L edge XAS. In L edge RIXS, the dynamical effects will be more pronounced due to the longer lifetime of the S2p−1 core excited states compared to the S1s−1 core excited states. [ABSTRACT FROM AUTHOR]

Photochemistry and photophysics processes involve structures far from equilibrium. In these reactions, there is often strong coupling between nuclear and electronic degrees of freedom. For first-row transition metals, Kβ X-ray emission spectroscopy (XES) is a sensitive probe of electronic structure due to the direct overlap between the valence orbitals and the 3p hole in the final state. Here the sensitivity of Kβ mainline (Kβ1,3) XES to structural dynamics is analyzed by simulating spectral changes along the excited state dynamics of an iron photosensitizer [FeII(bmip)2]2+ [bmip = 2,6-bis(3-methyl-imidazole-1-ylidine)-pyridine], using both restricted active space (RAS) multiconfigurational wavefunction theory and a one-electron orbital-energy approach in density-functional theory (1-DFT). Both methods predict a spectral blue-shift with increasing metal–ligand distance, which changes the emission intensity for any given detection energy. These results support the suggestion that the [FeII(bmip)2]2+ femtosecond Kβ XES signal shows oscillations due to coherent wavepacket dynamics. Based on the RAS results, the sensitivity to structural dynamics is twice as high for Kβ compared to Kα, with the drawback of a lower signal-to-noise ratio. Kβ sensitivity is favored by a larger spectral blue-shift with increasing metal–ligand distance and larger changes in spectral shape. Comparing the two simulations methods, 1-DFT predicts smaller energy shifts and lower sensitivity, likely due to missing final-state effects. The simulations can be used to design and interpret XES probes of non-equilibrium structures to gain mechanistic insights in photocatalysis. [ABSTRACT FROM AUTHOR]

Aims: The transcriptome of different dissociated pancreatic islet cells has been described in enzymatically isolated islets in both health and disease. However, the isolation, culturing, and dissociation procedures likely affect the transcriptome profiles, distorting the biological conclusions. The aim of the current study was to characterize the cells of the islets of Langerhans from subjects with and without type 1 diabetes in a way that reflects the in vivo situation to the highest possible extent. Methods: Islets were excised using laser capture microdissection directly from frozen pancreatic tissue sections obtained from organ donors with (n = 7) and without (n = 8) type 1 diabetes. Transcriptome analysis of excised samples was performed using AmpliSeq. Consecutive pancreatic sections were used to estimate the proportion of beta-, alpha-, and delta cells using immunofluorescence and to examine the presence of CD31 positive endothelial regions using immunohistochemistry. Results: The proportion of beta cells in islets from subjects with type 1 diabetes was reduced to 0% according to both the histological and transcriptome data, and several alterations in the transcriptome were derived from the loss of beta cells. In total, 473 differentially expressed genes were found in the islets from subjects with type 1 diabetes. Functional enrichment analysis showed that several of the most upregulated gene sets were related to vasculature and angiogenesis, and histologically, vascular density was increased in subjects with type 1 diabetes. Downregulated in type 1 diabetes islets was the gene set epithelial mesenchymal transition. Conclusion: A number of transcriptional alterations are present in islets from subjects with type 1 diabetes. In particular, several gene sets related to vasculature and angiogenesis are upregulated and there is an increased vascular density, suggesting an altered microvasculature in islets from subjects with type 1 diabetes. By studying pancreatic islets extracted directly from snap-frozen pancreatic tissue, this study reflects the in vivo situation to a high degree and gives important insights into islet pathophysiology in type 1 diabetes. [ABSTRACT FROM AUTHOR]

Manganese–oxo species catalyze key reactions, including C–H bond activation or dioxygen formation in natural photosynthesis. To better understand relevant reaction intermediates, we characterize electronic states and geometric structures of [MnOn]+ manganese–oxo complexes that represent a wide range of manganese oxidation states. To this end, we apply soft X-ray spectroscopy in a cryogenic ion trap, combined with multiconfigurational wavefunction calculations. We identify [MnO2]+ as a rare high-spin manganese(V) oxo complex with key similarities to six-coordinated manganese(V) oxo systems that are proposed as reaction intermediates in catalytic dioxygen bond formation. [ABSTRACT FROM AUTHOR]

Featured Application: Herein, an innovative methodology, called X-ray chronoscopy, is proposed for exploration of ultrafast processes in matter with attosecond precision using current XFEL sources. The method is based on measuring the change in an X-ray pulse temporal profile induced by interaction with a medium. X-ray free electron lasers (XFELs) have provided scientists opportunities to study matter with unprecedented temporal and spatial resolutions. However, access to the attosecond domain (i.e., below 1 femtosecond) remains elusive. Herein, a time-dependent experimental concept is theorized, allowing us to track ultrafast processes in matter with sub-fs resolution. The proposed X-ray chronoscopy approach exploits the state-of-the-art developments in terahertz streaking to measure the time structure of X-ray pulses with ultrahigh temporal resolution. The sub-femtosecond dynamics of the saturable X-ray absorption process is simulated. The employed rate equation model confirms that the X-ray-induced mechanisms leading to X-ray transparency can be probed via measurement of an X-ray pulse time structure. [ABSTRACT FROM AUTHOR]

