Polyphenols in cocoa and cocoa products: is there a link between antioxidant properties and health?

Cocoa and cocoa products have received much attention due to their significant polyphenol contents. Cocoa and cocoa products, namely cocoa liquor, cocoa powder and chocolates (milk and dark chocolates) may present varied polyphenol contents and possess different levels of antioxidant potentials. For the past ten years, at least 28 human studies have been conducted utilizing one of these cocoa products. However, questions arise on which of these products would deliver the best polyphenol contents and antioxidant effects. Moreover, the presence of methylxanthines, peptides, and minerals could synergistically enhance or reduce antioxidant properties of cocoa and cocoa products. To a greater extent, cocoa beans from different countries of origins and the methods of preparation (primary and secondary) could also partially influence the antioxidant polyphenols of cocoa products. Hence, comprehensive studies on the aforementioned factors could provide the understanding of health-promoting activities of cocoa or cocoa products components.     

An alternative strategy for count and storage of Kekulé and longer range resonance valence bond structures

In this paper, we suggest a simple representation for notation of Kekulé valence bond (KVB) structures and longer range resonance valence bond (RVB) structures, which is called "the adjacency bonding array". In this representation, only an N component one-dimensional array is needed for inscribing each KVB or longer range RVB structure for an N-carbon system. Based on the adjacency bonding arrays, we develop very efficient algorithms for the systematic search of KVB and RVB structures as well as evaluation of the basis set overlap and Hamiltonian matrices.     

DNA microarrays: is there a role for analytical chemistry?

DNA microarrays, or "DNA chips", represent a relatively new technology that is having a profound impact on biology and medicine, yet analytical research into this area is somewhat sparse. This article presents an overview of DNA microarrays and their application to gene expression analysis from the perspective of analytical chemistry, treating aspects of array platforms, measurement, image analysis, experimental design, normalization, and data analysis. Typical approaches are described and unresolved issues are discussed, with a view to identifying some of the contributions that might be made by analytical chemists.     

Supramolecular engineering of a 2D Kagomé lattice: synthesis, structures, and magnetic properties

Two 2D Mn (II) complexes, [Mn3(TzDC)2(phen)3] x 2 H2O (1; H3TzDC = 1,2,3-triazole-4,5-dicarboxylic acid, phen = 1,10-phenanthroline) and [Mn3(TzDC)2(bipy)3] x 4 H2O (2; bipy = 2,2'-bipyridine), were synthesized by hydrothermal reactions and characterized magnetically, and complex 1 was the first example of the chiral complex with a Kagomé lattice connectivity obtained through spontaneous resolution.     

Hydrogen bonding to pi-systems of indole and 1-methylindole: is there any OH...phenyl bond?

The weak hydrogen-bonded complexes between proton donors and the pi-cloud of indole and 1-methylindole (MI) are investigated theoretically by three different methods: DFT/B3LYP, MPW1B95, and MP2. This study addresses the question as to whether the 1:1 complex can only form between the proton and the pi-cloud of the pyrrole part of indole or if there also exists a 1:1 complex between the proton and the pi-cloud of the phenyl ring. For the water-indole system, the more elaborate MP2 and MPW1B95 methods yield only one minimum with a hydrogen bond to the pyrrole part and weak secondary interactions to the phenyl ring, in agreement with a recent criticism by Van Mourik (Chem. Phys. 2004, 304, 317-319) that the B3LYP functional is unable to account for the dispersion interaction. However, for the 1:1 complexes between MI and 2-propanol, all three methods indicate that both the five-membered and the six-membered rings of the indole chromophore can form pi-complexes. For the MI-trifluoroethanol (TFE) system, it is shown that the ethanol conformation is specific for the interaction site: for the complex to the five-membered ring, TFE is in the cis-gauche conformation, while for the complex to the six-membered ring site, it is in the trans conformation. These results are discussed as a function of local interactions in the systems.     

Note: Counterintuitive gauge-dependence of nuclear magnetic resonance shieldings for rare-gas dimers: does a natural gauge-origin for spherical atoms exist?

A counterintuitive gauge-dependence of NMR shieldings for rare-gas dimers is presented and analyzed. It is shown that common belief about the existence of a natural gauge-origin for spherical atoms with respect to NMR shielding calculations is wrong.     

