43 results on '"Markus Doerr"'
Search Results
2. Función de los confórmeros de ataque cercano en la acilación enantioselectiva del (R,S)-propranolol catalizada por lipasa B de Candida antarctica
- Author
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Daniel Iván Barrera Valderrama, Markus Doerr, and Martha Cecilia Daza Espinosa
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enzimología ,antagonistas adrenérgicos beta ,dominio catalítico ,simulación por computador. ,Biotechnology ,TP248.13-248.65 - Abstract
La lipasa B de Candida antarctica (CalB) se ha utilizado en la acilación quimio- y enantioselectiva del racemato (R,S)-propranolol. CalB tiene enantioselectividad moderada (E=63) por el R-propranolol. La enantioselectividad, se origina en la reacción de transferencia del grupo acilo desde la serina catalítica, acilada, al propranolol. La fase inicial de esta reacción involucra la formación de complejos de Michaelis y posteriormente conformaciones de ataque cercano. El análisis de las conformaciones de ataque cercano ha permitido en varios casos explicar el origen de la catálisis o reproducir el efecto catalítico. En este trabajo se profundiza en la comprensión la función de las conformaciones de ataque cercano en la enantioselectividad de la acilación del (R,S)-propranolol catalizada por CalB. Para lo anterior se realizó un estudio detallado de los complejos de Michaelis y de las conformaciones de ataque cercano del paso enantioselectivo de la reacción de acilación del (R,S)-propranolol utilizando un protocolo de dinámica molecular QM/MM (SCCDFTB/CHARMM) utilizando 6 distribuciones de velocidades iniciales y simulaciones de 2,5 ns. Se estudiaron 7 complejos CalB-propranolol. Los enlaces de hidrógeno del sitio activo de CalB acilada relevantes para la actividad catalítica fueron estables en todas las simulaciones. Las poblaciones de los complejos de Michaelis y de las conformaciones de ataque cercano son dependientes de la distribución de las velocidades iniciales de la dinámica molecular. La enantioselectividad moderada de CalB acilada, encontrada experimentalmente, puede ser parcialmente atribuida a la alta población de conformaciones de ataque cercano observada para el S-propranolol.
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- 2018
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3. Effects of the molecular structure on the electronic vertical spectrum of oxoglaucine
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Martha Cecilia Daza Espinosa, Diana Marcela Hernández, Angela Susana Rodriguez-Serrano, and Markus Doerr
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Oxoglaucina ,fitoalexinas ,Espectro vertical ,DFT/MRCI ,TDDFT ,Chemistry ,QD1-999 - Abstract
The vertical electronic spectrum of oxoglaucine by means of a multireference configuration interaction method (DFT/MRCI) was studied. The effect of both methyl and methoxy groups on the geometries and energetic distribution of the low-lying excited states was analyzed. The results show that, by means of the TZVP basis set, at the ground state minima of oxoglaucine, oxoglaucine without methyl and methoxy groups, the lowest excited singlet states are of nπ* (S1) and ππ* (S2) type. Triplet states of ππ* (T1) and nπ* (T2) type are energetically accessible from S1. From the energetic point of view, it can be proposed that the channel for an efficient intersystem crossing 1(nπ*)⇝3(ππ*) is plausible. Although the presence of the methyl and methoxyl groups distort the planarity of the rings system, the effect in the vertical distribution of the lowest lying singlet and triplet states can be considered as negligible.
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- 2018
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4. SYNTHESIS OF NEW N-PHENYL-N-(1-PHENYLHEX-5-EN-1-YL)ACETAMIDES AND THEIR 1H-NMR CONFORMATIONAL STUDY
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Mauricio Acelas, Elizabeth Gil, Markus Doerr, Martha Daza, and Juan Manuel Urbina
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Chemistry ,QD1-999 - Abstract
The synthesis and characterization of different N-phenyl-N-(1-phenylhex-5-en-1-yl)acetamides is presented. Two conformational isomers were observed for one of the compounds in their1H/13C-NMR spectra. Computational calculations and dihedral angle comparison using the allylic system coupling constants (J) were carried out to determine the isomeric structures responsible for signals duplicity and chemical shifting.
- Published
- 2014
5. Proton transfer from 1,4-pentadiene to superoxide radical anion: a QTAIM analysis
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Angela Rodríguez-Serrano, Martha Daza, Markus Doerr, and Jose Luis Villaveces
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superoxide radical anion, density functional theory, QTAIM, reaction mechanism, proton transfer, 1,4-pentadiene ,Chemistry ,QD1-999 - Abstract
We studied the bis-allylic proton transferreaction from 1,4-pentadiene to superoxideradical anion (O2·־). Minima andtransition state geometries, as well asthermochemical parameters were computedat the B3LYP/6-311+G(3df,2p)level of theory. The electronic wavefunctions of reactants, intermediates,and products were analyzed within theframework of the Quantum Theory ofAtoms in Molecules. The results showthe formation of strongly hydrogen bondedcomplexes between the 1,4-pentadien-3-yl anion and the hydroperoxylradical as the reaction products. Theseproduct complexes (PCs) are more stablethan the isolated reactants and muchmore stable than the isolated products.This reaction occurs via pre-reactivecomplexes which are more stable thanthe PCs and the transition states. This isin agreement with the fact that the netproton transfer reaction that leads to freeproducts is an endothermic and nonspontaneousprocess.
- Published
- 2014
6. On the separation of enantiomers by drift tube ion mobility spectrometry
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Roberto Fernandez-Maestre and Markus Doerr
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General Chemical Engineering ,Ion Mobility Spectrometry ,General Engineering ,Stereoisomerism ,Amino Acids ,Mass Spectrometry ,Analytical Chemistry - Abstract
Racemic mixtures of twelve common a-amino acids and three chiral drugs were tested for the separation of their enantiomers by ion mobility spectrometry (IMS)-quadrupole mass spectrometry (MS). Separations were tested by introducing chiral selectors in the mobility spectrometer buffer gas. (R)-α-(trifluoromethyl) benzyl alcohol, (R)-tetrahydrofuran-2-carbonitrile, (L)-ethyl lactate, methyl (S)-2-chloropropionate, and the R and S enantiomers of 2-butanol and 1-phenyl ethanol were evaluated as chiral selectors. Experimental conditions were varied during the tests including buffer gas temperature, concentration, and type of chiral selectors, analyte concentration, electrospray voltage, electrospray (ESI) solvent pH, and buffer gas flow. The individual enantiomers yielded different drift times for periods of up to 8 hours in a few experiments; such drift times were sufficiently different (~ 0.3 ms) to partially resolve the enantiomers in racemic mixtures, but these mixtures always yielded a single mobility peak at the experimental conditions tested with a drift time similar to that of one of the enantiomers. Energy calculations of the chiral selector –ion interactions showed that these separations are unlikely using 2-butanol as chiral selector but they might be feasible depending on the nature of chiral selectors and the type of enantiomers.
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- 2022
7. QM/MM calculation of solvent effects on absorption spectra of guanine.
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Maja Parac, Markus Doerr, Christel M. Marian, and Walter Thiel
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- 2010
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8. QM/MM study of the absorption spectra of DsRed.M1 chromophores.
