A comparative molecular similarity index analysis (CoMSIA) study identifies an HLA-A2 binding supermotif

The 3D-QSAR CoMSIA technique was applied to a set of 458 peptides binding to the five most widespread HLA-A2-like alleles: A^*0201, A^*0202, A^*0203, A^*0206 and A^*6802. Models comprising the main physicochemical properties (steric bulk, electron density, hydrophobicity and hydrogen-bond formation abilities) were obtained with acceptable predictivity (q ² ranged from 0.385 to 0.683). The use of coefficient contour maps allowed an A2-supermotif to be identified based on common favoured and disfavoured areas. The CoMSIA definition for the best HLA-A2 binder is as follows: hydrophobic aromatic amino acid at position 1; hydrophobic bulky side chains at positions 2, 6 and 9; non-hydrogen-bond-forming amino acids at position 3; small aliphatic hydrogen-bond donors at position 4; aliphatic amino acids at position 5; small aliphatic side chains at position 7; and small aliphatic hydrophilic and hydrogen-bond forming amino acids at position 8.     

Characterizing Enzyme Cooperativity with Imaging SAMDI-MS

This paper describes a method that combines a microfluidic device and self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI) mass spectrometry to calculate the cooperativity in binding of calcium ions to peptidylarginine deiminase type 2 (PAD2). This example uses only 120 μL of enzyme solution and three fluidic inputs. This microfluidic device incorporates a self-assembled monolayer that is functionalized with a peptide substrate for PAD2. The enzyme and different concentrations of calcium ions are flowed through each of eight channels, where the position along the channel corresponds to reaction time and position across the channel corresponds to the concentration of Ca²⁺. Imaging SAMDI (iSAMDI) is then used to determine the yield for the enzyme reaction at each 200 μm pixel on the monolayer, providing a time course for the reactions. Analysis of the peptide conversion as a function of position and time gives the degree of cooperativity (n) and the concentration of ligand required for half maximal activity (K_0.5) for the Ca²⁺ – dependent activation of PAD2. This work establishes a high-throughput and label-free method for studying enzyme-ligand binding interactions and widens the applicability of microfluidics and matrix-assisted laser desorption/ionization mass spectrometry (MALDI) imaging mass spectrometry.     

Novel Delta‐Opioid‐Receptor‐Selective Ligands in the 14‐Alkoxy‐Substituted Indolo‐ and Benzofuromorphinan Series

Several new indolo‐ and benzofuromorphinans substituted at the positions 5 and 14 were prepared and tested in vitro by means of opioid‐receptor binding and functional ([³⁵S]GTPγS binding) assays. All compounds 1 – 11 displayed high affinity for δ opioid‐binding sites (Table 1). Compound 4 proved to be an agonist, and all other compounds were antagonists. The presence of a Me group at position 5 induced no change in δ affinity (see 1 vs. 3 ), but decreased the μ and κ affinities. An EtO group at position 14 conferred a very high affinity and also high selectivity to δ opioid receptors (see 2 and 10 ). Chain elongation of the 14‐alkoxy group resulted in compounds with reduced δ affinity and selectivity (see 4 and 11 and also 5 – 9 ). The results of the present study indicate that the 5‐ and 14‐positions of indolo‐ and benzofuromorphinans represent critical sites that could be a trigger to develop new compounds with increased δ affinity and/or selectivity.     

Attachment of 80S ribosome to lipid monolayers at air/water interface: An electron microscopy study

The adsorption of 80S ribosome from rat liver to the surface of lipid monolayers at the air/water interface was examined by electron microscopy (EM) using a negative staining method. The results showed that, a large number of 80S ribosomes can be adsorbed to the lipid monolayers containing positively charged octadecylamine (SA), whereas the adsorption of ribosomes to the surface of neutral or negatively charged lipid monolayers was negligible. There existed a proper ratio of SA to complemented neutral lipids which facilitated the maximum binding of ribosomes. Increasing the subphase pH value will enhance the adsorption of ribosome, but when raising the subphase concentrations of K⁺, Mg²⁺ and glycerol, the adsorption of ribosomes can be weakened, suggesting that the driving forces of the adsorption mainly come from the electrostatic interactions between the ribosome and the lipids. The important characteristics of such interactions between the 80S rat liver ribosomes and the lipid membranes, as revealed by this new technology, which may help in the further understanding of the protein biosynthesis is discussed.     

