A critical comparison of approximation methods and models for equilibrium properties of low-barrier hydrogen bonds

Recent experimental evidence has led to the conclusion that short, strong hydrogen bonds can stabilize transition states of enzyme catalyzed biochemical reactions. Evidence for such hydrogen bonds is the low value of the isotopic fractionation factor, phi, which is defined as the equilibrium constant for the generic reaction, R-H + DOH <--> R-D + HOH, where H is the hydrogen atom participating in the low-barrier hydrogen bond in a molecule R-H. In this work we assess two approximation methods for computing the isotopic fractionation factors for single and multidimensional systems containing a low-barrier hydrogen bond. These methods are WKB and an approach that corrects the classical partition function via a quantum correction factor. We find that the latter approach is universally accurate and applicable in both single and multidimensional systems containing a low-barrier hydrogen bond. We also assess two different models for the coupling of a molecule's low-barrier hydrogen bond to other degrees of freedom, both internal and external to the molecule, and show that each leads to a lowering of the fractionation factor.     

Some ruthenium complexes containing cyanocarbon ligands: syntheses, structures and extent of electronic communication in binuclear systems

The preparation of several ruthenium complexes containing cyanocarbon anions is reported. Deprotonation (KOBu^t) of [Ru(NCCH₂CN)(PPh₃)₂Cp]PF₆ (1) gives Ru{NCCH(CN)}(PPh₃)₂Cp (2), which adds a second [Ru(PPh₃)₂Cp]⁺ unit to give [{Ru(PPh₃)₂Cp}₂(μ-NCCHCN)]⁺ (3). Attempted deprotonation of the latter to give the μ-NCCCN complex was unsuccessful. Similar chemistry with tricyanomethanide anion gives Ru{NCC(CN)₂}(PPh₃)₂Cp (4) and [{Ru(PPh₃)₂Cp}₂{μ-NCC(CN)CN}]PF₆ (5), and with pentacyanopropenide, Ru{NCC(CN)C(CN)C(CN)₂}(PPh₃)₂Cp (6) and [{Ru(PPh₃)₂Cp}₂{μ-NCC(CN)C(CN)C(CN)CN}]PF₆ (7). The Ru(dppe)Cp* analogues of 6 and 7 (8 and 9) were also prepared. Thermolysis of 6 (refluxing toluene, 12 h) results in loss of PPh₃ and formation of the binuclear cyclic complex {Ru(PPh₃)Cp[μ-NC{C(CN)C(CN)₂}CN]}₂ (10). The solid-state structures of 2-4 and 8-10 have been determined and the nature of the isomers shown to be present in solutions of the binuclear cations 7 and 9 by NMR studies has been probed using Hartree-Fock and density functional theory.     

Tetranuclear and Octanuclear Manganese Carboxylate Clusters: Preparation and Reactivity of (NBu(n)(4))[Mn(4)O(2)(O(2)CPh)(9)(H(2)O)] and Synthesis of (NBu(n)(4))(2)[Mn(8)O(4)(O(2)CPh)(12)(Et(2)mal)(2)(H(2)O)(2)] with a "Linked-Butterfly" Structure

