Publications by authors named "Oliver Weingart"

38 Publications

Capture and Separation of SO Traces in Metal-Organic Frameworks via Pre-Synthetic Pore Environment Tailoring by Methyl Groups.

Angew Chem Int Ed Engl 2021 Aug 9;60(33):17998-18005. Epub 2021 Jul 9.

Hoffmann Institute of Advanced Materials, Shenzhen Polytechnic, 7098 Liuxian Blvd, Nanshan District, Shenzhen, 518055, China.

Herein, we report a pre-synthetic pore environment design strategy to achieve stable methyl-functionalized metal-organic frameworks (MOFs) for preferential SO binding and thus enhanced low (partial) pressure SO adsorption and SO /CO separation. The enhanced sorption performance is for the first time attributed to an optimal pore size by increasing methyl group densities at the benzenedicarboxylate linker in [Ni (BDC-X) DABCO] (BDC-X=mono-, di-, and tetramethyl-1,4-benzenedicarboxylate/terephthalate; DABCO=1,4-diazabicyclo[2,2,2]octane). Monte Carlo simulations and first-principles density functional theory (DFT) calculations demonstrate the key role of methyl groups within the pore surface on the preferential SO affinity over the parent MOF. The SO separation potential by methyl-functionalized MOFs has been validated by gas sorption isotherms, ideal adsorbed solution theory calculations, simulated and experimental breakthrough curves, and DFT calculations.
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http://dx.doi.org/10.1002/anie.202105229DOI Listing
August 2021

Zirconium and Aluminum MOFs for Low-Pressure SO Adsorption and Potential Separation: Elucidating the Effect of Small Pores and NH Groups.

ACS Appl Mater Interfaces 2021 Jun 11;13(24):29137-29149. Epub 2021 Jun 11.

Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany.

Finding new adsorbents for the desulfurization of flue gases is a challenging task but is of current interest, as even low SO emissions impair the environment and health. Four Zr- and eight Al-MOFs (Zr-Fum, DUT-67(Zr), NU-1000, MOF-808, Al-Fum, MIL-53(Al), NH-MIL-53(Al), MIL-53(tdc)(Al), CAU-10-H, MIL-96(Al), MIL-100(Al), NH-MIL-101(Al)) were examined toward their SO sorption capability. Pore sizes in the range of about 4-8 Å are optimal for SO uptake in the low-pressure range (up to 0.1 bar). Pore widths that are only slightly larger than the kinetic diameter of 4.1 Å of the SO molecules allow for multi-side-dispersive interactions, which translate into high affinity at low pressure. Frameworks NH-MIL-53(Al) and NH-MIL-101(Al) with an NH-group at the linker tend to show enhanced SO affinity. Moreover, from single-gas adsorption isotherms, ideal adsorbed solution theory (IAST) selectivities toward binary SO/CO gas mixtures were determined with selectivity values between 35 and 53 at a molar fraction of 0.01 SO (10.000 ppm) and 1 bar for the frameworks Zr-Fum, MOF-808, NH-MIL-53(Al), and Al-Fum. Stability tests with exposure to dry SO during ≤10 h and humid SO during 5 h showed full retention of crystallinity and porosity for Zr-Fum and DUT-67(Zr). However, NU-1000, MOF-808, Al-Fum, MIL-53(tdc), CAU-10-H, and MIL-100(Al) exhibited ≥50-90% retained Brunauer-Emmett-Teller (BET)-surface area and pore volume; while NH-MIL-100(Al) and MIL-96(Al) demonstrated a major loss of porosity under dry SO and MIL-53(Al) and NH-MIL-53(Al) under humid SO. SO binding sites were revealed by density functional theory (DFT) simulation calculations with adsorption energies of -40 to -50 kJ·mol for Zr-Fum and Al-Fum and even above -50 kJ·mol for NH-MIL-53(Al), in agreement with the isosteric heat of adsorption near zero coverage (Δ). The predominant, highest binding energy noncovalent binding modes in both Zr-Fum and Al-Fum feature μ-OH···OSO hydrogen bonding interactions. The small pores of Al-Fum allow the interaction of two μ-OH bridges from opposite pore walls with the same SO molecule via OH···OSO···HO hydrogen bonds. For NH-MIL-53(Al), the DFT high-energy binding sites involve NH···OS together with the also present Al-μ-OH···OS hydrogen bonding interactions and C-π···SO, N···SO interactions.
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http://dx.doi.org/10.1021/acsami.1c06003DOI Listing
June 2021

Encapsulation of Phosphorescent Pt(II) Complexes in Zn-Based Metal-Organic Frameworks toward Oxygen-Sensing Porous Materials.

Inorg Chem 2020 May 7;59(10):7252-7264. Epub 2020 May 7.

CiMIC, SoN, Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, 48149 Münster, Germany.