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Elsa Sánchez-García, Markus Doerr, and Walter Thiel
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- 2010
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9. Effect of the CER[NP]:CER[AP] a ratio on the structure of a stratum corneum model lipid matrix - a molecular dynamics study
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Natalia Rivero, Martha C. Daza, and Markus Doerr
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Organic Chemistry ,Cell Biology ,Molecular Biology ,Biochemistry - Abstract
In some dermal diseases with evident skin dehydration and desquamation, the natural ratio of CER[NP]:CER[AP] is altered in the extracellular matrix of the stratum corneum by increasing the concentration of CER[AP]. The extracellular matrix of the stratum corneum is composed of several stacked lipid bilayers. Molecular dynamics simulations were used to investigate the molecular nanostructure of CER[NP], CER[AP], cholesterol and lignoceric acid models of the extracellular matrix of the stratum corneum with a nativelike CER[NP]:CER[AP] 2:1 ratio and a CER[NP]:CER[AP] ratio of 1:2. Despite the very minor chemical difference between CER[NP] and CER[AP], which is only a single OH group, it was possible to observe differences between the structural influence of the two ceramides. In the models with 1:2 ratio, the higher CER[AP] content leads to a larger inclination of the acyl chains and a smaller overlap in the lamellar midplane, with a small increase of the repeat distance compared to the model with higher CER[NP] concentration. Because CER[AP] forms more H-bonds than CER[NP], the total number of hydrogen bonds in the headgroup region is larger in the models with higher CER[AP] concentration, reducing the mobility of the lipids towards the centre of the bilayer and resulting in less overlap and increased tilt angles.
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- 2023
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10. Effect of the acyl-group length on the chemoselectivity of the lipase-catalyzed acylation of propranolol-a computational study
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Martha C. Daza, Markus Doerr, and Alexander Romero
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Models, Molecular ,Stereochemistry ,Protein Conformation ,Acylation ,Molecular Dynamics Simulation ,010402 general chemistry ,01 natural sciences ,Catalysis ,Enzyme catalysis ,Substrate Specificity ,Inorganic Chemistry ,Fungal Proteins ,chemistry.chemical_compound ,Nucleophile ,0103 physical sciences ,Physical and Theoretical Chemistry ,Chemoselectivity ,Lipase ,010304 chemical physics ,biology ,Basidiomycota ,Organic Chemistry ,Computational Biology ,biology.organism_classification ,Propranolol ,0104 chemical sciences ,Computer Science Applications ,Kinetics ,Computational Theory and Mathematics ,chemistry ,Docking (molecular) ,biology.protein ,lipids (amino acids, peptides, and proteins) ,Candida antarctica ,Acyl group - Abstract
The selective N-acylation of 1,2-amino alcohols has been proposed to occur through the proton shuttle mechanism. However, the O-acetylation of propranolol catalyzed by Candida antarctica lipase B is an exception. We investigated the relation between the chemoselectivity of this reaction and the acyl group length. For this purpose, we compared the acyl groups: ethanoyl, butanoyl, octanoyl, and hexadecanoyl. We studied the Michaelis complexes between serine-acylated Candida antarctica lipase B and propranolol, employing a computational approach that involved sampling Michaelis complex conformations through ensemble docking plus consensus scoring and molecular dynamics simulations. The conformations were then classified as near attack conformations for acylation of the amino or hydroxy group. The relative populations of these two classes of conformations were found to be consistent with the experimentally observed chemoselective O-acetylation. We predict that increasing the length of the hydrocarbon chain of the acyl group will cause O-acylation to be unfavorable with respect to N-acylation. The nucleophilic attack of propranolol to the acylated lipase was found to be more favorable through the classical mechanism when compared with the proton shuttle mechanism.
- Published
- 2021
11. Lipase-catalyzed O-acylation of (RS)-propranolol is determined by the acyl group length
- Author
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Martha C. Daza, Gilberto A. Zapata-Romero, and Markus Doerr
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O acylation ,chemistry.chemical_compound ,chemistry ,biology ,Stereochemistry ,medicine ,biology.protein ,Propranolol ,Lipase ,Acyl group ,Catalysis ,medicine.drug - Abstract
We employed a computational modeling approach to study the Michaelis complexes of (R)- and (S)-propranolol with serine-acylated Candida antarctica lipase B using four acyl groups: ethanoyl, butanoyl, octanoyl and hexadecanoyl. Our methodology involves sampling Michaelis complex conformations, first through ensemble docking using consensus scoring, and second by molecular dynamics simulations employing a quantum mechanics/molecular mechanics approach. The conformations are then categorized into two classes of near attack conformations, according to the distance of (a) the amino and (b) the hydroxy group of propranolol to the catalytic residues. The relative populations of these two classes of conformations was found to be consistent with the experimentally-observed exclusive chemoselectivity toward O-acylation with ethanoyl. Furthermore, we predict that increasing the length of the hydrocarbon chain of the acyl group will cause O-acylation to be unfavorable.
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- 2020
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12. Erfolgreiches Zeitmanagement für Dummies
- Author
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Markus Dörr and Markus Dörr
- Abstract
Der Arbeitstag reicht nicht aus, um alle Aufgaben zu erledigen. Oft fehlt es an Prioritäten und einer guten Tagesstruktur und ständig wird die Arbeit durch Störungen und Ablenkungen unterbrochen. Trifft das auch auf Sie zu? Dann finden Sie in diesem Band sicher viele Impulse und Methoden, wie Sie mit weniger Zeit, mehr Aufgaben, sogar in höherer Qualität erledigen und zudem Ihre Zufriedenheit am Arbeitsplatz steigern können. Markus Dörr zeigt Ihnen, wie Sie Ihre Zeit selbstbestimmt einteilen, mit Störungen und Zeitdieben umgehen und der ständigen Erreichbarkeit durch die unterschiedlichen Medien begegnen, die Technik aber gleichzeitig sinnvoll nutzen. Lernen Sie, Prioritäten zu setzen, Ihrem Tag eine gute Struktur zu geben, Meetings effizient durchzuführen und den Stress für sich und andere zu reduzieren. Schon bald werden Sie feststellen, wie Ihr?neues? Zeitmanagement Ihnen mehr Lebensqualität und Erfolg ermöglicht.
- Published
- 2022
13. Finite-temperature effect in the O-acylation of (R,S)-propranolol catalyzed by Candida antarctica lipase B
- Author
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Markus Doerr, Martha C. Daza, and Daniel Iván Barrera Valderrama
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Stereochemistry ,Acylation ,010402 general chemistry ,01 natural sciences ,Catalysis ,Reaction coordinate ,Kinetic resolution ,Fungal Proteins ,Tetrahedral carbonyl addition compound ,Materials Chemistry ,Physical and Theoretical Chemistry ,Spectroscopy ,biology ,010405 organic chemistry ,Chemistry ,Temperature ,Enantioselective synthesis ,Substrate (chemistry) ,Stereoisomerism ,Lipase ,biology.organism_classification ,Propranolol ,Computer Graphics and Computer-Aided Design ,0104 chemical sciences ,lipids (amino acids, peptides, and proteins) ,Candida antarctica ,Umbrella sampling - Abstract
CalB is a triacylglycerol hydrolase (E.C.3.1.1.3) used in the O-acylation of the beta-adrenergic blocking agent (R,S)-propranolol. The catalytic mechanism involves two steps: enzyme acylation and enzyme deacylation. The enantioselectivity of the O-acylation of (R,S)-propranolol originates from the second step, where the acyl-enzyme transfers the acyl group to the racemic substrate. This step occurs via an initial Michaelis complex (MCC) and a tetrahedral intermediate (TI-2). To gain more insight into the molecular basis of this reaction, we performed an exhaustive conformational sampling along the reaction coordinate of the enantioselective step of the reaction (MCC→TI-2→EPC) applying a QM/MM MD protocol (SCC-DFTB/CHARMM) in combination with umbrella sampling and the weighted histogram analysis method. To identify finite temperature effects we compare the PMF and the potential energy pathway. It is found that the effect of the finite temperature in this reaction is a destabilization of the tetrahedral intermediate and an increase of the barrier height of its formation. This increase is higher for the S-enantiomer.
