Equilibrium and <Superscript>1</Superscript>H NMR Kinetic Study of the Reactions of Dichlorido [S-Methyl-L-Cysteine(N,S)]Platinum(II) Complex with Some Relevant Biomolecules

The formation equilibria of the [Pt(SMC)(H₂O)₂]⁺ complex with some biologically relevant ligands such as L-methionine (L-met) and glutathione (GSH) were studied. The stoichiometry and stability constants of the formed complexes are reported, and the concentration distribution of the various complex species has been evaluated as a function of pH. The reaction between [PtCl₂(SMC)] and guanosine-5′-monophosphate (5′-GMP) was studied by ¹H NMR spectroscopy. The NMR spectra indicated that first step is the hydrolysis of the [PtCl₂(SMC)] complex and second step is the substitution of an aqua ligand, either in the cis or trans position with guanosine-5′-monophosphate in molar ratio 1:1. The values of rate constant showed faster substitution of coordinated H₂O in the trans position to the S donor atom of S-methyl-L-cysteine, whereas the slower reaction was assigned to the displacement of the cis coordinated aqua molecule. This is due to the strong trans labilization effect of coordinated sulfur. Electronic Supplementary Material  The online version of this article () contains supplementary material, which is available to authorized users.     

Interference between the hydrogen bonds to the two rings of nicotine

The biochemical transport and binding of nicotine depends on the hydrogen bonding between water and binding site residues to the pyridine ring and the protonated pyrrolidinium ring. To test the independence of these two moderately separated hydrogen-bonding sites, we have calculated the structures of clusters of protonated nicotine with water and a bicarbonate anion, benzene, indole, or a second water molecule. Unprotonated nicotine-water clusters have also been studied for contrast. The potential energy surfaces are first explored with an intermolecular anisotropic atom-atom model potential. Full geometry optimizations are then carried out using density functional theory to include nonadditive terms in the interaction energies. The presence of the charge on the pyrrolidine nitrogen removes the conventional hydrogen-bonding site on the pyridine ring. The hydrogen-bond ability of this site is nearly recovered when the protonated pyrrolidinium ring is bound to a bicarbonate anion, whereas its interaction with benzene shows a much smaller effect. Indole appears to partially restore the hydrogen-bond ability of the pyridine nitrogen, although indole and benzene both pi-bond to the pyrrolidinium ring. A second hydrogen-bonding water produces a significant conformational distortion of the nicotine. This demonstrates the limitations of the conventional qualitative predictions of hydrogen bonding based on the independence of molecular fragments. It also provides benchmarks for the development of atomistic modeling of biochemical systems.     

Chemical composition and antimicrobial activity of essential oils from Centaurea pannonica and C. jacea

The chemical composition and antimicrobial activity of the essential oils obtained by hydrodistillation from Centaurea pannonica (Heufel) Simonkai and C. jacea L. (Asteraceae), were investigated. The essential oils were analyzed by GC and GC-MS. Forty five and twenty nine compounds were identified in the two oils, respectively. C. pannonica oil was rich in fatty acids (43.7%), with 9-octadecanoic acid (34.0%) and (Z,Z)-9,12-octadecadienoic acid (8.6%) as the major compounds. In contrast, the essential oil of C. jacea was dominated by oxygenated sesquiterpenes (43.2%), among which caryophyllene oxide (23.5%) and spathulenol (8.9%) were the major constituents. However, the oil was also characterized by an important fatty acid fraction (15.5%), with 9-octadecanoic acid (8.9%) and hexadecanoic acid (6.6%) being the main components. The antimicrobial activities of the essential oils were evaluated by the microdilution method against three Gram-positive and three Gram-negative bacteria, and one yeast. Both oils exhibited significant antimicrobial activity, especially against Gram-positive bacteria.     

DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates

We apply DFT calculations to deoxydinucleoside monophosphates (dDMPs) which represent minimal fragments of the DNA chain to study the molecular basis of stability of the DNA duplex, the origin of its polymorphism and conformational heterogeneity. In this work, we continue our previous studies of dDMPs where we detected internal energy minima corresponding to the “classical” B conformation (BI‐form), which is the dominant form in the crystals of oligonucleotide duplexes. We obtained BI local energy minima for all existing base sequences of dDMPs. In the present study, we extend our analysis to other families of DNA conformations, successfully identifying A, BI, and BII energy minima for all dDMP sequences. These conformations demonstrate distinct differences in sugar ring puckering, but similar sequence‐dependent base arrangements. Internal energies of BI and BII conformers are close to each other for nearly all the base sequences. The dGpdG, dTpdG, and dCpdA dDMPs slightly favor the BII conformation, which agrees with these sequences being more frequently experimentally encountered in the BII form. We have found BII‐like structures of dDMPs for the base sequences both existing in crystals in BII conformation and those not yet encountered in crystals till now. On the other hand, we failed to obtain dDMP energy minima corresponding to the Z family of DNA conformations, thus giving us the ground to conclude that these conformations are stabilized in both crystals and solutions by external factors, presumably by interactions with various components of the media. Overall the accumulated computational data demonstrate that the A, BI, and BII families of DNA conformations originate from the corresponding local energy minimum conformations of dDMPs, thus determining structural stability of a single DNA strand during the processes of unwinding and rewinding of DNA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2548–2559, 2010     