Synthesis and magnetic properties comparison of M-Cu(II) and M-VO(II) Schiff base-porphyrazine complexes: what is the mechanism for spin-coupling?

Dimetallic Schiff base-porphyrazine (pz) compounds, denoted 1[M(1); M(2); R], have been prepared, where metal ion M(1) is incorporated into the pz core, and metal ion M(2) is bound to a bis(5-tert-butylsalicylidenimine) chelate built onto two amino nitrogens attached to the pz periphery; R is a solubilizing group (either propyl (Pr) or 3,4,5-trimethoxyphenyl (TMP)) attached to the remaining carbons of the pz periphery. The synthesis of 1[Cu; Cu; R], 1[Cu; VO; R], 1[ClMn; Cu; Pr], and 1[ClMn; VO; Pr] is discussed, the crystal structures of 1[Cu; Cu; TMP] and 1[ClMn; VO; Pr] are presented, and the magnetic properties of these compounds are compared. The pattern of ligand-mediated exchange coupling in these complexes is startling: for the Cu-M(2) complexes 1[Cu; VO; R] and 1[Cu; Cu; R], 2 x 10(2) < or = |J(Cu-VO)/J(Cu-Cu)|; for the ClMn-M(2) complexes 1[ClMn; Cu; Pr] and 1[ClMn; VO; Pr], J(ClMn-VO)/J(ClMn-Cu) approximately 1/3, an inverse ratio from that of the Cu-M(2) complexes, but with lesser discrimination. This coupling pattern is explained in terms of a novel orientation relative to the M(1)-M(2) direction: the "square-planar" Schiff base ligand set of M(2) is rotated in-plane by 45 degrees relative to the effectively coplanar pz ligand set of M(1).     

p-Phenylenecarbenonitrene and its halogen derivatives: how does resonance interaction between a nitrene and a carbene center affect the overall electronic configuration?

A series of para-conjugatively coupled phenylenecarbenonitrenes [(4-nitrenophenyl)methylene (3a), (4-nitrenophenyl)fluoromethylene (3b), (4-nitrenophenyl)chloromethylene (3c), and (4-nitrenophenyl)bromomethylene (3d)] were generated in argon matrix at low temperature (10 or 13 K) and characterized by IR and UV/vis spectroscopy. Density functional theory (B3LYP/6-31G(d)) and ab initio (MCSCF, CASPT2) methods were used to study the ground- and some low-lying excited states of 3a-d. The experimental and computational data suggest that 3a-d have singlet ground states (S0) and can be thought of as quinonoidal biradicals. In all cases, the lowest triplet (T1) and quintet (Q1) states lie about 2 kcal mol(-1) and 28-29 kcal mol(-1), respectively, higher in energy than S0. On the other hand the substituent is found to have a significant effect on the relative energy of the second excited triplet (T2) state. This state tends to become relatively more stable as the ability of the substituent to enforce a closed-shell configuration at the carbene subunit increases. Interestingly, the energy difference between the T2 and S0 states in 3a-d is found to depend linearly on the S-T gap of the corresponding phenylcarbenes 7a-d. This relationship is helpful in predicting when a substituted p-phenylenecarbenonitrene may have a triplet ground state instead of a singlet one.     

The heat capacities and standard entropies of corresponding potassium and ammonium ion species: is there a constant difference?

It is found that there is a nearly constant difference between the normalized values of the heat capacities and standard entropies of potassium and ammonium ion salts in the condensed phase, both solid salts and their aqueous solutions. Extension to the free gaseous ions remains moot.     

Effect of ortho-SR groups on O-H bond strength and H-atom donating ability of phenols: a possible role for the Tyr-Cys link in galactose oxidase active site?