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- 2021
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14. Protonation-State-Driven Photophysics in Phenothiazinium Dyes: Intersystem Crossing and Singlet-Oxygen Production
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Martha C. Daza, Jörg Tatchen, Angela Rodriguez-Serrano, Markus Doerr, and Christel M. Marian
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Aqueous solution ,010405 organic chemistry ,Singlet oxygen ,Organic Chemistry ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Thionine ,0104 chemical sciences ,Analytical Chemistry ,chemistry.chemical_compound ,Intersystem crossing ,chemistry ,Excited state ,Singlet fission ,Physical and Theoretical Chemistry ,Chemical equilibrium ,Triplet state - Abstract
The impact of altering the solvent pH value on the photodynamic action of thionine has been studied computationally by means of density functional theory and multi-reference interaction methods. To this end, we have investigated the electronic structure of the ground and excited states of diprotonated (TH₂²+) and neutral imine (T) forms of thionine (TH+). It is well known experimentally that the T₁ state of TH+ undergoes acid-base equilibrium reactions resulting in a pronounced pH effect for the efficiency of singlet oxygen (¹O₂) production. Our results show that the energy transfer reactions from the T₁ state of TH₂²+ and T to ³O₂ correspond to reversible equilibrium processes, whereas in TH+ this process is very exothermic in vacuum (-0.66 eV) and in aqueous solution (-0.49 eV). These facts explain the experimental observation of a much smaller efficiency of ¹O₂ production for TH₂²+ than for TH+. Moreover, we found that the pH value significantly affects the intersystem crossing (ISC) kinetics impacting the concentration of triplet state species available for energy transfer. In very acidic aqueous solution (pH 10⁷s-1). According to these results, maximum ISC efficiency is expected for intermediate acidic pH values (TH+, ∼10⁹ s-1).
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- 2017
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15. Quantum Mechanics/Molecular Mechanics Insights into the Enantioselectivity of the O-Acetylation of (R,S)-Propranolol Catalyzed by Candida antarctica Lipase B
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Martha C. Daza, Markus Doerr, Walter Thiel, Andrés M. Escorcia, and Kakali Sen
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biology ,010405 organic chemistry ,Stereochemistry ,Chemistry ,General Chemistry ,010402 general chemistry ,biology.organism_classification ,01 natural sciences ,Molecular mechanics ,Catalysis ,0104 chemical sciences ,Enzyme catalysis ,Molecular dynamics ,Tetrahedral carbonyl addition compound ,Quantum mechanics ,Stereoselectivity ,Candida antarctica ,Density functional theory - Abstract
Classical molecular dynamics (MD) simulations and combined quantum mechanics/molecular mechanics (QM/MM) calculations were used to investigate the origin of the enantioselectivity of the Candida antarctica lipase B (CalB) catalyzed O-acetylation of (R,S)-propranolol. The reaction is a two-step process. The initial step is the formation of a reactive acyl enzyme (AcCalB) via a tetrahedral intermediate (TI-1). The stereoselectivity originates from the second step, when AcCalB reacts with the racemic substrate via a second tetrahedral intermediate (TI-2). Reaction barriers for the conversion of (R)- and (S)-propranolol to O-acetylpropranolol were computed for several distinct conformations of TI-2. In QM/MM geometry optimizations and reaction path calculations the QM region was described by density functional theory (B3LYP/TZVP) and the MM region by the CHARMM force field. The QM/MM calculations show that the formation of TI-2 is the rate-determining step. The energy barrier for transformation of (R)-propran...
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- 2016
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16. Electronically Excited States of Higher Acenes up to Nonacene: A Density Functional Theory/Multireference Configuration Interaction Study
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Christina Tönshoff, Elsa Sanchez-Garcia, Markus Doerr, and Holger F. Bettinger
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010304 chemical physics ,Oscillator strength ,Chemie ,Multireference configuration interaction ,010402 general chemistry ,01 natural sciences ,Molecular physics ,0104 chemical sciences ,Computer Science Applications ,Pentacene ,chemistry.chemical_compound ,chemistry ,Computational chemistry ,Excited state ,0103 physical sciences ,Energy level ,Density functional theory ,Physical and Theoretical Chemistry ,HOMO/LUMO ,Acene - Abstract
While the optical spectra of the acene series up to pentacene provide textbook examples for the annulation principle, the spectra of the larger members are much less understood. The present work provides an investigation of the optically allowed excited states of the acene series from pentacene to nonacene, the largest acene observed experimentally, using the density functional based multireference configuration method (DFT/MRCI). For this purpose, the ten lowest energy states of the B2u and B3u irreducible representations were computed. In agreement with previous computational investigations, the electronic wave functions of the acenes acquire significant multireference character with increasing acene size. The HOMO → LUMO excitation is the major contributor to the (1)La state (p band, B2u) also for the larger acenes. The oscillator strength decreases with increasing length. The (1)Lb state (α band, B3u), so far difficult to assign for the larger acenes due to overlap with photoprecursor bands, becomes almost insensitive to acene length. The (1)Bb state (β band, B3u) also moves only moderately to lower energy with increasing acene size. Excited states of B3u symmetry that formally result from double excitations involving HOMO, HOMO-1, LUMO, and LUMO+1 decrease in energy much faster with system size. One of them (D1) has very small oscillator strength but becomes almost isoenergetic with the (1)La state for nonacene. The other (D2) also has low oscillator strength as long as it is higher in energy than (1)Bb. Once it is lower in energy than the (1)Bb state, both states interact strongly resulting in two states with large oscillator strengths. The emergence of two strongly absorbing states is in agreement with experimental observations. The DFT/MRCI computations reproduce experimental excitation energies very well for pentacene and hexacene (within 0.1 eV). For the larger acenes deviations are larger (up to 0.2 eV), but qualitative agreement is observed.
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- 2015
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17. Internal heavy atom effects in phenothiazinium dyes: enhancement of intersystem crossing via vibronic spin–orbit coupling
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Markus Doerr, Vidisha Rai-Constapel, Martha C. Daza, Angela Rodriguez-Serrano, and Christel M. Marian
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Photosensitizing Agents ,Molecular Structure ,Chemistry ,Relaxation (NMR) ,General Physics and Astronomy ,Quantum yield ,Spin–orbit interaction ,Photochemistry ,Photoexcitation ,Selenium ,Intersystem crossing ,Reaction rate constant ,Phenothiazines ,Excited state ,Quantum Theory ,Physical and Theoretical Chemistry ,Ground state ,Fluorescent Dyes - Abstract
The effect of substituting the intra-cyclic sulphur of thionine by oxygen (oxonine) and selenium (selenine) on the intersystem crossing (ISC) efficiency has been studied using high level quantum mechanical methods. The ISC rate constants are considerably increased when going from O towards Se while the fluorescence rate constants remain unchanged. For the three dyes, all accessible ISC channels are driven by vibronic spin-orbit coupling (SOC) between ππ* states. The interplay between the ground and low-lying excited states has been investigated in order to determine the dominant relaxation pathways. In oxonine the relaxation to the ground state after photoexcitation in water proceeds essentially via fluorescence from the S1(πHπL*) bright state (kF = 2.10 × 10(8) s(-1)), in agreement with the high experimental fluorescence quantum yield. In aqueous solution of thionine, the ISC rate constant (kISC ∼ 1 × 10(9) s(-1)) is one order of magnitude higher than fluorescence (kF = 1.66 × 10(8) s(-1)) which is consistent with its high triplet quantum yield observed in water (ϕT = 0.53). Due to a stronger vibronic SOC in selenine, the ISC rate is very high (kISC ∼ 10(10) s(-1)) and much faster than fluorescence (kF = 1.59 × 10(8) s(-1)). This suggests selenine-based dyes as very efficient triplet photosensitizers.