Insulin secretion is impaired with increasing age. In this study, we aimed to determine whether aging induces specific transcriptional changes in human islets. Laser capture microdissection was used to extract pancreatic islet tissue from 37 deceased organ donors aged 1–81 years. The transcriptomes of the extracted islets were analysed using Ion AmpliSeq sequencing. 346 genes that co-vary significantly with age were found. There was an increased transcription of genes linked to senescence, and several aspects of the cell cycle machinery were downregulated with increasing age. We detected numerous genes not linked to aging in previous studies likely because earlier studies analysed islet cells isolated by enzymatic digestion which might affect the islet transcriptome. Among the novel genes demonstrated to correlate with age, we found an upregulation of SPP1 encoding osteopontin. In beta cells, osteopontin has been seen to be protective against both cytotoxicity and hyperglycaemia. In summary, we present a transcriptional profile of aging in human islets and identify genes that could affect disease course in diabetes. [ABSTRACT FROM AUTHOR]

The metal L-edge (2p → 3d) X-ray absorption spectra are affected by a number of different interactions: electron-electron repulsion, spin-orbit coupling, and charge transfer between metal and ligands, which makes the simulation of spectra challenging. The core restricted active space (RAS) method is an accurate and flexible approach that can be used to calculate X-ray spectra of a wide range of medium-sized systems without any symmetry constraints. Here, the applicability of the method is tested in detail by simulating three ferric (3d5) model systems with well-known electronic structure, viz., atomic Fe3+, high-spin [FeCl6]³- with ligand donor bonding, and low-spin [Fe(CN)6]3- that also has metal backbonding. For these systems, the performance of the core RAS method, which does not require any system-dependent parameters, is comparable to that of the commonly used semi-empirical charge-transfer multiplet model. It handles orbitally degenerate ground states, accurately describes metal-ligand interactions, and includes both single and multiple excitations. The results are sensitive to the choice of orbitals in the active space and this sensitivity can be used to assign spectral features. A method has also been developed to analyze the calculated X-ray spectra using a chemically intuitive molecular orbital picture. [ABSTRACT FROM AUTHOR]

Developing new transition metal catalysts requires understanding of how both metal and ligand properties determine reactivity. Since metal complexes bearing ligands of the Py5 family (2,6-bis-[(2-pyridyl)methyl]pyridine) have been employed in many fields in the past 20 years, we set out here to understand their redox properties by studying a series of base metal ions (M = Mn, Fe, Co, and Ni) within the Py5OH (pyridine-2,6-diylbis[di-(pyridin-2-yl)methanol]) variant. Both reduced (MII) and the one-electron oxidized (MIII) species were carefully characterized using a combination of X-ray crystallography, X-ray absorption spectroscopy, cyclic voltammetry, and density-functional theory calculations. The observed metal–ligand interactions and electrochemical properties do not always follow consistent trends along the periodic table. We demonstrate that this observation cannot be explained by only considering orbital and geometric relaxation, and that spin multiplicity changes needed to be included into the DFT calculations to reproduce and understand these trends. In addition, exchange reactions of the sixth ligand coordinated to the metal, were analysed. Finally, by including published data of the extensively characterised Py5OMe (pyridine-2,6-diylbis[di-(pyridin-2-yl)methoxymethane])complexes, the special characteristics of the less common Py5OH ligand were extracted. This comparison highlights the non-innocent effect of the distal OH functionalization on the geometry, and consequently on the electronic structure of the metal complexes. Together, this gives a complete analysis of metal and ligand degrees of freedom for these base metal complexes, while also providing general insights into how to control electrochemical processes of transition metal complexes. [ABSTRACT FROM AUTHOR]

Recently, coherent structural dynamics in the excited state of an iron photosensitizer was observed through oscillations in the intensity of Kα x-ray emission spectroscopy (XES). Understanding the origin of the unexpected sensitivity of core-to-core transitions to structural dynamics is important for further development of femtosecond time-resolved XES methods and, we believe, generally necessary for interpretation of XES signals from highly non-equilibrium structures that are ubiquitous in photophysics and photochemistry. Here, we use multiconfigurational wavefunction calculations combined with atomic theory to analyze the emission process in detail. The sensitivity of core-to-core transitions to structural dynamics is due to a shift of the minimum energy metal–ligand bond distance between 1s and 2p core-hole states. A key effect is the additional contraction of the non-bonding 3s and 3p orbitals in 1s core-hole states, which decreases electron–electron repulsion and increases overlap in the metal–ligand bonds. The effect is believed to be general and especially pronounced for systems with strong bonds. The important role of 3s and 3p orbitals is consistent with the analysis of radial charge and spin densities and can be connected to the negative chemical shift observed for many transition metal complexes. The XES sensitivity to structural dynamics can be optimized by tuning the emission energy spectrometer, with oscillations up to ±4% of the maximum intensity for the current system. The theoretical predictions can be used to design experiments that separate electronic and nuclear degrees of freedom in ultrafast excited state dynamics. [ABSTRACT FROM AUTHOR]

Hard X-ray spectroscopy selectively probes metal sites in complex environments. Resonant inelastic X-ray scattering (RIXS) makes it is possible to directly study metal–ligand interactions through local valence excitations. Here multiconfigurational wavefunction simulations are used to model valence K pre-edge RIXS for three metal-hexacyanide complexes by coupling the electric dipole-forbidden excitations with dipole-allowed valence-to-core emission. Comparisons between experimental and simulated spectra makes it possible to evaluate the simulation accuracy and establish a best-modeling practice. The calculations give correct descriptions of all LMCT excitations in the spectra, although energies and intensities are sensitive to the description of dynamical electron correlation. The consistent treatment of all complexes shows that simulations can rationalize spectral features. The dispersion in the manganese(III) spectrum comes from unresolved multiple resonances rather than fluorescence, and the splitting is mainly caused by differences in spatial orientation between holes and electrons. The simulations predict spectral features that cannot be resolved in current experimental data sets and the potential for observing d–d excitations is also explored. The latter can be of relevance for non-centrosymmetric systems with more intense K pre-edges. These ab initio simulations can be used to both design and interpret high-resolution X-ray scattering experiments. [ABSTRACT FROM AUTHOR]