In this work, we synthesized two tailored phosphorescent Pt(II) complexes bearing a cyclometalating tridentate thiazole-based C^N*N pincer luminophore () and exchangeable chlorido () or cyanido () coligands. While both complexes showed photoluminescence from metal-perturbed ligand-centered triplet states (MP-LC), reached the highest phosphorescence quantum yields and displayed a significant sensitivity toward quenching by O. We encapsulated them into two Zn-based metal-organic frameworks, namely, and . The incorporation of the organometallic compounds in the resulting composites , , , and was verified by powder X-ray diffractometry, scanning electron microscopy, time-resolved photoluminescence spectroscopy and microscopy, as well as N- and Ar-gas sorption studies. The amount of encapsulated complex was determined by graphite furnace atomic absorption spectroscopy, showing a maximum loading of 3.7 wt %. If compared with their solid state forms, the solid-solution composites showed prolonged O-sensitive excited state lifetimes for the complexes at room temperature, reaching up to 18.4 μs under an Ar atmosphere, which is comparable with the behavior of the complex in liquid solutions or even frozen glassy matrices at 77 K.
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http://dx.doi.org/10.1021/acs.inorgchem.0c00678DOI Listing
May 2020

Coordinatively unsaturated metal sites (open metal sites) in metal-organic frameworks: design and applications.

Chem Soc Rev 2020 May 1;49(9):2751-2798. Epub 2020 Apr 1.

Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, D-40204 Düsseldorf, Germany.

Metal-organic frameworks (MOFs) can contain open metal sites (OMS) or coordinatively unsaturated sites (CUS) or open coordination sites (OCS) when vacant Lewis acid sites on the metal ions or cluster nodes have been generated. This review combines for the first time all aspects of OMS in MOFs, starting from different preparation strategies over theoretical studies on the effects of OMS with host-guest interactions up to distinct OMS-MOF applications. In the experimental part the focus of this review is on MOFs with proven OMS formation which are not only invoked but are clearly verified by analytical methods.
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http://dx.doi.org/10.1039/c9cs00609eDOI Listing
May 2020

Fluorinated azobenzenes as supramolecular halogen-bonding building blocks.

Beilstein J Org Chem 2019 23;15:2013-2019. Epub 2019 Aug 23.

Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany.

-Fluoroazobenzenes are a remarkable example of bistable photoswitches, addressable by visible light. Symmetrical, highly fluorinated azobenzenes bearing an iodine substituent in -position were shown to be suitable supramolecular building blocks both in solution and in the solid state in combination with neutral halogen bonding acceptors, such as lutidines. Therefore, we investigate the photochemistry of a series of azobenzene photoswitches. Upon introduction of iodoethynyl groups, the halogen bonding donor properties are significantly strengthened in solution. However, the bathochromic shift of the π→π* band leads to a partial overlap with the n→π* band, making it slightly more difficult to address. The introduction of iodine substituents is furthermore accompanied with a diminishing thermal half-life. A series of three azobenzenes with different halogen bonding donor properties are discussed in relation to their changing photophysical properties, rationalized by DFT calculations.
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http://dx.doi.org/10.3762/bjoc.15.197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6720338PMC
August 2019

In vitro quantification of botulinum neurotoxin type A1 using immobilized nerve cell-mimicking nanoreactors in a microfluidic platform.

Analyst 2019 Sep;144(19):5755-5765

Institute for Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland.

The bacterial toxin botulinum neurotoxin A (BoNT/A) is not only an extremely toxic substance but also a potent pharmaceutical compound that is used in a wide spectrum of neurological disorders and cosmetic applications. The quantification of the toxin is extremely challenging due to its extraordinary high physiological potency and is further complicated by the toxin's three key functionalities that are necessary for its activity: receptor binding, internalization-translocation, and catalytic activity. So far, the industrial standard to measure the active toxin has been the mouse bioassay (MBA) that is considered today as outdated due to ethical issues. Therefore, recent introductions of cell-based assays were highly anticipated; their impact however remains limited due to their labor-intensive implementation. This report describes a new in vitro approach that combines a nanosensor based on the use of nerve cell-mimicking nanoreactors (NMN) with microfluidic technology. The nanosensor was able to measure all three key functionalities, and therefore suitable to quantify the amount of physiologically active BoNT/A. The integration of such a sensor in a microfluidic device allowed the detection and quantification of BoNT/A amounts in a much shorter time than the MBA (<10 h vs. 2-4 days). Lastly, the system was also able to reliably quantify physiologically active BoNT/A within a simple final pharmaceutical formulation. This complete in vitro testing system and its unique combination of a highly sensitive nanosensor and microfluidic technology represent a significant ethical advancement over in vivo measures and a possible alternative to cell-based in vitro detection methods.
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http://dx.doi.org/10.1039/c9an00817aDOI Listing
September 2019

Impact of fluorination on the photophysics of the flavin chromophore: a quantum chemical perspective.

Phys Chem Chem Phys 2019 May;21(19):9912-9923

Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.