TFD: Torsion Fingerprints as a new measure to compare small molecule conformations

Advantages like intuitive interpretation, objectivity, general applicability, and its easy, automated calculation make the rmsd (root-mean-squared deviation) the measure of choice for the investigation of the accuracy of conformational model generators. For comparing conformations of a single molecule this is a clearly superior method. Single molecule analysis is, however, a rare scenario. Typically, conformations are generated for huge corporate or external vendor databases of high diversity which are then further investigated with high-throughput computational methods like docking or pharmacophore searching, in virtual screening campaigns. Representative subsets for accuracy investigations of computational methods need to mimic this diversity. Averaged rmsd values over these data sets are frequently used to assess the accuracy of the methods. There are, however, significant weaknesses in rmsd comparisons for such kind of data sets. The interpretation is for example no longer intuitive because what can be expected in terms of good or bad rmsd values crucially depends on the data set composition like size or number of rotatable bonds of the underlying molecules. Further, rmsd lacks normalization which might result in very high averaged rmsd values for highly flexible molecules and thus might completely skew results. We have developed a novel measure to compare conformations of molecules called Torsion Fingerprint Deviation (TFD). It extracts, weights, and compares Torsion Fingerprints from a query molecule and generated conformations under consideration of acyclic bonds as well as ring systems. TFD is alignment-free and overcomes major limitations of rmsd while retaining its advantages.     

Angular Benzoperylenetetracarboxylic Bisimides

Benzoperylene derivatives with two angularly attached dicarboxylic imide rings, which were prepared by the Diels–Alder‐Reaction, exhibit strong fluorescence and their free peri positions allow either control of the UV/Vis spectra through their substituents or form anchor positions for the attachment of functional units. The angular chromophore 3 may be used both for fluorescent labeling such as for primary amines or enzymes or as building blocks for more complex assemblies where they may act as energy donors for FRET or electron acceptors in PET such as for photovoltaic solar cells.     

Pr(BO2)3 und PrCl(BO2)2: Zwei meta‐Borate des Praseodyms im Vergleich

Pr(BO₂)₃ and PrCl(BO₂)₂: Two Praseodymium meta‐Borates in Comparison Single‐crystalline PrCl(BO₂)₂ can be obtained by the reaction of praseodymium, Pr₆O₁₁ and PrCl₃ with a small excess of B₂O₃ in evacuated silica tubes after seven days at 850 °C. If NaCl is additionally used as flux, single crystals of Pr(BO₂)₃ dominate the main product. Both praseodymium(III) meta‐borates are air and water stable. The crystals of PrCl(BO₂)₂ emerge as long, thin, pale green needles which tend to severe twinning due to their fibrous habit. The crystal structure (triclinic, P1¯; a = 420.56(4), b = 655.42(7), c = 808.34(8) pm, α = 82.361(8), β = 89.173(9), γ = 71.980(7)°, Z = 2) exhibits zigzag chains {[(B1)o^t_1/1O^e_2/2(B2)O^t_1/1O^e_2/2]²⁻} (≡ {[BO₂]⁻}) of corner‐linked [BO₃]³⁻ triangles with syndiotactic orientation of the terminal oxygen atoms which are running parallel to the [100] direction. The Pr³⁺ cations are surrounded by three Cl⁻ and seven O²⁻ anions with the shape of a tetracapped trigonal prism. The green, transparent crystals of Pr(BO₂)₃ (monoclinic, C2/c; a= 984.98(9), b = 809.57(8), c = 641.02(6) pm, β = 126.783(9)°, Z = 4) appear either lath‐shaped or rather spherical. In the crystal structure the B³⁺ cations reside both in trigonal planar as well as in tetrahedral coordination of oxygen atoms. Both types of borate polyhedra ([BO₃]³⁻ and [BO₄]⁵⁻) are linked via corners to form chains of the composition {[(B2)‐O^t_1/1O^e_2/2(B1)O^e_4/2(B2)O^t_1/1O^e_2/2]³⁻} (≡ {[BO₂]⁻}) which run parallel [101]. The coordination sphere of the Pr³⁺ cations consists of ten oxide anions which build up a bicapped square antiprism.