Ferrous chloride complexes [FeIILxCl] commonly attain a high-spin state independently of the supporting ligand(s) and temperature. Herein, we present the first report of a complete spin crossover with T1/2 = 80 K in [FeII(Py5OH)Cl]+ (Py5OH = pyridine-2,6-diylbis[di(pyridin-2-yl)methanol]). Both spin forms of the complex are analyzed by X-ray spectroscopy and DFT calculations. [ABSTRACT FROM AUTHOR]

The self-interaction error in density-functional theory leads to artificial stabilization of delocalized states, most evident in systems with an odd number of electrons. Clear examples are dissociations of carbocation radicals that often give delocalized states at long distances and large errors in computed binding energies. On the other hand, many mixed-valence transition-metal dimers known to exhibit valence trapping are correctly predicted to be localized. To understand the effects of the self-interaction error on these different systems, energy differences between delocalized and localized states are calculated with B3LYP. In the dissociation of radicals into symmetric fragments at infinite distance, this energy difference equals the error of the density-functional treatment. The energy difference decreases with increasing size of the system, from 55 kcal/mol in H2+ to 15 kcal/mol for C12H26+. Solvent corrections stabilize the localized state and result in smaller errors. Most reactions are asymmetric and this decreases the effect of the self-interaction error. In many systems, delocalization will not occur if the cost to move the electron from one fragment to the other is 70–80 kcal/mol (3.0–3.5 eV). This estimate refers to a situation where the distance between the fragments is infinite. The limit decreases with decreasing fragment distance. B3LYP calculations on the ferromagnetic state of a Mn(III,IV) dimer predict that the correct localized state is 22 kcal/mol more stable than the incorrect delocalized state. At short metal–metal distances the effect of the self-interaction error is predicted to be small. However, as the distance between the two manganese centers is increased to 7 Å, the dimer starts to delocalize and the energy artificially decreases. In the dissociation limit, the error is 10 kcal/mol. This is interpreted as an artifact originating from the self-interaction error. Delocalization is not encountered in many systems due to relatively short metal–metal distances and asymmetric ligand environments. However, some charge-transfer complexes cannot be properly calculated and delocalized states may become a problem in large models of enzyme systems with multiple transition-metal complexes. [ABSTRACT FROM AUTHOR]

Electronically excited states play important roles in many chemical reactions and spectroscopic techniques. In quantum chemistry, a common technique to solve excited states is the multiroot Davidson algorithm, but it is not designed for processes like X‐ray spectroscopy that involves hundreds of highly excited states. We show how the use of a restricted active space wavefunction together with a projection operator to remove low‐lying electronic states offers an efficient way to reach single and double‐core‐hole states. Additionally, several improvements to the stability and efficiency of the configuration interaction (CI) algorithm for a large number of states are suggested. When applied to a series of transition metal complexes the new CI algorithm does not only resolve divergence issues but also leads to typical reduction in computational time by 70%, with the largest savings for small molecules and large active spaces. Together, the projection operator and the improved CI algorithm now make it possible to simulate a wide range of single‐ and two‐photon spectroscopies. © 2019 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Light emission from luminol is probably one of the most popular chemiluminescence reactions due to its use in forensic science, and has recently displayed promising applications for the treatment of cancer in deep tissues. The mechanism is, however, very complex and distinct possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism has been studied in three steps: 1) luminol oxygenation to generate the chemiluminophore, 2) a chemiexcitation step, and 3) generation of the light emitter. The findings demonstrate that the luminol double‐deprotonated dianion activates molecular oxygen, diazaquinone is not formed, and the chemiluminophore is formed through the concerted addition of oxygen and concerted elimination of nitrogen. The peroxide bond, in comparison to other isoelectronic chemical functionalities (−NH−NH−, −N−−N−−, and −S−S−), is found to have the best chemiexcitation efficiency, which allows the oxygenation requirement to be rationalized and establishes general design principles for the chemiluminescence efficiency. Electron transfer from the aniline ring to the OO bond promotes the excitation process to create an excited state that is not the chemiluminescent species. To produce the light emitter, proton transfer between the amino and carbonyl groups must occur; this requires highly localized vibrational energy during chemiexcitation. Luminol chemiluminescence: Light emission from luminol is a popular chemiluminescence reaction. However, the mechanism is complex and different possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism of luminol has been elucidated. [ABSTRACT FROM AUTHOR]

The reaction occurring during artificial maturation of [FeFe] hydrogenase has been recreated using molecular systems. The formation of a miniaturized [FeFe] hydrogenase model system, generated through the combination of a [4Fe4S] cluster binding oligopeptide and an organometallic Fe complex, has been monitored by a range of spectroscopic techniques. A structure of the final assembly is suggested based on EPR and FTIR spectroscopy in combination with DFT calculations. The capacity of this novel H-cluster model to catalyze H2 production in aqueous media at mild potentials is verified in chemical assays. [ABSTRACT FROM AUTHOR]

