An ab initio study of S(N)2 reactivity at C6 in hexopyranose derivatives. II. Role of populations, barriers, and reaction path curvature

This paper continues our investigation into a simple dipole-dipole interaction model proposed to explain the dramatically reduced S(N)2 reactivity at the primary C6 position of galacto-configured pyranose systems relative to their gluco isomers. We present ab initio calculations (B3LYP/6-31+G(d,p)) on six model structures that show that this effect is not a major influence. Reactant rotameric equilibria as well as free-energy reaction barriers and reaction path curvature were evaluated. Results point to a number of other factors that could account for the observed reactivity differences. Our results cast doubt on the general relevance of transition structure dipole-dipole repulsions to S(N)2 reactivity.     

kT-scale colloidal interactions in high-frequency inhomogeneous AC electric fields. II. Concentrated ensembles

We report nonintrusive optical microscopy measurements of ensembles of polystyrene colloids in inhomogeneous AC electric fields as a function of field frequency and particle size. By using an inverse Monte Carlo (MC) simulation analysis of time-averaged particle microstructures, we sensitively measure induced dipole-dipole interactions on the kT energy scale. Measurements are reported for frequencies when the particle polarizability is greater and less than the medium, as well as the crossover between these conditions when dipole-dipole interactions vanish. By using measured single dipole-field interactions and associated parameters from Part I as input in the inverse analysis, the dipole-dipole interactions in this work are accurately modeled with no adjustable parameters for conditions away from the crossover frequency (i.e., |f(CM)| > 0). As dipolar interactions vanish at the crossover, a single frequency-dependent parameter is introduced to account for microstructures that appear to result from weak AC electro-osmotic flow induced interactions. By connecting quantitative measures of equilibrium microstructures and kT-scale dipole-field and dipole-dipole interactions, our findings provide a basis to understand colloidal assembly in inhomogeneous AC electric fields.     

High resolution infrared spectroscopy of carbon dioxide clusters up to (CO2)13

Thirteen specific infrared bands in the 2350 cm(-1) region are assigned to carbon dioxide clusters, (CO(2))(N), with N = 6, 7, 9, 10, 11, 12 and 13. The spectra are observed in direct absorption using a tuneable infrared laser to probe a pulsed supersonic jet expansion of a dilute mixture of CO(2) in He carrier gas. Assignments are aided by cluster structure calculations made using two reliable CO(2) intermolecular potential functions. For (CO(2))(6), two highly symmetric isomers are observed, one with S(6) symmetry (probably the more stable form), and the other with S(4) symmetry. (CO(2))(13) is also symmetric (S(6)), but the remaining clusters are asymmetric tops with no symmetry elements. The observed rotational constants tend to be slightly (≈2%) smaller than those from the predicted structures. The bands have increasing vibrational blueshifts with increasing cluster size, similar to those predicted by the resonant dipole-dipole interaction model but significantly larger in magnitude.     

Intramolecular nonbonded S...N interaction in rabeprazole

Intramolecular nonbonded S...N interactions in the crystal structures of the derivatives (7a-d) of sodium rabeprazole (1) and an intermolecular nonbonded S...N interaction between ethylmethylsulfoxide and pyridine in a solution were recognized. These results made us estimate that the intramolecular nonbonded S...N interaction existed in 1 and its derivatives in a solution, and formed the 4-membered quasi-ring in 2 (Fig. 1) followed by the increase of the reactivity of 2 to give the putative spiro sulfoxide 3, which is the key intermediate in the reaction cascade of 1 (Chart 1).     

A probable hydrogen-bonded Meisenheimer complex: an unusually high S(N)Ar reactivity of nitroaniline derivatives with hydroxide ion in aqueous media

Observations show that nitroanilines exhibit an unusually high S(N)Ar reactivity with OH(-) in aqueous media in reactions that produce nitrophenols. S(N)Ar reaction of 4-nitroaniline (2a) in aqueous NaOH for 16 h yields 4-nitrophenol (4a) quantitatively, whereas a similar reaction of 4-nitrochlorobenzene (1a) gave 4a in 2% yield together with recovered 1a in 97%, suggesting that the leaving ability of the NH(2) group far surpasses that of Cl under these conditions. An essential feature of S(N)Ar reactions of nitroanilines is probably that the NH(2) leaving group participates in a hydrogen-bonding interaction with H(2)O. Density functional theory (DFT) calculations for a set of 4-nitroaniline, OH(-), and H(2)O suggest a possible formation of a Meisenheimer complex stabilized by hydrogen-bonding interactions and a six-membered ring structure. The results obtained here contrast with conventional S(N)Ar reactivity profiles in which nitroanilines are nearly unreactive with nucleophiles in organic solvents.     

