Molecular volume calculation using AM1 semi-empirical method toward diffusion coefficients and electrophoretic mobility estimates in aqueous solution

Diffusion coefficients and electrophoretic mobility are two important physicochemical parameters used in mass transport phenomenon studies. The volume of the solute is required to determine or estimate these parameters. Classical methods, such as the LeBas method are commonly used. However, although valid, this method may represent a boring and time-consuming task, depending on the nature and number of compounds to be calculated. In this study, the volumes of a series of neutral and charged substances of the main functional groups present in organic molecules, amino acids, drugs and diverse compounds, such as cytosine and glucose, were calculated according to the LeBas method (V_M) and the AM1 semi-empirical method, V_W(AM1). The latter showed to be statistically coincident with the former. Employed as a pure value or corrected by the LeBas molar volume, the AM1 molecular volume was also demonstrated to estimate the diffusion coefficients in infinite aqueous dilution within an acceptable average error, according to the Othmer–Thakar, Wilke–Chang and Hayduk–Laudie methods, as well as the electrophoretic mobility of charged substances, such as carboxylates and protonated amines. According to these results, the AM1 method was seen to be statistically valid to calculate molecular volume. Many advantages in the construction of most diverse structures were noted, as well as a reduction in time and an increase in the quality of the information, when run on molecular modeling software.     

Stability constants of iron(II) sulfate complexes

The complex formation equilibria between iron(II) and sulfate ions have been studied at 25 degrees C in 3 M NaClO4 ionic medium by measuring with a glass electrode the competition of Fe2+ and H+ ions for the sulfate ion. The concentrations of the metal and of the ligand were varied in the ranges 0.01 to 0.125 and 0.01 to 0.250 M, respectively. The analytical concentration of strong acid was chosen to be 0.01 or 0.03 M. The potentials of the glass electrode, corrected for the effect of replacement of medium ions with reagent species, have been interpreted with the equilibria [formula: see text] Stability constants valid in the infinite dilution reference state, logK zero = 1.98 +/- 0.16, log beta 1 zero = 2.1(5) +/- 0.2 and log beta 2 = 2.5 +/- 0.2, have been estimated by assuming the validity of the specific interaction theory.     

Second harmonic generation in polymers containing a new azo chromophore based on phenylnitrobenzoxazole

The synthesis of the new chromophores 2‐{4‐[4‐(N,N‐dihydroxyethylamino)‐phenylazo]‐phenyl}‐6‐nitrobenzoxazole ( 1 ) and 4‐[4‐(N,N‐dihydroxyethylamino)phenylazo]‐benzoic acid ( 2 ) is described. Three homopolymers obtained by the polycondensation of 1 with propyloxy‐terephthalic acid and 1 and 2 with 2,4‐tolylenediisocianate as well as two copolymers obtained by polycondensation of appropriate mixtures of chromophores 1 and 2 with 2,4‐tolylene‐diisocianate were prepared and characterized. All as‐prepared polymers but one (homopolyurethane of 1 ) were amorphous and exhibited good optical clarity, good thermal stability above the glass transition, and solubility in organic solvents. The second‐order nonlinear optical behavior of the amorphous polymers was investigated on spin‐coated corona‐poled films through second harmonic generation (SHG) experiments at 1064 nm. At this wavelength, resonance‐enhanced values of the SHG coefficient d₃₃ were found in the range between 6 and 34 pm/V where higher values were observed for polymers with a higher molar content of 1 . © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1468–1475, 2002     

Fluorescence resonance energy transfer between quantum dot donors and dye-labeled protein acceptors

We used luminescent CdSe-ZnS core-shell quantum dots (QDs) as energy donors in fluorescent resonance energy transfer (FRET) assays. Engineered maltose binding protein (MBP) appended with an oligohistidine tail and labeled with an acceptor dye (Cy3) was immobilized on the nanocrystals via a noncovalent self-assembly scheme. This configuration allowed accurate control of the donor-acceptor separation distance to a range smaller than 100 A and provided a good model system to explore FRET phenomena in QD-protein-dye conjugates. This QD-MBP conjugate presents two advantages: (1) it permits one to tune the degree of spectral overlap between donor and acceptor and (2) provides a unique configuration where a single donor can interact with several acceptors simultaneously. The FRET signal was measured for these complexes as a function of both degree of spectral overlap and fraction of dye-labeled proteins in the QD conjugate. Data showed that substantial acceptor signals were measured upon conjugate formation, indicating efficient nonradiative exciton transfer between QD donors and dye-labeled protein acceptors. FRET efficiency can be controlled either by tuning the QD photoemission or by adjusting the number of dye-labeled proteins immobilized on the QD center. Results showed a clear dependence of the efficiency on the spectral overlap between the QD donor and dye acceptor. Apparent donor-acceptor distances were determined from efficiency measurements and corresponding F?rster distances, and these results agreed with QD bioconjugate dimensions extracted from structural data and core size variations among QD populations.     

