Sorbate properties of xenon in cloverite: A molecular dynamics study

Molecular dynamics calculations on xenon adsorbed in the cubic cavity of cloverite, a gallophosphate, is presented. Guest-host radial distribution functions, guest-host energy distribution functions, power spectra, and diffusion coefficients for xenon are reported at 397, 494, and 716 K. Results suggest that xenon is highly mobile at 700 K. A shift in the peak position of the power spectra toward lower frequency is observed with increase in temperature. (C) 1994 Academic Press, Inc.

Studies on molecular evolution and structural features of double-headed inhibitors of ?-amylase and trypsin in plants

Plant seeds usually have high concentrations of proteinase and amylase inhibitors. These inhibitors exhibit a wide range of specificity, stability and oligomeric structure. In this communication, we report analysis of sequences that show statistically significant similarity to the double-headed alpha-amylase/trypsin inhibitor of ragi (Eleusine coracana). Our aim is to understand their evolutionary and structural features. The 14 sequences of this family that are available in the SWISSPROT database form three evolutionarily distinct branches. The branches relate to enzyme specificities and also probably to the oligomeric state of the proteins and not to the botanical class of the plant from which the enzymes are derived. This suggests that the enzyme specificities of the inhibitors evolved before the divergence of commercially cultivated cereals. The inhibitor sequences have three regions that display periodicity in hydrophobicity. It is likely that this feature reflects extended secondary structure in these segments. One of the most variable regions of the polypeptide corresponds to a loop, which is most probably exposed in the native structure of the inhibitors and is responsible for the inhibitory property.

Synthesis and characterization of barium bis(citrato) oxozirconate(iv) tetrahydrate--A new molecular precursor for fine particle BaZrO3

Barium metazirconate (BaZrO3) fine powder has been produced by thermally decomposing a molecular precursor, barium bis(citrato)oxozirconate(IV) tetrahydrate at about 700-degrees-C. The precursor, Ba[ZrO(C6H6O7)2] . 4H2O (BZO) has been synthesized and characterized by employing a combination of spectroscopic and thermoanalytical techniques. The precursor undergoes thermal decomposition in three major stages: (i) dehydration to give an anhydrous barium zirconyl citrate, (ii) decomposition of the anhydrous citrate in a multistep process to form an ionic oxycarbonate intermediate, Ba2Zr2O5CO3, and (iii) decomposition of the oxycarbonate to produce BaZrO3 fine powder. The particle size of the resultant BaZrO3 is about 0.2 mum, and the surface area is found to be 4.0 m2 g-1.

Asymmetric synthesis of steroidal Tröger's base analogues. X-Ray molecular structure of methyl 3?,12?-{6H,12H-5,11-methanodibenzo[b,f][1,5]diazocine-2,8-bisacetoxy}-5?-cholan-24-oate

Cyclization of compound 5c in trifluoroacetic acid/hexamethylenetetramine produces Tröger's base analogue 6c in 75% yield with 70% diastereoselectivity.

Constructions of 2D-Metallamacrocycles Using Half-Sandwich Ru-2(II) Precursors: Synthesis, Molecular Structures, and Self-Selection for a Single Linkage Isomer

Coordination-driven self-assembly of oxalato-bridged half-sandwich p-cymene ruthenium complex Ru-2(mu-eta(4)-C2O4)(MeOH)(2)(eta(6)-p-cymene)(2)] (O3SCF3)(2) (1a) with several ditopic donors (L-a-L-d) in methanol affords a series of bi- and tetranuclear metallamacrocycles (2a and 3-5). Similarly, the combination of 2,5-dihydroxy-1,4-benzoquinonato (dhbq)-bridged binuclear complex Ru-2(mu-eta(4)-C6H2O4)(MeOH)(2)(eta(6)-p-cymene)(2)](O3SCF3)(2) (1b) with a flexible bidentate amide linker (L-a) in 1:1 molar ratio gave the corresponding tetranuclear complex 2b. All the macrocycles were isolated as their triflate salts in high yields and were fully characterized by various spectroscopic techniques. Finally, the molecular structures of all the assemblies were determined unambiguously by single-crystal X-diffraction analysis. Interestingly, the combination of acceptor 1a or 1b with an unsymmetrical linear ditopic donor L-a results in a self-sorted linkage isomeric (head-to-tail) macrocycle (2a or 2b) despite the possibility of formation of two different isomeric macrocycles (head-to-head or head-to-tail) due to different connectivity of the donor. Molecular structures of the complexes 2a and 2b showed tetranuclear rectangular geometry with dimensions of 5.51 angstrom x 13.29 angstrom for 2a and 7.91 angstrom x 13.46 angstrom for 2b. In both cases, two binuclear Ru-2(II) building blocks are connected by a mu-N-(4-pyridyl)isonicotinamide donor in a head-to-tail fashion. Surprisingly, the macrocycle 2a loses one counteranion and cocrystallizes with monodeprotonated 1,3,5-trihydroxybenzene via strong intermolecular pi-pi stacking and hydrogen bonding. The tweezer complex 3 showed strong fluorescence in solution, and it showed fluorescence sensing toward nitroaromatic compounds. A fluorescence study demonstrated a marked quenching of the initial fluorescence intensity of the macrocycle 3 upon gradual addition of trinitrotoluene and exhibits significant fluorescence quenching response only for nitroaromatic compounds compared to various other aromatic compounds tested.