10-Methylisoalloxazine (MIA) and its mono-fluorinated derivatives (6-9F-MIA) were investigated by means of quantum chemistry, looking into the influence of fluorination on fluorescence, absorption and inter-system crossing (ISC). A maximized fluorescence quantum yield (ΦFl) of this chromophore is desirable for application as a potential fluorescence marker in biodiagnostics/photobiological studies. An enhanced triplet quantum yield ΦT on the other hand may open a perspective for photodynamic therapies (PDT) in cancer treatment. Determination of equilibrium geometries was carried out employing (time-dependent) Kohn-Sham density functional theory and electronic properties were obtained using a combined density functional theory and multi-reference configuration interaction (DFT/MRCI) method. In the gas phase, El-Sayed-favored 1(ππ*) [radiolysis arrow - arrow with voltage kink] 3(nπ*)-ISC enables population transfer to the triplet domain on a timescale of 109 s-1, i.e. significantly faster than fluorescence (kFl ≈ 107 s-1). Two different models were applied to investigate the influence of aqueous medium on absorption and relaxation: the implicit solvation model A is the well-established conductor-like screening model (COSMO) and hybrid model B combines quantum mechanical micro-hydration and conductor-like screening. A polar, protic environment leads to a significant blue-shift of the nπ* potentials, slowing down the ISC process to 107-108 s-1, now enabled by vibronic spin-orbit coupling. Simple principles are derived that demonstrate the effect of fluorination at different positions on the spectroscopic properties. These principles can be utilized with respect to multiply fluorinated derivatives and even further substitution to enlarge effects on the population decay and quantum yields.
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http://dx.doi.org/10.1039/c9cp00805eDOI Listing
May 2019

Metal-Organic Frameworks with Potential Application for SO Separation and Flue Gas Desulfurization.

ACS Appl Mater Interfaces 2019 May 2;11(19):17350-17358. Epub 2019 May 2.

Hoffmann Institute of Advanced Materials , Shenzhen Polytechnic , 7098 Liuxian Blvd. , Nanshan District, Shenzhen 518055 , China.

Sulfur dioxide (SO) is an acidic and toxic gas and its emission from utilizing energy from fossil fuels or in industrial processes harms human health and environment. Therefore, it is of great interest to find new materials for SO sorption to improve classic flue gas desulfurization. In this work, we present SO sorption studies for the three different metal-organic frameworks MOF-177, NH-MIL-125(Ti), and MIL-160. MOF-177 revealed a new record high SO uptake (25.7 mmol·g at 293 K and 1 bar). Both NH-MIL-125(Ti) and MIL-160 show particular high SO uptakes at low pressures ( p < 0.01 bar) and thus are interesting candidates for the removal of remaining SO traces below 500 ppm from flue gas mixtures. The aluminum furandicarboxylate MOF MIL-160 is the most promising material, especially under application-orientated conditions, and features excellent ideal adsorbed solution theory selectivities (124-128 at 293 K, 1 bar; 79-95 at 353 K, 1 bar) and breakthrough performance with high onset time, combined with high stability under both humid and dry SO exposure. The outstanding sorption capability of MIL-160 could be explained by DFT simulation calculations and matching heat of adsorption for the binding sites O···S and OH···O (both ∼40 kJ·mol) and O···S (∼55-60 kJ·mol).
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http://dx.doi.org/10.1021/acsami.9b00029DOI Listing
May 2019

On the large apparent Stokes shift of phthalimides.

Phys Chem Chem Phys 2019 Feb;21(9):4839-4853

Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.

The photophysics of N-methylphthalimide (MP) in solution (cyclohexane, ethanol, acetonitrile, and water) was characterized by steady state as well as time resolved fluorescence and absorption spectroscopy. In all solvents the compound exhibits an unusually large Stokes shift of ∼10 000 cm-1. It is attributed to an ultrafast (<100 fs) depletion of the initially excited state, which results in the population of a weakly emitting state. Quantum chemical computations (DFT-MRCI) support this. They identify two energetically low-lying singlet ππ* excitations of different oscillator strength. Whereas the Stokes shift and thereby the ultrafast depletion of the initial excitation are hardly affected by the solvent later processes respond strongly. The fluorescence lifetime varies from ∼10 ps (cyclohexane) to ∼3 ns (water). This is attributed to a varying energetic accessibility of nπ* excitations.
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http://dx.doi.org/10.1039/c8cp07795aDOI Listing
February 2019

COBRAMM 2.0 - A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations.

J Mol Model 2018 Sep 3;24(9):271. Epub 2018 Sep 3.

Dipartimento di Chimica "G. Ciamician", Universita' degli Studi di Bologna, Via Selmi 2, 40126, Bologna, Italy.