Neutral versus charged species in enzyme catalysis. Classical and free energy barriers for oxygen atom transfer from C4a-hydroperoxyflavin to dimethyl sulfide

Theoretical calculations at the B3LYP/6-31+G(d,p) level have been used to study the oxidation of dimethyl sulfide by a series of bicyclic and tricyclic model C4a-flavin hydroperoxides. The intrinsic gas-phase reactivity of tricyclic C4a-hydroperoxyflavin 4 is ca. 10(9) greater than t-BuOOH but is ca. 10(7) less reactive toward the oxidation of dimethyl sulfide than peroxyformic acid. The SN2-like attack of the nucleophile on the distal oxygen of the hydroperoxide and the relative reactivity of the peracid are in excellent agreement with the earlier experimental data of Bruice. The effect of N1 or N5 hydrogen-bonding interactions on the activation barriers for oxygen atom transfer have been examined. Classical energy barriers for oxygen atom transfer from neutral and ion-paired forms of C4a-hydroperoxyflavin to dimethyl sulfide are predicted to differ by a small margin, suggesting that proton distribution exerts a relatively small influence on the reactivity of alkyl hydroperoxides. Isolated N1- and N5-protonated cations exhibit artificially low barriers as a consequence of their location in a high energy region of the potential energy surface domain.     

Construction of Heterometallic Clusters in a Small Peptide Scaffold as [NiFe]-Hydrogenase Models: Development of a Synthetic Methodology

[NiFe]-hydrogenases are enzymes that catalyze the reversible interconversion of protons and hydrogen at a heterobimetallic site containing Ni and Fe. This organometallic site has served as an inspiration for the synthesis of a number of biomimetic complexes, but, unfortunately, most close structural mimics have shown little to no reactivity with either of the substrates for hydrogenases. This suggests that interactions between the metallo-active site and the protein scaffold are crucial in tuning reactivity. As a first step toward development of peptide-based models, in this paper we demonstrate a synthetic strategy for construction of peptide coordinated, cysteinyl thiolate bridged Ni-M complexes in which M is a hetero-organometallic fragment. We utilize the seven amino acid peptide ACDLPCG as a scaffold for construction of these peptide-coordinated metallocenters. This peptide binds Ni in an N(2)S(2) environment consisting of the amino terminus, an amide nitrogen, and the two cysteinyl thiolates. We show that these thiolates serve as reactive sites for formation of heterometallic complexes in which they serve as bridging ligands. The method is general, and a number of heterometallic fragments including Ru(η(6)-arene)(2+), M(CO)(4)(piperidine) for M = Mo and W, and Fe(2)(CO)(6) were successfully incorporated, and the resulting metallopeptides characterized via a range of spectroscopic techniques. This methodology serves as the first step to construction of hydrogenase peptidomimetics that incorporate defined outer coordination sphere interactions intended to tune reactivity.     

Borohydride, azide, and chloride anions as terminal ligands on Fe/Mo/S clusters. Synthesis, structure and characterization of [(Cl4-cat)(PPr3) MoFe3S4(X)2]2(Bu4N)4 and [(Cl4-cat)(PPr3)MoFe3S4 (PPr3)(X)]2(Bu4N)2 (X = N3-, BH4-, Cl-) double-fused cubanes. NMR reactivity studies of [(Cl4-cat)(PPr3) MoFe3S4(BH4)2]2(Bu4N)4

