The structure factor for liquid lead

Abstract

The structure factor for liquid lead at the temperatures 613 K, 643 K, 863 K and 1163 K are measured by neutron diffraction. Extensive comparisons to earlier measurements are made as well as comparisons to different hard-core models.     

Configurational and Conformational Properties of 1,3,7,9-Tetraphospha-Cyclododeca-1,2,7,8-tetraene: An Ab Initio Study and NBO Analysis

An investigation employing the ab initio molecular orbital (MO) and density functional theory (DFT) methods to calculate structural optimization and conformational interconversion pathways for the two diastereoisomeric forms, (±) and meso configurations of 1,3,7,9-tetraphospha-cyclododeca-1,2,7,8-tetraene (1) was undertaken. Two axial symmetrical conformations are found for (±)-1 configuration. (±)-1-TB axial symmetrical form is found to be about 0.35 and 0.99 kcal mol^?1 more stable than (±)-1-Crown axial symmetrical conformation, as calculated by HF/6-31G*//HF/6-31G* and B3LYP/6-31G*//HF/6-31G* levels of theory, respectively. The unsymmetrical meso-1-TBCC form is found to be the most stable geometry, among the various conformations of meso-1 configuration. HF/6-31G*//HF/6-31G* and B3LYP/6-31G*//HF/6-31G* results showed that between the two most stable conformations of (±) and meso configurations, (±)-1-TB is more stable than meso-1-TBCC by about 3.35 and 2.43 kcal mol^?1, respectively. In addition, MP2/6-31G* and B3LYP/6-311+G** results showed that the (±)-1-TB form is about 1.10 and 2.36 kcal mol^?1 more stable than the meso-1-TBCC form. Further, NBO results revealed that in the most stable form of meso configuration (meso-1-TBCC), the sum of the π* allenic antibonding orbital occupancies (Σ π *_occupancy) is greater than dl configuration ((±)-1-TB). Also, NBO results indicated that in the (±)-1-TB conformer, the sum of σ and π allenic moieties bonding orbital deviations (Σ σ _dev+Σ π _dev) from their normal values, is lower than in the meso-1-TBCC form.     

PSEUDOHALOGEN CHEMISTRY. PART IV. HETEROLYTIC ADDITION OF THIOCYANOGEN TO ALKENES

Abstract

Thiocyanogen reacts slowly with alkenes, in the presence of a radical inhibitor in benzene or acetic acid in the dark at 25°, to yield α,β-dithiocyanates, α-isothiocyanates-β-thiocyanates and, in acetic acid, α-acetoxy-β-thiocyanates in varying proportions. The additions to alkyl alkenes are trans-stereospecific, and, in the case of the α-isothiocyanato-β-thiocyanates, non-regiospecific. The additions to aryl alkenes are trans-stereoselective and regiospecific, yielding the Markownikov-orientated α-isothiocyanato-β-thiocyanates. A heterolytic mechanism involving a two-step, kinetically controlled addition, with the formation of a cyano-sulfonium ion intermediate, e.g., 35, in the case of alkyl alkenes and an open carbonium ion, e.g., 36, in the case of aryl alkenes, is suggested. The diothiocyanate: isothiocyanato-thiocyanate ratios are discussed in terms of kinetic and steric control of reaction.     

AB INITIO MOLECULAR ORBITAL STUDY OF 1,2-DITHIANE AND 1,2,4,5-TETRATHIANE

Ab initio calculations at HF/6-31+G? level of theory for geometry optimization, and MP2/6-31+G?//HF/6-31+G? and B3LYP/6-31+G?//HF/6-31+G? levels for a single-point total energy calculation, are reported for the chair and twist conformations of 1,2-dithiane (1), 3,3,6,6-tetramethyl-1,2-dithiane (2), 1,2,4,5-tetrathiane (3), and 3,3,6,6-tetramethyl-1,2,4,5-tetrathiane (4). The C₂ symmetric chair conformations of 1 and 2 are calculated to be 21.9 and 8.6 kJ mol^?1 more stable than the corresponding twist forms. The calculated energy barriers for chair-to-twist processes in 1 and 2 are 56.3 and 72.8 kJ mol^?1, respectively. The C_2h symmetric chair conformation of 3 is 10.7 kJ mol^?1 more stable than the twist form. Interconversion of these forms takes place via a C₂ symmetric transition state, which is 67.5 kJ mol^?1 less stable than 3-Chair. The D₂ symmetric twist-boat conformation of 4 is calculated to be 4.0 kJ mol^?1 more stable than the C_2h symmetric chair form. The calculated strain energy for twist to chair process is 61.1 kJ mol^?1.     

Ab Initio Study of Conformational Properties of Heteroatom-Containing 1,2-Bisketene Analogues

Abstract

Minimum-energy and transition-state geometries of 4-oxobuta-1,3-diene-1-thione, buta-1,3-diene-1,4-dithione, 4-selenoxobuta-1,3-diene-1-thione, 4-selenoxobuta-1,3-diene-1-one, and buta-1,3-diene-1,4-diselenone were calculated using HF, B3LYP, and MP2 levels of theory and 6–31 + G* basis set by rotation around the related ?C?C? single bonds. In all of the above-mentioned molecules, the s-trans conformation was obtained as the most stable conformer with the 180° dihedral angle. In buta-1,3-diene-1,4-dithione, 4-selenoxobuta-1,3-diene-1-thione, and buta-1,3-diene-1,4-diselenone, the s-cis form of these compounds corresponded to the other energy-minimum geometry. Their skew geometries, with torsional angles approximately 100°, were a transition state for conformational interconversion between the two global minima forms. In 4-oxobuta-1,3-diene-1-thione and 4-selenoxobuta-1,3-diene-1-one, geometries with the C?C?C?C dihedral angles about 51 and 43° (respectively) were attributed to the second energy-minimum geometry. Transition-state structures from both molecules were found in the torsional angles at about 0 and 100°.

Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file.

GRAPHICAL ABSTRACT     

Supramolecular heterogeneity in β-turn forming synthetic tripeptides nucleated by isomers of fluorinated phenylalanine and aib as corner residues

The influences of fluorines in chemistry have emerged as a breakthrough in various arenas of bio-organic and medicinal chemistry. But its incorporation in β-turn design and its implications for supramolecular chemistry remains in a rudimentary stage. Inspired by the diversity displayed by the isomers of mono-fluorinated phenylalanine in biological sciences, here our effort is to modulate the solid state conformational analysis of three terminally protected synthetic tripeptides Boc-(Y)-F-Phe-Aib-Xaa-OMe, where (Y is (2)-F-Phe, Xaa; Leu in peptide I, (3)-F-Phe, Xaa; Leu in peptide II and (4)-F-Phe, Xaa; Ile in peptide III). Interestingly, all the three peptides display a conformational preference for β-turns, stabilized by 4→1 intramolecular hydrogen bonding. Our investigation further demonstrates that mere interchange of positions of fluorines in mono-fluorinated phenylalanine in peptides I–III introduces significant diversity in supramolecular chemistry. X-ray crystallography sheds some light at atomic resolution. Furthermore, this supramolecular heterogeneous behavior is evident from the morphologies obtained from the materials of all the three peptides grown from acetone to petroleum ether solution, studied by field emission scanning electron microscopy. Thus, these monofluorinated peptides I–III may serve as prominent candidates in understanding the structure and function of misfolded disease causing peptides like prion and Alzheimer's amyloid.     

Structural Transformation of Bovine Serum Albumin Induced by Dimethyl Sulfoxide and Probed by Fluorescence Correlation Spectroscopy and Additional Methods

Determining the structure of a protein and its transformation under different conditions is key to understanding its activity. The structural stability and activity of proteins in aqueous–organic solvent mixtures, which is an intriguing topic of research in biochemistry, is dependent on the nature of the protein and the properties of the medium. Herein, the effect of a commonly used cosolvent, dimethyl sulfoxide (DMSO), on the structure and conformational dynamics of bovine serum albumin (BSA) protein is studied by fluorescence correlation spectroscopy (FCS) measurements on fluorescein isothiocyanate (FITC)‐labeled BSA. The FCS study reveals a change of the hydrodynamic radius of BSA from 3.7 nm in the native state to 7.0 nm in the presence of 40 % DMSO, which suggests complete unfolding of the protein under these conditions. Fluorescence self‐quenching of FITC has been exploited to understand the conformational dynamics of BSA. The time constant of the conformational dynamics of BSA is found to change from 35 μs in its native state to 50 μs as the protein unfolds with increasing DMSO concentration. The FCS results are corroborated by the near‐UV circular dichroism spectra of the protein, which suggest a loss of its tertiary structure with increasing concentration of DMSO. The intrinsic fluorescence of BSA and the fluorescence response of 1‐anilinonaphthalene‐8‐sulfonic acid, used as a probe molecule, provide information that is consistent with the FCS measurements, except that aggregation of BSA is observed in the presence of 40 % DMSO in the ensemble measurements.     

Sterically congested macrobicycles with heteroatomic bridgehead functionality

A series of cyclophanes composed of two triarylelement caps linked by two-atom bridges has been synthesized. The bridgehead functional groups include phosphines in combination with amines, hydrosilanes, methylsilanes, and ethoxysilanes. Computational studies accurately predicted that when the bridgehead substituents are small (lone pairs or protons), an in_,in bridgehead stereochemistry is strongly favored, but larger bridgehead substituents favor the formations of in_,out stereoisomers. The X-ray structures, spectra, and reactivity of these compounds are discussed, as well as the resolution of one of the cyclophanes into pure enantiomers.     

FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm

The accurate prediction of protein–ligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible protein–ligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross‐docking experiments of 74 protein–ligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland‐crossdock‐set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross‐docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm‐based algorithms in dealing with highly flexible docking problems. © 2012 Wiley Periodicals, Inc.     

Batch tautomer generation with MolTPC

Besides all their conformational degrees of freedom, drug‐like molecules and natural products often also undergo tautomeric interconversions. Compared to the huge efforts made in experimental investigation of tautomerism, open and free algorithmic solutions for prototropic tautomer generation are surprisingly rare. The few freely available software packages limit their output to a subset of the possible configurational space by sometimes unwanted prior assumptions and complete neglection of ring‐chain tautomerism. Here, we describe an adjustable fully automatic tautomer enumeration approach, which is freely available and also incorporates the detection of ring‐chain variants. The algorithm is implemented in the MolTPC framework and accessible on SourceForge. © 2013 Wiley Periodicals, Inc.