Selectively Deoxyfluorinated N-Acetyllactosamine Analogues as 19F NMR Probes to Study Carbohydrate-Galectin Interactions

Galectins are widely expressed galactose-binding lectins implied, for example, in immune regulation, metastatic spreading, and pathogen recognition. N-Acetyllactosamine (Galβ1-4GlcNAc, LacNAc) and its oligomeric or glycosylated forms are natural ligands of galectins. To probe substrate specificity and binding mode of galectins, we synthesized a complete series of six mono-deoxyfluorinated analogues of LacNAc, in which each hydroxyl has been selectively replaced by fluorine while the anomeric position has been protected as methyl β-glycoside. Initial evaluation of their binding to human galectin-1 and -3 by ELISA and ¹⁹F NMR T₂-filter revealed that deoxyfluorination at C3, C4′ and C6′ completely abolished binding to galectin-1 but very weak binding to galectin-3 was still detectable. Moreover, deoxyfluorination of C2′ caused an approximately 8-fold increase in the binding affinity towards galectin-1, whereas binding to galectin-3 was essentially not affected. Lipophilicity measurement revealed that deoxyfluorination at the Gal moiety affects log P very differently compared to deoxyfluorination at the GlcNAc moiety.     

Structure of the Complex of [Ru(tpm)(dppz)py]2+ with a B‐DNA Oligonucleotide—A Single‐Substituent Binding Switch for a Metallo‐Intercalator

We report the synthesis of three new complexes related to the achiral [Ru(tpm)(dppz)py]²⁺ cation (tpm=tripyridazole methane, dppz=dipyrido[3,2‐a:2′,3′‐c]phenazine, py=pyridine) that contain an additional single functional group on the monodentate ancillary pyridyl ligand. Computational calculations indicate that the coordinated pyridyl rings are in a fixed orientation parallel to the dppz axis, and that the electrostatic properties of the complexes are very similar. DNA binding studies on the new complexes reveal that the nature and positioning of the functional group has a profound effect on the binding mode and affinity of these complexes. To explore the molecular and structural basis of these effects, circular dichroism and NMR studies on [Ru(tpm)(dppz)py]Cl₂ with the octanucleotides d(AGAGCTCT)₂ and d(CGAGCTCG)₂, were carried out. These studies demonstrate that the dppz ligand intercalates into the G²–A³ step, with {Ru(tpm)py} in the minor groove. They also reveal that the complex intercalates into the binding site in two possible orientations with the pyridyl ligand of the major conformer making close contact with terminal base pairs. We conclude that substitution at the 2‐ or 3‐position of the pyridine ring has little effect on binding, but that substitution at the 4‐position drastically disrupts intercalative binding, particularly with a 4‐amino substituent, because of steric and electronic interactions with the DNA. These results indicate that complexes derived from these systems have the potential to function as sequence‐specific light‐switch systems.     

Site-specific control of N7-metal coordination in DNA by a fluorescent purine derivative

