In the present study a benchmark set of medium-sized and large aromatic organic molecules with 10-78 atoms is presented. For this test set 0-0 transition energies measured in supersonic jets are ...compared to those calculated with DFT and the B3LYP functional, ADC(2), CC2 and the spin-scaled CC2 variants SOS-CC2 and SCS-CC2. Geometries of the ground and excited states have been optimized with these methods in polarized triple zeta basis sets. Zero-point vibrational corrections have been calculated with the same methods and basis sets. In addition the energies have been corrected by single point calculations with a triple zeta basis augmented with diffuse functions, aug-cc-pVTZ. The deviations of the theoretical results from experimental electronic origins, which have all been measured in the gas phase with high-resolution techniques, were evaluated. The accuracy of SOS-CC2 is comparable to that of unscaled CC2, whereas ADC(2) has slightly larger errors. The lowest errors were found for SCS-CC2. All correlated wave function methods provide significantly better results than DFT with the B3LYP functional. The effects of the energy corrections from the augmented basis set and the method-consistent calculation of the zero-point vibrational corrections are small. With this benchmark set reliable reference data for 0-0 transition energies for larger organic chromophores are available that can be used to benchmark the accuracy of other quantum chemical methods such as new DFT functionals or semi-empirical methods for excitation energies and structures and thereby augments available benchmark sets augments present benchmark sets which include mainly smaller molecules.
Chlorophylls are light-capturing units found in photosynthetic proteins. We study here the ground and excited state properties of monomeric, dimeric, and tetrameric models of the special ...chlorophyll/bacteriochlorophyll (Chl/BChl) pigment (P) centers P700 and P680/P870 of type I and type II photosystems, respectively. In the excited state calculations, we study the performance of the algebraic diagrammatic construction through second-order (ADC(2)) method in combination with the reduced virtual space (RVS) approach and the recently developed Laplace-transformed scaled-opposite-spin (LT-SOS) algorithm, which allows us, for the first time, to address multimeric effects at correlated ab initio levels using large basis sets. At the LT-SOS-RVS-ADC(2)/def2-TZVP level, we obtain vertical excitation energies (VEEs) of 2.00–2.07 and 1.52–1.62 eV for the P680/P700 and the P870 pigment models, respectively, which agree well with the experimental absorption maxima of 1.82, 1.77, and 1.43 eV for P680, P700, and P870, respectively. In the P680/P870 models, we find that the photoexcitation leads to a π → π* transition in which the exciton is delocalized between the adjacent Chl/BChl molecules of the central pair, whereas the exciton is localized to a single chlorophyll molecule in the P700 model. Consistent with experiments, the calculated excitonic splittings between the central pairs of P680, P700, and P870 models are 80, 200, and 400 cm–1, respectively. The calculations show that the electron affinity of the radical cation of the P680 model is 0.4 V larger than for the P870 model and 0.2 V larger than for P700. The chromophore stacking interaction is found to strongly influence the electron localization properties of the light-absorbing pigments, which may help to elucidate mechanistic details of the charge separation process in type I and type II photosystems.
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► Laplace errors for 0–0 transition energies and excited state structures are small. ► Timings for ground and excited state gradient calculations are reported. ► Applications to a ...chlorophyll and a bis(terpyridine) with 160 atoms are presented.
An implementation of analytical gradients, transition moments and excited state properties for scaled opposite-spin (SOS) CC2 and a SOS variant of the algebraic diagrammatic construction through second order ADC(2) is presented. The time-determining fifth order scaling steps in the algorithms are replaced by schemes with only fourth order scaling computational costs using a “resolution of the identity” approximation for the electron repulsion integrals and a numerical Laplace transformation of the orbital energy denominators. This leads to a significant reduction of the computational costs for geometry optimizations of large systems.
This work is an extension to the recently presented quartic scaling algorithm for SOS–CC2 energies for ground and excited states. The Laplace error for adiabatic electronic excitation energies and excited state structures is found to be very small. SOS–ADC(2) provides for adiabatic electronic excitation energies, excited state structure parameters, harmonic vibrational frequencies as well as dipole moments and transition strengths an accuracy similar to SOS–CC2. Timings for ground and excited state calculations are reported and applications to a chlorophyll molecule and a ditopic 2,2′:6′,2″-bis(terpyridine) with 160 atoms demonstrate how the new implementation extends the applicability of these methods for large systems.