Hemoglobin and myoglobin are oxygen-binding proteins with S = 0 heme {FeO2}8 active sites. The electronic structure of these sites has been the subject of much debate. This study utilizes Fe K-edge X-ray absorption spectroscopy (XAS) and 1s2p resonant inelastic X-ray scattering (RIXS) to study oxyhemoglobin and a related heme {FeO2}8 model compound, [(pfp)Fe(1-MeIm)(O2)] (pfp = meso-tetra(α,α,α,α-o-pivalamido-phenyl)porphyrin, or TpivPP, 1- MeIm = 1-methylimidazole) (pfpO2), which was previously analyzed using L-edge XAS. The K-edge XAS and RIXS data of pfpO2 and oxyhemoglobin are compared with the data for low-spin FeII and FeIII [Fe(tpp)(Im)2]0/+ (tpp = tetra-phenyl porphyrin) compounds, which serve as heme references. The X-ray data show that pfpO2 is similar to FeII, while oxyhemoglobin is qualitatively similar to FeIII, but with significant quantitative differences. Density-functional theory (DFT) calculations show that the difference between pfpO2 and oxyhemoglobin is due to a distal histidine H bond to O2 and the less hydrophobic environment in the protein, which lead to more backbonding into the O2. A valence bond configuration interaction multiplet model is used to analyze the RIXS data and show that pfpO2 is dominantly FeII with 6-8% FeIII character, while oxyhemoglobin has a very mixed wave function that has 50-77% FeIII character and a partially polarized Fe-O2 π-bond. [ABSTRACT FROM AUTHOR]

In this study, mechanisms of hydrolysis of all four chemically diverse cleavage sites of human serum albumin (HSA) by [Zr(OH)(PW11O39)]4− (ZrK) have been investigated using the hybrid two‐layer QM/MM (ONIOM) method. These reactions have been proposed to occur through the following two mechanisms: internal attack (IA) and water assisted (WA). In both mechanisms, the cleavage of the peptide bond in the Cys392‐Glu393 site of HSA is predicted to occur in the rate‐limiting step of the mechanism. With the barrier of 27.5 kcal/mol for the hydrolysis of this site, the IA mechanism is found to be energetically more favorable than the WA mechanism (barrier = 31.6 kcal/mol). The energetics for the IA mechanism are in line with the experimentally measured values for the cleavage of a wide range of dipeptides. These calculations also suggest an energetic preference (Cys392‐Glu393, Ala257‐Asp258, Lys313‐Asp314, and Arg114‐Leu115) for the hydrolysis of all four sites of HSA. © 2018 Wiley Periodicals, Inc. Mechanisms for the hydrolysis of all four chemically distinct cleavage sites of human serum albumin (HSA) catalyzed by a Zr‐containing polyoxometalate [Zr(OH)(PW11O39)]4−. They are proposed using the hybrid two‐layer QM/MM (ONIOM) calculations. [ABSTRACT FROM AUTHOR]

X-ray induced sample damage can impede electronic and structural investigations of radiation-sensitive samples studied with X-rays. Here we quantify dose-dependent sample damage to the prototypical MnIII(acac)3 complex in solution and at room temperature for the soft X-ray range, using X-ray absorption spectroscopy at the Mn L-edge. We observe the appearance of a reduced MnII species as the X-ray dose is increased. We find a half-damage dose of 1.6 MGy and quantify a spectroscopically tolerable dose on the order of 0.3 MGy (1 Gy = 1 J kg−1), where 90% of MnIII(acac)3 are intact. Our dose-limit is around one order of magnitude lower than the Henderson limit (half-damage dose of 20 MGy) which is commonly employed for protein crystallography with hard X-rays. It is comparable, however, to the dose-limits obtained for collecting un-damaged Mn K-edge spectra of the photosystem II protein, using hard X-rays. The dose-dependent reduction of MnIII observed here for solution samples occurs at a dose limit that is two to four orders of magnitude smaller than the dose limits previously reported for soft X-ray spectroscopy of iron samples in the solid phase. We compare our measured to calculated spectra from ab initio restricted active space (RAS) theory and discuss possible mechanisms for the observed dose-dependent damage of MnIII(acac)3 in solution. On the basis of our results, we assess the influence of sample damage in other experimental studies with soft X-rays from storage-ring synchrotron radiation sources and X-ray free-electron lasers. [ABSTRACT FROM AUTHOR]

We describe how inversion symmetry separation of electronic state manifolds in resonant inelastic soft X-ray scattering (RIXS) can be applied to probe excited-state dynamics with compelling selectivity. In a case study of Fe L3-edge RIXS in the ferricyanide complex Fe(CN)63−, we demonstrate with multi-configurational restricted active space spectrum simulations how the information content of RIXS spectral fingerprints can be used to unambiguously separate species of different electronic configurations, spin multiplicities, and structures, with possible involvement in the decay dynamics of photo-excited ligand-to-metal charge-transfer. Specifically, we propose that this could be applied to confirm or reject the presence of a hitherto elusive transient Quartet species. Thus, RIXS offers a particular possibility to settle a recent controversy regarding the decay pathway, and we expect the technique to be similarly applicable in other model systems of photo-induced dynamics. [ABSTRACT FROM AUTHOR]

To elucidate the etiology of type 1 diabetes, the affected pancreas needs to be thoroughly characterized. Pancreatic innervation has been suggested to be involved in the pathology of the disease and a reduction of sympathetic innervation of the islets was recently reported. In the present study, we hypothesized that parasympathetic innervation would be altered in the type 1 diabetes pancreas. Human pancreatic specimens were obtained from a unique cohort of individuals with recent onset or long standing type 1 diabetes. Density of parasympathetic axons was assessed by immunofluorescence and morphometry. Our main finding was a reduced density of parasympathetic axons in the exocrine, but not endocrine compartment of the pancreas in individuals with recent onset type 1 diabetes. The reduced density of parasympathetic axons in the exocrine compartment could have functional implications, e.g. be related to the exocrine insufficiency reported in type 1 diabetes patients. Further studies are needed to understand whether reduced parasympathetic innervation is a cause or consequence of type 1 diabetes. [ABSTRACT FROM AUTHOR]

