Showing papers in "Journal of the American Chemical Society in 1995"

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

Abstract: We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are determined using a 6-31G* basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small molecules to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the molecular conformation used in the charge determination. The new van der Waals parameters have been derived from liquid simulations and include hydrogen parameters which take into account the effects of any geminal electronegative atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce experimental vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et al., but a complex set of 4 and yj parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides has been developed for the peptide backbone.

Hydrothermal Synthesis of a Metal-Organic Framework Containing Large Rectangular Channels

Abstract: The great importance of microporous solids such as zeolites in adsorption, ion exchange, and shape-selective catalysis has stemmed from their ability to reversibly bind molecules and ions within their extended channels.' Recently, a major research effort has focused on using the molecular building block approach to generate analogous materials with 3-D organic? metal-~rganic,~ and inorganic4 frameworks. Strategies for the construction of these solids have respectively utilized hydrogenbonding interactions, metal-ligand coordination, and metalcluster copolymerization reactions to link their molecular components. A number of such frameworks have been found to exhibit desirable zeolitic properties such as stability and microporosity of the f r a m e w ~ r k , ~ ~ . ~ guest e x ~ h a n g e , ~ ~ , ~ and selective catalytic activityS6 In this report we present hydrothermal synthesis as a route to accessing crystalline, metal-organic, open frameworks having extended channel systems and composed of uncommon metal coordination. This will be demonstrated by describing the synthesis, structure, and properties of the extended network in crystalline Cu(4,4'-bpy)1 .s*NO~(HZO)I.Z~. A mixture of Cu(NO3)2*2.5H20 (0.17 g, 0.74 mmol), 4,4'bpy (0.17 g, 1.1 1 mmol), and 1,3,5-triazine (0.040 g, 0.49 \"01) in 15 mL of deionized water was transferred to a stainless steel bomb, which was sealed and placed in a programmable fumace. The temperature was raised to 140 \"C at 5 deglmin and held at that temperature for 24 h, then cooled at 0.1 deglmin to 90 OC and held for 12 h, then cooled at the same rate to 70 \"C and held for another 12 h, and finally cooled down to room temperature at 0.1 deglmin. The resulting rectangular parallelepiped orange crystals of Cu(4,4'-bpy), .5*N03(H20)1.25 were collected and washed with deionized water (3 x 5 mL) and ethanol (2 x 5 mL) and then air dried to give 0.25 g (87% yield based on b p ~ ) . ~ , ~ This compound is stable in air and is insoluble in water and common organic solvents. X-ray structure determination9 on a single crystal isolated from the reaction mixture was performed to reveal an extended cationic framework constructed from the building unit shown in Figure 1. Here, symmetry equivalent and slightly distorted trigonal planar copper(1) centers (N7-Cu-N1 = 125.4(2)\", N13a-Cu-N1 = 125.7(2)\", and N13a-Cu-N7 = 108.5(2)\")

Assembly of multicomponent protein films by means of electrostatic layer-by-layer adsorption

Abstract: Multilayer films which contain ordered layers of more than one protein species were assembled by means of altemate electrostatic adsorption mostly with positively charged poly(ethy1enimine) (PEI) or with negatively charged poly(styrenesu1fonate) (PSS). Water-soluble proteins used are cytochrome c (Cyt), myoglobin (Mb), lysozyme (Lys), histone f3, hemoglobin (Hb), glucoamylase (GA), and glucose oxidase (GOD). Charged protein layers formed multilayers with linear polymers acting as glue or filler. The assembly was monitored by a quartz crystal microbalance and W spectroscopy. Linear film growth was observed up to at least 25 molecular layers. The assembly of Mb and Lys, both positively-charged, was realized in altemation with PSS in the form of {PEI/PSS + (Mb/PSS)2 + (MbPSS/Lys/PSS)d}. The assembly of oppositely-charged (at pH 6.5) Lys and GOD consists from Lys and GOD layers separated by a polycatiodpolyanion bilayer: {PEYPSSPEI f (PSS/Lys)2 + PSSPEI f (GOD/PEI)6}. Hb was assembled as “positive” unit at pH 4.5 (in alternation with PSS) and as “negative” unit at pH 9.2 (in altemation with PEI). A multilayer consisting of alternating montmorillonite, PEI, and GOD layers was also assembled. These biomolecular architecture open a way to construct artificially orchestrated protein systems that can carry out complex enzymic reactions.