A synthetic strategy that utilizes O6‐protected 8‐bromoguanosine gives broad access to C8‐guanine derivatives with phenyl, pyridine, thiophene, and furan substituents. The resulting 8‐substituted 2′‐deoxyguanosines are push–pull fluorophores that can exhibit environmentally sensitive quantum yields (Φ=0.001–0.72) due to excited‐state proton‐transfer reactions with bulk solvent. Changes in nucleoside fluorescence were used to characterize metal‐binding affinity and specificity of 8‐substituted 2′‐deoxyguanosines. One derivative, 8‐(2‐pyridyl)‐2′‐deoxyguanosine (2PyG), exhibits selective binding of Cu^II, Ni^II, Cd^II, and Zn^II through a bidentate effect provided by the N7 position of guanine and the 2‐pyridyl nitrogen atom. Upon incorporation into DNA, 2‐pyridine‐modified guanine residues selectively bind to Cu^II and Ni^II with equilibrium dissociation constants (K_d) that range from 25 to 850 nM ; the affinities depend on the folded state of the oligonucleotide (duplex>G‐quadruplex) as well as the identity of the metal ion (Cu>Ni?Cd). These binding affinities are approximately 10 to 1 000 times higher than for unmodified metal binding sites in DNA, thereby providing site‐specific control of metal localization in alternatively folded nucleic acids. Temperature‐dependent circular‐dichroism studies reveal metal‐dependent stabilization of duplexes, but destabilization of G‐quadruplex structures upon adding Cu^II to 2PyG‐modified oligonucleotides. These results demonstrate how the addition of a single pyridine group to the C8 position of guanine provides a powerful new tool for studying the effects of N7 metalation on the structure, stability, and electronic properties of nucleic acids.     

On Ammonia Binding to the Oxygen‐Evolving Complex of Photosystem II: A Quantum Chemical Study

A recent EPR study (M. Perrez Navarro et al., Proc. Natl. Acad. Sci.­ 2013 , 110, 15561) provided evidence that ammonia binding to the oxygen‐evolving complex (OEC) of photosystem II in its S₂ state takes place at a terminal‐water binding position (W1) on the “dangler” manganese center Mn_A. This contradicted earlier interpretations of ¹⁴N electron‐spin‐echo envelope modulation (ESEEM) and extended X‐ray absorption fine‐structure (EXAFS) data, which were taken to indicate replacement of a bridging oxo ligand by an NH₂ unit. Here we have used systematic broken‐symmetry density functional theory calculations on large (ca. 200 atom) model clusters of an extensive variety of substitution patterns and core geometries to examine these contradictory pieces of evidence. Computed relative energies clearly favor the terminal substitution pattern over bridging‐ligand arrangements (by about 20–30 kcal mol^?1) and support W1 as the preferred binding site. Computed ¹⁴N EPR nuclear‐quadrupole coupling tensors confirm previous assumptions that the appreciable asymmetry may be accounted for by strong, asymmetric hydrogen bonding to the bound terminal NH₃ ligand (mainly by Asp61). Indeed, bridging NH₂ substitution would lead to exaggerated asymmetries. Although our computed structures confirm that the reported elongation of an Mn–Mn distance by about 0.15 Å inferred from EXAFS experiments may only be reproduced by bridging NH₂ substitution, it seems possible that the underlying EXAFS data were skewed by problems due to radiation damage. Overall, the present data clearly support the suggested terminal NH₃ coordination at the W1 site. The finding is significant for the proposed mechanistic scenarios of OEC catalysis, as this is not a water substrate site, and effects of this ammonia binding on catalysis thus must be due to more indirect influences on the likely substrate binding site at the O5 bridging‐oxygen position.     

A Functional Role for Aβ in Metal Homeostasis? N‐Truncation and High‐Affinity Copper Binding

Accumulation of the β‐amyloid (Aβ) peptide in extracellular senile plaques rich in copper and zinc is a defining pathological feature of Alzheimer′s disease (AD). The Aβ1–x (x=16/28/40/42) peptides have been the primary focus of Cu^II binding studies for more than 15 years; however, the N‐truncated Aβ4–42 peptide is a major Aβ isoform detected in both healthy and diseased brains, and it contains a novel N‐terminal FRH sequence. Proteins with His at the third position are known to bind Cu^II avidly, with conditional log K values at pH 7.4 in the range of 11.0–14.6, which is much higher than that determined for Aβ1–x peptides. By using Aβ4–16 as a model, it was demonstrated that its FRH sequence stoichiometrically binds Cu^II with a conditional K_d value of 3×10⁻¹⁴ M at pH 7.4, and that both Aβ4–16 and Aβ4–42 possess negligible redox activity. Combined with the predominance of Aβ4–42 in the brain, our results suggest a physiological role for this isoform in metal homeostasis within the central nervous system.     