Rotation about the Ar-S bond in ortho-(alkylthio)phenols strongly affects the bond dissociation enthalpy (BDE) and the reactivity of the OH group. Newly synthesized sulfur containing heterocycles 3 and 4, where the -SR group is almost coplanar with the phenolic ring, are characterized by unusually low BDE(O-H) values (79.6 and 79.2 kcal/mol, respectively) and by much higher reactivities toward peroxyl radicals than the ortho-methylthio derivative 1 (82.0 kcal/mol). The importance of the intramolecular hydrogen bond (IHB) in determining the BDE(O-H) was demonstrated by FT-IR experiments, which showed that in heterocycles 3 and 4 the IHB between the phenolic OH group and the S atom is much weaker than that present in 1. Since the IHB can be formed only if the -SR group adopts an out-of-plane geometry, this interaction is possible only in the methylthio derivative 1 and not in 3 and 4. The additive contribution to the phenolic BDE(O-H) of the -SR substituent therefore varies from -3.1 to +2.8 kcal/mol for the in-plane and out-of-plane conformations, respectively. These results may be relevant to understanding the role of the tyrosine-cysteine link in the active site of galactose oxidase, an important enzyme that catalyzes the two-electron aerobic oxidation of primary alcohols to aldehydes. The switching of the ortho -SR substituent between perpendicular and planar conformations may account for the catalytic efficiency of this enzyme.     

π-Extended and six-coordinate iron(II) complexes: structures, magnetic properties, and the electrochemical synthesis of a conducting iron(II) metallopolymer

Herein, we describe the preparation of three new bidentate π-extended derivatives of the ligand N-phenyl-2-pyridinalimine (ppi) containing a 3-thienyl (4) substituent at position 4 of the aniline ring or 2-thienyl (6) or phenyl (2) substituents at each of the 2,5 positions of the aniline rings. Three iron(2+) complexes (7-9) containing these ligands were prepared by combining two equivalents each of 2, 4, or 6 with Fe(NCS)(2), and the resulting neutral, six-coordinate complexes were fully characterized, including with single crystal X-ray diffraction experiments in the case of complexes 7 and 9. Variable temperature magnetic susceptibility and Mo?ssbauer experiments confirm the presence of spin-crossover in complexes 7 and 8, and the unusual solid state variable temperature magnetic properties of complex 9 likely result from crystal packing forces. Electropolymerization of the 2,5-dithienyl-substituted complex (9) produces a conducting and electrochromic metallopolymer film (poly-9).     

Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: does a stronger acid make a stiffer hydrogen bond?

Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m(-1) for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.     

Halogen bonding between substituted chlorobenzene and trimethylamine: Decisive role of σ–hole and C?Cl bond breaking energy

Theoretical studies have been carried out on the halogen bonding interaction between para substituted chlorobenzene (Y C₆H₄Cl, Y = H, NH₂, CH₃, F, CN, NO₂) and N(CH₃)₃ using ab initio MP2/aug‐cc‐pVDZ and DFT based wB97XD/6‐311++G(d,p) methods. The positive electrostatic potential (V_S,max) on the Cl atom and the heterolytic bond breaking enthalpy of the C Cl bond have been calculated and their role on halogen bonding is discussed. The heterolytic bond breaking enthalpy of the C Cl bond is proposed as a measure of the strength of the σ‐hole on Cl atom. The binding strength of the complexes ranging between −6.13 kJ mol⁻¹ and −9.29 kJ mol⁻¹ are linearly related to the V_S,max of the Cl atom and the bond breaking enthalpy of the C Cl bond. In addition, energy decomposition analysis was performed on the halogen bonded complexes via symmetry adapted perturbation theory (SAPT) to predict the dominant energy component and the nature of the N···Cl interaction.     

Enthalpy recovery in polymeric glasses: Does a correlation exist between the empirical (T-N-M) relationship parameters and the glass structures?

To characterize the enthalpy recovery which appears during physical aging in glassy materials and especially in glassy polymers, the empirical Tool-Narayanaswamy-Moynihan (TNM) relationship for the relaxation time is widely used. This relationship depends essentially on three parameters, the apparent activation energy Δh*, the non linearity parameter x and the fictive temperature T_f. Even if a great amount of data (x, Δ*) can be found in the literature, no direct correlation between the values of these parameters and the engaged structures are available. On the one hand, using some polymers like Poly(ethylene terephthalate), Polymethyl(α-n-alkyl)acrylates and three dimensional epoxy networks for which structural changes are controlled and on the other hand, using some recently published results concerning other materials including inorganic polymers (Ge-Se and Ge-Te glasses), we show that it is possible to propose some interesting tendencies. In particular it is shown that the value of x depends on the intermolecular strength for organic polymers and on the connectivity for inorganic polymer.