The reaction of Mn(O(2)CPh)(2).2H(2)O and PhCO(2)H in EtOH/MeCN with NBu(n)(4)MnO(4) gives (NBu(n)(4))[Mn(4)O(2)(O(2)CPh)(9)(H(2)O)] (4) in high yield (85-95%). Complex 4 crystallizes in monoclinic space group P2(1)/c with the following unit cell parameters at -129 degrees C: a = 17.394(3) ?, b = 19.040(3) ?, c = 25.660(5) ?, beta = 103.51(1) degrees, V = 8262.7 ?(3), Z = 4; the structure was refined on F to R (R(w)) = 9.11% (9.26%) using 4590 unique reflections with F > 2.33sigma(F). The anion of 4 consists of a [Mn(4)(&mgr;(3)-O)(2)](8+) core with a "butterfly" disposition of four Mn(III) atoms. In addition to seven bridging PhCO(2)(-) groups, there is a chelating PhCO(2)(-) group at one "wingtip" Mn atom and terminal PhCO(2)(-) and H(2)O groups at the other. Complex 4 is an excellent steppingstone to other [Mn(4)O(2)]-containing species. Treatment of 4 with 2,2-diethylmalonate (2 equiv) leads to isolation of (NBu(n)(4))(2)[Mn(8)O(4)(O(2)CPh)(12)(Et(2)mal)(2)(H(2)O)(2)] (5) in 45% yield after recrystallization. Complex 5 is mixed-valent (2Mn(II),6Mn(III)) and contains an [Mn(8)O(4)](14+) core that consists of two [Mn(4)O(2)](7+) (Mn(II),3Mn(III)) butterfly units linked together by one of the &mgr;(3)-O(2)(-) ions in each unit bridging to one of the body Mn atoms in the other unit, and thus converting to &mgr;(4)-O(2)(-) modes. The Mn(II) ions are in wingtip positions. The Et(2)mal(2)(-) groups each bridge two wingtip Mn atoms from different butterfly units, providing additional linkage between the halves of the molecule. Complex 5.4CH(2)Cl(2) crystallizes in monoclinic space group P2(1)/c with the following unit cell parameters at -165 degrees C: a = 16.247(5) ?, b = 27.190(8) ?, c = 17.715(5) ?, beta = 113.95(1) degrees, V = 7152.0 ?(3), Z = 4; the structure was refined on F to R (R(w)) = 8.36 (8.61%) using 4133 unique reflections with F > 3sigma(F). The reaction of 4 with 2 equiv of bpy or picolinic acid (picH) yields the known complex Mn(4)O(2)(O(2)CPh)(7)(bpy)(2) (2), containing Mn(II),3Mn(III), or (NBu(n)(4))[Mn(4)O(2)(O(2)CPh)(7)(pic)(2)] (6), containing 4Mn(III). Treatment of 4 with dibenzoylmethane (dbmH, 2 equiv) gives the mono-chelate product (NBu(n)(4))[Mn(4)O(2)(O(2)CPh)(8)(dbm)] (7); ligation of a second chelate group requires treatment of 7 with Na(dbm), which yields (NBu(n)(4))[Mn(4)O(2)(O(2)CPh)(7)(dbm)(2)] (8). Complexes 7 and 8 both contain a [Mn(4)O(2)](8+) (4Mn(III)) butterfly unit. Complex 7 contains chelating dbm(-) and chelating PhCO(2)(-) at the two wingtip positions, whereas 8 contains two chelating dbm(-) groups at these positions, as in 2 and 6. Complex 7.2CH(2)Cl(2) crystallizes in monoclinic space group P2(1) with the following unit cell parameters at -170 degrees C: a = 18.169(3) ?, b = 19.678(4) ?, c = 25.036(4) ?, beta = 101.49(1) degrees, V = 8771.7 ?(3), Z = 4; the structure was refined on F to R (R(w)) = 7.36% (7.59%) using 10 782 unique reflections with F > 3sigma(F). Variable-temperature magnetic susceptibility studies have been carried out on powdered samples of complexes 2 and 5 in a 10.0 kG field in the 5.0-320.0 K range. The effective magnetic moment (&mgr;(eff)) for 2 gradually decreases from 8.61 &mgr;(B) per molecule at 320.0 K to 5.71 &mgr;(B) at 13.0 K and then increases slightly to 5.91 &mgr;(B) at 5.0 K. For 5, &mgr;(eff) gradually decreases from 10.54 &mgr;(B) per molecule at 320.0 K to 8.42 &mgr;(B) at 40.0 K, followed by a more rapid decrease to 6.02 &mgr;(B) at 5.0 K. On the basis of the crystal structure of 5 showing the single Mn(II) ion in each [Mn(4)O(2)](7+) subcore to be at a wingtip position, the Mn(II) ion in 2 was concluded to be at a wingtip position also. Employing the reasonable approximation that J(w)(b)(Mn(II)/Mn(III)) = J(w)(b)(Mn(III)/M(III)), where J(w)(b) is the magnetic exchange interaction between wingtip (w) and body (b) Mn ions of the indicated oxidation state, a theoretical chi(M) vs T expression was derived and used to fit the experimental molar magnetic susceptibility (chi(M)) vs T data. The obtained fitting parameters were J(w)(b) = -3.9 cm(-)(1), J(b)(b) = -9.2 cm(-)(1), and g = 1.80. These values suggest a S(T) = (5)/(2) ground state spin for 2, which was confirmed by magnetization vs field measurements in the 0.5-50.0 kG magnetic field range and 2.0-30.0 K temperature range. For complex 5, since the two bonds connecting the two [Mn(4)O(2)](7+) units are Jahn-Teller elongated and weak, it was assumed that complex 5 could be treated, to a first approximation, as consisting of weakly-interacting halves; the magnetic susceptibility data for 5 at temperatures >/=40 K were therefore fit to the same theoretical expression as used for 2, and the fitting parameters were J(w)(b) = -14.0 cm(-)(1) and J(b)(b) = -30.5 cm(-)(1), with g = 1.93 (held constant). These values suggest an S(T) = (5)/(2) ground state spin for each [Mn(4)O(2)](7+) unit of 5, as found for 2. The interactions between the subunits are difficult to incorporate into this model, and the true ground state spin value of the entire Mn(8) anion was therefore determined by magnetization vs field studies, which showed the ground state of 5 to be S(T) = 3. The results of the studies on 2 and 5 are considered with respect to spin frustration effects within the [Mn(4)O(2)](7+) units. Complexes 2 and 5 are EPR-active and -silent, respectively, consistent with their S(T) = (5)/(2) and S(T) = 3 ground states, respectively.     