A Functional Role for Aβ in Metal Homeostasis? N‐Truncation and High‐Affinity Copper Binding

Accumulation of the β‐amyloid (Aβ) peptide in extracellular senile plaques rich in copper and zinc is a defining pathological feature of Alzheimer′s disease (AD). The Aβ1–x (x=16/28/40/42) peptides have been the primary focus of Cu^II binding studies for more than 15 years; however, the N‐truncated Aβ4–42 peptide is a major Aβ isoform detected in both healthy and diseased brains, and it contains a novel N‐terminal FRH sequence. Proteins with His at the third position are known to bind Cu^II avidly, with conditional log K values at pH 7.4 in the range of 11.0–14.6, which is much higher than that determined for Aβ1–x peptides. By using Aβ4–16 as a model, it was demonstrated that its FRH sequence stoichiometrically binds Cu^II with a conditional K_d value of 3×10^?14 M at pH 7.4, and that both Aβ4–16 and Aβ4–42 possess negligible redox activity. Combined with the predominance of Aβ4–42 in the brain, our results suggest a physiological role for this isoform in metal homeostasis within the central nervous system.     

Kinetic Study of Hydrogen–Deuterium Exchange of Glutamic Acid in Deuterated Hydrochloric Acid Solution

The kinetics of the hydrogen–deuterium (H–D) exchange at both the methine (alpha) and methylene (gamma) positions of glutamic acid in deuterated hydrochloric acid solution has been studied in the temperature range of 383–433 K by ¹H NMR detection. The reaction rates of H–D exchange at the two positions were described by applying multivariable linear regression (MLR) analysis and are determined as v = k[Glu]^3.3[D₃O⁺]^1.5 mol L^?1 h^?1 with k = 3.52 × 10¹⁶ × exp (–1.37 × 10⁵/RT) mol^?3.8 L h^?1 for the alpha position as well as v = k[Glu]^1.0[D₃O⁺]^0.45 mol L^?1 h^?1 with k = 1.77 × 10¹² × exp (–0.99 × 10⁵/RT) mol^?0.45 L h^?1 for the gamma position. The Arrhenius activation energy (E_a) at the gamma position is less than that at the alpha position, which implies that the deuteration reaction at the gamma position proceeded more easily.     

Synthesis of Unnatural Lipohilic N-(9H-Fluoren-9-ylmethoxy)carbonyl-Substituted α-Amino Acids and Their Incorporation into Cyclic RGD-Peptides: A structure-activity study

The α_v/β₃ integrin is implicated in human tumor metastasis and angiogenesis. It has been shown that structures of the sequence cyclo(-Arg¹-Gly²-Asp³-D -Phe⁴-Xaa⁵-) ( I ) and cyclo(-Arg¹-Gly²-Asp³-Phe⁴-D -Xaa⁵-) ( II ) bind with high affinity and the latter with high selectivity to this receptor. The residues Xaa and D -Xaa accept a broad variety of amino acids. Here, we report on the synthesis, activities, and conformational analysis of cyclic Arg-Gly-Asp (RGD) peptides containing liophilic amino acids Xaa or D -Xaa in position 5. For I , these were (2S)-2-aminohexadecanoic acid (Ahd) and N′-hexadecylglycine (Hd-Gly) and in II , D -Ahd and Hd-Gly, and, for control purposes, Ahd were incorporated (Fig. 1). The enantiomerically pure a-amino acids were obtained by non-enantioselective synthesis and subsequent enzymatic separation of isomers using acylase I (Scheme). Hd-Gly was prepared in a modified procedure according to Stewart from ethyl bromoacetate and hexadecylamine (Scheme). The synthesis and physicochemical properties of the corresponding (9H-fluoren-9-ylmethoxy)carbonyl (Fmoc) derivatives, compatible with solid-phase peptide synthesis, are described. Structure elucidation by NMR reveals that the lipid modification has no significant impact on the template structures when incorporated into them. For peptides I with Xaa = Ahd or Hd-Gly ( 1 or 2 ), a βII′/γ-turn-like arrangement with D -Phe in i+1 position of the β-turn is found. Peptides II with D -Xaa = D -Ahd or Hd-Gly ( 3 or 4 ) exhibit a βII′/γ-turn conformation with Gly in i+1 position of the β-turn, whereas II with Ahd instead of D -Xaa, i.e., lacking a D -amino acid in position 4 or 5 ( 5 ). adopts no defined conformation. However, in assays of receptor specificity employing human α_vv/β₃ integrin, the compounds exhibit IC₅₀ values ranging from nanomolar to less than millimolar. These results indicate that although the arrangement of the pharmacophoric groups is preserved in the target compounds, the biological activity is highly dependent on spatial requirements of the lipid anchor in the receptor binding pocket. Obviously, only certain positions do not affect the binding.     