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- 2015
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18. Concerted double proton-transfer electron-transfer between catechol and superoxide radical anion
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Jorge Quintero-Saumeth, Markus Doerr, David A. Rincón, and Martha C. Daza
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Reaction mechanism ,010405 organic chemistry ,Chemistry ,Superoxide ,General Physics and Astronomy ,Hydrogen atom ,010402 general chemistry ,Photochemistry ,01 natural sciences ,0104 chemical sciences ,Adduct ,Electron transfer ,chemistry.chemical_compound ,Reaction rate constant ,Reactivity (chemistry) ,Physical and Theoretical Chemistry ,Proton-coupled electron transfer - Abstract
We have carried out a computational study on the reactivity of catechol (1,2-dihydroxybenzene) towards superoxide radical anion (O2˙−) in water, N,N-dimethylformamide (DMF), pentyl ethanoate (PEA) and vacuum using density functional theory and the coupled cluster method. Five reaction mechanisms were studied: (i) sequential proton transfer followed by hydrogen atom transfer (PT-HT), (ii) sequential hydrogen atom transfer followed by proton transfer (HT-PT), (iii) single electron transfer (SET), (iv) radical adduct formation (RAF) and (v) concerted double proton-transfer electron-transfer (denoted as global reaction, GR). Our results show that catechol and superoxide do not react via a sequential reaction mechanism (initial PT, initial HAT or SET). Instead, the reaction proceeds via a concerted double proton-transfer electron-transfer mechanism yielding hydrogen peroxide and catechol radical anion. The protons are transferred asynchronously between the σ orbitals of the catechol oxygen atoms to superoxide, while the electron is transferred between oxygen π orbitals in the same direction. The calculated rate constants in aqueous media agree with the experimental values reported in the literature. This suggests that the mechanism proposed in this work is adequate to describe this reaction. In addition, our results show that the reaction exhibits a large tunneling effect.
- Published
- 2017
19. Computational study of the enantioselectivity of the O-acetylation of (R,S)-propranolol catalyzed by Candida antarctica lipase B
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Andrés M. Escorcia, Markus Doerr, and Martha C. Daza
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chemistry.chemical_classification ,biology ,Chemistry ,Stereochemistry ,Process Chemistry and Technology ,Substrate (chemistry) ,Bioengineering ,biology.organism_classification ,Biochemistry ,Catalysis ,Transition state ,Molecular dynamics ,Enzyme ,Acetylation ,Candida antarctica ,Enantiomer - Abstract
Candida antarctica lipase B (CalB) displays moderate enantioselectivity when it catalyzes the acetylation of (R,S)-propranolol, favoring the faster transformation of the R-propranolol. With the aim to better understand the enantioselectivity of this reaction, we have performed a molecular dynamics (MD) study of the enzyme substrate complexes. Reactive enzyme substrate complexes were identified for both enantiomers of propranolol, which differ in their temporal stability and in their ability to reach the corresponding transition states (TS). Reactive complexes of R-propranolol present a better ability to be transformed by CalB than those of S-propranolol. This allows us to explain the enantioselectivity. Analysis of the enzyme–substrate interactions suggests that the CH-π interactions between the naphthyl rings of propranolol and the residues of the CalB binding pocket may play an important role in stabilizing the transition states involved in the transformation of the R-propranolol. The residues Ile189, Ala282 and Leu278 were identified as key residues for the enantioselectivity of CalB.
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- 2014
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20. Erfolgreiches Zeitmanagement für Dummies
- Author
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Markus Dörr and Markus Dörr
- Abstract
»Du hast keinen Plan.« Wie oft haben Sie das zu jemandem gesagt oder auch schon auf sich selbst bezogen? Aber nur wer einen Plan hat, kann beruflich oder privat die vielen Aufgaben erledigen, ohne völlig in Hektik zu verfallen. Markus Dörr zeigt Ihnen, wie erfolgreiches Zeitmanagement funktioniert, wie Sie Ihre Zeit wieder selbstbestimmt einteilen können, wie Sie mit Störungen und Zeitdieben umgehen und wie Sie die ständige Erreichbarkeit durch E-Mail, Smartphone und Co. eindämmen und gleichzeitig die Technik sinnvoll nutzen können. Lernen Sie, Prioritäten zu setzen, Meetings effektiv zu planen und durchzuführen und den Stress für sich und andere zu reduzieren. Und schon bald werden Sie feststellen, wie erfolgreiches Zeitmanagement Ihre Lebensqualität erhöht.
- Published
- 2016
21. Acetylation of (R,S)-propranolol catalyzed by Candida antarctica lipase B: An experimental and computational study
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Daniel Molina, Markus Doerr, Andrés M. Escorcia, and Martha C. Daza
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biology ,Chemistry ,Process Chemistry and Technology ,Substrate (chemistry) ,Bioengineering ,Nuclear magnetic resonance spectroscopy ,biology.organism_classification ,Biochemistry ,Catalysis ,chemistry.chemical_compound ,Vinyl acetate ,Organic chemistry ,Candida antarctica ,Methanol ,Chemoselectivity ,Solubility - Abstract
The chemo- and enantioselectivity of the Candida antarctica lipase B (CalB)-catalyzed acetylation reaction of (R,S)-propranolol using vinyl acetate as acyl donor and toluene as organic solvent was studied. Because of the poor solubility of propranolol in toluene small quantities of methanol were added as cosolvent. The effects of the propranolol/vinyl acetate ratio, the enzyme purification procedure and the methanol concentration on the reaction were investigated. The reactions occurring in the system were quantitatively investigated using 1H and 13C NMR spectroscopy. The major reactions were the hydrolysis and alcoholysis of vinyl acetate, as a consequence of the presence of residual water and methanol in the reaction medium. Furthermore, the NMR analysis confirmed that O-acetyl-propranolol was formed exclusively. The reaction was also found to be enantioselective favoring the faster transformation of the R-propranolol. In addition to the experiments, molecular modeling was used to study the formation of the reactive Michaelis complexes between propranolol and acetylated CalB, using a combined molecular docking and molecular dynamics (MD) procedure. Only for the O-acetylation we found binding modes of the substrate leading to formation of the product, which explains the experimentally observed chemoselectivity of CalB.
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- 2013
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22. A quantum chemical investigation of the electronic structure of thionine
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Markus Doerr, Christel M. Marian, Angela Rodriguez-Serrano, and Martha C. Daza
- Subjects
Models, Molecular ,Chemistry ,Relaxation (NMR) ,Molecular Conformation ,Electrons ,Electronic structure ,Configuration interaction ,Phenothiazines ,Excited state ,Solvents ,Quantum Theory ,Density functional theory ,Physical and Theoretical Chemistry ,Solvent effects ,Atomic physics ,Ground state ,Basis set - Abstract
We have examined the electronic and molecular structure of 3,7-diaminophenothiazin-5-ium dye (thionine) in the electronic ground state and in the lowest excited states. The electronic structure was calculated using a combination of density functional theory and multi-reference configuration interaction (DFT/MRCI). Equilibrium geometries were optimized employing (time-dependent) density functional theory (B3LYP functional) combined with the TZVP basis set. Solvent effects were estimated using the COSMO model and micro-hydration with up to five explicit water molecules. Our calculated electronic energies are in good agreement with experimental data. We find the lowest excited singlet and triplet states at the ground state geometry to be of π→π* (S(1), S(2), T(1), T(2)) and n→π* (S(3), T(3)) character. This order changes when the molecular structure in the electronically excited states is relaxed. Geometry relaxation has almost no effect on the energy of the S(1) and T(1) states (~0.02 eV). The relaxation effects on the energies of S(2) and T(2) are moderate (0.14-0.20 eV). The very small emission energy results in a very low fluorescence rate. While we were not able to locate the energetic minimum of the S(3) state, we found a non-planar minimum for the T(3) state with an energy which is very close to the energy of the S(1) minimum in the gas phase (0.04 eV above). When hydration effects are taken into account, the n→π* states S(3) and T(3) are strongly blueshifted (0.33 and 0.46 eV), while the π→π* states are only slightly affected (0.06 eV).
