A Monte Carlo Simulation of Nematic and Discotic Ordering in a Polymeric Liquid Crystal

A cyclic polymeric liquid crystal system is simulated using the Metropolis Monte Carlo method in the NVT ensemble. The polymeric system consists of mesogenic moieties attached by alkyl chain spacers to siloxane ring polymers. In the model, the mesogenic moieties are represented individually by an anisotropic Lennard-Jones potential and the polymer ring is represented solely as a constraint on the relative motions of the attached mesogens. A transition from calamitic ordering to discotic ordering is observed as the ring-mesogen bond is varied from full flexible to rigid.     

Synthesis, crystal structures and density functional theory study of dimeric copper(II) complexes of a tridentate Schiff-base ligand

Oxalate- or 4,4′-bipyridine-bridged dimeric copper(II) complexes, [Cu₂L₂(μ-ox)] (1) and [Cu₂L₂(μ-bipy)](BF₄)₂ (2) [where ox = oxalate, bipy = 4,4′-bipyridine, HL = N-(1H-pyrrol-2-ylmethylene)-2-pyridineethanamine, L⁻ = HL−H⁺], have been synthesised and characterised by elemental analysis, IR, UV-Vis and single crystal X-ray diffraction. Crystal structure determinations carried out on 1 and 2 reveal that 1 is an oxalate-bridged centrosymmetrical square pyramidal dimeric copper(II) complex while 2 is a 4,4′-bipyridine-bridged non-centrosymmetric square planar dinuclear copper(II) complex. Comparison of the optimised geometries with the corresponding crystal structures suggests that the B3LYP/LANL2DZ level can reproduce the structures of 1 and 2 on the whole. The electronic spectra of 1 and 2 predicted by B3LYP/LANL2DZ method show some blue shifts compared with their experimental data. Thermal analysis carried out on 1 shows that there is only one exothermal peak at about 260 °C and the residue is presumably Cu₂O₄N₆.     

Towards a quantitative rationalization of multicomponent glass properties by means of molecular dynamics simulations

This review summarizes the achievements obtained by making use of molecular dynamics (MD) simulations in the elucidation of the structure of multicomponent glasses exerting bioactive properties. Emphasis on critical aspects of MD simulations for oxide glasses treatment is given. The potentiality of the quantitative structure–property relationships (QSPR) analysis as a tool for interpretative and predictive purposes is highlighted.     

Molecular Dynamics Simulations of Chlorambucil/DNA Adducts. A Structural Basis for the 5′ -GNC Interstrand DNA Crosslink Formed by Nitrogen Mustards

Abstract

The alkylation of DNA by chlorambucil has been studied using a computational approach. Molecular dynamics simulations were performed on the fully solvated non-covalent complex, two monoadducts and a crosslinked diadduct of chlorambucil with the d(CGG₃G₂CGC).- d(GCG₁CCCG) duplex, in which the N7 atoms of G₁, G₂ and G₃ are potential alkylation sites. The results provide a structural basis for the preference of nitrogen mustards to crosslink DNA duplexes at a 5′-GNC site (a 1,3 crosslink, G₁ -G₃) rather than at a 5′-GC sites (a 1,2 crosslink, G₁ -G₂).

In the non-covalent complex simulation the drug reoriented from a non-interstrand crosslinking location to a position favorable for G₁ -G₃ diadduct formation. It proved possible to construct a G₁ -G₃ diadduct from a structure from the non-covalent simulation, and continue the molecular dynamics calculation without further disruption of the DNA structure. A crosslinked diadduct developed with four B_II conformations on the 3′ side of each alkylated guanine and of their respective complementary cytosine. In the first monoadduct simulation the starting point was the same DNA conformation used in the crosslinked diadduct simulation with alkylation at G₁. In this simulation the DNA deformation was reduced, with the helix returning to a more canonical form. A second monoadduct simulation was started from a canonical DNA conformation alkylated at G₃. Here, no significant motion towards a potential crosslinking conformation occurred. Collectively, the results suggest that crosslink formation is dependent upon the drug orientation prior to alkylation and the required deformation of the DNA to permit 1,3 crosslinking can largely be achieved in the non-covalent complex.     