Aims/hypothesis: According to the consensus criteria developed for type 1 diabetes, an individual can be diagnosed with insulitis when ≥ 15 CD45 cells are found within the parenchyma or in the islet-exocrine interface in ≥ 3 islets. The aim of this study was to determine the frequency of individuals with type 2 diabetes fulfilling these criteria with reference to non-diabetic and type 1 diabetic individuals. Methods: Insulitis was determined by examining CD45 cells in the pancreases of 50, 13 and 44 organ donors with type 2 diabetes, type 1 diabetes and no diabetes, respectively. CD3 cells (T cells) infiltrating the islets were evaluated in insulitic donors. In insulitic donors with type 2 diabetes, the pancreases were characterised according to the presence of CD68 (macrophages), myeloperoxidase (MPO; neutrophils), CD3, CD20 (B cells) and HLA class I hyperstained islets. In all type 2 diabetic donors, potential correlations of insulitis with dynamic glucose-stimulated insulin secretion in vitro or age, BMI, HbA or autoantibody positivity were examined. Results: Overall, 28% of the type 2 diabetic donors fulfilled the consensus criteria for insulitis developed for type 1 diabetes. Of the type 1 diabetic donors, 31% fulfilled the criteria. None of the non-diabetic donors met the criteria. Only type 1 diabetic donors had ≥ 15 CD3 cells in ≥ 3 islets. Type 2 diabetic donors with insulitis also had a substantial number of CD45 cells in the exocrine parenchyma. Macrophages constituted the largest fraction of CD45 cells, followed by neutrophils and T cells. Of type 2 diabetic pancreases with insulitis, 36% contained islets that hyperstained for HLA class I. Isolated islets from type 2 diabetic donors secreted less insulin than controls, although with preserved dynamics. Insulitis in the type 2 diabetic donors did not correlate with glucose-stimulated insulin secretion, the presence of autoantibodies, BMI or HbA. Conclusions/interpretation: The current definition of insulitis cannot be used to distinguish pancreases retrieved from individuals with type 1 diabetes from those with type 2 diabetes. On the basis of our findings, we propose a revised definition of insulitis, with a positive diagnosis when ≥ 15 CD3 cells, not CD45 cells, are found in ≥ 3 islets. [ABSTRACT FROM AUTHOR]

X-ray absorption spectroscopy (XAS) in the metal K pre-edge is a standard probe of electronic and geometric structure of transition metal complexes. Simulating the K pre-edge spectra requires contributions beyond the electric dipole, but if that term is non-zero, the second-order terms, e.g. electric quadrupoles, are no longer origin-independent. In the velocity representation, complete origin independence can be achieved by including all terms to the same order in the oscillator strength. Here, we implement that approach in the length representation and use it for restricted active space (RAS) simulations of metal K pre-edges of iron monomers and dimers. Complete origin independence is not achieved and the size of the remaining errors depends on the electric dipole oscillator strength and its ratio in length and velocity representations. The error in the origin independence is in the ANO basis sets two orders of magnitude smaller than the value of the individual contributions. For systems with strong electric dipole contributions, the errors are not significant within 3 Å from a metal centre, far enough to handle many multi-metal systems. Furthermore, we discuss the convergence of the multipole expansion, the possibility to assign spectral contributions, and the origin of negative absorption intensities. [ABSTRACT FROM AUTHOR]

A primary insult to the pancreatic islets of Langerhans, leading to the activation of innate immunity, has been suggested as an important step in the inflammatory process in type 1 diabetes (T1D). The aim of this study was to examine whether interferon (IFN)-stimulated genes (ISGs) are overexpressed in human T1D islets affected with insulitis. By using laser capture microdissection and a quantitative PCR array, 23 of 84 examined ISGs were found to be overexpressed by at least fivefold in insulitic islets from living patients with recent-onset T1D, participating in the Diabetes Virus Detection (DiViD) study, compared with islets from organ donors without diabetes. Most of the overexpressed ISGs, including GBP1, TLR3, OAS1, EIF2AK2, HLA-E, IFI6, and STAT1, showed higher expression in the islet core compared with the peri-islet area containing the surrounding immune cells. In contrast, the T-cell attractant chemokine CXCL10 showed an almost 10-fold higher expression in the peri-islet area than in the islet, possibly partly explaining the localization of T cells mainly to this region. In conclusion, insulitic islets from recent-onset T1D subjects show overexpression of ISGs, with an expression pattern similar to that seen in islets infected with virus or exposed to IFN-γ/interleukin-1β or IFN-α. [ABSTRACT FROM AUTHOR]

Many non-heme iron enzymes have similar sets of ligands but still catalyze widely different reactions. A key question is, therefore, the role of the protein in controlling reactivity and selectivity. Examples from multiscale simulations, primarily QM/MM, of both mono- and binuclear non-heme iron enzymes are used to analyze the stability of these models and what they reveal about the protein effects. Consistent results from QM/MM modeling are the importance of the hydrogen bond network to control reactivity and electrostatic stabilization of electron transfer from second-sphere residues. The long-range electrostatic effects on reaction barriers are small for many systems. In the systems where large electrostatic effects have been reported, these lead to higher barriers. There is thus no evidence of any significant long-range electrostatic effects contributing to the catalytic efficiency of non-heme iron enzymes. However, the correct evaluation of electrostatic contributions is challenging, and the correlation between calculated residue contributions and the effects of mutation experiments is not very strong. The largest benefits of QM/MM models are thus the improved active-site geometries, rather than the calculation of accurate energies. Reported differences in mechanistic predictions between QM and QM/MM models can be explained by differences in hydrogen bonding patterns in and around the active site. Correctly constructed cluster models can give results with similar accuracy as those from multiscale models, but the latter reduces the risk of drawing the wrong mechanistic conclusions based on incorrect geometries and are preferable for all types of modeling, even when using very large QM parts. [ABSTRACT FROM AUTHOR]