- Published
- 2012
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23. QM/MM Study of the Monomeric Red Fluorescent Protein DsRed.M1
- Author
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Markus Doerr, Elsa Sanchez-Garcia, Ya-Wen Hsiao, and Walter Thiel
- Subjects
Chemistry ,Chemie ,Water ,Charge density ,Hydrogen Bonding ,Protonation ,Crystal structure ,Molecular Dynamics Simulation ,Physik (inkl. Astronomie) ,Chromophore ,Surfaces, Coatings and Films ,QM/MM ,Luminescent Proteins ,Molecular dynamics ,Crystallography ,Isomerism ,Computational chemistry ,Materials Chemistry ,Quantum Theory ,Density functional theory ,Physical and Theoretical Chemistry ,Conformational isomerism - Abstract
We report a combined quantum mechanical/molecular mechanical (QM/MM) study of the DsRed.M1 protein using as QM component the self-consistent charge density functional tight-binding (SCC-DFTB) method in molecular dynamics (MD) simulations and hybrid density functional theory (DFT, B3LYP functional) in QM/MM geometry optimizations. We consider different variants of the chromophore (including the cis- and trans-acylimine and peptide forms) as well as different protonation states of environmental residues. The QM/MM calculations provide insight into the role of nearby residues concerning their interactions with the chromophore and their influence on structural and spectroscopic properties. QM/MM optimizations yield a single conformer for the anionic acylimine chromophore, whereas there are distinct cis- and trans-conformers in the anionic peptide chromophore, the latter being more stable. The calculated vertical excitation energies (DFT/MRCI) for the anionic chromophores agree well with experiment. The published crystal structure of DsRed.M1 with an anionic acylimine chromophore indicates a quinoid structure, while the QM/MM calculations predict the phenolate form to be more stable.
- Published
- 2009
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24. The 15N chemical shifts in mixed NB2Si and NBSi2 environments of Si3B3N7—A theoretical investigation
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Markus Doerr and Christel M. Marian
- Subjects
Nuclear and High Energy Physics ,Radiation ,Silicon ,Chemical shift ,Ab initio ,Analytical chemistry ,chemistry.chemical_element ,General Chemistry ,Nitride ,Quantum chemistry ,Amorphous solid ,chemistry ,Computational chemistry ,Molecule ,Boron ,Instrumentation - Abstract
Nuclear magnetic resonance (NMR) chemical shifts in solids may be calculated by ab initio methods approximating the solid state by molecular clusters. We employed this technique to obtain estimates of (15)N chemical shifts in NB(2)Si and NBSi(2) environments in the solid state. Such nitrogen environments are found in amorphous (Si/B/N-)ceramics which exhibit very interesting features such as high thermal and mechanical stability. We based our calculations on cutouts of hypothetical Si(3)B(3)N(7) crystals suggested by Kroll and Hoffmann [Silicon boron nitrides: hypothetical polymorphs of Si(3)B(3)N(7), Angew. Chem. Int. Ed. 37 (1998) 2527]. Taking the systematic errors of our calculations into account we expect the chemical shifts in NBSi(2) environments around -293+/-5ppm. Chemical shifts in NB(2)Si environments are expected at -272+/-6ppm. The range of the calculated chemical shifts in NBSi(2) environments coincides with experimental chemical shifts in molecular compounds. Experimental chemical shifts of NB(2)Si nitrogen in molecules appear at lower field than our calculated chemical shifts in the solid state.
- Published
- 2006
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25. Novel new ester quaternaries for improved performance benefits as rinse cycle fabric softeners
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Owen Portwood, Markus Doerr, Robert O. Keys, Floyd E. Friedli, Dave Whittlinger, and C. Joe Toney
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Dimethylethanolamine ,chemistry.chemical_classification ,Diethanolamine ,Degree of unsaturation ,General Chemical Engineering ,Fabric softener ,Aminoethylethanolamine ,Biodegradation ,Surfaces, Coatings and Films ,chemistry.chemical_compound ,chemistry ,Triethanolamine ,medicine ,Organic chemistry ,Physical and Theoretical Chemistry ,Alkyl ,medicine.drug - Abstract
A number of new diesterquats and anidoester quats were synthesized and tested for biodegradation and softening. Methyldiethanolamine, 3-methoxylpropylamine, diethanolaminopropylamine, aminoethylethanolamine, dimethylethanolamine, and diethanolamine were reacted, either “as is” or after alkoxylation, with tallow fatty acid and further converted into dialkyl quats. The diesterquat from diethanolisopropanolamine was by far the best of the ester quats synthesized in overall biodegradation, softening, and cost/ease of manufacture. It appears that two ester groups are needed for ready biodegradation as opposed to an amide-ester combination. Increasing unsaturation of the alkyl chains within a molecule increases its rate of biodegradation slightly.
- Published
- 2001
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26. A theoretical study of thionine: spin-orbit coupling and intersystem crossing
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Martha C. Daza, Markus Doerr, Christel M. Marian, Angela Rodriguez-Serrano, and Vidisha Rai-Constapel
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education.field_of_study ,Vacuum ,Chemistry ,Population ,Quantum yield ,Water ,Spin–orbit interaction ,Models, Theoretical ,Photochemistry ,Fluorescence ,Reaction rate constant ,Intersystem crossing ,Phenothiazines ,Radiative transfer ,Quantum Theory ,Thermodynamics ,Singlet state ,Physical and Theoretical Chemistry ,Atomic physics ,education - Abstract
A study of the possible intersystem crossing (ISC) mechanisms (S→T) in thionine (3,7-diamino-phenothiazin-5-ium), which is conducive to the efficient population of the triplet manifold, is presented. The radiationless deactivation channels {S(1),S(2)(π → π*) → T(1),T(2)(π → π*)} have been examined. Since the direct ISC does not explain the high triplet quantum yield in this system, attention has been centered on the vibronic spin-orbit coupling between the low-lying singlet and triplet (π → π*) states of interest. An efficient population transfer from the S(1)(π(H) → π(L)*) state to the T(2)(π(H-1) → π(L)*) state via this channel is confirmed. The calculated ISC rate constant for this channel is k(ISC) ≈ 3.35 × 10(8) s(-1), which can compete with the radiative depopulation of the S(1)(π(H) → π(L)*) state via fluorescence (k(F) ≈ 1.66 × 10(8) s(-1)) in a vacuum. The S(1)(π(H) → π(L)*) → T(1)(π(H) → π(L)*) and {S(2)(π(H-1) → π(L)*) → T(1),T(2)(π → π*)} ISC channels have been estimated to be less efficient (k(ISC) ≈ 10(5)-10(6) s(-1)). Based on the computed ISC rate constants and excited-state solvent shifts, it is suggested that the efficient triplet quantum yield of thionine in water is primarily due to the S(1)(π(H) → π(L)*) → T(2)(π(H-1) → π(L)*) channel with a computed rate constant of the order of 10(8)-10(9) s(-1) which is in accord with the experimental finding (k(ISC) = 2.8 × 10(9) s(-1)).
- Published
- 2012
27. QM/MM studies of structural and energetic properties of the far-red fluorescent protein HcRed
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Markus Doerr, Sean C. Smith, Walter Thiel, Zhen Li, and Qiao Sun
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Models, Molecular ,Chemistry ,Hydrogen bond ,General Physics and Astronomy ,Protonation ,Chromophore ,Hydrogen-Ion Concentration ,Molecular Dynamics Simulation ,Fluorescence ,Bond length ,QM/MM ,Molecular dynamics ,Crystallography ,Luminescent Proteins ,Deprotonation ,Models, Chemical ,Computational chemistry ,Quantum Theory ,Physical and Theoretical Chemistry - Abstract
The far-red fluorescent protein HcRed was investigated using molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Three models of HcRed (anionic chromophore) were considered, differing in the protonation states of nearby Glu residues (A: Glu214 and Glu146 both protonated; B: Glu214 protonated and Glu146 deprotonated; C: Glu214 and Glu146 both deprotonated). SCC-DFTB/MM MD simulations of model B yield good agreement with the available crystallographic data at ambient pH. Bond lengths in the QM region are well reproduced, with a root mean square (rms) deviation between experimental and average MD data of 0.079 A; the chromophore is almost co-planar, which is consistent with experimental observation; and the five hydrogen bonds involving the chromophore are conserved. QM/MM geometry optimizations were performed on representative snapshot structures from the MD simulations for each model. They confirm the structural features observed in the MD simulations. According to the DFT(B3LYP)/MM results, the cis-conformation of the chromophore is more stable than the trans-form by 9.1-12.9 kcal mol(-1) in model B, and by 12.4-19.9 kcal mol(-1) in model C, consistent with the experimental preference for the cis-isomer. However, in model A when both Glu214 and Glu146 are protonated, the stability is inverted with the trans-form being favored. The different protonation states of the titratable active-site residues Glu214 and Glu146 thus critically influence the manner in which the relative stability and degree of planarity of the cis- and trans-conformers vary with pH. Coupled with the known correlation of chromophore conformation with fluorescence efficiency, this work provides a detailed structural basis for the observed phenomenon that red fluorescent proteins such as HcRed, mKate and Rtms5 show bright fluorescence at high pH.