Isotropic Spectra of Half-Integer Quadrupolar Spins from Bidimensional Magic-Angle Spinning NMR

Abstract: Interest in the solid state nuclear magnetic resonance (NMR) spectroscopy of half-integer quadrupolar spins is strongly stimulated by the roles that these isotopes play in a variety of important systems such as minerals, structural ceramics, semiconductors, glasses, and catalysts.' In spite of the partly ionic nature of these materials, quadrupole interactions with surrounding electric field gradients often broaden the solid state NMR line shapes of these nuclei into the MHz range. Although most of this broadening can be circumvented by limiting excitations to the central -l/2 +l/2 transition? second-order effects can widen the resulting resonances and prevent the resolution of chemically inequivalent sites. In contrast to what happens in spin-'/2 spectroscopy, no single-axis spinning techniques are available for canceling the effects of these second-order anisotropies. Still, as is briefly discussed in the present Communication, bidimensional NMR methods involving multiple-quantum excitation in combination with fixed-angle sample spinning are capable of refocusing second-order quadrupolar effects and can thus be used to acquire highly resolved spectra devoid from quadrupolar, shielding, or dipolar anisotropies. Central-transition NMR experiments manage to avoid firstorder quadrupolar broadenings owing to the Hamiltonian's quadratic dependence on the S, angular momentum.2 The following term in the quadrupolee the last two, however, are anisotropic and can broaden the central transitions of powdered samples over several kHz. The effects of these anisotropies can be scaled by rapidly spinning the sample at an axis Ps3 This leads to time averaged NMR frequencies

Monolayers in Three Dimensions: NMR, SAXS, Thermal, and Electron Hopping Studies of Alkanethiol Stabilized Gold Clusters

Abstract: Gold clusters stabilized by chemisorbed monolayers of octane-, dodecaneor hexadecanethiolate have been investigated in solution and in the solid phase. These materials can be pumped free of solvent to form a dark brown solid that can be re-dissolved in nonpolar solvents. Their exceptional stability suggests they be viewed as cluster compounds. The self-assembled alkanethiolate monolayers stabilizing the metal clusters can be investigated using techniques that are insufficiently sensitive for study of a monolayer on a flat surface, e.g., 'H and I3C NMR, elemental analysis, differential scanning calorimetry (DSC), thermogravimetry (TGA), and diffusion-ordered NMR spectroscopy (DOSY). Results from such measurements, combined with small-angle X-ray scattering (SAXS) data on solutions of the clusters and images from scanning tunneling (STM), and atomic force microscopy (AFM), are consistent with a small, monodisperse (12 8, radius) gold core, which modeled as a sphere contains -400 Au atoms and -126 alkanethiolate chains, or if modeled as a cuboctahedral structure contains 309 Au atoms and -95 alkanethiolate chains. High-resolution NMR spectra of cluster solutions display well-defined resonances except for methylenes nearest the gold interface; the absence of the latter resonances is attributed to a combination of broadening mechanisms based on the discontinuous change in magnetic susceptibility at the metal-hydrocarbon interface and residual dipolar interactions. Films of the dry, solid cluster compound on interdigitated array electrodes exhibit current-potential responses characteristic of electron hopping conductivity in which electrons tunnel from Au core to Au core. The electron hopping rate decreases and the activation barrier increases systematically at longer alkane chain length. The results are consistent with electron transport rate control being a combination of thermally activated electron transfer to create oppositely charged Au cores (cermet theory) and distance-dependent tunneling (8 = 1.2 A-1) through the oriented alkanethiolate layers separating them. The self-organization of alkanethiols chemisorbed on planar Au surfaces has generated intense interest in understanding its chemical basis.' The two-dimensional character of self-assembled monolayers places limits, however, on the experiments by which they can be probed when they are chemisorbed on planar Au surfaces, e.g.,I wetting, helium diffraction, scanning probe, interfacial electron transfers, FTIR spectroscopy, etc. An *Address correspondence to this author at the University of North +Department of Chemistry, University of Illinois, Urbana, IL. * W. R. Grace and Co, Washington Research Center, 7379 Route 32, 3 Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Department of Chemistry, University of Oregon, Eugene, OR97403II Oak Ridge National Laboratories. # Department of Physics and Astronomy. University of North Carolina. @ Abstract published in Advance ACS Abstracts, December 1, 1995. (1) (a) DuBois L. H.; Nuzzo, R. G. Annu. Rev. Chem. Phys. 1992, 43, 437. (b) Laibinis, P. E.; Whitesides, G. M.; Allara D. L.; Tao, Y.-T.; Parikh, A. N.; Nuzzo, R. G. J. Am. Chem. Soc. 1991,133, 7152. (c) Chidsey, C. E. D.; Liu, G.; Scoles, G.; Wang, J. Langmuir, 1990, 6, 1804. (d) Fenter, P.; Eisenberger, P.; Liang, K. S. Phys. Rev. Let?. 1993, 70, 2447. (e) Chidsey, C. E. D. Science 1991,251,919. (0 Chailapakul, 0.; Sun, L.; Xu C.; Crooks, R. M. J. Am. Chem. SOC. 1993, 115, 12439. (g) Nemetz, A; Fischer T.; Ulman, A,; Knoll, W. J. Chem. Phys. 1993, 987. (h) Schneider, T. W.; Buttry, D. A. J. Am. Chem. SOC. 1993,115, 12391. (i) Widrig, C. A,; Alves, C. A.; Porter, M. D. J. Am. Chem. Soc. 1991, 123, 2805. (j) Kim, Y.-T.; McCarley, R. L.; Bard A. J. J. Phys. Chem. 1992, 96, 7416. Carolina. Columbia, MD 2 1044-4098.