A conformational analysis of mono and dialkyl ethers of 2,2′-dihydroxy-1,1′-binaphthalene by circular dichroism spectroscopy and cholesteric induction in nematic liquid crystals

The coupling of the analysis of the absorption and circular dichroism (CD) spectra with that of the cholesteric mesophases induced in nematic liquid crystals indicated some interesting conformational features of bridged and nonbridged mono- and dialkylethers of optically active 2,2′-dihydroxy-1,1′-binaphthalene. Bridged derivatives are characterized by relatively small dihedral angles. Simple monoalkyl ethers are characterized by larger dihedral angles but they all assume an s-cis conformation, owing to the existence of intramolecular hydrogen bonds. Nonbridged dialkylethers prefer even larger dihedral angles and, depending on the bulkiness of the alkyl groups, the s-trans conformation can be found. Interestingly, the conformation of dialkylethers is strongly dependent on the structure of the liquid crystal solvent, because the intramolecular hydrogen bond is not possible there. © 1995 Wiley-Liss, Inc.     

Ideal enantiomeric resolution by recrystallization of a racemic compound (part 4): Relationship between enantiomeric resolution phenomenon and crystal properties

A new example of a racemate showing unusual enantiomeric resolution phenomenon, in which simple recrystallization of the racemate leads to remarkable enantiomeric enrichment of either enantiomer up to 100% ee in the mother liquor, has been found. This compound is (±)-[2-[4-(3-ethoxy-2-hydroxypropoxy)phenylcarbamoyl]-ethyl]dimethylsulfonium p-nitrobenzenesulfonate [EtOCH₂CH(OH)CH₂OC₆H₄NHCOCH₂CH₂SMe₂⁺O₂NC₆H₄SO₃⁻] [(±)-SN]. By repeating recrystallization of (±)-SN and the resulting deposited crystals successively and collecting the resulting enantiomerically enriched mother liquors with the same chirality sense, highly efficient enantiomeric resolution of the racemate into its separate enantiomers has been accomplished. The relationship between the occurrence of this enantiomeric resolution phenomenon and the crystal properties has been investigated with respect to SN and its aryl- and alkylsulfonate derivatives. The mode of enantiomeric resolution of (±)-SN was similar to that of para-substituted benzenesulfonate derivatives (±)-ST (4-MeC₆H₄SO₃⁻) and (±)-SC (4-ClC₆H₄SO₃⁻) previously reported, whereas the unsubstituted derivative (±)-SB (C₆H₅SO₃⁻) and alkysulfonate derivatives (±)-SO (n-C₈H₁₇SO₃⁻) and (±)-SM (CH₃SO₃⁻) did not show such an enantiomeric resolution phenomenon. The crystalline form of the former racemates that underwent the enantiomeric resolution was racemic compounds, while the latter were mixed crystals (solid solutions) composed of the respective optical antipodes. Chirality 9:220–224, 1997. © 1997 Wiley-Liss, Inc.     

New protein fold revealed by a 1.65 A resolution crystal structure of Francisella tularensis pathogenicity island protein IglC

Francisella tularensis is a highly infectious Gram-negative intracellular pathogen that causes the fulminating disease tularemia and is considered to be a potential bioweapon. F. tularensis pathogenicity island proteins play a key role in modulating phagosome biogenesis and subsequent bacterial escape into the cytoplasm of macrophages. The 23 kDa pathogenicity island protein IglC is essential for the survival and proliferation of F. tularensis in macrophages. Seeking to gain some insight into its function, we determined the crystal structure of IglC at 1.65 A resolution. IglC adopts a beta-sandwich conformation that exhibits no similarity with any known protein structure.     

A new theory of phototropism - its regulation by a light-induced gradient of auxin-inhibiting substances

Against the wholly indirect evidence of a lateral gradient of auxin as an explanation of phototropic curvature according to the Cholodny-Went theory, direct measurement of free. extractable or diffusable indoleacetic acid from phototropically curving hypocotyls and coleoptiles invariably shows an even distribution of auxin. On the contrary, growth inhibitors extracted or diffused from these organs turn out to be accumulated at the irradiated side, as proposed already by A. H. Blaauw (Z. Bot. 7: 465. 1915). the classical experiment by F. W. Went (Rec. Trav. Bot. Neerl. 25:1, 1928) has to be interpreted as evidence for a lateral gradient of substance(s) inhibiting auxin activity Phototropic curvature is thus a matter of differential auxin sensitivity across the unilaterally irradiated organ.     