Our explorations of the reactivity of Fe/Mo/S clusters of some relevance to the FeMoco nitrogenase have led to new double-fused cubane clusters with the Mo2Fe6S8 core as derivatives of the known (Cl4-cat)2Mo2Fe6S8(PPr3)6 (I) fused double cubane. The new clusters have been obtained by substitution reactions of the PPr3 ligands with Cl-, BH4-, and N3-. By careful control of the conditions of these reactions, the clusters [(Cl4-cat)(PPr3)MoFe3S4(BH4)2]2(Bu4N)4 (II), [(Cl4-cat)(PPr3)MoFe3S4(PPr3)(BH4)]2(Bu4N)2 (III), [(Cl4-cat)(PPr3)MoFe3S4(N3)2]2(Bu4N)4 (IV), [(Cl4-cat)(PPr3)MoFe3S4(PPr3)(N3)]2(Bu4N)2 (V), and [(Cl4-cat)(PPr3)MoFe3S4Cl2]2(Et4N)4 (VI) have been obtained and structurally characterized. A study of their electrochemistry shows that the reduction potentials for the derivatives of I are shifted to more positive values than those of I, suggesting a stabilization of the reduced clusters by the anionic ligands BH4- and N3-. Using 1H NMR spectroscopy, we have explored the lability of the BH4- ligand in II in coordinating solvents and its hydridic character, which is apparent in its reactivity toward proton sources such as MeOH or PhOH.     

Thermodynamic modeling of hydrogen sulfide solubility in ionic liquids using modified SAFT-VR and PC-SAFT equations of state

Equations of state based on the statistical associating fluid theory for potentials of variable range (SAFT-VR) and the perturbed chain statistical associating fluid theory (PC-SAFT) have been used to model the PVT behavior of ionic liquids and the solubility of H₂S in six imidazolium-based ionic liquids. The studied systems included [bmim][PF6], [hmim][PF6], [bmim][BF4], [hmim][BF4], [bmim][NTF2] and [hmim][NTF2] at various temperatures and pressures.For pure components, parameters of the models have been obtained by fitting the models to experimental data on liquid densities; the average relative deviation between the calculated and experimental densities for ionic liquids is less than 2.42% in the PC-SAFT model and 5.44% in the SAFT-VR approach, the latter which incorporates the square-well potential for short-range interactions. In both models an additional term has been added to account for dipole-dipole interactions between solute molecules resulting from the permanent charges on the chain molecules of the solvents. The model parameters have also been correlated as functions of the molecular weight of the solvents. For binary mixtures of ionic liquids and H₂S, the association interactions between H₂S molecules and between the ionic liquids and H₂S molecules have also been taken into account in both approaches, using binary interaction coefficients. The results show an average deviation of less than 5% in the calculation of the mole fraction of H₂S in the ionic liquids. The effect of inclusion of the polar term has been studied for binary systems in both models.     

Dipolar stabilization of emissive singlet charge transfer excited states in polyfluorene copolymers

The singlet excited-state dynamics in poly[(9,9-dioctylfluorene)-(dibenzothiophene-S,S-dioxide)] (PFSx ) random copolymers with different contents of dibenzothiophene-S,S-dioxide (S) units have been studied by steady-state and time resolved fluorescence spectroscopies. Emission from PFSx copolymers shows a pronounced solvatochromism in polar chloroform, relative to the less polar toluene. An excited intramolecular charge transfer state (ICT) is stabilized by dipole-dipole interactions with the polar solvent cage, and possibly accompanied by conformational rearrangement of the molecular structure, in complete analogy with their small oligomer counterparts. The spectral dynamics clearly show that the ICT stabilization is strongly affected by the surrounding medium. In the solid state, emission from PFSx copolymers depends on the content of S units, showing an increase of inhomogeneous broadening and a red shift of the optical transitions. This observation is consistent with stabilization of the emissive ICT state, by the local reorientation of the surrounding molecules at the location of the excited chromophore, which results in favorable dipole-dipole interactions driven by the increase in the dielectric constant of the bulk polymer matrix with increasing S content, in analogy to what happens in polar solvent studies. Furthermore, in clear agreement with the interpretation described above, a strong increase in the emission quantum efficiency is observed in the solid state by decreasing the temperature and freezing out the molecular torsions and dipole-dipole interactions necessary to stabilize the ICT state.     