- Published
- 2010
28. Quantum Refinement of Protein Structures : Implementation and Application to the Red Fluorescent Protein DsRed.M1
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Markus Doerr, Ya-Wen Hsiao, Elsa Sanchez-Garcia, and Walter Thiel
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Models, Molecular ,Molecular Structure ,Protein Conformation ,Chemistry ,Protein Data Bank (RCSB PDB) ,Chemie ,Molecular Dynamics Simulation ,Chromophore ,Physik (inkl. Astronomie) ,Surfaces, Coatings and Films ,Green fluorescent protein ,Bond length ,Luminescent Proteins ,Crystallography ,Protein structure ,Materials Chemistry ,Quantum Theory ,Moiety ,Physical and Theoretical Chemistry ,Quantum ,Fluorescent Dyes ,Macromolecule - Abstract
Quantum refinement is an improvement upon the molecular mechanics (MM)-based crystallographic refinement. In the latter, X-ray data are supplemented with additional chemical information through MM force fields, whereas quantum refinement describes crucial regions of interest in the macromolecule by quantum mechanics (QM) instead of MM. In this paper, we report the implementation of quantum refinement in the ChemShell QM/MM framework and its application in an investigation of the chromophore structure of the red fluorescent protein DsRed.M1. Both mechanical and electrostatic QM/MM embedding schemes are implemented and tested. In the quantum refinement of DsRed.M1, the anionic red acylimine chromophore adopts a nearly orthogonal arrangement (rather than a cis or trans form), and the bond lengths in the acylimine moiety are more consistent with a phenolate (rather than a quinoid) structure. These findings are in contrast to the structure deduced from a standard crystallographic refinement (PDB: 2VAD), but in agreement with our earlier results from a purely theoretical QM/MM study. On the other hand, the quantum refinement of the anionic acylimine form of DsRed.M1 yields a hydrogen bonding network around the chromophore, especially with regard to the arrangement of the water molecules and the Glu148 residue, that is closer to the 2VAD structure than to the previously optimized QM/MM structure. In our earlier study the initial classical molecular dynamics (MD) simulations during QM/MM setup apparently exaggerated the mobility of the water molecules around the chromophore. On the basis of the present results, it seems likely that the Glu148 residue is protonated in the DsRed.M1 protein. The calculation of electronic excitation energies allows for further assessment of the proposed structures, especially in the chromophore region. Using a combination of density functional theory and multireference configuration interaction (DFT/MRCI), we find excellent agreement between experiment and theory only for the structures obtained from quantum refinement and from QM/MM optimization, but not for the 2VAD structure. The present case study on DsRed.M1 thus demonstrates the merits of combining reliable theoretical and experimental information in the determination of protein structures.
- Published
- 2010
29. QM/MM calculation of solvent effects on absorption spectra of guanine
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Markus Doerr, Maja Parac, Christel M. Marian, and Walter Thiel
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Guanine ,Absorption spectroscopy ,Chemistry ,Molecular Conformation ,Multireference configuration interaction ,General Chemistry ,Time-dependent density functional theory ,Molecular Dynamics Simulation ,QM/MM ,Computational Mathematics ,Molecular dynamics ,Water environment ,Solvents ,Quantum Theory ,Density functional theory ,Solvent effects ,Atomic physics - Abstract
Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited-state calculations were extracted from ground-state molecular dynamics (MD) simulations using the self-consistent-charge density functional tight binding (SCC-DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited-state calculations used time-dependent density functional theory (TDDFT) and the DFT-based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto-N7H and keto-N9H guanine, with particular focus on solvent effects in the low-energy spectrum of the keto-N9H tautomer. When compared with the vertical excitation energies of gas-phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC-DFTB-based rather than B3LYP-based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas-phase and solution spectra, typically ca. 0.1-0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent-induced structural changes and from electrostatic solute-solvent interactions, the latter being dominant.
- Published
- 2009
30. Photophysics of phenalenone: quantum-mechanical investigation of singlet-triplet intersystem crossing
- Author
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Martha C. Daza, Markus Doerr, Susanne Salzmann, Christel M. Marian, and Walter Thiel
- Subjects
Intersystem crossing ,Condensed matter physics ,Chemistry ,Excited state ,Singlet fission ,General Physics and Astronomy ,Electronic structure ,Spin–orbit interaction ,Physical and Theoretical Chemistry ,Triplet state ,Internal conversion (chemistry) ,Phosphorescence ,Molecular physics - Abstract
We have examined the electronic and molecular structure of 1H-phenalen-1-one (phenalenone) in the electronic ground state and in the lowest excited states, as well as intersystem crossing. The electronic structure was calculated using a combination of density functional theory and multi-reference configuration interaction. Intersystem crossing rates were determined using Fermi's golden rule and taking direct and vibronic spin-orbit coupling into account. The required spin-orbit matrix elements were obtained applying a non-empirical spin-orbit mean-field approximation. Our calculated electronic energies are in good agreement with experimental data. We find the lowest excited singlet states to be of the npi* (S1) and pipi* (S2) type. Energetically accessible from S1 are two triplet states of the pipi* (T1) and npi* (T2) type, the latter being nearly degenerate to S1. This ordering of states is retained when the molecular structure in the electronically excited states is relaxed. We expect very efficient intersystem crossing between S1 and T1. Our calculated intersystem crossing rate is approximately 2 x 10(10) s(-1), which is in excellent agreement with the experimental value of 3.45 x 10(10) s(-1). Our estimated phosphorescence and fluorescence rates are many orders of magnitude smaller. Our results are in agreement with the experimentally observed behavior of phenalenone, including the high efficiency of 1O2 production.
- Published
- 2009
31. Magnetic properties of Mn-doped ZnO Nanowires
- Author
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Markus Doerr, S.A. Granovsky, A. S. Markosyan, Jia G. Lu, T. Papageorgiou, Jochen Wosnitza, C.J. Chien, and I.Yu. Gaidukova
- Subjects
Materials science ,Condensed matter physics ,Nanowire ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics ,Matrix (chemical analysis) ,Paramagnetism ,Dendrite (crystal) ,Magnetization ,Condensed Matter::Materials Science ,Ferromagnetism ,Impurity ,Condensed Matter::Superconductivity ,Curie temperature ,General Materials Science ,Condensed Matter::Strongly Correlated Electrons - Abstract
Structural, magnetic and transport properties of undoped and Mn-doped quasi one-dimensional ZnO nano-wires formed as dendrite crystals of different width have been studied. All Mn-doped nanowires (Mn content 16% and 27 %) exhibit a ferromagnetic behavior, which is significantly temperature dependent. A small magnetic signal detected up to the room temperature is supposed to be due to small amounts of magnetic impurities. Analysis of the temperature dependencies of magnetization shows that the observed magnetic properties can be caused by the host ferromagnetic matrix with Curie temperature TC 40 K.
