Hydrogen Bonding Regulates the Monomeric Nonradiative Decay of Adenine in DNA Strands

Lü, You; Lan, Zhenggang; Thiel, Walter

doi:10.1002/ange.201008146

Cited by 37 publications

(28 citation statements)

References 64 publications

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“…The multiple state interface is also being used to implement a surface hopping MD module for ChemShell based on the surface hopping routines in the MNDO semiempirical package . A development version of this module has been used to simulate the dynamical behavior of DNA bases in aqueous solution and the DNA environment …”

Section: Recent Developmentsmentioning

confidence: 99%

ChemShell—a modular software package for QM/MM simulations

Metz

Kästner

Sokol

et al. 2013

WIREs Comput Mol Sci

437

228

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1ChemShell is a modular computational chemistry package with a particular focus on hybrid quantum mechanical/molecular mechanical (QM/MM) simulations. A core set of chemical data handling modules and scripted interfaces to a large number of quantum chemistry and molecular modeling packages underpin a flexible QM/MM scheme. ChemShell has been used in the study of small molecules, molecular crystals, biological macromolecules such as enzymes, framework materials including zeolites, ionic solids, and surfaces. We outline the range of QM/MM coupling schemes and supporting functions for system setup, geometry optimization, and transition-state location (including those from the open-source DL-FIND optimization library). We discuss recently implemented features allowing a more efficient treatment of long range electrostatic interactions, X-ray based quantum refinement of crystal structures, free energy methods, and excited-state calculations. ChemShell has been ported to a range of parallel computers and we describe a number of options including parallel execution based on the message-passing capabilities of the interfaced packages and taskfarming for applications in which a number of individual QM, MM, or QM/MM calculations can performed simultaneously. We exemplify each of the features by brief reference to published applications. C

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Section: Recent Developmentsmentioning

confidence: 99%

ChemShell—a modular software package for QM/MM simulations

Metz

Kästner

Sokol

et al. 2013

WIREs Comput Mol Sci

437

228

View full text Add to dashboard Cite

show abstract

“…Given these encouraging features and the availability of an efficient MRCI code with analytic derivatives, several OM2/MRCI studies have recently been performed on the excited‐state dynamics of medium‐size organic molecules using trajectory surface hopping (TSH) . These TSH simulations have provided insight into the photostability of DNA bases in different environments (gas phase, aqueous solution, single‐stranded, and double‐stranded DNA oligomers), the mechanism of photoswitches and photoinduced molecular rotors, the complete photochemical cycle of a GFP chromophore with ultrafast excited‐state proton transfer, the chiral pathways and mode‐specific tuning of photo‐isomerization in azobenzenes, and the competition between concerted and stepwise mechanisms in the ultrafast photoinduced Wolff rearrangement of 2‐diaza‐1‐naphthoquinone . The results of these OM2/MRCI studies are generally consistent with the available experimental data and high‐level static calculations, but the dynamics often detects pathways and preferences between pathways that are not obvious from static calculations.…”

Section: Applicationsmentioning

confidence: 99%

Semiempirical quantum–chemical methods

Thiel

2013

WIREs Comput Mol Sci

Self Cite

292

302

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The semiempirical methods of quantum chemistry are reviewed, with emphasis on established neglect of diatomic differential overlap-based methods (MNDO, AM1, PM3) and on the more recent orthogonalization-corrected methods (OM1, OM2, OM3). After a brief historical overview, the methodology is presented in nontechnical terms, covering the underlying concepts, parameterization strategies, and computational aspects, as well as linear scaling and hybrid approaches. The application section addresses selected recent benchmarks and surveys ground-state and excited-state studies, including recent OM2-basedOne of the earliest semiempirical approaches in quantum chemistry was the π-electron method of Hückel, 1

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“…Such TSH simulations provided insight, for example, into the chiral pathways and mode‐specific tuning of photoisomerization in azobenzenes,84a the mechanism of fluorene‐based photoinduced molecular rotors,84b the complete photochemical cycle of a GFP chromophore with ultrafast excited‐state proton transfer,84c and the competition between concerted and stepwise mechanisms in the ultrafast photoinduced Wolff rearrangement 84d. The photodynamics of DNA nucleobases were simulated in the gas phase, in aqueous solution, and in solvated DNA single‐ and double‐strand models; the radiationless decay was found to be slowed down by about one order of magnitude in the DNA environment, with the preference between different decay channels being regulated by hydrogen bonding in the DNA double strand 85. In these and other studies, the TSH simulations often detected pathways and preferences between pathways that were not obvious from static calculations.…”

Section: Walter Thiel As Director Of the Department Of Theorymentioning

confidence: 99%

One Hundred Years of the Max‐Planck‐Institut für Kohlenforschung

Reetz

2014

Angew Chem Int Ed

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This Essay is an account of the institutional and scientific development of the Max‐Planck‐Institut für Kohlenforschung in Mülheim an der Ruhr (Germany), which is the successor to the Kaiser‐Wilhelm‐Institut für Kohlenforschung founded in 1914. The Essay is divided into four main parts, corresponding to the four major periods which are closely associated with the respective Directors of the Institute from 1914 to 2014: 1) Franz Fischer; 2) Karl Ziegler; 3) Günther Wilke; and 4) the period beginning with Manfred T. Reetz, who established a directorate comprising five Directors of equal status, each heading a different research department under the banner of catalysis. Along with key historical events associated with the Institute, research highlights of the four periods are featured.

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Hydrogen Bonding Regulates the Monomeric Nonradiative Decay of Adenine in DNA Strands

Cited by 37 publications

References 64 publications

ChemShell—a modular software package for QM/MM simulations

ChemShell—a modular software package for QM/MM simulations

Semiempirical quantum–chemical methods

One Hundred Years of the Max‐Planck‐Institut für Kohlenforschung

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