Polarizable contributions to the surface tension of liquid water

Surface tension, gamma, strongly affects interfacial properties in fluids. The degree to which polarizability affects gamma in water is thus far not well established. To address this situation, we carry out molecular dynamics simulations to study the interfacial forces acting on a slab of liquid water surrounded by vacuum using the Gaussian charge polarizable (GCP) model at 298.15 K. The GCP model incorporates both a fixed dipole due to Gaussian distributed charges and a polarizable dipole. We find a well-defined bulklike region forms with a width of approximately 31 A. The average density of the bulklike region agrees with the experimental value of 0.997 g/cm3. However, we find that the orientation of the molecules in the bulklike region is strongly influenced by the interfaces, even at a distance five molecular diameters from the interface. Specifically, the orientations of both the permanent and induced dipoles show a preferred orientation parallel to the interface. Near the interface, the preferred orientation of the dipoles becomes more pronounced and the average magnitude of the induced dipoles decreases monotonically. To quantify the degree to which molecular orientation affects gamma, we calculate the contributions to gamma from permanent dipolar interactions, induced dipolar interactions, and dispersion forces. We find that the induced dipole interactions and the permanent dipole interactions, as well as the cross interactions, have positive contributions to gamma, and therefore contribute stability to the interface. The repulsive core interactions result in a negative contribution to gamma, which nearly cancels the positive contributions from the dipoles. The large negative core contributions to gamma are the result of small oxygen-oxygen separation between molecules. These small separations occur due to the strong attractions between hydrogen and oxygen atoms. The final predicted value for gamma (68.65 m/Nm) shows a deviation of approximately 4% of the experimental value of 71.972 m/Nm. The inclusion of polarization is critical for this model to produce an accurate value.     

Diversity-oriented synthesis of functionalized pyrrolo[3,2-d]pyrimidines with variation of the pyrimidine ring nitrogen substituents

Nine 2,4-dioxo-2,3,4,5-tetrahydro-1H-pyrrolo[3,2-d]pyrimidine-6-carboxylic acid benzyl esters 12 were synthesized in four steps from 4-oxo-N-(PhF)proline benzyl ester 7 by a general method in which elements of molecular diversity were readily added onto the pyrimidine nitrogens. Conversion of 4-oxoproline 7 into the corresponding aminopyrrole 8 using benzyl-, allyl-, and isopropylamine followed by treatment with phenyl, allyl, and ethyl isocyanate gave nine different ureas 9. 4-Ureido-1H-pyrrole-2-carboxylic acid benzyl esters 9 were then converted into the respective pyrrolo[3,2-d]pyrimidines 12 using trichloroacetyl chloride in acetonitrile followed by treatment with Cs(2)CO(3). Crystallization from toluene gave the desired deazapurines in 37-55% overall yield from proline 7.     

The tuneable complexation of gold nanoparticles

Mixed monolayer protected gold nanoparticles have been fabricated incorporating 1,5-dialkyloxynaphthalene moieties that are capable of forming complexes with the tetracationic cyclophane cyclobis(paraquat-p-phenylene); electrochemical reduction of the cyclophane or the addition of tetrathiafulvalene results in disassembly of the complexes.     

Reactions SRN1 en serie heterocyclique: IV: Reactivite des sels du dimethyl-2,2 nitro-5 dioxanne-1,3

2-Alkyl 2-nitro 1,3-propanediol, 2-alkylidene 1,3-propanediol and 2-dialkylidene 1,3-propanediol are prepared via S_RN1 reactions with salts of 2,2-dimethyl 5-nitro 1,3-dioxane and acid-catalyzed cleavage of the resulting acetals.     

A tuneable self-complexing molecular switch

[reaction: see text] A new self-complexing donor-acceptor system has been synthesized that has the propensity to undergo intramolecular decomplexation under thermal and electrochemical perturbation and upon addition of a competitive guest for the cyclophane's cavity.     

Synthesis of new potentially bioactive bicyclic 2-pyridones

Three convenient methods of reduction of the nitro group of 5-nitroimidazoles and 5-nitrothiazole that bear a diethylmethylene malonate group in an ortho-like position with respect to the nitro group and cyclization of the resulting amino derivatives are reported. These reactions afforded the target bicyclic 2-pyridones in good to excellent yields.     

Exploring the conformational energy landscape of glassy disaccharides by cross polarization magic angle spinning 13C nuclear magnetic resonance and numerical simulations. II. Enhanced molecular flexibility in amorphous trehalose

This paper uses chemical shift surfaces to simulate experimental (13)C cross polarization magic angle spinning spectra for amorphous solid state disaccharides, paying particular attention to the glycosidic linkage atoms in trehalose, sucrose, and lactose. The combination of molecular mechanics with density functional theory/gauge invariant atomic orbital ab initio methods provides reliable structural information on the conformational distribution in the glass. The results are interpreted in terms of an enhanced flexibility that trehalose possesses in the amorphous solid state, at least on the time scale of (13)C nuclear magnetic resonance measurements. Implications of these findings for the fragility of trehalose glass and bioprotectant action are discussed.     

Total synthesis of (-)-spongidepsin

[structure: see text] A convergent and rapid stereoselective synthesis of (-)-spongidepsin has been achieved from the Roche ester in 14 steps with an overall yield of 13%.     

Crystal structure determination of 10-trifluoroacetylphenothiazine

The structure of the title compound has been determined by single crystal X-ray methods. The crystals are monoclinic, space group P2₁/n with four molecules in a cell of dimensions a = 14.365(4), b = 5.942 (2), c = 17.359(3) Å, β = 119.88(2)° and V = 1298.0(6) Å. The structure has been refined by full-matrix least-squares to R = 0.043 using 1650 observed reflections. This study shows that the folding angle between the two benzo planes is 131.8(1)°, one of the smallest values observed in phenothiazine derivatives. Also, the trifluoroacetyl group is perpendicular to the plane bisecting the tricyclic ring, in contrast to most 10-aryl-substituted phenothiazines where the substituent is approximately parallel to the plane bisecting the tricyclic ring.     

Adapting Poisson-Boltzmann to the self-consistent mean field theory: application to protein side-chain modeling

We present an extension of the self-consistent mean field theory for protein side-chain modeling in which solvation effects are included based on the Poisson-Boltzmann (PB) theory. In this approach, the protein is represented with multiple copies of its side chains. Each copy is assigned a weight that is refined iteratively based on the mean field energy generated by the rest of the protein, until self-consistency is reached. At each cycle, the variational free energy of the multi-copy system is computed; this free energy includes the internal energy of the protein that accounts for vdW and electrostatics interactions and a solvation free energy term that is computed using the PB equation. The method converges in only a few cycles and takes only minutes of central processing unit time on a commodity personal computer. The predicted conformation of each residue is then set to be its copy with the highest weight after convergence. We have tested this method on a database of hundred highly refined NMR structures to circumvent the problems of crystal packing inherent to x-ray structures. The use of the PB-derived solvation free energy significantly improves prediction accuracy for surface side chains. For example, the prediction accuracies for χ(1) for surface cysteine, serine, and threonine residues improve from 68%, 35%, and 43% to 80%, 53%, and 57%, respectively. A comparison with other side-chain prediction algorithms demonstrates that our approach is consistently better in predicting the conformations of exposed side chains.