We present a new version of the simulation software COBRAMM, a program package interfacing widely known commercial and academic software for molecular modeling. It allows a problem-driven tailoring of computational chemistry simulations with effortless ground and excited-state electronic structure computations. Calculations can be executed within a pure QM or combined quantum mechanical/molecular mechanical (QM/MM) framework, bridging from the atomistic to the nanoscale. The user can perform all necessary steps to simulate ground state and photoreactions in vacuum, complex biopolymer, or solvent environments. Starting from ground-state optimization, reaction path computations, initial conditions sampling, spectroscopy simulation, and photodynamics with deactivation events, COBRAMM is designed to assist in characterization and analysis of complex molecular materials and their properties. Interpretation of recorded spectra range from steady-state to time-resolved measurements. Various tools help the user to set up the system of interest and analyze the results.
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http://dx.doi.org/10.1007/s00894-018-3769-6DOI Listing
September 2018

Relationship between Excited State Lifetime and Isomerization Quantum Yield in Animal Rhodopsins: Beyond the One-Dimensional Landau-Zener Model.

J Phys Chem Lett 2018 Jun 6;9(12):3315-3322. Epub 2018 Jun 6.

Dipartimento di Chimica Industriale "Toso Montanari" , Università degli Studi di Bologna , Viale del Risorgimento , 4I-40136 Bologna , Italy.

We show that the speed of the chromophore photoisomerization of animal rhodopsins is not a relevant control knob for their light sensitivity. This result is at odds with the momentum-driven tunnelling rationale (i.e., assuming a one-dimensional Landau-Zener model for the decay: Zener, C. Non-Adiabatic Crossing of Energy Levels. Proc. R. Soc. London, Ser. A 1932, 137 (833), 696-702) holding that a faster nuclear motion through the conical intersection translates into a higher quantum yield and, thus, light sensitivity. Instead, a model based on the phase-matching of specific excited state vibrational modes should be considered. Using extensive semiclassical hybrid quantum mechanics/molecular mechanics trajectory computations to simulate the photoisomerization of three animal rhodopsin models (visual rhodopsin, squid rhodopsin and human melanopsin), we also demonstrate that phase-matching between three different modes (the reactive carbon and hydrogen twisting coordinates and the bond length alternation mode) is required to achieve high quantum yields. In fact, such "phase-matching" mechanism explains the computational results and provides a tool for the prediction of the photoisomerization outcome in retinal proteins.
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http://dx.doi.org/10.1021/acs.jpclett.8b01062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6650607PMC
June 2018

The effect of solvent relaxation in the ultrafast time-resolved spectroscopy of solvated benzophenone.

Photochem Photobiol Sci 2018 Mar;17(3):323-331

Université de Lorraine - Nancy, Laboratoire de Physique et Chimie Théoriques, UMR 7019, Vandoeuvre-lès-Nancy, 54506 France.

Benzophenone (BP) despite its relatively simple molecular structure is a paradigmatic sensitizer, featuring both photocatalytic and photobiological effects due to its rather complex photophysical properties. In this contribution we report an original theoretical approach to model realistic, ultra-fast spectroscopy data, which requires describing intra- and intermolecular energy and structural relaxation. In particular we explicitly simulate time-resolved pump-probe spectra using a combination of state-of-the art hybrid quantum mechanics/molecular mechanics dynamics to treat relaxation and vibrational effects. The comparison with experimental transient absorption data demonstrates the efficiency and accuracy of our approach. Furthermore the explicit inclusion of the solvent, water for simulation and methanol for experiment, allows us, despite the inherent different behavior of the two, to underline the role played by the H-bonding relaxation in the first hundreds of femtoseconds after optical excitation. Finally we predict for the first time the two-dimensional electronic spectrum (2DES) of BP taking into account the vibrational effects and hence modelling partially symmetric and asymmetric ultrafast broadening.
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http://dx.doi.org/10.1039/c7pp00439gDOI Listing
March 2018

Introduction-Festschrift in Honor of Prof. Volker Buß.

Photochem Photobiol 2017 11;93(6):1335

Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.

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http://dx.doi.org/10.1111/php.12850DOI Listing
November 2017

Dual Photochemical Reaction Pathway in Flavin-Based Photoreceptor LOV Domain: A Combined Quantum-Mechanics/Molecular-Mechanics Investigation.

J Phys Chem B 2017 10 4;121(41):9583-9596. Epub 2017 Oct 4.

Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstrasse 1, D-40225 Düsseldorf, Germany.