Molecular Simulation of Solution Conformations of the Amyloid β-Peptide Aβ(1–42) by a Backpropagation Neural Network Model

Abstract

The predictive power of solution-dependent conformational states of the Aβ(1–42) peptide of Alzheimer's disease by an optimized backpropagation neural network was tested. It was found that the neural network simulates well the solution-dependent conformations. The model was also examined by using geometry-optimized conformations (hybrid approach of Gasteiger charges plus MM+ molecular-mechanics) where the initial coordinates were obtained by NMR solution spectroscopy.     

First structural evidence of a specific inhibition of phospholipase A2 by alpha-tocopherol (vitamin E) and its implications in inflammation: crystal structure of the complex formed between phospholipase A2 and alpha-tocopherol at 1.8 A resolution

This is the first structural evidence of alpha-tocopherol (alpha-TP) as a possible candidate against inflammation, as it inhibits phospholipase A2 specifically and effectively. The crystal structure of the complex formed between Vipera russelli phospholipase A2 and alpha-tocopherol has been determined and refined to a resolution of 1.8 A. The structure contains two molecules, A and B, of phospholipase A2 in the asymmetric unit, together with one alpha-tocopherol molecule, which is bound specifically to one of them. The phospholipase A2 molecules interact extensively with each other in the crystalline state. The two molecules were found in a stable association in the solution state as well, thus indicating their inherent tendency to remain together as a structural unit, leading to significant functional implications. In the crystal structure, the most important difference between the conformations of two molecules as a result of their association pertains to the orientation of Trp31. It may be noted that Trp31 is located at the mouth of the hydrophobic channel that forms the binding domain of the enzyme. The values of torsion angles (phi, psi, chi(1) and chi(2)) for both the backbone as well as for the side-chain of Trp31 in molecules A and B are -94 degrees, -30 degrees, -66 degrees, 116 degrees and -128 degrees, 170 degrees, -63 degrees, -81 degrees, respectively. The conformation of Trp31 in molecule A is suitable for binding, while that in B hinders the passage of the ligand to the binding site. Consequently, alpha-tocopherol is able to bind to molecule A only, while the binding site of molecule B contains three water molecules. In the complex, the aromatic moiety of alpha-tocopherol is placed in the large space at the active site of the enzyme, while the long hydrophobic channel in the enzyme is filled by hydrocarbon chain of alpha-tocopherol. The critical interactions between the enzyme and alpha-tocopherol are generated between the hydroxyl group of the six-membered ring of alpha-tocopherol and His48 N(delta1) and Asp49 O(delta1) as characteristic hydrogen bonds. The remaining part of alpha-tocopherol interacts extensively with the residues of the hydrophobic channel of the enzyme, giving rise to a number of hydrophobic interactions, resulting in the formation of a stable complex.     

Insights into the role of oligomeric state on the biological activities of crotoxin: crystal structure of a tetrameric phospholipase A2 formed by two isoforms of crotoxin B from Crotalus durissus terrificus venom

Crotoxin B (CB or Cdt PLA(2)) is a basic Asp49-PLA(2) found in the venom of Crotalus durissus terrificus and it is one of the subunits that constitute the crotoxin (Cro). This heterodimeric toxin, main component of the C. d. terrificus venom, is completed by an acidic, nontoxic, and nonenzymatic component (crotoxin A, CA or crotapotin), and it is related to important envenomation effects such as neurological disorders, myotoxicity, and renal failure. Although Cro has been crystallized since 1938, no crystal structure of this toxin or its subunits is currently available. In this work, the authors present the crystal structure of a novel tetrameric complex formed by two dimers of crotoxin B isoforms (CB1 and CB2). The results suggest that these assemblies are stable in solution and show that Ser1 and Glu92 of CB1 and CB2, respectively, play an important role in the oligomerization. The tetrameric and dimeric conformations resulting from the association of the isoforms may increase the neurotoxicity of the toxin CB by the creation of new binding sites, which could improve the affinity of the molecular complexes to the presynaptic membrane.