Synthesis, crystal structure, magnetic properties, and electronic structure of the new ternary vanadate CuMnVO4

A new magnetic oxide, CuMnVO4, was prepared, and its crystal structure was determined by single-crystal X-ray diffraction. The magnetic properties of CuMnVO4 were characterized by magnetic susceptibility and specific heat measurements, and the spin exchange interactions of CuMnVO4 were analyzed on the basis of spin-polarized electronic band structure calculations. CuMnVO4 contains MnO4 chains made up of edge-sharing MnO6 octahedra containing high-spin Mn2+ cations. Our work shows that CuMnVO4 undergoes a three-dimensional antiferromagnetic transition at approximately 20 K. Both the intrachain and interchain spin exchanges are antiferromagnetic, and the interchain spin exchange is not negligible compared to the intrachain spin exchange.     

Dihydrogen complexes of rhodium: [RhH2(H2)x (PR3)2]+ (R = Cy, iPr; x = 1, 2)

Addition of H2 (4 atm at 298 K) to [Rh(nbd)(PR3)2][BAr(F)4] [R = Cy, iPr] affords Rh(III) dihydride/dihydrogen complexes. For R = Cy, complex 1a results, which has been shown by low-temperature NMR experiments to be the bis-dihydrogen/bis-hydride complex [Rh(H)2(eta2-H2)2(PCy3)2][BAr(F)4]. An X-ray diffraction study on 1a confirmed the {Rh(PCy3)2} core structure, but due to a poor data set, the hydrogen ligands were not located. DFT calculations at the B3LYP/DZVP level support the formulation as a Rh(III) dihydride/dihydrogen complex with cis hydride ligands. For R = iPr, the equivalent species, [Rh(H)2(eta2-H2)2(P iPr3)2][BAr(F)4] 2a, is formed, along with another complex that was spectroscopically identified as the mono-dihydrogen, bis-hydride solvent complex [Rh(H)2(eta2-H2)(CD2Cl2)(P iPr3)2][BAr(F)4] 2b. The analogous complex with PCy3 ligands, [Rh(H)2(eta2-H2)(CD2Cl2)(PCy3)2][BAr(F)4] 1b, can be observed by reducing the H2 pressure to 2 atm (at 298 K). Under vacuum, the dihydrogen ligands are lost in these complexes to form the spectroscopically characterized species, tentatively identified as the bis hydrides [Rh(H)2(L)2(PR3)2][BAr(F)4] (1c R = Cy; 2c R = iPr; L = CD2Cl2 or agostic interaction). Exposure of 1c or 2c to a H2 atmosphere regenerates the dihydrogen/bis-hydride complexes, while adding acetonitrile affords the bis-hydride MeCN adduct complexes [Rh(H)2(NCMe)2(PR3)2][BAr(F)4]. The dihydrogen complexes lose [HPR3][BAr(F)4] at or just above ambient temperature, suggested to be by heterolytic splitting of coordinated H2, to ultimately afford the dicationic cluster compounds of the type [Rh6(PR3)6(mu-H)12][BAr(F)4]2 in moderate yield.     

