Scaffold topologies. 2. Analysis of chemical databases

We have systematically enumerated graph representations of scaffold topologies for up to eight-ring molecules and four-valence atoms, thus providing coverage of the lower portion of the chemical space of small molecules (Pollock et al. J. Chem. Inf. Model., this issue). Here, we examine scaffold topology distributions for several databases: ChemNavigator and PubChem for commercially available chemicals, the Dictionary of Natural Products, a set of 2742 launched drugs, WOMBAT, a database of medicinal chemistry compounds, and two subsets of PubChem, "actives" and DSSTox comprising toxic substances. We also examined a virtual database of exhaustively enumerated small organic molecules, GDB (Fink et al. Angew. Chem., Int. Ed. 2005, 44, 1504-1508), and we contrast the scaffold topology distribution from these collections to the complete coverage of up to eight-ring molecules. For reasons related, perhaps, to synthetic accessibility and complexity, scaffolds exhibiting six rings or more are poorly represented. Among all collections examined, PubChem has the greatest scaffold topological diversity, whereas GDB is the most limited. More than 50% of all entries (13 000 000+ actual and 13 000 000+ virtual compounds) exhibit only eight distinct topologies, one of which is the nonscaffold topology that represents all treelike structures. However, most of the topologies are represented by a single or very small number of examples. Within topologies, we found that three-way scaffold connections (3-nodes) are much more frequent compared to four-way (4-node) connections. Fused rings have a slightly higher frequency in biologically oriented databases. Scaffold topologies can be the first step toward an efficient coarse-grained classification scheme of the molecules found in chemical databases.     

使用色散可调啁啾光纤光栅在常规单模光纤中实现超过100km,10Gb/s的转输 *

报道了用简单的应力方法使均匀光栅成为线性啁啾光纤光栅的技术 ,并推导出了相应理论 ,发现最大色散补偿带宽与色散的乘积近似为常数 .在常规单模光纤G652,10Gb/s系统中实现超过100km的色散补偿 .     

A Class of Integrable Flows on the Space of Symmetric Matrices

For a given skew symmetric real n × n matrix N, the bracket [X, Y] _N = XNY − YNX defines a Lie algebra structure on the space Sym(n, N) of symmetric n × n real matrices and hence a corresponding Lie-Poisson structure. The purpose of this paper is to investigate the geometry, integrability, and linearizability of the Hamiltonian system , or equivalently in Lax form, the equation on this space along with a detailed study of the Poisson geometry itself. If N has distinct eigenvalues, it is proved that this system is integrable on a generic symplectic leaf of the Lie-Poisson structure of Sym(n, N). This is established by finding another compatible Poisson structure. If N is invertible, several remarkable identifications can be implemented. First, (Sym(n, N), [·, ·]) is Lie algebra isomorphic with the symplectic Lie algebra associated to the symplectic form on given by N ⁻¹. In this case, the system is the reduction of the geodesic flow of the left invariant Frobenius metric on the underlying symplectic group Sp(n, N ⁻¹). Second, the trace of the product of matrices defines a non-invariant non-degenerate inner product on Sym(n, N) which identifies it with its dual. Therefore Sym(n, N) carries a natural Lie-Poisson structure as well as a compatible “frozen bracket” structure. The Poisson diffeomorphism from Sym(n, N) to maps our system to a Mischenko-Fomenko system, thereby providing another proof of its integrability if N is invertible with distinct eigenvalues. Third, there is a second ad-invariant inner product on Sym(n, N); using it to identify Sym(n, N) with itself and composing it with the dual of the Lie algebra isomorphism with , our system becomes a Mischenko- Fomenko system directly on Sym(n, N). If N is invertible and has distinct eigenvalues, it is shown that this geodesic flow on Sym(n, N) is linearized on the Prym subvariety of the Jacobian of the spectral curve associated to a Lax pair formulation with parameter of the system. If, on the other hand, N has nullity one and distinct eigenvalues, in spite of the fact that the system is completely integrable, it is shown that the flow does not linearize on the Jacobian of the spectral curve. Research partially supported by NSF grants CMS-0408542 and DMS-0604307. Research partially supported by the Swiss SCOPES grant IB7320-110721/1, 2005-2008, and MEdC Contract 2-CEx 06-11-22/25.07.2006. Research partially supported by the California Institute of Technology and NSF-ITR Grant ACI-0204932. Research partially supported by the Swiss NSF and the Swiss SCOPES grant IB7320-110721/1.     

Synthesis and structural characterization of amino-functionalized polysaccharides

A variety of carbohydrates, in particular polysaccharides can be subjected to chemical modification to obtain derivatives with amphiphilic properties, which enable biochemical or biological reactions at the polymer surface. In the present work, a polydisperse maltodextrin mixture of average molecular weight 3000 was coupled with 1,6-hexamethylenediamine (HMD) via reductive amination reaction. Resulting products were characterized by thermal analysis and positive nanoelectrospray quadrupole time-of-flight (Q-TOF) mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Both thermal analysis and MS screening confirmed the formation of the HMD-polysaccharide coupling products. Moreover, HMD-linked polysaccharide chains containing 2 to 26 glucose building blocks were identified by nanoESI Q-TOF MS. MS/MS fragmentation using collision-induced dissociation (CID) at low ion acceleration energies provided strong evidence for HMD-maltodextrin linkage formation and the set of sequence ions diagnostic for the composition and structure of a HMD-linked chain containing 18 glucose residues.      

三维光存储中折射率失配引起的球差补偿

为实现三维光存储中折射率失配引起的球差补偿,建立了光学存储系统模型,获得了折射率失配引起的波前偏差函数与存储深度的表达式.采用泽尔尼克循环多项式对波前偏差函数进行补偿展开.在双光子荧光和单光子共焦荧光读出方式下,均可获得读出荧光强度与存储深度的关系:在折射率失配引起的球差未得到补偿矫正的情况下,存储深度在200 μm左右读出荧光强度基本上下降为零;当折射率失配引起的初级球差被补偿矫正后,读出荧光强度随存储深度的下降得到较好改善;当折射率失配引起的二级球差被补偿矫正后,存储深度在1 mm内存储点强度随深度基本上没有明显地变化.并且对像差补偿方法进行了具体地分析.     

Exact geometric theory of dendronized polymer dynamics

Dendronized polymers consist of an elastic backbone with a set of iterated branch structures (dendrimers) attached at every base point of the backbone. The conformations of such molecules depend on the elastic deformation of the backbone and the branches, as well as on nonlocal (e.g., electrostatic, or Lennard–Jones) interactions between the elementary molecular units comprising the dendrimers and/or backbone. We develop a geometrically exact theory for the dynamics of such polymers, taking into account both local (elastic) and nonlocal interactions. The theory is based on applying symmetry reduction of Hamilton?s principle for a Lagrangian defined on the tangent bundle of iterated semidirect products of the rotation groups that represent the relative orientations of the dendritic branches of the polymer. The resulting symmetry-reduced equations of motion are written in conservative form.