人类A3腺苷受体拮抗剂1,2,4-三唑并[1,5-α]喹喔啉衍生物的QSAR研究

采用遗传算法构建了27种人类腺苷受体拮抗剂1,2,4-三唑并[1,5-α]喹喔啉衍生物与受体之间的亲和性的QSAR模型. 为得到理想模型, 计算了拓扑学、热力学、空间、电子拓扑状态和量子化学描述符. 结合这些参数得到最终模型: pK_i＝13.407－0.027*F_C－8^E－0.033*F_C－8^N＋0.845*Atype_C_28－19.493*Shadow_XYfrac.计算得到的统计学指标为: LOF＝0.291, r²＝0.766, r_adj²＝0.723, F-test＝17.974, PRESS＝3.469, CV-r²＝0.791. 通过对模型进行分析, 得到如下结论: 降低C-8位亲电、亲核原子的前线电子密度的权重和分子在XY平面的投影分数, 增加疏水性原子类型描述符Atpye_C_28的值, 都对增加化合物分子与受体的亲和性有利. 利用此模型合理的设计了两个新的化合物, 并预测具有较高的结合活性. 该研究为喹喔啉衍生物作为人类A₃腺苷受体拮抗剂的结构改造提供理论指导, 并为进一步研究受体与配体亲和性机理奠定理论基础.     

A Mini‐Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class

Nucleolytic ribozymes catalyze site‐specific cleavage of their phosphodiester backbones. A minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved stem P1 while retaining wild‐type activity. Atomic mutagenesis revealed that nitrogen atoms N1 and N3 of the adenine‐6 at the cleavage site are indispensable for cleavage. By NMR spectroscopy, a pK_a value of 5.1 was determined for a ¹³C2‐labeled adenine at this position in the twister ribozyme, which is significantly shifted compared to the pK_a of the same adenine in the substrate alone. This finding pinpoints at a potential role for adenine‐6 in the catalytic mechanism besides the previously identified invariant guanine‐48 and a Mg²⁺ ion, both of which are directly coordinated to the non‐bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence stems from the observation that Mn²⁺ or Cd²⁺ accelerated cleavage of phosphorothioate substrates. The relevance of this metal ion binding site is further emphasized by a new 2.6 Å X‐ray structure of a 2′‐OCH₃‐U5 modified twister ribozyme.     