This paper gives an overview of activities regarding RDM in Germany including the national political context as well as initiatives on federal state level. The knowledge about Germany's federal ...system, which also entails the autonomy of the federal states regarding the higher education system, is fundamental to understand the different approaches towards RDM in Germany. The state initiatives of Thuringia, Baden-Wuerttemberg and Hesse are described to compare them to the state initiative (Landesinitiative NFDI) of Germany's most populous state of North-Rhine Westphalia (NRW). The aim of the initiative in NRW is to initiate the collaboration between institutions, to link current RDM activities in NRW and to prepare the local institutions for the participation in a National Research Data Infrastructure (Nationale Forschungsdateninfrastruktur, NFDI).
HMGA2 is an architectonic transcription factor abundantly expressed during embryonic and fetal development and it is associated with the progression of malignant tumors. The protein harbours three ...basically charged DNA binding domains and an acidic protein binding C-terminal domain. DNA binding induces changes of DNA conformation and hence results in global overall change of gene expression patterns. Recently, using a PCR-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure two consensus sequences for HMGA2 binding have been identified.
In this investigation chromatin immunoprecipitation (ChIP) experiments and bioinformatic methods were used to analyze if these binding sequences can be verified on chromatin of living cells as well.
After quantification of HMGA2 protein in different cell lines the colon cancer derived cell line HCT116 was chosen for further ChIP experiments because of its 3.4-fold higher HMGA2 protein level. 49 DNA fragments were obtained by ChIP. These fragments containing HMGA2 binding sites have been analyzed for their AT-content, location in the human genome and similarities to sequences generated by a SELEX study. The sequences show a significantly higher AT-content than the average of the human genome. The artificially generated SELEX sequences and short BLAST alignments (11 and 12 bp) of the ChIP fragments from living cells show similarities in their organization. The flanking regions are AT-rich, whereas a lower conservation is present in the center of the sequences.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Background: Recently, it has become obvious that the HMGB1 protein can act as a proinflammatory and proangiogenic mediator
when actively secreted by macrophages or passively released from necrotic ...cells playing an important role in the pathogenesis
of several diseases including cancer. Materials and Methods: The absolute and relative amount of HMGB1 was measured with an
ELISA in different effusion types. Results: The amount of HMGB1 protein in the samples differed between 0.0004% and 0.0025%
of the total sample protein. The mean values of transudates were significantly (p<0.001) lower than the mean values of exudates.
Conclusion: HMGB1, a so-called danger signalling protein, was found to be highly expressed in human pleural and peritoneal
effusions due to cancer and inflammation. Compared to transudates the average level of HMGB1 was significantly higher in exudates.
These results underline the characteristics of HMGB1 as a possible target for treatment in advanced cancer as well.
Die GSS bietet ihren Mitgliedern eine exzellente Infrastruktur für ihre Forschung im Promotionsprozess und ein internationales und interdisziplinäres Ausbildungsprogramm auf dem Gebiet der ...Solvatationswissenschaft. Mit 30 % internationalen Mitgliedern und einem Ausbildungsprogramm auf Englisch wird Internationalität und interkulturelle Vielfalt aktiv gelebt. Die GSS‐Mitglieder, die in unterschiedlichen Gebieten der Chemie, Physik, Biologie und der Verfahrenstechnik arbeiten, tauschen sich auf regelmäßigen Veranstaltungen und Workshops aus und lernen dabei von Beginn der Promotion an eine interdisziplinäre Denkweise kennen.
The GSS offers its members an excellent infrastructure for their PhD research and a unique, international and interdisciplinary training program in the area of Solvation Science. With 30% international members and a training program in English internationality and intercultural diversity is part of everyday life in the GSS. The about 100 GSS members, working in the fields of chemistry, physics, biology and engineering, discuss their work during regular events and workshops and thereby learn to think interdisciplinary from the beginning of their PhD thesis.