The restricted active-space (RAS) approach can accurately simulate metal L-edge X-ray absorption spectra of first-row transition metal complexes without the use of any fitting parameters. These characteristics provide a unique capability to identify unknown chemical species and to analyze their electronic structure. To find the best balance between cost and accuracy, the sensitivity of the simulated spectra with respect to the method variables has been tested for two models, [FeCl6]3- and [Fe(CN)6]3-. For these systems, the reference calculations give deviations, when compared with experiment, of ≤1 eV in peak positions, ≤30% for the relative intensity of major peaks, and ≤50% for minor peaks. When compared with these deviations, the simulated spectra are sensitive to the number of final states, the inclusion of dynamical correlation, and the ionization potential electron affinity shift, in addition to the selection of the active space. The spectra are less sensitive to the quality of the basis set and even a double- ζ basis gives reasonable results. The inclusion of dynamical correlation through second-order perturbation theory can be done efficiently using the state-specific formalism without correlating the core orbitals. Although these observations are not directly transferable to other systems, they can, together with a cost analysis, aid in the design of RAS models and help to extend the use of this powerful approach to a wider range of transition metal systems. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The intensities and relative energies of metal K pre-edge features are sensitive to both geometric and electronic structures. With the possibility to collect high-resolution spectral data it is important to find theoretical methods that include all important spectral effects: ligand-field splitting, multiplet structures, 3d–4p orbital hybridization, and charge-transfer excitations. Here the restricted active space (RAS) method is used for the first time to calculate metal K pre-edge spectra of open-shell systems, and its performance is tested against on six iron complexes: [FeCl6]n−, [FeCl4]n−, and [Fe(CN)6]n− in ferrous and ferric oxidation states. The method gives good descriptions of the spectral shapes for all six systems. The mean absolute deviation for the relative energies of different peaks is only 0.1 eV. For the two systems that lack centrosymmetry [FeCl4]2−/1−, the ratios between dipole and quadrupole intensity contributions are reproduced with an error of 10%, which leads to good descriptions of the integrated pre-edge intensities. To gain further chemical insight, the origins of the pre-edge features have been analyzed with a chemically intuitive molecular orbital picture that serves as a bridge between the spectra and the electronic structures. The pre-edges contain information about both ligand-field strengths and orbital covalencies, which can be understood by analyzing the RAS wavefunction. The RAS method can thus be used to predict and rationalize the effects of changes in both the oxidation state and ligand environment in a number of hard X-ray studies of small and medium-sized molecular systems. [ABSTRACT FROM AUTHOR]

Excited-state chemistry is usually ascribed to photo-induced processes, such as fluorescence, phosphorescence, and photochemistry, or to bio- and chemiluminescence, in which light emission originates from a chemical reaction. A third class of excited-state chemistry is, however, possible. It corresponds to the photochemical phenomena produced by chemienergizing certain chemical groups without light – chemiexcitation. By studying Dewar dioxetane, which can be viewed as the combination of 1,2-dioxetane and 1,3-butadiene, we show here how the photo-isomerization channel of 1,3-butadiene can be reached at a later stage after the thermal decomposition of the dioxetane moiety. Multi-reference multiconfigurational quantum chemistry methods and accurate reaction-path computational strategies were used to determine the reaction coordinate of three successive processes: decomposition of the dioxetane moiety, non-adiabatic energy transfer from the ground to the excited state, and finally non-radiative decay of the 1,3-butadiene group. With the present study, we open a new area of research within computational photochemistry to study chemically-induced excited-state chemistry that is difficult to tackle experimentally due to the short-lived character of the species involved in the process. The findings shall be of relevance to unveil “dark” photochemistry mechanisms, which might operate in biological systems under conditions of lack of light. These mechanisms might allow reactions that are typical of photo-induced phenomena. [ABSTRACT FROM AUTHOR]

Low-density lipoprotein receptor-related protein 1 (LRP1) is an endocytic and multi-functional type I cell surface membrane protein, which is known to be phosphorylated by the activated platelet-derived growth factor receptor (PDGFR). The tyrosine kinase inhibitor imatinib, which inhibits PDGFR and c-Abl, and which has previously been reported to counteract β-cell death and diabetes, has been suggested to reduce atherosclerosis by inhibiting PDGFR-induced LRP1 phosphorylation. The aim of the present study was to study LRP1 function in β-cells and to what extent imatinib modulates LRP1 activity. LRP1 and c-Abl gene knockdown was performed by RNAi using rat INS-1 832/13 and human EndoC1-βH1 cells. LRP1 was also antagonized by treatment with the antagonist low-density lipoprotein receptor-related protein associated protein 1 (LRPAP1). We have used PDGF-BB, a PDGFR agonist, and apolipoprotein E (ApoE), an LRP1 agonist, to stimulate the activities of PDGFR and LRP1 respectively. Knockdown or inhibition of LRP1 resulted in increased hydrogen peroxide (H²O²)- or cytokine-induced cell death, and glucose-induced insulin release was lowered in LRP1-silenced cells. These results indicate that LRP1 function is necessary for β-cell function and that LRP1 is adversely affected by challenges to β-cell health. PDGF-BB, or the combination of PDGF-BB+ApoE, induced phosphorylation of extracellular-signal-regulated kinase (ERK), Akt and LRP1. LRP1 silencing blocked this event. Imatinib blocked phosphorylation of LRP1 by PDGFR activation but induced phosphorylation of ERK. LRP1 silencing blocked imatinib-induced phosphorylation of ERK. Sunitinib also blocked LRP1 phosphorylation in response to PDGF-BB and induced phosphorylation of ERK, but this latter event was not affected by LRP1 knockdown. siRNA-mediated knockdown of the imatinib target c-Abl resulted in an increased ERK phosphorylation at basal conditions, with no further increase in response to imatinib. Imatinib-induced cell survival of tunicamycin-treated cells was partially mediated by ERK activation. We have concluded that imatinib promotes LRP1-dependent ERK activation, possibly via inhibition of c-Abl, and that this could contribute to the pro-survival effects of imatinib on β-cells. [ABSTRACT FROM AUTHOR]