Multiple-Quantum Magic-Angle Spinning NMR: A New Method for the Study of Quadrupolar Nuclei in Solids

Abstract: Whereas solid state isotropic spectra can be obtained from spin-'/2 nuclei by fast magic-angle spinning (MAS), this methodology fails when applied on half-integer quadrupoles due to the presence of non-negligible secondorder anisotropic effects. Very recently, however, we have shown that the combined use of MAS and bidimensional multiple-quantum (MQ) spectroscopy can refocus these anisotropies; the present paper discusses theoretical and experimental aspects of this novel MQMAS methodology and illustrates its application on a series of sodium salts. It is shown that even under fixed magnetic field operation, a simple model-free inspection of the peaks in a bidimensional MQMAS NMR spectrum can separate the contributions of isotropic chemical and isotropic quadrupolar shifts for different chemical sites. Moreover the anisotropic line shapes that can be resolved from these spectra are almost unaffected by excitation distortions and can thus be used to discern the values of a site's quadrupolar coupling constant and asymmetry parameter. The conditions that maximize the MQMAS signal-to-noise ratio for a ~pin-~/z are then explored with the aid of a simple analytical model, which can also be used to explain the absence of distortions in the anisotropic line shapes. The MQMAS method thus optimized was applied to the high-resolution 23Na NMR analysis of the multi-site ionic compounds NazTeO3, Na2S03, Na3P5010, and Na2HP04; extensions of the MQMAS NMR methodology to the quantitative analysis of inequivalent sites are also discussed and demonstrated.

Fluorescent Chemosensors Based on Energy Migration in Conjugated Polymers: The Molecular Wire Approach to Increased Sensitivity

Abstract: We demonstrate herein how conjugated polymers (molecular wires) can be used to interconnect (wire in series) receptors to produce fluorescent chemosensory systems with sensitivity enhancements over single receptor analogues. The enhancement mechanism in the polyreceptor materials is based on an energy migration scheme in which excitations, diffuse along the polymer backbone. Analyte binding produces trapping sites for the excitations which results in greatly attenuated emission intensity. Three different cyclophane-based receptor systems that bind paraquat were investigated. These systems are quenched by paraquat binding, and the quenching enhancements relative to a monomeric model compound were used to determine the efficiency of energy migration. Two polymers with related poly(phenyleneethyny1ene) structures were investigated, and the all-para system was found to exhibit more facile energy migration than the more electronically localized analogue that contained meta linkages. The para polyreceptor system was found to display a 65-fold enhancement in sensitivity to paraquat as compared to a model monoreceptor fluorescent chemosensor. However, we have determined that delocalization alone is not sufficient to produce facile energy migration, and the more delocalized polythiophenes appear to be less effective at energy migration than the para poly(phenyleneethyny1ene) material. Paraquat-induced fluorescent quenching studies on homologous polymers that lacked the cyclophane receptors were also performed. These results indicate that diffusive quenching by paraquat is enhanced by energy migration.