The primary photochemical reaction of the light, oxygen, and voltage (LOV) domain of the blue-light photosensor YtvA of Bacillus subtilis were investigated using high-level QM(DFT/MRCI)/MM methods. After blue-light excitation, the S atom of the reactive cysteine forms a covalent bond with the C of the flavin mononucleotide (FMN) ring. Two conformations for the side chain of reactive cysteine with occupancies of 70% (conf A) and 30% (conf B) are observed in the X-ray crystallographic structures of the YtvA-LOV ( Möglich , A. ; Moffat , K. J. Mol. Biol. 2007 , 373 , 112 - 126 ). In conf A, the thiol group is directed toward the dimethylbenzene moiety of the FMN ring whereas it is placed directly above the N atom of the FMN ring in conf B. Starting from both conformations, the singlet and triplet excited pathways were evaluated. The singlet states excited from conf A decay nonradiatively to the triplet states by intersystem crossing (ISC). After the formation of a neutral biradical, the triplet states cross over to the electronic ground state by a second ISC and the adducts are efficiently formed. The singlet states excited from conf B are located near the S/S conical intersection (CIn). A major fraction returns to the initial states through the CIn. The rest may directly reach the adduct state. Thus, the photoexcitation has a dual reaction pathway. In YtvA-LOV, it is inferred that the efficient triplet excitation from conf A was chosen by bypassing the less efficient singlet excitation from conf B.
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http://dx.doi.org/10.1021/acs.jpcb.7b09207DOI Listing
October 2017

New Perspectives on an Old Issue: A Comparative MS-CASPT2 and OM2-MRCI Study of Polyenes and Protonated Schiff Bases.

Photochem Photobiol 2017 11 16;93(6):1345-1355. Epub 2017 Oct 16.

Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany.

Polyenic systems are involved in light perception of numerous living organisms. Although a π-conjugated backbone is a common feature of all polyenes, their photophysics may vary. We provide a comparative quantum mechanical study of low-lying S and S excited states in short (3-5 double bonds) symmetric all-trans linear polyenes and corresponding protonated Schiff bases. In our investigation, we use the well-established ab initio multireference CASPT2 approach and benchmark the efficient semiempirical OM2-MRCI approach against it. For all protonated Schiff bases, MS-CASPT2 results in two distinct S minima with inverted and noninverted bond length pattern, respectively. We find that OM2-MRCI is a computationally affordable and reliable alternative to MS-CASPT2 for investigations of polyenic systems, particularly when highly demanding calculations (e.g. excited-state dynamics) need to be performed.
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http://dx.doi.org/10.1111/php.12833DOI Listing
November 2017

Nerve cell-mimicking liposomes as biosensor for botulinum neurotoxin complete physiological activity.

Toxicol Appl Pharmacol 2016 Dec 12;313:16-23. Epub 2016 Oct 12.

Institute for Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, CH-8092 Zurich, Switzerland.

Botulinum neurotoxins (BoNT) are the most toxic substances known, and their neurotoxic properties and paralysing effects are exploited for medical treatment of a wide spectrum of disorders. To accurately quantify the potency of a pharmaceutical BoNT preparation, its physiological key activities (binding to membrane receptor, translocation, and proteolytic degradation of SNARE proteins) need to be determined. To date, this was only possible using animal models, or, to a limited extent, cell-based assays. We here report a novel in vitro system for BoNT/B analysis, based on nerve-cell mimicking liposomes presenting motoneuronal membrane receptors required for BoNT binding. Following triggered membrane translocation of the toxin's Light Chain, the endopeptidase activity can be quantitatively monitored employing a FRET-based reporter assay within the functionalized liposomes. We were able to detect BoNT/B physiological activity at picomolar concentrations in short time, opening the possibility for future replacement of animal experimentation in pharmaceutical BoNT testing.
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http://dx.doi.org/10.1016/j.taap.2016.10.010DOI Listing
December 2016

Femtosecond Spectroscopy of Calcium Dipicolinate-A Major Component of Bacterial Spores.

J Phys Chem B 2016 09 29;120(35):9376-86. Epub 2016 Aug 29.

Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf , Universitätstr. 1, D-40225 Düsseldorf, Germany.

Bacterial spores are rich in calcium dipicolinate (CaDPA). The role of this compound in the high UV resistance of spore DNA and their unique DNA photochemistry is not yet clarified. Here, the photophysical properties of CaDPA dissolved in water are studied by means of steady-state and time-resolved spectroscopy as well as quantum chemistry. Upon 255 nm excitation, a fluorescence emission with a yield of 1.7 × 10(-5) is detected. This low yield is in line with a measured fluorescence lifetime of 110 fs. Transient absorption experiments point to further transitions with time constants of 92 ps and 6.8 μs. The microsecond time constant is assigned to the decay of a triplet state. The yield of this state is close to unity. With the aid of quantum chemistry (TD-DFT, DFT-MRCI), the following transitions are identified. The primarily excited (1)ππ* state depletes within 110 fs. The depletion results in the population of an energetically close lying (1)nπ* state. An El-Sayed allowed intersystem crossing process with a time constant of 92 ps ensues. Implications of these findings on the interaction between photoexcited CaDPA and spore DNA are discussed.
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http://dx.doi.org/10.1021/acs.jpcb.6b06230DOI Listing
September 2016

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

J Comput Chem 2016 Feb 12;37(5):506-41. Epub 2015 Nov 12.

Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA.

