Hydrogen bonding of the nucleobase mimic 2-pyridone to fluorobenzenes: an ab initio investigation

The hydrogen-bonded complexes of the nucleobase mimic 2-pyridone (2PY) with seven different fluorinated benzenes (1-, 1,2-, 1,4-, 1,2,3-, 1,3,5-, 1,2,3,4-, and 1,2,4,5-fluorobenzene) are important model systems for investigating the relative importance of hydrogen bonding versus pi-stacking interactions in DNA. We have shown by supersonic-jet spectroscopy that these dimers are hydrogen bonded and not pi-stacked at low temperature (Leist, R.; Frey, J. A.; Leutwyler, S. J. Phys. Chem. A 2006, 110, 4180). Their geometries and binding energies D(e) were calculated using the resolution of identity (RI) M?ller-Plesset second-order perturbation theory method (RIMP2). The most stable dimers are bound by antiparallel N-H...F-C and C-H...O=C hydrogen bonds. The binding energies are extrapolated to the complete basis set (CBS) limit, , using the aug-cc-pVXZ basis set series. The CBS binding energies range from -D(e,CBS) = 6.4-6.9 kcal/mol and the respective dissociation energies from -D(0,CBS) = 5.9-6.3 kcal/mol. In combination with experiment, the latter represent upper limits to the dissociation energies of the pi-stacked isomers (which are not observed experimentally). The individual C-H...O=C and N-H...F-C contributions to D(e) can be approximately separated. They are nearly equal for 2PY.fluorobenzene; each additional F atom strengthens the C-H...O=C hydrogen bond by approximately 0.5 kcal/mol and weakens the C-F...H-N hydrogen bond by approximately 0.3 kcal/mol. The single H-bond strengths and lengths correlate with the gas-phase acid-base properties of the C-H and C-F groups of the fluorobenzenes.     

An ab initio benchmark study of hydrogen bonded formamide dimers

The five singly and doubly hydrogen bonded dimers of formamide are calculated at the correlated level by using resolution of identity M?ller-Plesset second-order perturbation theory (RIMP2) and the coupled cluster with singles, doubles, and perturbative triples [CCSD(T)] method. All structures are optimized with the Dunning aug-cc-pVTZ and aug-cc-pVQZ basis sets. The binding energies are extrapolated to the complete basis set (CBS) limit by using the aug-cc-pVXZ (X = D, T, Q) basis set series. The effect of extending the basis set to aug-cc-pV5Z on the geometries and binding energies is studied for the centrosymmetric doubly N-H...O bonded dimer FA1 and the doubly C-H...O bonded dimer FA5. The MP2 CBS limits range from -5.19 kcal/mol for FA5 to -14.80 kcal/mol for the FA1 dimer. The DeltaCCSD(T) corrections to the MP2 CBS limit binding energies calculated with the 6-31+G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are mutually consistent to within < or =0.03 kcal/mol. The DeltaCCSD(T) correction increases the binding energy of the C-H...O bonded FA5 dimer by 0.4 kcal/mol or approximately 9% over the distance range +/-0.5 Angstrom relative to the potential minimum. This implies that the ubiquitous long-range C-H...O interactions in proteins are stronger than hitherto calculated.     

Development of a chiral micellar electrokinetic chromatography–tandem mass spectrometry assay for simultaneous analysis of warfarin and hydroxywarfarin metabolites: Application to the analysis of patients serum samples

The enantioseparation of warfarin (WAR) along with the five positional and optical isomers is challenging because of the difficulty to simultaneously separate and quantitate these chiral compounds. Currently, no effective chiral CE–MS methods exist for the simultaneous enantioseparation of WAR and all its hydroxylated metabolites in a single run. Polymeric surfactants (aka. molecular micelles) are particularly compatible with micellar electrokinetic chromatography–mass spectrometry (MEKC–MS) because they have a wider elution window for enantioseparation and do not interfere with the MS detection of chiral drugs. Using polysodium N-undecenoyl-l,l-leucylvalinate (poly-l,l-SULV) as a chiral pseudophase in MEKC–MS baseline separation of WAR, its five metabolites along with the internal standard was obtained in 45 min. This is in comparison to 100 min required for separation of the same mixture with packed column CEC–MS using a vancomycin chiral stationary phase. Serum samples were extracted with mixed-mode anion-exchange (MAX) cartridge with recoveries of greater than 85.2% for all WAR and hydroxywarfarin (OH-WAR) metabolites. Utilizing the tandem MS and multiple reaction monitoring mode, the MEKC–MS/MS method was used to simultaneously generate calibration curves over a concentration range from 2 to 5000 ng/mL for R- and S-warfarin, 5 to 1000 ng/mL for R- and S-6-, 7-, 8- and 10-OH-WAR and 10 to 1000 ng/mL for R and S-4′-OH-WAR. For the first time, the limits of detection and quantitation for most WAR metabolites by MEKC–MS/MS were found to be at levels of 2 and 5 ng/mL, respectively. The method was successfully applied for the first time to analyze WAR and its metabolites in plasma samples of 55 patients undergoing WAR therapy, demonstrating the potential of chiral MEKC–MS/MS method to accurately quantitate with high sensitivity.     