- Published
- 2009
32. Stepwise Conversion of a Single Source Precursor into Crystalline AlN by Transamination Reaction
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Christel M. Marian, Markus Doerr, Stephan Schulz, Wilfried Hoffbauer, Jörn Schmedt auf der Günne, Tillmann Bauer, and Wilfried Assenmacher
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Chemistry ,Electron energy loss spectroscopy ,Analytical chemistry ,Chemie ,Reaction intermediate ,Nitride ,Condensed Matter Physics ,Electronic, Optical and Magnetic Materials ,Inorganic Chemistry ,Solid-state nuclear magnetic resonance ,Differential thermal analysis ,X-ray crystallography ,Materials Chemistry ,Ceramics and Composites ,Physical chemistry ,Physical and Theoretical Chemistry ,Spectroscopy ,Pyrolysis - Abstract
Ammonolysis of the monomeric, base-stabilized trisaminoalane Me 3 N-Al[N(H)Dipp)] 3 (Dipp=2,6- i Pr 2 –C 6 H 3 ) yielded Al–N oligomers, which were characterized in detail by solid state NMR spectroscopy ( 1 H, 13 C, 15 N, 27 Al) and TGA/DTA. Pyrolysis of as-prepared oligomers at different temperatures in an argon steam yielded carbon-containing black solids, whereas pyrolysis under a steady flow of NH 3 produced pure aluminum nitride (AlN). The role of the pyrolysis temperature and the influence of NH 3 on the formation of crystalline materials were investigated. As-prepared AlN was characterized by solid state NMR spectroscopy ( 15 N, 27 Al), X-ray diffraction (XRD), transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS). Theoretical calculations were performed in order to identify potential reaction intermediates.
- Published
- 2008
33. Reverse Monte Carlo modelling of amorphous Si3B3N7using scattering and15N NMR data
- Author
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Markus Doerr and Christel M. Marian
- Subjects
Internal energy ,Scattering ,Chemistry ,business.industry ,Chemical shift ,Nuclear magnetic resonance spectroscopy ,Reverse Monte Carlo ,Condensed Matter Physics ,Amorphous solid ,Computational physics ,Superposition principle ,Optics ,General Materials Science ,business ,Electron scattering - Abstract
We present an enhanced reverse Monte Carlo approach that includes fitting to NMR data in the form of chemical shifts in addition to the usually used scattering data. Furthermore, the internal energy is accounted for in the cost function to prevent unphysical structures. This approach was applied to generate structural models of amorphous Si3B3N7, which is a prototype of a new class of high performance ceramics exhibiting interesting features like high thermal and mechanical stability. We fitted our structural models in direct space to radial distribution functions from x-ray, neutron and electron scattering experiments, and to the 15N NMR spectrum of the ceramic. This spectrum could not be interpreted before since it exhibits a broad structureless signal which is a superposition of peaks related to different chemical environments NBxSi3−x (x = 0–3) whose chemical shifts were only partly known experimentally. Therefore we based the calculation of NMR data in the reverse Monte Carlo optimizations on previous theoretical work that was done in our group. All generated models reproduce the experimental radial distribution functions very well. This good agreement does not deteriorate when the NMR data are taken into account. Fitting the models to 15N NMR chemical shifts in addition to scattering data results in structural changes that not only improve the agreement with the experimental magic-angle spinning (MAS) NMR spectrum but yield also significantly better second-nearest neighbour coordination statistics.
- Published
- 2007
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34. Why are the Homoleptic Diyl Complexes M(InR)4 with M = Ni and Pt Stable Compounds while only Ni(CO)4 but not Pt(CO)4 can become Isolated? A Theoretical Study of M(EMe)44 and M(CO)4 (M = Ni, Pd, Pt; E = B, Al, Ga, In, Tl)
- Author
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Gernot Frenking and Markus Doerr
- Subjects
Inorganic Chemistry ,chemistry.chemical_compound ,Electron density distribution ,Crystallography ,Electrostatic attraction ,Covalent bond ,Chemistry ,Stereochemistry ,Density functional theory ,Electronic structure ,Bond energy ,Homoleptic ,Bond-dissociation energy - Abstract
The equilibrium geometries and first bond dissociation energies of the homoleptic complexes M(EMe)4 and M(CO)4 with M = Ni, Pd, Pt and E = B, Al, Ga, In, Tl have been calculated at the gradient corrected DFT level using the BP86 functionals. The electronic structure of the metal-ligand bonds has been examined with the topologial analysis of the electron density distribution. The nature of the bonding is revealed by partitioning the metal-ligand interaction energies into contributions by electrostatic attraction, covalent bonding and Pauli repulsion. The calculated data show that the M-CO and M-EMe bonding is very similar. However, the M-EMe bonds of the lighter elements E are much stronger than the M-CO bonds. The bond energies of the latter are as low or even lower than the M-TlMe bonds. The main reason why Pd(CO)4 and Pt(CO)4 are unstable at room temperature in a condensed phase can be traced back to the already rather weak bond energy of the Ni-CO bond. The Pd-L bond energies of the complexes with L = CO and L = EMe are always 10 — 20 kcal/mol lower than the Ni-L bond energies. The calculated bond energy of Ni(CO)4 is only Do = 27 kcal/mol. Thus, the bond energy of Pd(CO)4 is only Do = 12 kcal/mol. The first bond dissociation energy of Pt(CO)4 is low because the relaxation energy of the Pt(CO)3 fragment is rather high. The low bond energies of the M-CO bonds are mainly caused by the relatively weak electrostatic attraction and by the comparatively large Pauli repulsion. The σ and π contributions to the covalent M-CO interactions have about the same strength. The π bonding in the M-EMe bonds is less than in the M-CO bonds but it remains an important part of the bond energy. The trends of the electrostatic and covalent contributions to the bond energies and the σ and π bonding in the metal-ligand bonds are discussed. Theoretische Studien anorganischer Verbindungen. 17 Warum sind die homoleptischen Diyl-Komplexe M(InR)4 mit M = Pt und Ni stabile Verbindungen obwohl nur Ni(CO)4 nicht aber Pt(CO)4 isoliert werden kann? Eine theoretische Untersuchung von M(EMe)4 und M(CO)4(M = Ni, Pd, Pt; E 5 B, Al, Ga, In, Tl) Die Geometrien und erste Dissoziationsenergien der homoleptischen Komplexe M(EMe)4 und M(CO)4 mit M = Ni, Pd, Pt und E = B, Al, Ga, In, Tl wurden mit gradientenkorrigierten Dichtefunktionalen unter Verwendung von BP86 berechnet. Die elektronische Struktur der Metall-Ligand-Bindungen ist mit der topologischen Analyse der Elektronendichteverteilung untersucht worden. Die Natur der chemischen Bindung wurde durch eine Energieanalyse aufgeklart, mit deren Hilfe die Beitrage der elektrostatischen Anziehung, der kovalenten Bindung und der Pauli-Abstosung zu den Metall-Ligand-Wechselwirkungen ermittelt wurden. Die Ergebnisse zeigen, dass die M-CO- and M-EMe-Bindungen sehr ahnlich sind. Die M-EMe-Bindungen der leichteren Elemente E sind aber wesentlich starker als die M-CO-Bindungen. Die Metall-Carbonyl-Bindungen haben eine ahnlich geringe Bindungsenergie wie die M-TlR-Bindungen. Die Erklarung, warum Pd(CO)4 und Pt(CO)4 in kondensierter Phase bei Raumtemperatur instabil sind, findet ihren Ursprung in der bereits geringen Bindungsenergie des Ni(CO)4. Die Pd-L-Bindungsenergien der Komplexe mit L = CO und L = EMe sind immer 10 — 20 kcal/mol niedriger als die Bindungsenergien der Ni-L-Bindungen. Da die berechnete Bindungsenergie des Ni(CO)4 lediglich Do = 27 kcal/mol betragt, sinkt die Bindungsenergie des Pd(CO)4 auf nur noch Do = 12 kcal/mol. Die erste Bindungsdissoziationsenergie des Pt(CO)4 ist niedrig, weil die Relaxationsenergie des Pt(CO)3-Fragments recht hoch ist. Die relativ niedrigen Wechselwirkungsenergien der M-CO-Bindungen konnen mit der im Vergleich zur M-ER-Bindung schwachen elektrostatischen Anziehung und der starken Pauli-Abstosung erklart werden. Die kovalente M-CO-Bindung hat etwa gleichstarke σ- und π-Beitrage. Die σ-Beitrage in den M-EMe-Bindungen sind schwacher als in den M-CO-Bindungen aber sie bleiben wichtig fur die Bindungsenergie. Die Trends der elektrostatischen und der kovalenten Beitrage zu den Bindungsenergien und die σ- und π-Anteile der Metall-Ligand-Bindungen werden diskutiert.