Probing charge-transfer processes in helium nanodroplets by optically selected mass spectrometry (OSMS): charge steering by long-range interactions

Electron impact ionization of a helium atom in a helium nanodroplet is followed by rapid charge migration, which can ultimately result in the localization of the charge on an atomic or molecular solute. This process is studied here for the cases of hydrogen cyanide, acetylene, and cyanoacetylene in helium, using a new experimental method we call optically selected mass spectrometry (OSMS). The method combines infrared laser spectroscopy with mass spectrometry to separate the contributions to the overall droplet beam mass spectrum from the various species present under a given set of conditions. This is done by vibrationally exciting a specific species that exists in a subset of the droplets (for example, the droplets containing a single HCN molecule). The resulting helium evaporation leads to a concomitant reduction in the ionization cross sections for these droplets. This method is used to study the charge migration in helium and reveals that the probability of charge transfer to a solvated molecule does not approach unity for small droplets and depends on the identity of the solvated molecule. The experimental results are explained quantitatively by considering the effect of the electrostatic potential (between the charge and the embedded molecule) on the trajectory of the migrating charge.     

The effect of the counterion on water mobility in reverse micelles studied by molecular dynamics simulations

In this study, mobility and structure of water molecules in Aerosol OT (bis(2-ethylhexyl) sulfosuccinate, AOT) reverse micelles with water content w0 = 5 and Na+, K+, Cs+ counterions have been explored with molecular dynamics (MD) simulations. Using the Faeder/Ladanyi model (J. Phys. Chem. B, 2000, 104, 1033) of the reverse micelle interior, MD simulations were performed to calculate the self-intermediate scattering function, FS(Q,t), for water hydrogen atoms that could be measured in a quasielastic neutron scattering experiment. Separate intermediate scattering functions FRS(Q,t) and FCMS(Q,t) were determined for rotational and translational motion. We find that the decay of FCMS(Q,t) is nonexponential and our analysis of the MD data indicates that this behavior arises from decreased water mobility for molecules close to the interface and from confinement-induced restrictions on the range of translational displacements. Rotational relaxation also exhibits nonexponential decay, which is consistent with relatively rapid restricted rotation and slower rotational relaxation over the full angular range. Rotational relaxation is anisotropic, with the O-H bond short-time rotational mobility considerably higher than that of the molecular dipole. This behavior is related to the decreased density of water-water hydrogen bonds in the vicinity of the interface compared to core or bulk water. We find that the interfacial mobility of water molecules is quite different for the three counterion types, but that the core mobility exhibits weak counterion dependence. Differences in interfacial mobility are strongly correlated with structural features, especially ion-water coordination, and the extent of disruption by the counterions of the water hydrogen bond network.     