In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.
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http://dx.doi.org/10.1002/jcc.24221DOI Listing
February 2016

The photoformation of a phthalide: a ketene intermediate traced by FSRS.

Phys Chem Chem Phys 2015 Jan;17(1):376-86

Heinrich Heine Universität, Institut für Physikalische Chemie, Universitätsstraße 1, 40225 Düsseldorf, Germany.

The photo-isomerization of o-acetylbenzaldehyde (oABA) in acetonitrile was studied by femto- and nanosecond transient absorption spectroscopy. Spectroscopic signatures are assigned with the aid of TD-DFT, TD-CAM-DFT and DFT-MRCI computations. The isomerization yields a lactone, 3-methylphthalide (3MP), with a quantum yield of 0.3 (30%). As evidenced by femtosecond stimulated Raman spectroscopy (FSRS), the isomerization proceeds via a ketene intermediate. It is formed within ∼2-3 ps after photo-excitation. Intersystem crossing (ISC) populating the triplet state of oABA seems to compete with the ketene formation. Experiments on the non-reactive meta- and para-derivatives, which undergo efficient ISC with time constants of 5 ps, support this statement. The triplet state of oABA also contributes to the ketene formation, presumably involving a biradical intermediate. The ketene exhibits a lifetime of 1.4 μs and generates an additional intermediate in the cascade towards the lactone.
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http://dx.doi.org/10.1039/c4cp03351eDOI Listing
January 2015

Modelling time-resolved two-dimensional electronic spectroscopy of the primary photoisomerization event in rhodopsin.

J Phys Chem B 2014 Jul 8;118(28):8396-405. Epub 2014 May 8.

Université de Lyon , CNRS, Institut de Chimie de Lyon, École Normale Supérieure de Lyon, 46 Allée d'Italie, F-69364 Lyon Cedex 07, France.

Time-resolved two-dimensional (2D) electronic spectra (ES) tracking the evolution of the excited state manifolds of the retinal chromophore have been simulated along the photoisomerization pathway in bovine rhodopsin, using a state-of-the-art hybrid QM/MM approach based on multiconfigurational methods. Simulations of broadband 2D spectra provide a useful picture of the overall detectable 2D signals from the near-infrared (NIR) to the near-ultraviolet (UV). Evolution of the stimulated emission (SE) and excited state absorption (ESA) 2D signals indicates that the S1 → SN (with N ≥ 2) ESAs feature a substantial blue-shift only after bond inversion and partial rotation along the cis → trans isomerization angle, while the SE rapidly red-shifts during the photoinduced skeletal relaxation of the polyene chain. Different combinations of pulse frequencies are proposed in order to follow the evolution of specific ESA signals. These include a two-color 2DVis/NIR setup especially suited for tracking the evolution of the S1 → S2 transitions that can be used to discriminate between different photochemical mechanisms of retinal photoisomerization as a function of the environment. The reported results are consistent with the available time-resolved pump-probe experimental data, and may be used for the design of more elaborate transient 2D electronic spectroscopy techniques.
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http://dx.doi.org/10.1021/jp502538mDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216198PMC
July 2014

Wavepacket splitting and two-pathway deactivation in the photoexcited visual pigment isorhodopsin.

Angew Chem Int Ed Engl 2014 Feb 31;53(9):2504-7. Epub 2014 Jan 31.

IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza L. da Vinci, 32, 20133 Milano (Italy); Center for Nano Science and Technology @Polimi, Italian Institute of Technology, Via G. Pascoli 70/3, 20133 Milano (Italy).

Isorhodopsin is the visual pigment analogue of rhodopsin. It shares the same opsin environment but it embeds 9-cis retinal instead of 11-cis. Its photoisomerization is three times slower and less effective. The mechanistic rationale behind this observation is revealed by combining high-level quantum-mechanical/molecular-mechanical simulations with ultrafast optical spectroscopy with sub-20 fs time resolution and spectral coverage extended to the near-infrared. Whereas in rhodopsin the photoexcited wavepacket has ballistic motion through a single conical intersection seam region between the ground and excited states, in isorhodopsin it branches into two competitive deactivation pathways involving distinct conical intersection funnels. One is rapidly accessed but unreactive. The other is slower, as it features extended steric interactions with the environment, but it is productive as it follows forward bicycle pedal motion.
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http://dx.doi.org/10.1002/anie.201309867DOI Listing
February 2014

Periodic decay in the photoisomerisation of p-aminoazobenzene.

Phys Chem Chem Phys 2013 Jul 12;15(28):11814-21. Epub 2013 Jun 12.

Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.