Density functional theory calculations on the neutral [Mn12]0 molecular magnet and super‐reduced [Mn12]8– cluster were employed to investigate the experimental geometrical changes observed during discharging in a molecular cluster battery. It was found that for relevant low‐spin states the eight electrons added in [Mn12]8– are mainly added to the outer eight Mn atoms, causing elongation of the bonds between outer Mn and their surrounding O atoms, while the inner Mn4 cluster is less affected by the reduction. Schematic representation of the spin density of the neutral [Mn12]0 cluster and its super‐reduced state [Mn12]8–, for which several possible spin states were found. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) Part of Focus Issue on “Functional Oxides” (Eds.: T. Frauenheim, J. M. Knaup, P. Broqvist, S. Ramanathan) DFT‐based theoretical studies describe the changes in molecular and electronic structures during the super‐reduction of the Mn12 cluster by the uptake of 8 excess electrons in the gas phase. The results agree largely with experimental observations obtained in a molecular cluster battery setup. [ABSTRACT FROM AUTHOR]

It has previously been shown that self-consistent-charge density-functional tight-binding (SCC-DFTB) suffers from a self-interaction error that leads to artificial stabilization of delocalized states. The effects of the error are similar to those appearing for many density functionals. In SCC-DFTB, the delocalization error is inherently related to the use of a Hubbard-like term to describe on-site charge interactions. The mathematical simplicity of this Hubbard-like term makes it easy to estimate if a complex system is subject to artificial stabilization of delocalized states and to quantitatively predict the delocalization error in the system energy at large fragment separation. The error is directly proportional to the on-site charge interaction term but decreases as the fragments become more asymmetric. The difference in orbital energies required to eliminate the delocalization error becomes equal to the Hubbard-like parameter of the fragment with the highest electron affinity. However, in most cases, the localized state will be favored by spin polarization, fragment repulsion, solvent effects, and large reorganization energies, in analogy to density functional theory, from which SCC-DFTB is derived. The presented analysis gives an early indication whether the standard approach is suitable, or if a different method is required to correct the delocalization error. In addition to cationic dimers, we discuss the effects of the delocalization error for asymmetric systems, bond dissociation of neutral molecules, and the description of mixed valence transition metal systems, exemplified by the enzyme cytochrome oxidase. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012 [ABSTRACT FROM AUTHOR]

QM:QM' models, where QM' is a fast molecular orbital method, offers advantages over standard quantum mechanics: molecular mechanics (QM:MM) models, especially in the description of charge transfer and mutual polarization between layers. The ONIOM QM:QM' scheme also allows for reactions across the layer boundary, but the understanding of these events is limited. To explain the factors that affect cross-boundary events, a set of proton transfer processes, including the acylation reaction in serine protease, have been investigated. For reactions inside out, that is, when a group breaks a bond in the high layer and forms a new bond with a group in the low layer, QM' methods that are overbinding relative to the QM method, for example, Hartree-Fock versus B3LYP, can severely overestimate the exothermicity of the reaction. This might lead to artificial reactivity across the QM:QM' boundary, a phenomenon called model escape. The accuracy for reactions that occur outside in, that is, when a group in the low layer forms a new bond with the high layer, is mainly determined by the QM' calculation. Cross-boundary reactions should generally be avoided in the present ONIOM scheme. Fortunately, a better understanding of these events makes it easy to design stable ONIOM QM:QM' models, for example, by choosing a proper model system. Importantly, an accurate description of cross-boundary reactions would open up possibilities to simulate chemical reactions without a priori limiting the reactivity in the design of the computational model. Challenges to implement a simulation scheme (ONIOM-XR) that can automatically handle chemical reactions between different layers are briefly discussed. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012 [ABSTRACT FROM AUTHOR]

We present the theoretical and implementation details of the DFTB method with analytical gradients into the Gaussian package. SCF optimization performance with DIIS method is compared with modified Broyden method and Anderson methods, from which DIIS method is to be preferred. The number of geometry optimization steps can be significantly decreased with the Berny algorithm compared to the conjugated gradient method. From the comparison of geometry parameters as well as trends in the change of HOMO and LUMO energies, the results show clearly that DFTB can reproduce values obtained at the B3LYP/6-31G(d) level well. We also investigated the DFTB method as the low level quantum mechanical (QM) method in an ONIOM (QM:QM′) description for an amino acid model system and found DFTB promising as a method to describe polarization and charge-transfer effects in large systems. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [ABSTRACT FROM AUTHOR]

Water exchange on Mn centers in proteins has been modeled with density functional theory using the B3LYP functional. The reaction barrier for dissociative water exchange on [MnIV(H2O)2(OH)4] is only 9.6 kcal mol-1, corresponding to a rate of 6×105 s-1. It has also been investigated how modifications of the model complex change the exchange rate. Three cases of water exchange on Mn dimers have been modeled. The reaction barrier for dissociative exchange of a terminal water ligand on [(H2O)2(OH)2MnIV(μ-O)2MnIV(H2O)2(OH)2] is 8.6 kcal mol-1, while the bridging oxo group exchange with a ring-opening mechanism has a barrier of 19.2 kcal mol-1. These results are intended for interpretations of measurements of water exchange for the oxygen evolving complex of photosystem II. Finally, a tautomerization mechanism for exchange of a terminal oxyl radical has been modeled for the synthetic O2 catalyst [(terpy)(H2O)MnIV(μ-O)2MnIV(O•)(terpy)]3+ (terpy=2,2′:6,2″-terpyridine). The calculated reaction barrier is 14.7 kcal mol-1. [ABSTRACT FROM AUTHOR]

