Initial dynamics of the Norrish Type I reaction in acetone: probing wave packet motion

The Norrish Type I reaction in the S(1) (nπ*) state of acetone is a prototype case of ketone photochemistry. On the basis of results from time-resolved mass spectrometry (TRMS) and photoelectron spectroscopy (TRPES) experiments, it was recently suggested that after excitation the wave packet travels toward the S(1) minimum in less than 30 fs and stays there for more than 100 picoseconds [Chem. Phys. Lett.2008, 461, 193]. In this work we present simulated TRMS and TRPES signals based on ab initio multiple spawning simulations of the dynamics during the first 200 fs after excitation, getting quite good agreement with the experimental signals. We can explain the ultrafast decay of the experimental signals in the following manner: the wave packet simply travels, mainly along the deplanarization coordinate, out of the detection window of the ionizing probe. This window is so narrow that subsequent revival of the signal due to the coherent deplanarization vibration is not observed, meaning that from the point of view of the experiment the wave packets travels directly to the S(1) minimum. This result stresses the importance of pursuing a closer link to the experimental signal when using molecular dynamics simulations in interpreting experimental results.     

Selective oxidation of propylene to acrolein by silica-supported bismuth molybdate catalysts

Silica-supported bismuth molybdate catalysts have been prepared by impregnation, structurally characterized and examined as improved catalysts for the selective oxidation of propylene to acrolein. Catalysts with a wide range of loadings (from 10 to 90 wt%) of beta bismuth molybdate (??-Bi₂Mo₂O₉) were studied to provide a better understanding about the distribution of active sites, and to elucidate the role of lattice oxygen in the reaction. The catalyst containing 50 wt% of beta bismuth molybdate on SiO₂ was found to possess good distribution of active sites and sufficiently high lattice oxygen, which resulted in an extraordinary increase of the catalytic activity.     

Synergy effects in mixed Bi2O3, MoO3 and V2O5 catalysts for selective oxidation of propylene

In this work, the possible synergy effects between Bi₂O₃, MoO₃ and V₂O₅, and between Bi₂Mo₃O₁₂ and BiVO₄, were investigated. The catalytic activity of the ??mechanical mixture?? of these compounds was measured. The mixture containing 36.96?mol% Bi₂O₃, 39.13?mol% MoO₃ and 23.91?mol% V₂O₅ (21.43?mol% Bi₂Mo₃O₁₂ and 78.57?mol% BiVO₄), corresponding to the compound Bi_1?x/3V_1?x Mo _x O₄ with x?=?0.45 (Bi_0.85V_0.55Mo_0.45O₄), exhibited the highest activity for the selective oxidation of propylene to acrolein. The mixed sample prepared chemically by a sol?Cgel method possessed higher activity than that of mechanical mixtures.     

Transient convection, diffusion, and adsorption in surface-based biosensors

This paper presents a theoretical and computational investigation of convection, diffusion, and adsorption in surface-based biosensors. In particular, we study the transport dynamics in a model geometry of a surface plasmon resonance (SPR) sensor. The work, however, is equally relevant for other microfluidic surface-based biosensors, operating under flow conditions. A widely adopted approximate quasi-steady theory to capture convective and diffusive mass transport is reviewed, and an analytical solution is presented. An expression of the Damk?hler number is derived in terms of the nondimensional adsorption coefficient (Biot number), the nondimensional flow rate (Péclet number), and the model geometry. Transient dynamics is investigated, and we quantify the error of using the quasi-steady-state assumption for experimental data fitting in both kinetically limited and convection-diffusion-limited regimes for irreversible adsorption, in specific. The results clarify the conditions under which the quasi-steady theory is reliable or not. In extension to the well-known fact that the range of validity is altered under convection-diffusion-limited conditions, we show how also the ratio of the inlet concentration to the maximum surface capacity is critical for reliable use of the quasi-steady theory. Finally, our results provide users of surface-based biosensors with a tool for correcting experimentally obtained adsorption rate constants.     

