A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems

The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.     

Charged particle multiplicity distributions ine + e − annihilation at 29 GeV: a comparison with hadronic data

The charged particle multiplicity distributions for two-jet events ine ⁺ e ^? annihilation at 29 GeV have been measured using the High Resolution Spectrometer at PEP. A Poisson distribution describes the data for both the complete event and for the single jets. In addition, no correlation is observed between the multiplicities in the two jets of an event. For fixed values of the prong number of the complete event, the multiplicity sharing between the two jets is in good agreement with a binomial distribution. The rapidity gap distribution is exponential with a slope equal to the mean rapidity density. These observations, which are consistent with a picture of independent emission of single particles, are contrasted to the results from soft hadronic collisions and conclusions are drawn about the nature of clusters.     

S-wave structure in the Kπ system

We have analysed the Kπ spectrum (4 827 events) of the reaction K⁺n→K⁺π^?p at 9 GeV/c and find evidence of a broad S-wave enhancement which may be interpreted as a resonance. For production of Kπ masses above 890 GeV/c², we have assumed the dominance of pion exchange.     

Inhibitors of Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1)

FAH domain containing protein 1 (FAHD1) acts as oxaloacetate decarboxylase in mitochondria, contributing to the regulation of the tricarboxylic acid cycle. Guided by a high-resolution X-ray structure of FAHD1 liganded by oxalate, the enzymatic mechanism of substrate processing is analyzed in detail. Taking the chemical features of the FAHD1 substrate oxaloacetate into account, the potential inhibitor structures are deduced. The synthesis of drug-like scaffolds afforded first-generation FAHD1-inhibitors with activities in the low micromolar IC₅₀ range. The investigations disclosed structures competing with the substrate for binding to the metal cofactor, as well as scaffolds, which may have a novel binding mode to FAHD1.