On-line identification of non-linear hysteretic structures using an adaptive tracking technique

System identification and damage detection based on vibration data have received considerable attention recently because of their importance to structural health monitoring. Various technical approaches have been proposed in the literature; however, the on-line identification of the changes of parameters for non-linear structures due to damages is still a challenging problem. In this paper, we propose an on-line adaptive tracking technique, based on the least-square estimation, to identify the system parameters and their changes of non-linear hysteretic structures. The method proposed is capable of tracking abrupt or slow changes of the system parameters from which the damage event and the severity of the structural damage can be detected and evaluated. Simulation results for tracking the parametric changes of non-linear hysteretic structures are presented to demonstrate the application and effectiveness of the proposed technique in detecting the structural damages.     

O-H small middle dot small middle dot small middle dotPt(II): Hydrogen Bond with a Strong Dispersion Component

An MP2 ab initio study of the interaction between a H(2)O molecule and trans-[Pt(OH)(2)(NH(3))(2)] revealed a HO-H small middle dot small middle dot small middle dotPt(II) hydrogen bond (see picture) with a strong dispersion component (ca. 4 kcal mol(-1)). This dispersion interaction is independent of the charge on the complex and is likely to be ubiquitous in aqueous solutions of Pt(II) complexes.     

Solvent interactions and conformational choice in a core N-glycan segment: gas phase conformation of the central, branching trimannose unit and its singly hydrated complex

The intrinsic conformational preferences and structures of the branched trimannoside, alpha-phenyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside (which contains the same carbohydrates found in a key subunit of the core pentasaccharide in N-glycans) and its singly hydrated complex, have been investigated in the gas phase isolated at low temperature in a molecular beam expansion. Conformational assignments of their infrared ion dip spectra, based on comparisons between experiment and ONIOM (B3LYP/6-31+G(d):HF/6-31G(d)) and single-point MP2 calculations have identified their preferred structures and relative energies. The unhydrated trimannoside populates a unique structure supported by two strong, central hydrogen bonds linking the central mannose unit (CM), and its two branches (3M and 6M) closely together, through a cooperative hydrogen-bonding network: OH4(CM)-->OH6(3M)-->OH6(6M). A closely bound structure is also retained in the singly hydrated oligosaccharide, with the water molecule bridging across the 3M and 6M branches to provide additional bonding. This structure contrasts sharply with the more open, entropically favored trimannoside structure determined in aqueous solution at 298 K. In principle this structure can be accessed from the isolated trimannoside structure by a simple conformational change, a twist about the alpha(1,3) glycosidic linkage, increasing the dihedral angle psi[C1(3M)-O3(3M)-C3(CM)-C2(CM)] from approximately 74 degrees to approximately 146 degrees to enable accommodation of a water molecule at the centrally bound site occupied by the hydroxymethyl group on the 3M ring and mediation of the water-linked hydrogen-bonded network: OH4(CM) -->OH(W)-->OH6(6M). The creation of a "water pocket" motif localized at the bisecting axis of the trimannoside is strikingly similar to the structure of more complex N-glycans in water, suggesting perhaps a general role for the "bisecting" OH4 group in the central (CM) mannose unit.     

Scope and limitations of the SCS-MP2 method for stacking and hydrogen bonding interactions

