Conformational variety for the ansa chain of rifamycins: Comparison of observed crystal structures and molecular dynamics simulations

The antibiotic activity (via inhibition of DNA-dependent RNA polymerase, DDRP) of rifamycins has been correlated to the conformation of the ansa chain, which can be described by means of 17 torsion angles defined along the ansa backbone. It has been shown that favourable or unfavourable conformations of the ansa chain in rifamycin crystals are generally diagnostic of activity or inactivity against isolated DDRP. The principles of structure correlation suggest that the torsional variety observed in rifamycin crystals should mimic the dynamic flexibility of the ansa chain in solution. Twenty-six crystal structures of rifamycins are grouped into two classes (active and non-active). For each class the variance of the 17 ansa backbone torsion angles is analysed. Active compounds show a well-defined common pattern, while non-active molecules are more scattered, mainly due to steric constraints forcing the molecules into unfavourable conformations. The experimental distributions of torsion angles are compared to the torsional freedom of the ansa chain simulated by molecular dynamics calculations performed at different temperatures and conditions on rifamycin S and rifamycin O, which represent a typical active and a typical sterically constrained molecule, respectively. It is shown that the torsional variety found in the crystalline state samples the dynamic behaviour of the ansa chain for active compounds. The methods of circular statistics are illustrated to describe torsion angle distributions.     

Design of a two-element airfoil in a range of angles of attack

A numerical-analytical solution of an inverse boundary-value problem of aerohydrodynamics is obtained for a two-element airfoil in the full formulation, based on the velocity distribution defined on the sought airfoil contours in a range of angles of attack. It is demonstrated that flow separation does not occur in the entire range considered for a specified non-separated velocity distribution on the upper surfaces at the maximum angle of attack and on the lower surface at the minimum angle of attack. An example of constructing a sectional airfoil is given; verification of the results obtained is performed with the use of the Fluent software package. __________ Translated from Prikladnaya Mekhanika i Tekhnicheskaya Fizika, Vol. 49, No. 6, pp. 107–114, November–December, 2008.     

Doublet and quartet states of Li 2 −

Electronic states of the molecular lithium anion are investigated by configuration-interaction calculations. Comparison with the analogously computed potential energy curves for the lowest singlet and triplet states of the neutral Li₂ shows that in addition to the well-known stable ground state X there also exist metastable excited states of Li ₂ ^- . Within the quartet sector, two candidates for such long-lived states are identified and their spectroscopic properties studied. Received 23 March 1999     

Synthesis and Crystal Structure of 3,6-Dimethyl- 9-（4-b rom o p h enyl）- 1,8-oxo-2,7,10-trioxanth ene

The crystal structure of the title compound (C19H13BrO5) has been determined by single-crystal X-ray diffraction. The crystal is of monoclinic,space group P21/c,with a=10.508(4),b=11.354(4),c=14.522(5),β=106.255(4)°,V=1663.4(10)3,Mr=401.20,Z=4,Dc=1.602 g/cm3,λ=0.71073,F(000)=808,μ= 2.498 mm-1,R=0.0337 and wR=0.0837 for 2200 observed reflections (I>2σ(I)). X-ray analysis reveals that the dihedral angles between planes 1 and 2,1 and 3,1 and 4,2 and 3,2 and 4,and 3 and 4 are 78.6,82.5,87.4,5.6,9.5 and 4.9°,respectively. There exists a conjugated system in the molecular structure.     

Modeling and Simulation for Urban Rail Traffic Problem Based on Cellular Automata

Based on the Nagel-Schreckenberg model, we propose a new cellular automata model to simulate the urban rail traffic flow under moving block system and present a new minimum instantaneous distance formula under pure moving block. We also analyze the characteristics of the urban rail traffic flow under the influence of train density, station dwell times, the length of train, and the train velocity. Train delays can be decreased effectively through flexible departure intervals according to the preceding train type before its departure. The results demonstrate that a suitable adjustment of the current train velocity based on the following train velocity can greatly shorten the minimum departure intervals and then increase the capacity of rail transit.     

Unique Euler angles and self‐consistent multiplication tables for double point groups

The standard Euler angle parameterization of rotations is not unique. This is a particular problem when considering spinor representations. We enlarge the domain of the Euler angles from an SO₃ covering to an SU₂ covering, 0≤α<2π, 0≤β≤π, 0≤γ<4π. With this modification we can find unique Euler angles for operations of the double groups and thus construct self‐consistent group tables for those groups. Factor systems can then be described for the projective representations. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 1–9, 1999     

Sugar Puckering Drives G-Quadruplex Refolding: Implications for V-Shaped Loops

A DNA G-quadruplex adopting a (3+1) hybrid structure was modified in two adjacent syn positions of the antiparallel strand with anti-favoring 2′-deoxy-2′-fluoro-riboguanosine (^FrG) analogues. The two substitutions promoted a structural rearrangement to a topology with the 5′-terminal G residue located in the central tetrad and the two modified residues linked by a V-shaped zero-nucleotide loop. Strikingly, whereas a sugar pucker in the preferred north domain is found for both modified nucleotides, the ^FrG analogue preceding the V-loop is forced to adopt the unfavored syn conformation in the new quadruplex fold. Apparently, a preferred C3′-endo sugar pucker within the V-loop architecture outweighs the propensity of the ^FrG analogue to adopt an anti glycosidic conformation. Refolding into a V-loop topology is likewise observed for a sequence modified at corresponding positions with two riboguanosine substitutions. In contrast, 2′-F-arabinoguanosine analogues with their favored south-east sugar conformation do not support formation of the V-loop topology. Examination of known G-quadruplexes with a V-shaped loop highlights the critical role of the sugar conformation for this distinct structural motif.     

Consistent valence force-field parameterization of bond lengths and angles with quantum chemical ab initio methods applied to some heterocyclic dopamine D3-receptor agonists

To secure a broad utilization of molecular mechanics in medicinal chemistry appropriate parameters (e.g., reference values and force constants) are required to describe correctly all possible atomic interactions. For this purpose parameters for bond lengths and bond angles were derived for some heterocyclic dopamine D₃-receptor agonists. Some new atom types were introduced and consistent valence force-field (CVFF) was supplied with several bond-stretching and angle-bending force constants as well as reference values. Representative fragments containing these missing parameters were minimized at the HF/6-31G* level of theory using Gaussian-92. After frequency calculation, corresponding force constants were extracted from the Hessian matrix. The values were then appropriately converted and scaled. Also, reference values were taken from quantum mechanically minimized structures, applying the same basis set. The transferability of the calculated force constants to CVFF was investigated using fragments with already known parameters. The quality of the extended force field was checked in comparison with “automatic parameters” and ab initio-minimized structures. Finally, the evaluated procedure was applied successfully to related structures. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 935–946, 1998     

群组决策特征根法

本文提出了一个群组决策的特征根法GEM（Groupeigenvaluemethod），它彻底克服了判断矩阵的不一致性，为决策支持系统中的专家选择开辟了新路．