Wie wird der wissenschaftliche Nachwuchs heutzutage ausgebildet? Wie können die Randbedingungen einer Promotion den veränderten Anforderungen von Hochschule und Gesellschaft gerecht werden? Welche Kompetenzen und Fähigkeiten sollen dabei erlernt und wie können diese vermittelt werden? Solche und ähnliche Fragen werden im Bereich der Hochschulpolitik zunehmend diskutiert. Eine Antwort darauf versucht die Ausbildung von Doktoranden in Graduiertenschulen zu geben. Welche Ziele die Doktorandenausbildung im Exzellenzcluster RESOLV verfolgt und wie diese umgesetzt werden, wird hier dargestellt.
Abstract
Die GSS bietet ihren Mitgliedern eine exzellente Infrastruktur für ihre Forschung im Promotionsprozess und ein internationales und interdisziplinäres Ausbildungsprogramm auf dem Gebiet der ...Solvatationswissenschaft. Mit 30 % internationalen Mitgliedern und einem Ausbildungsprogramm auf Englisch wird Internationalität und interkulturelle Vielfalt aktiv gelebt. Die GSS‐Mitglieder, die in unterschiedlichen Gebieten der Chemie, Physik, Biologie und der Verfahrenstechnik arbeiten, tauschen sich auf regelmäßigen Veranstaltungen und Workshops aus und lernen dabei von Beginn der Promotion an eine interdisziplinäre Denkweise kennen.
The GSS offers its members an excellent infrastructure for their PhD research and a unique, international and interdisciplinary training program in the area of Solvation Science. With 30% international members and a training program in English internationality and intercultural diversity is part of everyday life in the GSS. The about 100 GSS members, working in the fields of chemistry, physics, biology and engineering, discuss their work during regular events and workshops and thereby learn to think interdisciplinary from the beginning of their PhD thesis.
Die GSS bietet ihren Mitgliedern eine exzellente Infrastruktur fur ihre Forschung im Promotionsprozess und ein internationales und interdisziplinäres Ausbildungsprogramm auf dem Gebiet der ...Solvatationswissenschaft. Mit 30 % internationalen Mitgliedern und einem Ausbildungsprogramm auf Englisch wird Internationalität und interkulturelle Vielfalt aktiv gelebt. Die GSS-Mitglieder, die in unterschiedlichen Gebieten der Chemie, Physik, Biologie und der Verfahrenstechnik arbeiten, tauschen sich auf regelmäßigen Veranstaltungen und Workshops aus und lernen dabei von Beginn der Promotion an eine interdisziplinäre Denkweise kennen. The GSS offers its members an excellent infrastructure for their PhD research and a unique, international and interdisciplinary training program in the area of Solvation Science. With 30% international members and a training program in English internationality and intercultural diversity is part of everyday life in the GSS. The about 100 GSS members, working in the fields of chemistry, physics, biology and engineering, discuss their work during regular events and workshops and thereby learn to think interdisciplinary from the beginning of their PhD thesis.
In the present study a benchmark set of medium-sized and large aromatic organic molecules with 10-78 atoms is presented. For this test set 0-0 transition energies measured in supersonic jets are ...compared to those calculated with DFT and the B3LYP functional, ADC(2), CC2 and the spin-scaled CC2 variants SOS-CC2 and SCS-CC2. Geometries of the ground and excited states have been optimized with these methods in polarized triple zeta basis sets. Zero-point vibrational corrections have been calculated with the same methods and basis sets. In addition the energies have been corrected by single point calculations with a triple zeta basis augmented with diffuse functions, aug-cc-pVTZ. The deviations of the theoretical results from experimental electronic origins, which have all been measured in the gas phase with high-resolution techniques, were evaluated. The accuracy of SOS-CC2 is comparable to that of unscaled CC2, whereas ADC(2) has slightly larger errors. The lowest errors were found for SCS-CC2. All correlated wave function methods provide significantly better results than DFT with the B3LYP functional. The effects of the energy corrections from the augmented basis set and the method-consistent calculation of the zero-point vibrational corrections are small. With this benchmark set reliable reference data for 0-0 transition energies for larger organic chromophores are available that can be used to benchmark the accuracy of other quantum chemical methods such as new DFT functionals or semi-empirical methods for excitation energies and structures and thereby augments available benchmark sets augments present benchmark sets which include mainly smaller molecules.
A new test set for 0-0 transition energies in organic molecules, consisting of 66 electronic origins taken from high-resolution measurements in supersonic jets, has been compiled and evaluated for second-order wave function methods and DFT/B3LYP.
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