- Published
- 2002
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35. Quantum Refinement of Protein Structures: Implementation and Application to the Red Fluorescent Protein DsRed.M1.
- Author
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Ya-Wen Hsiao, Elsa Sanchez-Garcia, Markus Doerr, and Walter Thiel
- Published
- 2010
- Full Text
- View/download PDF
36. On the mechanism of the di-.pi.-methane rearrangement of bicyclo[3.2.1]octa-2,6-diene: deuterium labeling and generation of diradical intermediates via photolysis and thermolysis of appropriate azoalkanes
- Author
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Waldemar Adam, Ottorino De Lucchi, and Markus Doerr
- Subjects
Bicyclic molecule ,Diene ,Diradical ,Quantum yield ,General Chemistry ,Reaction intermediate ,Photochemistry ,Biochemistry ,Chemical reaction ,Catalysis ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,chemistry ,Di-pi-methane rearrangement ,Benzophenone - Abstract
The direct (254 nm) and acetone-sensitized (300 nm) photolyses of 2,4,4-trideuteriobicyclo(3.2.1)octa-2,6-diene (D-1) gave exclusively 3,5,5-trideuteriotricyclo(4.2.0.0)oct-3-ene (D-7) and 2,6,6-trideuteriotricyclo(3.2.1.0)oct-3-ene (D-8) but no rearranged diene, namely, 2,8,8-trideuteriobicyclo(3.2.1)octa-2,6-diene (D-1{prime}). Pyrolysis (400{degree}C) and direct (334 nm) and benzophenone-sensitized (364 nm) photolyses of the azoalkane 3,5,5-trideuterio-9,10-diazatricyclo(4.4.0.0)deca-3,9-diene (D-9) afforded a mixture of tricyclooctenes D-7 (major product) and D-8 and bicyclooctadiene D-1, but no rearranged diene D-1{prime}. These three modes of denitrogenation of the azoalkane 2,2,7-trideuterio-4,5-diazatricyclo(4.3.1.0)deca-4,8-diene (D-10) led only to the tricyclooctene D-8 (major product) and equal amounts of the bicyclooctadienes D-1 and D-1{prime}. Distinct temperature profiles were observed in the product fingerprints of the direct photolysis (334 nm) of the azoalkanes 9 and 10. For both azoalkanes 9 and 10 the quantum yields of denitrogenation increased with rising temperature. In none of these transformations could bicyclo(3.3.0)octa-2,7-diene (2) be detected. These results imply that the di-{pi}-methane rearrangement of the bicyclooctadienes 1 (D-1) and the denitrogenations of the azoalkanes 9 (D-9) and 10 (D-10) are disjoint chemical events. The intervention of diazenyl diradicals (one-bond cleavage of the azoalkanes) is postulated to be responsible for this disparity. The intervention of cyclopropyldicarbinyl diradical 3 as bona fide reaction intermediate in the di-{pi}-methane rearrangement of bicyclooctadiene 1 is questioned.
- Published
- 1989
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37. Synthesis, photolysis, and thermolysis of azoalkanes derived from spirocyclopropane-substituted norbornenes: competitive nitrogen loss and diazoalkane formation
- Author
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Waldemar Adam, Markus Doerr, Karl Peters, Hans Georg von Schnering, Eva Maria Peters, and Karlheinz Hill
- Subjects
chemistry.chemical_classification ,chemistry.chemical_compound ,Hydrocarbon ,Azo compound ,chemistry ,Organic Chemistry ,Thermal decomposition ,Photodissociation ,Organic chemistry ,chemistry.chemical_element ,Photochemistry ,Pyrolysis ,Nitrogen - Published
- 1985
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38. Wagner-Meerwein rearrangements of radical cations generated by triphenylpyrylium tetrafluoroborate photosensitized electron transfer of azoalkanes
- Author
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Waldemar Adam and Markus Doerr
- Subjects
chemistry.chemical_classification ,Azo compound ,Tetrafluoroborate ,Bicyclic molecule ,General Chemistry ,Visible radiation ,Electron acceptor ,Photochemistry ,Biochemistry ,Catalysis ,chemistry.chemical_compound ,Electron transfer ,Colloid and Surface Chemistry ,chemistry ,Radical ion - Abstract
In contrast to the direct or acetone-sensitized irradiation of the azoalkane (I), which leads exclusively to the product of cyclization (III), a rearranged product (IV) is formed in the presence of the electron acceptor triphenylpyrylium tetrafluoroborate (TPT) via the radical cation (II) and the TPT radical.
- Published
- 1987
- Full Text
- View/download PDF
39. ChemInform Abstract: Wagner-Meerwein Rearrangements of Radical Cations Generated by Triphenylpyrylium Tetrafluoroborate Photosensitized Electron Transfer of Azoalkanes
- Author
-
Markus Doerr and Waldemar Adam
- Subjects
chemistry.chemical_classification ,chemistry.chemical_compound ,Electron transfer ,Tetrafluoroborate ,chemistry ,Radical ion ,General Medicine ,Electron acceptor ,Radiation chemistry ,Photochemistry - Abstract
In contrast to the direct or acetone-sensitized irradiation of the azoalkane (I), which leads exclusively to the product of cyclization (III), a rearranged product (IV) is formed in the presence of the electron acceptor triphenylpyrylium tetrafluoroborate (TPT) via the radical cation (II) and the TPT radical.
- Published
- 1987
- Full Text
- View/download PDF
40. ChemInform Abstract: Mechanism of the Di-π-methane Rearrangement of Bicyclo(3.2.1)octa-2,6-diene: Deuterium Labeling and Generation of Diradical Intermediates via Photolysis and Thermolysis of Appropriate Azoalkanes
- Author
-
O. De Lucchi, Waldemar Adam, and Markus Doerr
- Subjects
chemistry.chemical_compound ,Deuterium ,Bicyclic molecule ,chemistry ,Diene ,Diradical ,Thermal decomposition ,Photodissociation ,General Medicine ,Photochemistry ,Methane - Published
- 1989
- Full Text
- View/download PDF
41. ChemInform Abstract: Evidence for Diazenyl Diradicals in the Photoisomerization of 4-Methylene-3,3,5,5-tetramethylpyrazoline
- Author
-
Markus Doerr and Waldemar Adam
- Subjects
chemistry.chemical_compound ,chemistry ,Photoisomerization ,General Medicine ,Methylene ,Photochemistry - Published
- 1987
- Full Text
- View/download PDF
42. SYNTHESIS OF NEW N -PHENYL- N - (1 -PHENYLHEX-5 - EN -1 -YL)ACETAMIDES AND THEIR 1 H-NMR CONFORMATIONAL STUDY
- Author
-
Mauricio Acelas, Elizabeth Gil, Markus Doerr, Daza, Martha C., and Juan-Manuel Urbina
43. Evidence for diazenyl diradicals in the photoisomerization of 4-methylene-3,3,5,5-tetramethylpyrazoline
- Author
-
Markus Doerr and Waldemar Adam
- Subjects
chemistry.chemical_compound ,Colloid and Surface Chemistry ,Bicyclic molecule ,Photoisomerization ,chemistry ,General Chemistry ,Thermal reaction ,Methylene ,Photochemistry ,Biochemistry ,Isomerization ,Catalysis - Published
- 1987
- Full Text
- View/download PDF
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