Reaction of [CpRu(CH3CN)3]PF6 with bidentate ligands: structural characterization of [{CpRu(CH3CN)2}2(μ-η-dppe)](PF6)2 [dppe=1,2-bis(diphenylphosphino)ethane]

The reaction of [CpRu(CH₃CN)₃]PF₆ with the bidentate ligands L-L=1,2-bis(diphenylphosphino)ethane, dppe, and (1-diphenylarsino-2-diphenylphosphino)ethane, dpadppe, affords mononuclear or dinuclear complexes of formula [CpRu(η²-L-L)(CH₃CN)]PF₆, [{CpRu(CH₃CN)₂}₂(μ-η^1:1-L-L)](PF₆)₂ and [{CpRu(CH₃CN)}₂(μ-η^1:1-L-L)₂](PF₆)₂ (L-L=dppe, dpadppe). All of the compounds are characterized by microanalysis and NMR [¹H and ³¹P{¹H}] spectroscopy. The crystal structure of [{CpRu(CH₃CN)₂}₂(μ-η^1:1-dppe)](PF₆)₂ has been determined by X-ray diffraction analysis. The complex exhibits a dppe ligand bridging two CpRu(CH₃CN)₂ fragments.     

Organocatalytic asymmetric alpha-bromination of aldehydes and ketones

The first organocatalytic enantioselective alpha-bromination of aldehydes and ketones is presented; a C2-symmetric diphenylpyrrolidine catalyst afforded the alpha-brominated aldehydes in good yields and up to 96% ee, while ketones were alpha-brominated by a C2-symmetric imidazolidine in up to 94% ee; furthermore, the organocatalytic enantioselective alpha-iodination of aldehydes is also demonstrated to proceed with up to 89% ee.     

A simple approach for improving the hybrid MMVB force field: application to the photoisomerization of s-cis butadiene

MMVB is a QM/MM hybrid method, consisting of a molecular mechanics force field coupled to a valence bond Heisenberg Hamiltonian parametrized from ab initio CASSCF calculations on several prototype molecules. The Heisenberg Hamiltonian matrix elements Q(ij) and K(ij), whose expressions are partitioned here into a primary contribution and second-order correction terms, are calculated analytically in MMVB. When the original MMVB force field fails to produce potential energy surfaces accurate enough for dynamics calculations, we show that significant improvements can be made by refitting the second-order correction terms for the particular molecule(s) being studied. This "local" reparametrization is based on values of K(ij) extracted (using effective Hamiltonian techniques) from CASSCF calculations on the same molecule(s). The method is demonstrated for the photoisomerization of s-cis butadiene, and we explain how the correction terms that enabled a successful MMVB dynamics study [Garavelli, M.; Bernardi, F.; Olivucci, M.; Bearpark, M. J.; Klein, S.; Robb, M. A. J Phys Chem A 2001, 105, 11496] were refitted.     

Staphylococcus aureus bicomponent gamma-hemolysins, HlgA, HlgB, and HlgC, can form mixed pores containing all components

Staphylococcal gamma-hemolysins are bicomponent toxins forming a protein family with leucocidins and alpha-toxin. Two active toxins (AB and CB) can be formed combining one of the class-S components, HlgA or HlgC, with the class-F component HlgB. These two gamma-hemolysins form pores with marked similarities to alpha-toxin in terms of conductance, nonlinearity of the current-voltage curve, and channel stability in the open state. AB and CB pores, however, are cation-selective, whereas alpha-toxin is anion-selective. gamma-Hemolysins' pores are hetero-oligomers formed by three or four copies of each component (indicated as 3A3B and 3C3B or 4A4B and 4C4B). Point mutants located on a beta-strand of the class-S component that forms part of the protomer-protomer contact region can prevent oligomer assembly. Interestingly, these mutants inhibit growth of pores formed not only by their natural components but also by nonstandard components. This lead to the hypothesis that mixed ABC pores could also be formed. By studying the conductance of pores, assembled in the presence of all three components (in different ratios), it was observed that the magnitudes expected for mixed pores were, indeed, present. We conclude that the gamma-hemolysin/leucocidin bicomponent toxin family may form a larger than expected number of active toxins by cross-combining various S and F components.     

2,4‐Dioxa‐7‐aza‐, 2,4‐Dioxa‐8‐aza‐, and 2,4‐Dioxa‐9‐aza‐3‐phosphadecalins as Rigid Acetylcholine Mimetics: Syntheses and Characterization

Phosphorylation of suitable piperidine precursors yielded a series of novel decalin‐type O,N,P‐heterocycles. The title compounds, P(3)‐axially and P(3)‐equatorially X‐substituted, cis‐ and trans‐configurated 2,4‐dioxa‐7‐aza‐, 2,4‐dioxa‐8‐aza‐, and 2,4‐dioxa‐9‐aza‐3‐phosphabicyclo[4.4.0]decane 3‐oxides (X=Cl, F, 4‐nitrophenoxy, and 2,4‐dinitrophenoxy), are configuratively fixed and conformationally constrained P‐analogues of acetylcholine and as such represent acetylcholine (7‐aza and 9‐aza isomers) or γ‐homo‐acetylcholine mimetics (8‐aza isomers). Being irreversible inhibitors of acetylcholinesterase (AChE), the compounds are considered to be suitable probes for the investigation of the stereochemical course of the inhibition reaction by ³¹P‐NMR spectroscopy. Moreover, the design of these mimetics will enable studies of molecular interactions with AChE, in particular, the recognition conformation of acetylcholine.     

Stereoselective Synthesis of Selenium-Containing Glycoconjugates via the Mitsunobu Reaction

A simple and efficient route for the synthesis of new glycoconjugates has been developed. The approach acts as a model for a mini-library of compounds with a deoxy-selenosugar core joined to a polyphenolic moiety with well-known antioxidant properties. An unexpected stereocontrol detected in the Mitsunobu key reaction led to the most attractive product showing a natural d-configuration. Thus, we were able to obtain the target molecules from the commercially available d-ribose via a shorter and convenient sequence of reactions.