The mechanism of orotidine 5-monophosphate decarboxylase (ODCase) has been modeled using hybrid Density Functional Theory (B3LYP functional). The main goal of the present study was to investigate if much larger quantum chemical models of the active site than previously used could shed new light on the mechanism. The models used include the five conserved amino acids expected to be the most important ones for catalysis. One result of this model is that a mechanism involving a direct cleavage of the C–C bond followed by a protonation of C6 by Lys93 appears unlikely, with a barrier for decarboxylation 20 kcal mol–1 too high. Additional effects like electrostatic stress and ground-state destabilization have been estimated to have only a minor influence on the reaction barrier. The conclusion from the calculations is that the negative charge developing on the substrate during decarboxylation must be stabilized by a protonation of the carbonyl O2 of the substrate. For this mechanism, the addition of the catalytic amino acids decreases the reaction barrier by 25 kcal mol–1, but full agreement with experimental results has still not been reached. Further modifications of this mechanism are discussed. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located a http://dx.doi.org/10.1007/s00894-002-0080-2. [ABSTRACT FROM AUTHOR]

In the preceding paper results are presented, which are in serious conflict with state-of-the-art ab initio method. Based on these new results the authors propose a new explanation of the reason for the preferential production of a phosphorescent state. Here we show that these controversial results are flawed, since the model use exclude biradical electron structures. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Stochastic processes are highly relevant in research fields as different as neuroscience, economy, ecology, chemistry, and fundamental physics. However, due to their intrinsic unpredictability, stochastic mechanisms are very challenging for any kind of investigations and practical applications. Here we report the deliberate use of stochastic X-ray pulses in two-dimensional spectroscopy to the simultaneous mapping of unoccupied and occupied electronic states of atoms in a regime where the opacity and transparency properties of matter are subject to the incident intensity and photon energy. A readily transferable matrix formalism is presented to extract the electronic states from a dataset measured with the monitored input from a stochastic excitation source. The presented formalism enables investigations of the response of the electronic structure to irradiation with intense X-ray pulses while the time structure of the incident pulses is preserved. Free electron X-ray laser pulses, generated by self-amplified spontaneous emission, are stochastic in nature. Here the authors present a reconstruction method for 2D spectroscopy while preserving the intrinsic properties of the incident pulses and apply it to a study towards X-ray intensity induced effects. [ABSTRACT FROM AUTHOR]

Quantum‐chemistry determinations of the luminol chemiluminescence mechanism have made it possible to: first, clarify the spin inversion of the reaction; secondly, to determine the concerted nature of the two steps of 3O2 addition and 1N2 elimination; thirdly, to answer why such oxygen by nitrogen substitution must occur for an efficient excited‐state population; fourthly, to describe the electronic‐structure properties of the chemiexcitation; and finally, to distinguish the paths producing light emission versus those giving rise to radiationless decay. More information can be found in the Full Paper by A. Giussani, D. Roca‐Sanjuán, et al. on page 5202. [ABSTRACT FROM AUTHOR]

The anti-inflammatory cytokine IL-35 is produced by regulatory T (Treg) cells to suppress autoimmune and inflammatory responses. The role of IL-35 in type 1 diabetes (T1D) remains to be answered. To elucidate this, we investigated the kinetics of Treg cell response in the multiple low dose streptozotocin induced (MLDSTZ) T1D model and measured the levels of IL-35 in human T1D patients. We found that Treg cells were increased in MLDSTZ mice. However, the Treg cells showed a decreased production of anti-inflammatory (IL-10, IL-35, TGF-β) and increased pro-inflammatory (IFN-γ, IL-2, IL-17) cytokines, indicating a phenotypic shift of Treg cells under T1D condition. IL-35 administration effectively both prevented development of, and counteracted established MLDSTZ T1D, seemingly by induction of Eos expression and IL-35 production in Treg cells, thus reversing the phenotypic shift of the Treg cells. IL-35 administration reversed established hyperglycemia in NOD mouse model of T1D. Moreover, circulating IL-35 levels were decreased in human T1D patients compared to healthy controls. These findings suggest that insufficient IL-35 levels play a pivotal role in the development of T1D and that treatment with IL-35 should be investigated in treatment of T1D and other autoimmune diseases. [ABSTRACT FROM AUTHOR]

Quantum chemical investigations of the neutral [Mn12O12(CH3COO)16(H2O)4]0 molecular magnet cluster (abbreviated as [Mn12]0) are complicated by the energetic multitude of spin states due to weak spin–spin couplings between the twelve Mn centers. The situation becomes even more serious for this cluster in its super‐reduced [Mn12]8– state, which was recently introduced by the Awaga group [Wang et al., Chemistry – Asian J. 6, 1074 (2011)] as the cathode‐active material of the molecular cluster battery (MCB). In their work on pp. 517–521, Nishimoto et al. theoretically investigate the geometrical changes observed experimentally during discharging in the MCB using standard geometry optimization and direct first principles molecular dynamics simulations to include temperature effects. The spin‐polarized, broken‐symmetry density functional theory (DFT) calculations on 15 candidate electronic states suggest that for relevant low‐spin states the eight electrons added in [Mn12]8– are mainly, but not completely transferred to the outer eight Mn atoms, causing elongation of the bonds between outer Mn and their surrounding O atoms, while the inner Mn4O4 cluster is less affected by the reduction (only one electron can be picked up in the lowest‐energy spin state). [ABSTRACT FROM AUTHOR]