Structure-reactivity relationships among metallothionein three-metal domains: role of non-cysteine amino acid residues in lobster metallothionein and human metallothionein-3

Metallothionein (MT) domains of different origins, exhibiting distinct, highly conserved cysteine positions, show differences in metal-cysteine coordination and reactivity. Lobster MT, which includes two Cd3S9 beta domains, was chosen as a basic model to study the structure-function relationship among the clusters. The possible influence of (1) the position of the cysteine residues and (2) the steric and electrostatic effects of neighboring amino acids on the folding and stability of MT clusters have been examined with the native lobster beta C and beta N domains, each having nine cysteines and binding three M2+ ions, and a modified domain beta C-->N, in which the cysteines of the C-terminal domain are relocated so they are spaced as in the N-terminal domain. Each has been synthesized and characterized by UV, CD, 113Cd NMR, and 1H NMR spectroscopies. The synthetic native domains (Cd3 beta C and Cd3 beta N) displayed spectroscopic properties, metal-binding affinities, and kinetic reactivity similar to those of the holo protein. In contrast, the modified Cd3 beta C-->N domain was unusually reactive and, in the presence of Chelex, a metal-ion chelating resin, was converted to a Cd5(beta C-->N)2 dimer. These differences in structure and reactivity demonstrate that the requirements for formation of a stable type-B, Cd3S9, beta cluster are more stringent than simply the sequential positions of the cysteines along the peptide chain and include specific interactions with neighboring amino acids. Molecular mechanics calculations suggest that changes of even a single amino acid in lobster Cd3 beta N toward lobster Cd3 beta C-->N or in mammalian MT1 or MT2 toward Cd3 beta-MT3 (GIF) can destabilize their structures.     

Anisotropic local motions and location of amide protons in proteins

A new method has been developed to obtain dynamic and structural information about peptide planes in proteins by a combination of measurements of weak short-range cross-correlation rates R(H(N)N/NC') that are due to concerted fluctuations of the H(N)-N and N-C' dipole-dipole interactions and stronger long-range cross-correlation rates R(C'H(N)/H(N)N) and R(NH(N)/H(N)C(alpha)). The rates were interpreted using the axially symmetric Gaussian axial fluctuation model (GAF). The oscillation amplitudes as well as the positions of H(N) atoms with respect to peptide planes in ubiquitin were determined. Most N-H(N) bonds were found not to lie exactly along the bisector of the N-C' and N-C(alpha) bonds but to be slightly tilted toward the carbon-terminal side of the peptide.     

UF6分子的模型伸缩振动能级的计算

利用一个四参数非线性模型,对处于电子基态下的XY6型分子的X-Y键的伸缩振动进行了描述,并将其应用于计算UF6分子中U-F键的伸缩振动能级.计算中引入的模型Hamilton算符所包含的描述U-F键非谐振动的参数λ和描述U-F键之间的偶极-偶极相互作用参数ε1, ε2由实验值得出,波函数|ψn〉按形式为|n,α〉=|n1〉|n2〉|n3〉|n4〉|n5〉|n6〉的基函数集展开,从而把复杂的Hamilton方程转化为简单的矩阵代数方程.结果显示,该非线性模型能够较好地描述UF6分子的振动( 计算误差在1.0 cm-1之内 ),同时合理地预测了一些至今还未观测到的能级值.     

Characterization and dioxygen reactivity of a new series of coordinatively unsaturated thiolate-ligated manganese(II) complexes