Exploring the Effect of Ligand Structural Isomerism in Langmuir–Blodgett Films of Chiral Luminescent EuIII Self‐Assemblies

Here we have investigated the influence of the antenna group position on both the formation of chiral amphiphilic Eu^III‐based self‐assemblies in CH₃CN solution and, on the ability to form monolayers on the surface of quartz substrates using the Langmuir–Blodgett technique, by changing from the 1‐naphthyl ( 2(R) , 2(S) ) to the 2‐naphthyl ( 1(R) , 1(S) ) position. The evaluation of binding constants of the self‐ assemblies in CH₃CN solution was achieved using conventional techniques such as UV/Visible and luminescence spectroscopies along with more specific circular dichroism (CD) spectroscopy. The binding constants obtained for EuL , EuL₂ and EuL₃ species in the case of 2‐naphthyl derivatives were comparable to those obtained for 1‐naphthyl derivatives. The analysis of the changes in the CD spectra of 1(R) and 1(S) upon addition of Eu^III not only allowed us to evaluate the values of the binding constants but the resulting recalculated spectra may also be used as fingerprints for assignment of the chiral self‐assembly species formed in solution. The obtained monolayers were predominantly formed from EuL₃ (≈85 %) with the minor species present in ≈15 % EuL₂ .     

Relative binding orientations of adenosine A1 receptor ligands — A test case for Distributed Multipole Analysis in medicinal chemistry

Summary The electrostatic properties of adenosine-based agonists and xanthine-based antagonists for the adenosine A₁ receptor were used to assess various proposals for their relative orientation in the unknown binding site. The electrostatic properties were calculated from distributed multipole representations of SCF wavefunctions. A range of methods of assessing the electrostatic similarity of the ligands were used in the comparison. One of the methods, comparing the sign of the potential around the two molecules, gave inconclusive results. The other approaches, however, provided a mutually complementary and consistent picture of the electrostatic similarity and dissimilarity of the molecules in the three proposed relative orientations. This was significantly different from the results obtained previously with MOPAC AM1 point charges. In the standard model overlay, where the aromatic nitrogen atoms of both agonists and antagonists are in the same position relative to the binding site, the electrostatic potentials are so dissimilar that binding to the same receptor site is highly unlikely. Overlaying the N⁶-region of adenosine with that near C8 of theophylline (the N⁶-C8 model) produces the greatest similarity in electrostatic properties for these ligands. However, N⁶-cyclopentyladenosine (CPA) and 1,3-dipropyl-8-cyclopentylxanthine (DPCPX) show greater electrostatic similarity when the aromatic rings are superimposed according to the flipped model, in which the xanthine ring is rotated around its horizontal axis. This difference is mainly attributed to the change in conformation of N⁶-substituted adenosines and could result in a different orientation for theophylline and DPCPX within the receptor binding site. However, it is more likely that DPCPX also binds according to the N⁶-C8 model, as this model gives the best steric overlay and would be favoured by the lipophilic forces, provided that the binding site residues could accommodate the different electrostatic properties in the N⁶/N7-region. Finally, we have shown that Distributed Multipole Analysis (DMA) offers a new, feasible tool for the medicinal chemist, because it provides the use of reliable electrostatic models to determine plausible relative binding orientations.Abbreviations DMA distributed multipole analysis - SCF self-consistent field - CPA N⁶-cyclopentyladenosine - DPCPX 1,3-dipropyl-8-cyclopentylxanthine - R-PIA R-1-phenyl-2-propyladenosine - S-PIA S-1-phenyl-2-propyladenosine     

Syntheses of Biphenyl Analogues of AP7, a New Class of Competitive N-Methyl-D-aspartate (NMDA) Receptor Antagonists

Syntheses of a series of enantiomerically pure, substituted analogues 7b–t of SDZ EAB 515 ( 7a ) were described (Schemes 1 and 2). Affinites for the NMDA receptor were measured ([³H]CGP-39653 binding assay) and competitive NMDA antagonistic potencies determined in a functional test (rat neocortical slice preparation). Structure-activity relationships show that attachment of an OH group at position 4 of the chain-inserted benzene ring of the biphenyl moiety and/or expansion of the angle between the planes of the two benzene rings by ortho-substituents increase in vitro activities into the low nanomolar range.     