Fluorobenzenes are pi-acceptor synthons that form pi-stacked structures in molecular crystals as well as in artificial DNAs. We investigate the competition between hydrogen bonding and pi-stacking in dimers consisting of the nucleobase mimic 2-pyridone (2PY) and all fluorobenzenes from 1-fluorobenzene to hexafluorobenzene (n-FB, with n = 1-6). We contrast the results of high level ab initio calculations with those obtained using ultraviolet (UV) and infrared (IR) laser spectroscopy of isolated and supersonically cooled dimers. The 2PY.n-FB complexes with n = 1-5 prefer double hydrogen bonding over pi-stacking, as diagnosed from the UV absorption and IR laser depletion spectra, which both show features characteristic of doubly H-bonded complexes. The 2-pyridone.hexafluorobenzene dimer is the only pi-stacked dimer, exhibiting a homogeneously broadened UV spectrum and no IR bands characteristic for H-bonded species. MP2 (second-order M?ller-Plesset perturbation theory) calculations overestimate the pi-stacked dimer binding energies by about 10 kJ/mol and disagree with the experimental observations. In contrast, the MP2 treatment of the H-bonded dimers appears to be quite accurate. Grimme's spin-component-scaled MP2 approach (SCS-MP2) is an improvement over MP2 for the pi-stacked dimers, reducing the binding energy by approximately 10 kJ/mol. When applied to explicitly correlated MP2 theory (SCS-MP2-R12 approach), agreement with the corresponding coupled-cluster binding energies [at the CCSD(T) level] is very good for the pi-stacked dimers, within +/- 1 kJ/mol for the 2PY complexes with 1-fluorobenzene, 1,2-difluorobenzene, 1,2,4,5-tetrafluorobenzene, pentafluorobenzene and hexafluorobenzene. Unfortunately, the SCS-MP2 approach also reduces the binding energy of the H-bonded species, leading to disagreement with both coupled-cluster theory and experiment. The SCS-MP2-R12 binding energies follow the SCS-MP2 binding energies closely, being about 0.5 and 0.7 kJ/mol larger for the H-bonded and pi-stacked forms, respectively, in an augmented correlation-consistent polarized valence quadruple-zeta basis. It seems that the SCS-MP2 and SCS-MP2-R12 methods cannot provide sufficient accuracy to replace the CCSD(T) method for intermolecular interactions where H-bonding and pi-stacking are competitive.     

Wall Heat Flux and Thermal Stratification Investigations during the Compression Stroke of an engine-like Geometry: A comparison between LES and DNS

The near wall regions in internal combustion engines contain a significant amount of the gaseous mass in the cylinder and thus have a high relevance for the amount of unburned hydrocarbons, the wall heat transfer and the thermal stratification in the cylinder. In this context in the following study the predictive capability of Large Eddy Simulation (LES) with respect to wall heat flux and thermal stratification during the compression stroke i.e. under non-reactive conditions in an Internal Combustion Engine (ICE) are investigated based on a comparison with Direct Numerical Simulations (DNS). Two different modeling approaches for the near wall region, the low Reynolds damping approach and the LES adapted model from Plengsaard and Rutland, have been tested. During the first half of the compression stroke the low Reynolds damping approach agreed well with the DNS data, but increasing deviations were observed after 270° CA (piston halfway up). The underprediction of the wall heat flux at later stages was found to stem from the underestimation of the y ₊ values of the first cell centroid, compared to values obtained by evaluating the DNS data at the same location, and originates from the model used to determine the friction velocity. As a consequence of the underpredicted y ₊ value, the cell is not located in the viscous sublayer as expected, and the temperature gradient which is needed for the heat flux calculation is underpredicted. The results of the LES wall heat transfer model from Plengsaard and Rutland on the other hand showed overall reasonable agreement with the DNS data, but the model strongly depended on the modeling constants. With respect to the increasing thermal stratification during the compression both methods were found to significantly under predict the DNS results. These findings are especially relevant for LES of auto ignition phenomena in engines, since ignition timing and location are known to strongly depend on the temperature distribution.     

Synthesis,Characterization, and Theoretical Investigation of Two‐Coordinate Palladium(0) and Platinum(0) Complexes Utilizing π‐Accepting Carbenes

An elegant general synthesis route for the preparation of two coordinate palladium(0) and platinum(0) complexes was developed by reacting commercially available tetrakis(triphenylphosphine)palladium/platinum with π‐accepting cyclic alkyl(amino) carbenes (cAACs). The complexes are characterized by NMR spectroscopy, mass spectrometry, and single‐crystal X‐ray diffraction. The palladium complexes exhibit sharp color changes (crystallochromism) from dark maroon to bright green if the C‐Pd‐C bond angle is sharpened by approximately 6°, which is chemically feasible by elimination of one lattice THF solvent molecule. The analogous dark orange‐colored platinum complexes are more rigid and thus do not show this phenomenon. Additionally, [(cAAC)₂Pd/Pt] complexes can be quasi‐reversibly oxidized to their corresponding [(cAAC)₂Pd/Pt]⁺ cations, as evidenced by cyclic voltammetry measurements. The bonding and stability are studied by theoretical calculations.