Bile acids in asymmetric synthesis and molecular recognition

This account summarizes the progress made in our laboratory towards the development of new uses of naturally occurring bile acids. Applications in Asymmetric Synthesis (intramolecular coupling, and intermolecular reactions) and Molecular Recognition are described with suitable examples.

Design, synthesis, and evaluation of bile acid-based molecular tweezers

A family of bile acid-based molecular tweezers (7-9) has been constructed readily from simple precursors. Binding experiments with various electron deficient aromatic compounds showed that tweezer 8 binds trinitrofluorenone 10e with an association constant of 220 M(-1) in CDCl3. Single-crystal X-ray analysis of compound 8 shows aromatic-aromatic interactions producing a two-dimensional lattice of pyrene units. Tweezer 8 was immobilized on Merrifield resin, and binding studies have shown that these data compare well with those of the solution state studies.

Electron donor-acceptor complex of ICl with diethyl ether - He I photoelectron spectroscopy and ab initio molecular orbital study

The He I photoelectron spectrum of the diethyl ether-ICl complex has been obtained. The oxygen orbitals are shifted to higher binding energies and that of ICl to lower binding energies owing to complex formation. Ab initio molecular orbital (MO) calculations of the complex molecule showed that the bonding is between the sigma-type lone pair of oxygen and the I atom and that the complex has C-2v symmetry. The binding energy of the complex is computed to be 8.06 kcal mol(-1) at the MP2/3-21G* level. The orbital energies obtained from the photoelectron spectra of the complex are compared and assigned with orbital energies obtained by MO calculations. Natural bond orbital analysis (NBO) shows that charge transfer is from the sigma-type oxygen lone pair to the iodine atom and the magnitude of charge transfer is 0.0744 e.

Extended Huckel molecular orbital calculations on hydroxobridged heterotrinuclear cobalt(III) complexes

EHT calculations on heterotrinuclear cobalt(III) complexes of the type [Cu{(OH)(2)Co(L(4))}(2)](4+) where L(4) denotes (en)(2) or (NH3)(4), en = ethylenediamine and their component species have been carried out. The results regarding bonding and structure for the trinuclear complexes are compared with those for the monomer components such as [Co(en)(2)(OH)(2)](+), [Co(NH3)(4)(OH)(2)](+) and [Cu(OH)(4)](2-) are discussed.

Basis set dependence of the molecular electrostatic potential topography. A case study of substituted benzenes

The basis set dependence of the topographical structure of the molecular electrostatic potential (MESP), as well as the effect of substituents on the MESP distribution, has been investigated with substituted benzenes as test cases. The molecules are studied at HF-SCF 3�21G and 6�31G** levels, with a further MESP topographical investigation at the 3�21G, double-zeta, 6�31G*, 6�31G**, double-zeta polarized and triple-zeta polarized levels. The MESP critical points for a 3�21G optimized/6�31G** basis are similar to the corresponding 6�31G** optimized/6�31G** ones. More generally, the qualitative features of the MESP topography computed at the polarized level are independent of the level at which optimization is carried out. For a proper representation of oxygen lone pairs, however, optimization using a polarized basis set is required. The nature of the substituent drastically changes the MESP distribution over the phenyl ring. The values and positions of MESP minima indicate the most active site for electrophilic attack. This point is strengthened by a study of disubstituted benzenes.

Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

The various types of chain folding and possible intraloop as well as interloop base pairing in human telomeric DNA containing d(TTAG(3)) repeats have been investigated by model-building, molecular mechanics, and molecular dynamics techniques. Model-building and molecular mechanics studies indicate that it is possible to build a variety of energetically favorable folded-back structures with the two TTA loops on same side and the 5' end thymines in the two loops forming TATA tetrads involving a number of different intraloop as well as interloop A:T pairing schemes. In these folded-back structures, although both intraloop and interloop Watson-Crick pairing is feasible, no structure is possible with interloop Hoogsteen pairing. MD studies of representative structures indicate that the guanine-tetraplex stem is very rigid and, while the loop regions are relatively much more flexible, most of the hydrogen bonds remain intact throughout the 350-ps in vacuo simulation. The various possible TTA loop structures, although they are energetically similar, have characteristic inter proton distances, which could give rise to unique cross-peaks in two-dimensional nuclear Overhauser effect spectroscopy (NOESY) experiments. These folded-back structures with A:T pairings in the loop region help in rationalizing the data from chemical probing and other biochemical studies on human telomeric DNA.