Combining Bayes Classification and Point Group Symmetry under Boolean Framework for Enhanced Protein Quaternary Structure Inference

Our ability to infer the protein quaternary structure automatically from atom and lattice information is inadequate, especially for weak complexes, and heteromeric quaternary structures. Several approaches exist, but they have limited performance. Here, we present a new scheme to infer protein quaternary structure from lattice and protein information, with all-around coverage for strong, weak and very weak affinity homomeric and heteromeric complexes. The scheme combines naive Bayes classifier and point group symmetry under Boolean framework to detect quaternary structures in crystal lattice. It consistently produces >= 90% coverage across diverse benchmarking data sets, including a notably superior 95% coverage for recognition heteromeric complexes, compared with 53% on the same data set by current state-of-the-art method. The detailed study of a limited number of prediction-failed cases offers interesting insights into the intriguing nature of protein contacts in lattice. The findings have implications for accurate inference of quaternary states of proteins, especially weak affinity complexes.

Synthon polymorphism and pseudopolymorphism in co-crystals. The 4,4 `-bipyridine-4-hydroxybenzoic acid structural landscape

Co-crystals of 4,4'-bipyridine and 4-hydroxybenzoic acid (1 : 2) show synthon polymorphism with the former being more stable. A 2 : 1 co-crystal is pseudopolymorphic within the same structural landscape with the structural roles of the two bipyridine N-atoms being distinct, as evidenced by mimicry by 4-phenylpyridine.

Symmetry-breaking transition in a two-level system coupled to an Ohmic bath: A squeezed-state approach

Displaced squeezed states are proposed as variational ground states for phonons (Bose fields) coupled to two-level systems (spin systems). We have investigated the zero-temperature phase diagram for the localization-delocalization transition of a tunneling particle interacting with an Ohmic heat bath. Our results are compared with known existing approximate treatments. A modified phase diagram using the displaced squeezed state is presented.

Synthesis based on cyclohexadienes: Part 10 synthesis of 5,5-dimethyl-7-methoxy-4-oxatricyclo[4.3.1.0]decan-2-ones

Synthesis of 5, 5-dimethyl- 7-methoxy-4 -oxatricyclo[4,3,1,0(3,7)]- decan-2-one 3a, a novel heterocyclic ring system present in morellin 1, and its 3-substituted derivatives 3b-e, is described from the Diels-Alder adducts 7, available from 1-methoxycyclohexa-1,4-dienes 4. Two routes, which involved the halocyclisation and the oxidative addition, were investigated for the conversion of the adducts 7 into 3. While the halocyclisation method resulted in mixtures, excellent yields of the target molecule were obtained by the second method. Solvolysis of the bromoether 9 resulted in a mixture of rearranged products 10, 13, 15 and 16.

Synthesis of 5,5-Dimethyl-7-methoxy 4-oxatricyclo [4,3,1,03,7]decan-2-ones

Two new synthetic routes for the preparation of the title compound and its 3-substituted derivatives, a novel ring system present in morellin and other related natural products, are reported from the readily available dihydroanisoles.

Synthesis, Crystal Structure, and Magnetic Properties of a Ferromagnetically Coupled Angular Trinuclear Copper(11) Complex [Cu3(02CMe)4(bpy)s(HzO)](PF)62

The synthesis, X-ray crystal structure, and magnetic properties of an angular trinuclear copper(II) complex [Cu3(O2CMC)4(bpy)3(H2O)](PF6)2 (1), obtained from a reaction of Cu2(O2CMe)4(H2O)2 With 2,2'-bipyridine (bpy) and NH4PF6 in ethanol, are reported. Complex 1 crystallizes in triclinic space group P1BAR with a = 11.529(1) angstrom, b = 12.121(2) angstrom, c = 17.153(2) angstrom, alpha = 82.01(1)-degrees, beta = 79.42(1)-degrees, gamma = 89.62(1)-degrees, and Z = 2. A total of 6928 data with I > 2.5sigma(I) were refined to R = 0.0441 and R(w) = 0.0557. The structure consists of a trinuclear core bridged by four acetate ligands showing different bonding modes. The coordination geometry at each copper is distorted square-pyramidal with a CuN2O2...O chromophore. The Cu...Cu distances are 3.198(1) angstrom, 4.568(1) angstrom, and 6.277(1) angstrom. There are two monoatomic acetate bridges showing Cu-O-Cu angles of 93.1(1) and 97.5(1)-degrees. Magnetic studies in the temperature range 39-297 K show the presence of a strong ferromagnetically coupled dicopper(II) unit (2J = +158 cm-1) and an essentially isolated copper(II) center (2J' = -0.4 cm-1) in 1. The EPR spectra display an axial spectrum giving g(parallel-to) = 2.28 (A(parallel-to) = 160 X 10(-4) cm-1) and g(perpendicular-to) = 2.06 (A(perpendicular-to) = 12 X 10(-4) cm-1) for the normal copper and two intense isotropic signals with g values 2.70 and 1.74 for the strongly coupled copper pair. The structural features of 1 compare well with the first generation models for ascorbate oxidase.

