On the perception of molecules from 3D atomic coordinates

A method is presented for perceiving chemical types of atoms in molecules given 3D atomic coordinates and element identities. The method assigns hybridizations, bond orders, and formal charges for structures whether hydrogen atoms are present. The Maximum Weighted Matching algorithm for nonbipartite graphs is used to assign bond orders with weights derived from statistics of a large collection of organic molecules. Results form tests on a collection of functional groups, heterocycles, entries from the Protein Data Bank, and Cambridge Structural Database as well as a comparison to other methods, are presented and discussed.     

Pd2L2 metallacycles as molecular containers for small molecules

M(2)L(2) type metallacyclic complexes, [Pd(2)(L1)(2)Cl(4)]·1.5CH(2)Cl(2) (1), [Pd(2)(L1)(2)Cl(4)]·2CHCl(3) (2), [Pd(2)(L2)(2)Cl(4)]·2CH(2)Cl(2)·2CH(3)CN (3), [Pd(2)(L2)(2)Cl(4)]·2CHCl(3)·2CH(3)CN (4) and [Pd(2)(L3)(2)Cl(4)]·CH(2)Cl(2)·2CH(3)CN (5), have been prepared from three semi-rigid benzimidazol or benzotriazol ligands, 1,4-bis(benzimidazol-1-ylmethyl)-2,3,5,6-tetramethylbenzene (L1), 1,4-bis(5,6-dimethylbenzimidazol-1-ylmethyl)-2,3,5,6-tetramethylbenzene (L2) and 1,4-bis(benzotriazol-1-ylmethyl)-2,3,5,6-tetramethylbenzene (L3). All the complexes were structurally characterized by single-crystal X-ray diffraction and the phase purity was confirmed by powder X-ray diffraction (PXRD) measurements. The solution structure of representative complex 1 was studied by (1)H NMR titration and ESI mass spectroscopy. The thermal stability and guest-exchange properties of 1, 3 and 4 were investigated, revealing that the Pd(2)L(2) metallacycles can act as a selective receptor for CH(2)Cl(2) or CHCl(3) guest molecules. The catalytic activity of 1 in Suzuki-Miyaura coupling reaction was also studied and 1 could be recycled at least 5 times under heterogeneous conditions, indicative of a potential self-supported catalyst.     

Natural molecular shells as open subsystems of small molecules

We compare the first few natural molecular shells of several small molecules to the corresponding “restricted Hartree‐Fock,” “second‐order Møller‐Plesset,” and “local density approximation” molecular shells. Occupation probabilities of each molecular shell are computed ab initio, especially the single‐occupation and double‐occupation probabilities, that is, the probabilities that the molecular shell is occupied by exactly one electron or by exactly two electrons. We observe that among corresponding molecular shells, the natural molecular shell has the least single‐occupation probability and the greatest double‐occupation probability. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Polyoxolenes may provide a tool for designing paramagnetic molecules with predetermined spin topologies

The development of the chemistry of transition metal complexes formed by o-semiquinonato radical ligands has provided a useful topic for learning how to use chemical methods for obtaining systems with predetermined magnetic properties. Similar complexes can be used as building blocks for assembling magnetically coupled networks with multidimensional extended topologies. The examples reported here show how an appropriate strategy in designing linked semiquinonates can be used to fix the magnetic properties of a collection of paramagnetic centres. To cite this article: A. Bencini et al., C. R. Chimie 6 (2003).     

A general treatment of vibration-rotation coordinates for triatomic molecules

An exact, within the Born–Oppenheimer approximation, body-fixed Hamiltonian for the nuclear motions of a triatomic system is presented. This Hamiltonian is expressed in terms of two arbitrarily defined internal distances and the angle between them. The body-fixed axis system is related to these coordinates in a general fashion. Problems with singularities and the domain of the Hamiltonian are discussed using specific examples of axis embedding. A number of commonly used coordinate systems including Jacobi, bond-length-bond-angle, and Radau coordinates are special cases of this Hamiltonian. Sample calculations on the H₂S molecule are presented using all these and other coordinate systems. The possibility of using this Hamiltonian for reactive scattering calculations is also discussed.     

RGB small molecules based on a bipolar molecular design for highly efficient solution-processed single-layer OLEDs

In this paper, we describe a bipolar molecular design for small molecule solution-processed organic light emitting diodes (OLEDs). Combining the rigidity of the conjugated emissive cores and the flexibility of the peripheral alkyl-linked carbazole groups, two series of highly efficient bipolar RGB (red, green, blue) emitters have been synthesized and characterized. The emissive cores are composed of electron-withdrawing groups; the carbazole groups endow the materials electron-donating units. Such bipolar structures are advantageous for the carrier injection and balance. Four peripheral carbazole groups are introduced in T-series materials (TCDqC, TCSoC, TCBzC, TCNzC), and another four in O-series materials (OCDqC, OCSoC, OCBzC, OCNzC). With the single-layer device configuration of ITO/PEDOT:PSS/emitting layer/CsF/Al, two green devices exhibited excellent performance with a maximum luminescence efficiency of over 6.4 cd A(-1), and a high maximum luminance of more than 6700 cd m(-2). In addition, compared with the T-series, the luminescence efficiency of blue and red devices based on O-series materials increased from 1.6 to 2.8 cd A(-1) and 0.2 to 1.3 cd A(-1), respectively. To our knowledge, the performance of the blue device based on OCSoC is among the best of the blue small-molecule solution-processed single-layer devices reported so far.     

Angular distribution of photoelectrons in small molecules: a molecular quantum defect calculation

The molecular quantum defect orbital (MQDO) method, previously used in the determination of molecular photoionization cross sections, is applied here to calculate the angular distribution of photoelectrons arising from the molecular photoionization. Calculations are performed for the ionization from outer valence orbitals of HF, H(2)O, NH(3), N(2)O, and H(2)CO molecules. The results are compared with previous measurements and with theoretical curves found in the literature. Profiles of the angular distribution parameter as a function of photoelectron energy covering a range from the photoionization threshold to 120 eV are presented for the above molecules. The energy dependence of the angular distributions predicted by the MQDO calculations agrees fairly well with predictions from more sophisticated theories and with observed results.     

Prediction of vapour pressure using descriptors derived from molecular dynamics

Vapour pressures of organic materials can be predicted to high levels of accuracy using cohesive energies and solubility parameters derived from molecular dynamics simulations that use good forcefields. It is found that over 90% of the correlation with vapour pressure is accounted for by a single cross term involving the product of either the molecular weight or molar volume of a molecule and its cohesive energy density.