New sensitizer-modified calix[4]arenes enabling near-UV excitation of complexed luminescent lanthanide ions

Abstract: The synthesis is described of a series of calix[4]arenes with three different sensitizer chromophores (“antenna”) attached to the lower rim via a short spacer. In the Eu3+ and Tb3+ complexes of these calixarenes, photoexcitation of the antenna can induce lanthanide emission via intramolecular energy transfer. Although the higher energy of the Tb3+ luminescent state makes it more difficult to sensitize than in the case of Eu3+, especially a triphenylene antenna is found to have strong sensitizing ability toward not only Eu3+ but also Tb3+, allowing excitation of the lanthanide with wavelengths extending to 350 nm.

Excitation Sculpting in High-Resolution Nuclear Magnetic Resonance Spectroscopy: Application to Selective NOE Experiments

Abstract: Selective pulses are key elements in high-resolution NMR experiments, so great effort has been put into designing pulse shapes with desirable properties'-' In this communication we describe a selective excitation technique which, judged by the usual criteria, outdistances existing methods Our method gives constant phase and amplitude excitation over an easily adjustable bandwidth, can achieve given selectivity in a shorter time than existing methods, has no out-of-band sidelobes, and in exciting a multiplet, refocuses the evolution of scalar coupling The method is tolerant of radio-frequency (fl field inhomogeneity, and altering the net flip angle is easy The use of pulsed field gradients (PFGS)~,~ results in these crucial properties being achieved in a single scan, without difference spectroscopy or phase cycling: magnetization from outside the desired bandwidth is destroyed, thus simplifying the subsequent manipulation of the excited magnetization While PFGs have been used to tailor spectral response using single spin echoes, for example with the WATERGATE sequence,I0 and while selective 180" pulses have been used for selective excitation in conjunction with difference spectroscopy," the approach described here is more general The heart of the method is the double PFG spin echo (DPFGSE) sequence (-GI -S-GI-G~-S-G~-), in which S is any sequence of 13'pulses of any kind and the Gi are PFGs S induces the unitary transformation Us = R-,(/f?) R-y(t9) R,(a) R,(@ R,@) where, eg, R,(y) represents a rotation through an angle y about an axis E , and a, @, and 8 are arbitrary angles It can be shownI2 that applying a DPFGSE to isolated spins transforms a magnetization vector m = (m,,m,,m,) into a vector M with components

Self-assembled monolayers and multilayers of conjugated thiols, α,ω-dithiols, and thioacetyl-containing adsorbates. Understanding attachments between potential molecular wires and gold surfaces

Abstract: This paper describes tudies of the formation of self-assembled monolayers (SAMs) and multilayers on gold surfaces of rigid-rod conjugated oligomers that have thiol, cr,a.r-dithiol, thioacetyl, or cqor{'ithioacetyl end groups' The SAMs were analyzed usingillipsom-etry, X-ray photoelectron spectroscopy Q(PS), and infrared extemal reflectance spec6oscopy. The thiol moieties usually dominate adsorption on the gold sites; interactions with the conjugated z-systems are weaker. Rigid rod cr,al-dithiols form *r"*bli"r in which one thiol gouP binds to the surface while the second thiol moiety projects upward at the exposed surface of the SAlvl. ln sinr deprotection of the thiol moieties by deacylation of thioacetyl groups using NFlaOFtpermits formation of SAMs without having to isolate the oxidatively unstable free thiols. Moreover, directidsorption, without exogenous base, of the thioacetyl-terminated oligomers can be accomplished to generate gold surface-bound thiolates. However, in the non-base-promoted adsorptions, higher concentrations of the thioaietyl groups, relative to that of thiol groups, are required to achieve monolayer coverage in a given interval. A thiol-teinninated phenylene-ethynylene system was shown to have a tilt angle of the long molecular axis of <20o from the normal to the substrate surface. These aromatic o-ro-dithiol-derived monolayers provide the basis for studies leading to the design of molecular wires capable of bridging proximate

Superconducting and Semiconducting Magnetic Charge Transfer Salts: (BEDT-TTF)4AFe(C2O4)3.cntdot.C6H5CN (A = H2O, K, NH4)