The synthesis, structural, and spectroscopic characterization of four new coordinatively unsaturated mononuclear thiolate-ligated manganese(II) complexes ([Mn(II)(S(Me2)N(4)(6-Me-DPEN))](BF(4)) (1), [Mn(II)(S(Me2)N(4)(6-Me-DPPN))](BPh(4))·MeCN (3), [Mn(II)(S(Me2)N(4)(2-QuinoPN))](PF(6))·MeCN·Et(2)O (4), and [Mn(II)(S(Me2)N(4)(6-H-DPEN)(MeOH)](BPh(4)) (5)) is described, along with their magnetic, redox, and reactivity properties. These complexes are structurally related to recently reported [Mn(II)(S(Me2)N(4)(2-QuinoEN))](PF(6)) (2) (Coggins, M. K.; Kovacs, J. A. J. Am. Chem. Soc.2011, 133, 12470). Dioxygen addition to complexes 1-5 is shown to result in the formation of five new rare examples of Mn(III) dimers containing a single, unsupported oxo bridge: [Mn(III)(S(Me2)N(4)(6-Me-DPEN)](2)-(μ-O)(BF(4))(2)·2MeOH (6), [Mn(III)(S(Me2)N(4)(QuinoEN)](2)-(μ-O)(PF(6))(2)·Et(2)O (7), [Mn(III)(S(Me2)N(4)(6-Me-DPPN)](2)-(μ-O)(BPh(4))(2) (8), [Mn(III)(S(Me2)N(4)(QuinoPN)](2)-(μ-O)(BPh(4))(2) (9), and [Mn(III)(S(Me2)N(4)(6-H-DPEN)](2)-(μ-O)(PF(6))(2)·2MeCN (10). Labeling studies show that the oxo atom is derived from (18)O(2). Ligand modifications, involving either the insertion of a methylene into the backbone or the placement of an ortho substituent on the N-heterocyclic amine, are shown to noticeably modulate the magnetic and reactivity properties. Fits to solid-state magnetic susceptibility data show that the Mn(III) ions of μ-oxo dimers 6-10 are moderately antiferromagnetically coupled, with coupling constants (2J) that fall within the expected range. Metastable intermediates, which ultimately convert to μ-oxo bridged 6 and 7, are observed in low-temperature reactions between 1 and 2 and dioxygen. Complexes 3-5, on the other hand, do not form observable intermediates, thus illustrating the effect that relatively minor ligand modifications have upon the stability of metastable dioxygen-derived species.     

Effect of intermolecular dipole-dipole interactions on interfacial supramolecular structures of C3-symmetric hexa-peri-hexabenzocoronene derivatives

Two-dimensional (2D) supramolecular assemblies of a series of novel C(3)-symmetric hexa-peri-hexabenzocoronene (HBC) derivatives bearing different substituents adsorbed on highly oriented pyrolytic graphite were studied by using scanning tunneling microscopy at a solid-liquid interface. It was found that the intermolecular dipole-dipole interactions play a critical role in controlling the interfacial supramolecular assembly of these C(3)-symmetric HBC derivatives at the solid-liquid interface. The HBC molecule bearing three -CF(3) groups could form 2D honeycomb structures because of antiparallel dipole-dipole interactions, whereas HBC molecules bearing three -CN or -NO(2) groups could form hexagonal superstructures because of a special trimeric arrangement induced by dipole-dipole interactions and weak hydrogen bonding interactions ([C-H···NC-] or [C-H···O(2)N-]). Molecular mechanics and dynamics simulations were performed to reveal the physics behind the 2D structures as well as detailed functional group interactions. This work provides an example of how intermolecular dipole-dipole interactions could enable fine control over the self-assembly of disklike π-conjugated molecules.     

Anisotropy in the interaction of ultracold dysprosium

The nature of the interaction between ultracold atoms with a large orbital and spin angular momentum has attracted considerable attention. It was suggested that such interactions can lead to the realization of exotic states of highly correlated matter. Here, we report on a theoretical study of the competing anisotropic dispersion, magnetic dipole-dipole, and electric quadrupole-quadrupole forces between two dysprosium atoms. Each dysprosium atom has an orbital angular momentum of L = 6 and a magnetic moment of μ = 10 μ(B). We show that the dispersion coefficients of the ground state adiabatic potentials lie between 1865 a.u. and 1890 a.u., creating a non-negligible anisotropy with a spread of 25 a.u. and that the electric quadrupole-quadrupole interaction is weak compared to the other interactions. We also find that for interatomic separations R < 50a(0) both the anisotropic dispersion and magnetic dipole-dipole potential are larger than the atomic Zeeman splittings for external magnetic fields of order 10 G to 100 G. At these separations the atomic angular momentum can be reoriented. We finish by describing two scattering models for these inelastic m-changing collisions. A universal scattering theory is used to model loss due to the anisotropy in the dispersion and a Born approximation is used to model losses from the magnetic dipole-dipole interaction for the (164)Dy isotope. These models find loss rates that are of the same order of magnitude as the experimental value.     