Overtone spectroscopy of H2O clusters in the V(OH) = 2 manifold: infrared-ultraviolet vibrationally mediated dissociation studies

Spectroscopy and predissociation dynamics of (H2O)2 and Ar-H2O are investigated with vibrationally mediated dissociation (VMD) techniques, wherein upsilon(OH) = 2 overtones of the complexes are selectively prepared with direct infrared pumping, followed by 193 nm photolysis of the excited H2O molecules. As a function of relative laser timing, the photolysis breaks H2O into OH and H fragments either (i) directly inside the complex or (ii) after the complex undergoes vibrational predissociation, with the nascent quantum state distribution of the OH photofragment probed via laser-induced fluorescence. This capability provides the first rotationally resolved spectroscopic analysis of (H2O)2 in the first overtone region and vibrational predissociation dynamics of water dimer and Ar-water clusters. The sensitivity of the VMD approach permits several upsilon(OH) = 2 overtone bands to be observed, the spectroscopic assignment of which is discussed in the context of recent anharmonic theoretical calculations.     

EFFECT OF METAL IONS ON THE LUMINESCENCE OF ACRIDINE DYES BOUND TO DNA

Abstract— The luminescence of acridine dyes intercalated in DNA was studied as a function of the concurrent binding of metal ions to DNA, in an effort to deduce specific site interactions of the dyes. Two dyes, proflavine (PF) and acridine orange (AO), and two metal ions, silver and mercuric, were used. Both ions quench the fluorescence of the dyes in aqueous solution at room temperature. The metal ions have a different effect on the fluorescence of these dyes when they are intercalated between the base pairs of DNA. The fluorescence of AO is decreased when silver is bound, while the fluorescence of PF is enhanced. Since Ag⁺ initially binds to GC sites in DNA, which quench the PF fluorescence, it ostensibly 'turns off' the quenching by DNA at these sites, and this effect is greater than the quenching effect of the silver ion itself. Hg²⁺ ion initially binds to AT sites in DNA. Since both dyes fluoresce from AT sites, Hg²⁺ is expected to quench their fluorescence. This behavior is observed at low r (metal ion/base). At higher r values, however, where Hg²⁺ is expected to begin binding to GC sites, the fluorescence of PF is enhanced. These quenching turn-off effects are tentatively interpreted in terms of a change in the structure of the dye/DNA complex which occurs when a metal ion binds at the intercalation site. At 77 K. no fluorescence enhancement is observed when metal ions bind; Ag⁺ quenches the fluorescence and enhances the phosphorescence of both dyes. Qualitatively similar results are obtained with Hg²⁺.     

Nucleoside und Nucleotide. Teil 16. Verhalten von 1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)-pyrimidinon-5′-triphosphat, 1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)pyridinon-5′-triphosphat und 4-Amino-1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)-pyridinon-5′-triphosphat gegenüber DNA-Polymerase

Nucleosides and Nucleotides. Part 16. The Behaviour of 1-(2′-Deoxy-β-D -ribofuranosyl)-2(1H)-pyrimidinone-5′-triphosphate, 1-(2′-Deoxy-β-D -ribofuranosyl-2(1H))-pyridinone-5′-triphosphate and 4-Amino-1-(2′-desoxy-β-D -ribofuranosyl)-2(1H)-pyridinone-5′-triphosphate towards DNA Polymerase The behaviour of nucleotide base analogs in the DNA synthesis in vitro was studied. The investigated nucleoside-5′-triphosphates 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyrimidinone-5′-triphosphate (pppM_d), 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone-5′-triphosphate (pppII_d) and 4-amino-1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone-5′-triphosphate (pppZ_d) can be considered to be analogs of 2′-deoxy-cytidine-5′-triphosphate. However, their ability to undergo base pairing to the complementary guanine is decreased. When pppM_d, pppII_d or pppZ_d are substituted for pppC_d in the enzymatic synthesis of DNA by DNA polymerase no incorporation of these analogs is observed. They exhibit only a weak inhibition of the DNA synthesis. The mode of the inhibition is uncompetitive which shows that these nucleotide analogs cannot serve as substrates for the DNA polymerase.