A Crystallization Technique For the Enantiomer Resolution of Conglomerates- (+/-)-4-Methoxyphenyl 1-Phenylethyl Ketone

The sorting of crystals of (+/-)-4-methoxyphenyl 1-phenylethyl ketone into its enantiomers is facilitated by crystallisation in a cellular grid made of filter paper.

Levitation Effect: Role of Symmetry and Dependence of Diffusivity on the Bond Length of Homonuclear and Heteronuclear Diatomic Species

Molecular dynamics investigation of model diatomic species confined to the alpha-cages of zeolite NaY is reported. The dependence of self-diffusivity on the bond length of the diatomic species has been investigated. Three different sets of runs have been carried out. In the first set, the two atoms of the diatomic molecule interact with the zeolite atoms with equal strength (example, O-2, the symmetric case). In the second and third sets which correspond to asymmetric cases, the two atoms of the diatomic molecule interact with unequal strengths (example, CO). The result for the symmetric case exhibits a well-defined maximum in self-diffusivity for an intermediate bond length. In contrast to this, the intermediate asymmetry leads to a less pronounced maximum. For the large asymmetric case, the maximum is completely absent. These findings are analyzed by computing a number of related properties. These results provide a direct confirmation at the microscopic level of the suggestion by Derouane that the supermobility observed experimentally by Kemball has its origin in the mutual cancellation of forces. The maximum in diffusivity from molecular dynamics is seen at the value predicted by the levitation effect. Further, these findings suggest a role for symmetry in the existence of a diffusivity maximum as a function of diameter of the diffusant often referred to as the levitation effect. The nature of the required symmetry for the existence of anomalous diffusivity is interaction symmetry which is different from that normally encountered in crystallography.

Enantioselective Synthesis of Possible Diastereomers of Heptadeca-1-ene-4,6-diyne-3,8,9,10-tetrol; Putative Structure of a Conjugated Diyne Natural Product Isolated from Hydrocotyle leucocephala

Enantioselective synthesis of possible diastereomers of heptadeca-1-ene-4,6-diyne-3,8,9,10-tetrol, a structure proposed for the natural product isolated from Hydrocotyle leucocephala is accomplished. The reported spectral data of the natural product did not match those of any of the isomers that were synthesized and established that the structure proposed for the natural product is not correct and requires revision.

Cyclization of enediyne radical cations through chemical, photochemical, and electrochemical oxidation: The role of state symmetry

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4-Hydroxy-6-(4-methoxyphenyl)-4-phenyl-1,3-diazinane-2-thione

In the title compound, C17H18N2O2S, the 1,3-diazinane-2-thione ring system is not coplanar with the benzene ring and methoxyphenyl ring system, the dihedral angle between the planes being 65.58 (13) and 89.18 (10)degrees, respectively. The crystal structure is characterized by intermolecular O-H...S, N-H...S, N-H...O and C-H...S hydrogen bonding.

Enantioselective synthesis of both (+)- and (-)-derivatives of bicyclo[4.3.0]nonan-8-one and 3,8-diones from R-carvone

Enantioselective synthesis of both the enantiomeric forms of the hydrindane derivatives mentioned in the title, potential chiral precursors in terpenoid synthesis, starling from R-carvone employing two different cyclopentannulation methodologies is described.

Exceptionally long crystal formation from 4-(3-bromopropyloxy)salicylaldehyde. X-ray crystallographic investigation

Unusually long (>14 cm) crystalline needles grow from 4-(3-bromopropyloxy)salicylaldehyde 1 presumably as a consequence of Br ... Br interactions; the powdered form of 1 shows one order of magnitude greater SHG activity realtive to urea.

Linear electro-optic effect and temperature coefficient of birefringence in 4-nitro-4script-methylbenzylidene aniline single crystals

A study of the linear electro?optic effect in single crystals of the organic compound, 4?nitro�4??methylbenzylidene aniline is reported. The reduced half?wave voltages have been found to have values 2.8, 1.3, and 1.1 kV at 632.8, 514.5, and 488.0 nm, respectively and the corresponding values of the largest linear electro?optic coefficient have been calculated. The thermal variation of the birefringence has also been investigated and the temperature variation of the refractive index difference is found to have the value, d?n/dT = 15.8 × 10?5 K?1.