Studies on electron spin resonance spectroscopy of biradical molecules containing (14)N-O and (15)N-O moieties

The biradicals with (14)N-Oxide and (15)N-Oxide at the both ends of a molecule are synthesized for the molecular ruler of protein structure, and a potential device for quantum computing. We also establish a general synthetic method for reliable biradical formation. ESR spectra are recorded for the biradicals containing (15)N-Oxide and (14)N-Oxide with various interdistance separations. We find that two types of biradicals yielded different ESR spectra depending upon the distance between the (15)N-O and (14)N-O moieties in a molecule. This is due to electron spin dipole-dipole interaction occurring between the radicals. We also find that there is an indication of isotopic nuclear effects in the dipole-dipole interactions. The present study implies feasibility of the distance measurement between two different N-Oxides containing (14)N and (15)N isotopes. We conclude that quantum entanglement effects are observed through the dipolar interactions, which enable application of quantum computing devices operating in the liquid state.     

Enhancing reactivity via structural distortion

To examine how small structural changes influence the reactivity and magnetic properties of biologically relevant metal complexes, the reactivity and magnetic properties of two structurally related five-coordinate Fe(III) thiolate compounds are compared. (Et,Pr)-ligated [Fe(III)(S(2)(Me2)N(3)(Et,Pr))]PF(6) (3) is synthesized via the abstraction of a sulfur from alkyl persulfide ligated [Fe(III)(S(2)(Me2)N(3)(Et,Pr))-S(pers)]PF(6) (2) using PEt(3). (Et,Pr)-3 is structurally related to (Pr,Pr)-ligated [Fe(III)(S(2)(Me2)N(3)(Pr,Pr))]PF(6) (1), a nitrile hydratase model compound previously reported by our group, except it contains one fewer methylene unit in its ligand backbone. Removal of this methylene distorts the geometry, opens a S-Fe-N angle by approximately 10 degrees, alters the magnetic properties by stabilizing the S = 1/2 state relative to the S = 3/2 state, and increases reactivity. Reactivity differences between 3 and 1 were assessed by comparing the thermodynamics and kinetics of azide binding. Azide binds reversibly to both (Et,Pr)-3 and (Pr,Pr)-1 in MeOH solutions. The ambient temperature K(eq) describing the equilibrium between five-coordinate 1 or 3 and azide-bound 1-N(3) or 3-N(3) in MeOH is approximately 10 times larger for the (Et,Pr) system. In CH(2)Cl(2), azide binds approximately 3 times faster to 3 relative to 1, and in MeOH, azide dissociates 1 order of magnitude slower from 3-N(3) relative to 1-N(3). The increased on rates are most likely a consequence of the decreased structural rearrangement required to convert 3 to an approximately octahedral structure, or they reflect differences in the LUMO (vs SOMO) orbital population (i.e., spin-state differences). Dissociation rates from both 3-N(3) and 1-N(3) are much faster than one would expect for low-spin Fe(III). Most likely this is due to the labilizing effect of the thiolate sulfur that is trans to azide in these structures.     

Leaving group effects in gas-phase substitutions and eliminations

Using a methodology recently developed for studying the product distributions of gas-phase S(N)2 and E2 reactions, the effect of the leaving group on the reaction rate and branching ratio was investigated. Using a dianion as the nucleophile, reactions with a series of alkyl bromides, iodides, and trifluoroacetates were examined. The alkyl groups in the study are ethyl, n-propyl, n-butyl, isobutyl, isopropyl, sec-butyl, and tert-butyl. The data indicate that leaving group abilities are directly related to the exothermicities of the reaction processes in both the gas phase and the condensed phase. Gas-phase data give a reactivity order of iodide > trifluoroacetate > bromide for S(N)2 and E2 reactions. Previous condensed phase data indicate a reactivity order of iodide > bromide > trifluoroacetate for substitution reactions; however, the basicities of bromide and trifluoroacetate are reversed in the condensed phase so this reactivity pattern does reflect the relative reaction exothermicities. Aside from this variation, the gas-phase data parallel condensed phase data indicating that the substituent effects are rooted in the nature of the alkyl substrate rather than in differences in solvation. The experimental data are supported by calculations at the MP2/6-311+G(d,p)//MP2/6-31+(d) level.