Abstract: We have shown that the hexagonal layer motif [AM{sup III}(C{sub 2} O{sub 4}){sub 3}]{sup n-} containing bridging oxalate groups, which has been shown to form a wide variety of compounds with electronically inactive counter-cations having unusual cooperative magnetic properties, can also stabilize lattices containing the organic {pi}-donor BEDT-TTF. In the compounds whose structures we describe here, (BEDT-TTF){sub 4}AFe(C{sub 2}O{sub 4}){sub 3}.C{sub 6}H{sub 5} CN (A = H{sub 2}O, K, NH{sub 4}), the lattice is stabilized by C{sub 6} H{sub 5}CN molecules included in the hexagonal cavities. The packing of the BEDT-TTF in the A = K, NH{sub 4} phases is of a type not previously observed with spin-paired (BEDT-TTF){sub 2}{sup 2+} separated by closed shell (BEDT-TTF){sup 0}, while that in the superconductor is of {Beta}{double_prime} type. Both the superconducting A = H{sub 2}O and semiconducting A = K, NH{sub 4} phases contain high spin 3d{sup 5} Fe{sup III} with only very weak exchange interaction between them. Additional low temperature and high magnetic field experiments (e.g., of Schubnikov-de Haas oscillatory magnetoresistance) will be needed to delineate the Fermi surface in the superconductor. 36 refs., 11 figs., 4 tabs.

Chemical force microscopy: Exploiting chemically-modified tips to quantify adhesion, friction, and functional group distributions in molecular assemblies

Abstract: Chemical force microscopy (CFM) has been used to measure adhesion and friction forces between probe tips and substrates covalently modified with self-assembled monolayers (SAMs) that terminate in distinct functional groups. Robe tips have been modified with SAMs using a procedure that involves coating commercial Si3N4 cantilevedtip assemblies with a thin layer of polycrystalline Au followed by immersion in a solution of a functionalized thiol. This methodology provides a reproducible means for endowing the probe with different chemical functional groups. The spring constants and radii of the chemically modified cantilevedtip assemblies have been characterized to allow for quantitative friction and adhesion measurements. Au-coated Si and Si substrates have been treated with functionalized thiols and silanes, respectively, to produce SAM coated substrates terminating with different functional groups. A force microscope has been used to characterize the adhesive interactions between probe tips and substrates that have been modified with SAMs which terminate with COOH, CH3, and N H 2 functional groups in EtOH and HzO solvents. Force vs distance curves recorded under EtOH show that the interaction between functional groups decreases as follows: COOWCOOH > CHdCH3 > COOWCH3. The measured adhesive forces were found to agree well with predictions of the Johnson, Kendall, and Roberts (JKR) theory of adhesive contact and thus show that the observed adhesion forces correlate with the surface free energy of the molecular groups in EtOH. Electrostatic contributions to adhesive forces have also been studied using a COO-/NH3+ tip/surface in aqueous solution. Force vs distance curves recorded as a function of ionic strength show that the observed adhesive interaction decreases with increasing ionic strength. These results have been interpreted in terms of contact and noncontact contributions to the experimentally measured adhesive force. The friction forces between tips and samples modified with COOH and CH3 groups have also been measured as a function of applied load. The magnitude of the friction force was found to decrease in the following manner with different tip/sample functionalities: COOWCOOH > CH3/CH3 > COOWCH3. Friction forces between different chemical functional groups thus correlate directly with the adhesion forces between these same groups. Specifically, high friction is observed between groups that adhere strongly, while low friction is observed between weakly interacting functional groups. The dependence of friction forces on the tip and sample functionality is shown to be the basis for chemical force microscopy in which lateral force images are interpreted in terms of the strength of both adhesive groups.

Naked protein conformations : cytochrome c in the gas phase

Abstract: Ion mobility measurementsl have been used to obtain direct information about the conformers present for naked cytochrome c ions in the gas phase. The relative abundance of compact native-like conformations is negligible. However, a number of well-defined, partially folded conformers that are considerably more diffuse than the native structure are observed. These may be intermediates in the folding process. The results suggest that the gas phase is an environment that will allow access to complementary information about protein conformations and the dynamics of protein folding.' The development of gentle ionization techniques' has facilitated studies of biological molecules using mass spectrometry. Accurate measurements of molecular weigh& as well as sequence information*.h are becoming commonplace, and recently there have been several attempts to use mass spectrometry to deduce information about the three-dimensional structures of biological molecules. For example, the charge distribution generated by electrospray ionization' (ESI) has been shown to depend on the conformation of the protein in s o l u t i ~ n . ~ . ~ Mass spectrometry has been used to monitor 'W'H isotope exchange for proteins in solution\"' as well as in the gas phase.\".\" Finally, ion beam scattering experiment^'^.^^ have shown that protein ions in different charge states have different collision cross sections. The ion mobility measurementsl reported here resolve protein conformers on the basis of their different collision cross sections and provide precise cross sections for the conformers

Mechanism and Thermodynamics of Ion Selectivity in Aqueous Solutions of 18-Crown-6 Ether: A Molecular Dynamics Study