Nucleotide/Protein Interaction: Energetic and Structural Features of Na,K-ATPase

Microcalorimetric titrations allow to recognize and investigate high-affinity ligand binding to Na,K-ATPase. Titrations with the cardiac glycoside Ouabain, which acts as a specific inhibitor of the enzyme, have provided not only the thermodynamic parameters of high-affinity binding with a stoichiometric coefficient of about 0.6 but also evidence for low-affinity binding to the lipid. The marked enthalpic contribution of -95 kJ mol^-1 at 298.2 K is partially compensated by a large negative entropy change, attributed to an increased interaction between water and the protein. The calorimetric ADP and ATP titrations at 298.2 K are indicative of high-affinity nucleotide binding either in 3 mM NaCl, 3 mM MgCl₂ or at high ionic strength such as 120 mM choline chloride. However, no binding is detected in the buffer solution alone at low ionic strength. The affinities for ADP and ATP are similar, around 10⁶ M^-1 and the stoichiometric coefficients are close to that of Ouabain binding. The exothermic binding of ADP is characterized by a ΔH and ΔS value of -65 kJ mol^-1 and -100 J mol^-1 K^-1, respectively. TheΔH value for ATP binding is larger than for ADP and is compensated by a larger, unfavorable ΔS value. This leads to an enthalpy/entropy compensation, which could express that H-bond formation represents the major type of interaction. As for Ouabain, the negative ΔS values that are also characteristic of nucleotide binding can indicate an increase of solvate interaction with the protein due to a conformational transition occurring subsequent to the binding process. The resulting binding constants are discussed with regard to the results of other studies employing different techniques. A molecular interaction model for nucleotide binding is suggested. This revised version was published online in July 2006 with corrections to the Cover Date.     

Voltammetric studies of the interaction of quinacrine with DNA

The binding interaction of the antimalarial drug quinacrine with herring sperm deoxyribonucleic acid (DNA) has been studied by square wave voltammetry. The binding parameters, the binding constant K and the binding site size s, were obtained simultaneously by the analysis of bound and free quinacrine concentration corresponding to the limits of slow and fast binding kinetics compared to the experimental timescale. The binding constant and the binding site size for the interaction of quinacrine with DNA were K=1.59 (±0.18)×10⁵ M^–1 and s=7.1 (±0.15) base pairs and K=7.35 (±0.83)×10⁵ M^–1, s=6.2 (±0.02) base pairs for the limiting conditions of static and mobile binding equilibrium respectively. The standard Gibbs free energy change (G⁰=–RT ln K) is approximately –29.67 kJ/mol at 25 °C, which highlights the spontaneity of the binding of quinacrine with DNA. The binding of quinacrine to herring sperm DNA results in peak potential shifts in voltammetric and a red shift in UV-absorption measurements. The ionic strength dependence of the binding constant is not large. Furthermore, the relative viscosity of DNA increases in the presence of quinacrine. These characteristics strongly support the intercalation of quinacrine into DNA. The results also show that the intercalation of quinacrine into DNA may occur at approximately every seventh base pair.     

Design and Theoretical Study of Nickel Catalysts for Syndiotactic Polyolefins

A nickel catalyst was nodeled with ligand L^2,[NH=CH-CH=CH-0]^-,which should have potential use as a syndiotactic plyolefin catalyst,and the reaction mechanism was studied by theoretical calculations using the density functinal method at the B3LYP/LANL2MB level.The mechanism involves the formation of the intermediate [NiL^2Me]^ ,in which the metal occupies a T-shaped geometry.This intermediate has two possible structures with the methyl group trans either to the oxygen or to the nitrogen atom of L^2.The results show that both structures can lead to the desired product via similar reaction paths,A and B.Thus,the polymerization could be considered as taking place either with the alkyl group occupying the position trans to the Ni-0 or trans to the Ni-N bond in the catalyst.The polymerization process thus favors the catalysis of syndiotactic polyolefins.The syndiotactic synthesis effects could also be enhanced by varations in the ligand substituents.From energy considerations,we can conclude that it is more favorable for the methyl ttrans-O position to form a complex than to occupy the trans-N position.From bond length considerations,it is also more favoured for ethene to occupy the trans-O position than to occupy the trans-N position.