Semiempirical OM2/MRCI surface-hopping simulations have been performed to study the E→Z and Z→E isomerisations of p-aminoazobenzene upon photoexcitation to the S1 state (nπ*). The overall mechanism is similar to the one found previously for the unsubstituted parent system, although there is a moderate speedup of the decay to the ground state because of the steeper excited-state potential between the Franck-Condon region and the conical intersection seam. The decay dynamics to the ground state shows an oscillatory pattern that can be attributed to an out-of-plane rotation of the N2 moiety. The reaction is thus initially driven by N2 rotation, which triggers phenyl rotations around the C-N bonds. The Z isomer is produced most effectively when the phenyl rings rotate in phase.
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http://dx.doi.org/10.1039/c3cp51316eDOI Listing
July 2013

Interfacial States in Donor-Acceptor Organic Heterojunctions: Computational Insights into Thiophene-Oligomer/Fullerene Junctions.

J Chem Theory Comput 2013 Jan 4;9(1):533-42. Epub 2012 Dec 4.

Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, D-45470 Mülheim, Germany.

Donor-acceptor heterojunctions composed of thiophene oligomers and C60 fullerene were investigated with computational methods. Benchmark calculations were performed with time-dependent density functional theory. The effects of varying the density functional, the number of oligomers, the intermolecular distance, the medium polarization, and the chemical functionalization of the monomers were analyzed. The results are presented in terms of diagrams where the electronic states are classified as locally excited states, charge-transfer states, and delocalized states. The effects of each option for computational simulations of realistic heterojunctions employed in photovoltaic devices are evaluated and discussed.
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http://dx.doi.org/10.1021/ct300844yDOI Listing
January 2013

Sampling excited state dynamics: influence of HOOP mode excitations in a retinal model.

Phys Chem Chem Phys 2012 Nov;14(41):14299-305

Lehrstuhl für Theoretische Chemie, Fakultät für Chemie, Universität Duisburg-Essen, Germany.

Zero point energy and classical thermal sampling techniques are compared in semi-classical photodynamics of the pentadienyliminium cation, a minimal retinal model. Using both methods, the effects of vibrational hydrogen-out-of-plane (HOOP) excitations on the photo-reactivity are probed at the ab initio CASSCF level. With 2376 individual trajectories the calculations reveal a clear picture of the relation between the excited state reaction coordinate, surface crossing and product generation. The productivity is strongly coupled with hydrogen torsion and the number of hopping attempts before the molecule finally decays.
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http://dx.doi.org/10.1039/c2cp41994gDOI Listing
November 2012

Cooperating Dinitrogen and Phenyl Rotations in trans-Azobenzene Photoisomerization.

J Chem Theory Comput 2012 Jul 4;8(7):2352-8. Epub 2012 Jun 4.

Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.

Semiempirical OM2/MRCI surface-hopping simulations have been performed to study the trans-to-cis photoisomerization of azobenzene upon excitation to the S1 state. The decay dynamics to the ground state shows an oscillatory pattern that can be attributed to an out-of-plane rotation of the N2 moiety. The reaction is thus initially driven by N2 rotation which triggers phenyl rotations around the C-N bonds. The cis isomer is produced most effectively when the phenyl rings rotate in phase. Mode-specific excitations cause variations in the computed decay times and product yields.
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http://dx.doi.org/10.1021/ct300303sDOI Listing
July 2012

A bioanalytical platform for simultaneous detection and quantification of biological toxins.

Sensors (Basel) 2012 21;12(2):2324-39. Epub 2012 Feb 21.

Laboratory of Food Microbiology, Institute of Food, Nutrition and Health (IFNH), ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.

Prevalent incidents support the notion that toxins, produced by bacteria, fungi, plants or animals are increasingly responsible for food poisoning or intoxication. Owing to their high toxicity some toxins are also regarded as potential biological warfare agents. Accordingly, control, detection and neutralization of toxic substances are a considerable economic burden to food safety, health care and military biodefense. The present contribution describes a new versatile instrument and related procedures for array-based simultaneous detection of bacterial and plant toxins using a bioanalytical platform which combines the specificity of covalently immobilized capture probes with a dedicated instrumentation and immuno-based microarray analytics. The bioanalytical platform consists of a microstructured polymer slide serving both as support of printed arrays and as incubation chamber. The platform further includes an easy-to-operate instrument for simultaneous slide processing at selectable assay temperature. Cy5 coupled streptavidin is used as unifying fluorescent tracer. Fluorescence image analysis and signal quantitation allow determination of the toxin's identity and concentration. The system's performance has been investigated by immunological detection of Botulinum Neurotoxin type A (BoNT/A), Staphylococcal enterotoxin B (SEB), and the plant toxin ricin. Toxins were detectable at levels as low as 0.5-1 ng · mL(-1) in buffer or in raw milk.
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http://dx.doi.org/10.3390/s120202324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3304168PMC
July 2012

Nonadiabatic decay dynamics of a benzylidene malononitrile.

J Phys Chem A 2012 Feb 6;116(6):1510-8. Epub 2012 Feb 6.

Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101 Shandong, China.