Abstract: We have performed extensive classical molecular dynamics simulations to examine the mechanism and thermodynamics for ion selectivity of 18-crown-6 ether in aqueous solutions. We have computed the free energy profiles or potentials of mean force and the corresponding binding free energies for M{sup +}:18-crown-6 (M{sup +} = K{sup +}, Na{sup +}, Rb{sup +}, Cs{sup +}) complexation in water. To the best of our knowledge, the present work is the first to employ the potential of mean force approach to the evaluation of crown ether selectivity in an aqueous solution. The resultant potentials of mean force indicate that minima free energy surfaces for K{sup +} and Na{sup +} are located at the crown ether center-of-mass. A well-defined second minimum is also observed in the potential of mean force of the Na{sup +}:18-crown-6 complex in water. It appears that K{sup +} is selected over Na{sup +} because of the greater free energy penalty associated with displacing water molecules from Na{sup +} as it approaches the crown ether. This leads to a substantial increase in the activation free energy and a decrease in the corresponding binding free energy for Na{sup +}:18-crown-6 complexation as compared to K{sup +}:18-crown-6. The selection of K{sup +} overmore » Rb{sup +} and Cs{sup +} is due to the size of the cation relative to that of the crown ether cavity. 26 refs., 11 figs., 2 tabs.« less

Novel Saccharide-Photoinduced Electron Transfer Sensors Based on the Interaction of Boronic Acid and Amine

Abstract: Two boronic acid systems, monoboronic acid 3 and diboronic acid 8, were synthesized. When saccharides form cyclic boronate esters with these boronic acids, the Lewis acid-base interaction between the boronic acid moiety and tertiary amine is strengthened; when saccharides form cyclic boronate esters with boronic acids the acidity of the boronic acid is enhanced. The strength of this acid-base interaction modulates the photoinduced electron transfer (PET) from the amine to anthracene. Both of these compounds show increased fluoresecence at pH 7.77 through supression of the photoinduced electron transfer from nitrogen to anthracene on saccharide binding, a direct result of the stronger boron-nitrogen bond. Compound 3 shows the typical selectivity of monoboronic acids towards saccharides. Compound 8 which has a cleftlike structure is particularly selective and sensitive for, glucose due to the formation of an intramolecular 1:1 complex between the two boronic acids and the 1,2- and 4,6-hydroxyls of glucose. This is the first example in which ditopic recognition of monosaccharides is achieved in a PET sensor system.

Interaction of Delta- and Lambda-[Ru(phen)2DPPZ]2+ with DNA: A Calorimetric and Equilibrium Binding Study

Abstract: Fluorescence and absorption spectroscopy, isothermal titration calorimetry, and viscosity measurements have been used to characterize the interaction of Delta and Lambda [Ru(phen)(2)DPPZ](2+) with calf thymus DNA. The method of continuous variations revealed two distinct binding stoichiometries for both Delta- and Lambda-DPPZ, corresponding to 0.7 and 3 mol of base pair/mol of ligand. Binding isotherms were obtained for the two enantiomers, both of which show strong binding to DNA, with K = 3.2 x 10(6) M(-1) bp and 1.7 x 10(6) M(-1) bp for the Delta and Lambda isomers, respectively, at 25 degrees C in solutions containing 50 mM NaCl. Titration calorimetry gave Delta H values of +0.3 kcal mol(-1) for Delta-DPPZ and +2.9 kcal mol(-1) for Lambda-DPPZ for their interaction with DNA. These small positive enthalpies, which were confirmed using thermal difference spectroscopy, indicated that the binding of these compounds to DNA is entropically driven. An enthalpy of +2.5 kcal mol(-1) was obtained for the binding of the parent compound, tris(phenanthroline)-Ru(II), to DNA. Titration of all three compounds into buffer gave a nonnegligible heat of dilution. The salt dependence of the binding constant was examined for both isomers. The slope SK = (delta logK/delta log[Na+]) was found to be 1.9 and 2.1 for the Delta and Lambda isomers, respectively. By using polyelectrolyte theory to interpret the observed salt dependence of the equilibrium constant, it can be shown that there is a significant nonelectrostatic contribution to the binding constant. Relative viscosity experiments showed that both Delta- and Lambda-DPPZ increase the length of rod-like DNA, in a manner consistent with binding by classical intercalation. Fluorescence energy transfer experiments provided additional evidence for the intercalation of Delta- and Lambda-[Ru(phen)(2)DPPZ](2+) into DNA.