The photoinduced nonadiabatic decay dynamics of 2-[4-(dimethylamino)benzylidene]malononitrile (DMN) in the gas phase is investigated at the semiempirical OM2/MRCI level using surface hopping simulations. A lifetime of 1.2 ps is predicted for the S(1) state, in accordance with experimental observation. The dominant reaction coordinate is found to be the twisting around the C7═C8 double bond accompanied by pronounced pyramidalization at the C8 atom. Motion along this coordinate leads to the lowest-energy conical intersection (CI(01α)). Several other S(0)/S(1) conical intersections have also been located by full optimization but play no role in the dynamics. The time-resolved fluorescence spectrum of DMN is simulated by computing emission energies and oscillator strengths along the trajectories. It compares well with the experimental spectrum. The use of different active spaces in the OM2/MRCI calculations yields similar results and thus demonstrates their internal consistency.
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http://dx.doi.org/10.1021/jp2117888DOI Listing
February 2012

Product formation in rhodopsin by fast hydrogen motions.

Phys Chem Chem Phys 2011 Mar 18;13(9):3645-8. Epub 2011 Jan 18.

Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhem-Platz 1, 45470 Mülheim an der Ruhr, Germany.

The photochemical cis-trans isomerization of retinal in rhodopsin is investigated by structure sampling and excited state QM/MM trajectories with surface hopping. The calculations uncover the motions responsible for photoproduct formation and elucidate the reasons behind the efficient photoisomerization in the primary event of visual transduction.
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http://dx.doi.org/10.1039/c0cp02496aDOI Listing
March 2011

Conical intersection dynamics of the primary photoisomerization event in vision.

Nature 2010 Sep;467(7314):440-3

IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy.

Ever since the conversion of the 11-cis retinal chromophore to its all-trans form in rhodopsin was identified as the primary photochemical event in vision, experimentalists and theoreticians have tried to unravel the molecular details of this process. The high quantum yield of 0.65 (ref. 2), the production of the primary ground-state rhodopsin photoproduct within a mere 200 fs (refs 3-7), and the storage of considerable energy in the first stable bathorhodopsin intermediate all suggest an unusually fast and efficient photoactivated one-way reaction. Rhodopsin's unique reactivity is generally attributed to a conical intersection between the potential energy surfaces of the ground and excited electronic states enabling the efficient and ultrafast conversion of photon energy into chemical energy. But obtaining direct experimental evidence for the involvement of a conical intersection is challenging: the energy gap between the electronic states of the reacting molecule changes significantly over an ultrashort timescale, which calls for observational methods that combine high temporal resolution with a broad spectral observation window. Here we show that ultrafast optical spectroscopy with sub-20-fs time resolution and spectral coverage from the visible to the near-infrared allows us to follow the dynamics leading to the conical intersection in rhodopsin isomerization. We track coherent wave-packet motion from the photoexcited Franck-Condon region to the photoproduct by monitoring the loss of reactant emission and the subsequent appearance of photoproduct absorption, and find excellent agreement between the experimental observations and molecular dynamics calculations that involve a true electronic state crossing. Taken together, these findings constitute the most compelling evidence to date for the existence and importance of conical intersections in visual photochemistry.
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http://dx.doi.org/10.1038/nature09346DOI Listing
September 2010

The case of botulinum toxin in milk: experimental data.

Appl Environ Microbiol 2010 May 2;76(10):3293-300. Epub 2010 Apr 2.

Toxinology Group, Spiez Laboratory, 3700 Spiez, Switzerland.

Botulinum neurotoxin (BoNT) is the most toxic substance known to man and the causative agent of botulism. Due to its high toxicity and the availability of the producing organism Clostridium botulinum, BoNT is regarded as a potential biological warfare agent. Because of the mild pasteurization process, as well as rapid product distribution and consumption, the milk supply chain has long been considered a potential target of a bioterrorist attack. Since, to our knowledge, no empirical data on the inactivation of BoNT in milk during pasteurization are available at this time, we investigated the activities of BoNT type A (BoNT/A) and BoNT/B, as well as their respective complexes, during a laboratory-scale pasteurization process. When we monitored milk alkaline phosphatase activity, which is an industry-accepted parameter of successfully completed pasteurization, our method proved comparable to the industrial process. After heating raw milk spiked with a set amount of BoNT/A or BoNT/B or one of their respective complexes, the structural integrity of the toxin was determined by enzyme-linked immunosorbent assay (ELISA) and its functional activity by mouse bioassay. We demonstrated that standard pasteurization at 72 degrees C for 15 s inactivates at least 99.99% of BoNT/A and BoNT/B and at least 99.5% of their respective complexes. Our results suggest that if BoNTs or their complexes were deliberately released into the milk supply chain, standard pasteurization conditions would reduce their activity much more dramatically than originally anticipated and thus lower the threat level of the widely discussed "BoNT in milk" scenario.
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http://dx.doi.org/10.1128/AEM.02937-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869135PMC
May 2010
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