An endohedral single-molecule magnet with long relaxation times: DySc2N@C80

The magnetism of DySc(2)N@C(80) endofullerene was studied with X-ray magnetic circular dichroism (XMCD) and a magnetometer with a superconducting quantum interference device (SQUID) down to temperatures of 2 K and in fields up to 7 T. XMCD shows hysteresis of the 4f spin and orbital moment in Dy(III) ions. SQUID magnetometry indicates hysteresis below 6 K, while thermal and nonthermal relaxation is observed. Dilution of DySc(2)N@C(80) samples with C(60) increases the zero-field 4f electron relaxation time at 2 K to several hours.     

CDPM2: A damage-plasticity approach to modelling the failure of concrete

A constitutive model based on the combination of damage mechanics and plasticity is developed to analyse the failure of concrete structures. The aim is to obtain a model, which describes the important characteristics of the failure process of concrete subjected to multiaxial loading. This is achieved by combining an effective stress based plasticity model with a damage model based on plastic and elastic strain measures. The model response in tension, uni-, bi- and triaxial compression is compared to experimental results. The model describes well the increase in strength and displacement capacity for increasing confinement levels. Furthermore, the model is applied to the structural analyses of tensile and compressive failure.     

In silico prediction of drug solubility: 4. Will simple potentials suffice?

In view of the extreme importance of reliable computational prediction of aqueous drug solubility, we have established a Monte Carlo simulation procedure which appears, in principle, to yield reliable solubilities even for complex drug molecules. A theory based on judicious application of linear response and mean field approximations has been found to reproduce the computationally demanding free energy determinations by simulation while at the same time offering mechanistic insight. The focus here is on the suitability of the model of both drug and solvent, i.e., the force fields. The optimized potentials for liquid simulations all atom (OPLS‐AA) force field, either intact or combined with partial charges determined either by semiempirical AM1/CM1A calculations or taken from the condensed‐phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field has been used. The results illustrate the crucial role of the force field in determining drug solubilities. The errors in interaction energies obtained by the simple force fields tested here are still found to be too large for our purpose but if a component of this error is systematic and readily removed by empirical adjustment the results are significantly improved. In fact, consistent use of the OPLS‐AA Lennard‐Jones force field parameters with partial charges from the COMPASS force field will in this way produce good predictions of amorphous drug solubility within 1 day on a standard desktop PC. This is shown here by the results of extensive new simulations for a total of 47 drug molecules which were also improved by increasing the water box in the hydration simulations from 500 to 2000 water molecules. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

Peptide‐Directed DNA‐Templated Protein Labelling for The Assembly of a Pseudo‐IgM

The development of methods for conjugation of DNA to proteins is of high relevance for the integration of protein function and DNA structures. Here, we demonstrate that protein‐binding peptides can direct a DNA‐templated reaction, selectively furnishing DNA–protein conjugates with one DNA label. Quantitative conversion of oligonucleotides is achieved at low stoichiometries and the reaction can be performed in complex biological matrixes, such as cell lysates. Further, we have used a star‐like pentameric DNA nanostructure to assemble five DNA–Rituximab conjugates, made by our reported method, into a pseudo‐IgM antibody structure that was subsequently characterized by negative‐stain transmission electron microscopy (nsTEM) analysis.     

New exploratory clustering tool

This paper describes a clustering method on three‐way arrays making use of an exploratory visualization approach. The aim of this study is to cluster samples in the object mode of a three‐way array, which is done using the scores (sample loadings) of a three‐way factor model, for example, a Tucker3 or a PARAFAC model. Further, tools are developed to explore and identify reasons for particular clusters by visually mining the data using the clustering results as guidance. We introduce a three‐way clustering tool and demonstrate our results on a metabolite profiling dataset. We explore how high performance liquid chromatography (HPLC) measurements of commercial extracts of St. John's wort (natural remedies for the treatment of mild to moderate depression) differ and which chemical compounds account for those differences. Using common distance measures, for example, Euclidean or Mahalanobis, on the scores of a three‐way model, we verify that we can capture the underlying clustering structure in the data. Beside this, by making use of the visualization approach, we are able to identify the variables playing a significant role in the extracted cluster structure. The suggested approach generalizes straightforwardly to higher‐order data and also to two‐way data. Copyright © 2007 John Wiley & Sons, Ltd.     

On the convergence of zero-point vibrational corrections to nuclear shieldings and shielding anisotropies towards the complete basis set limit in water

ABSTRACT

The method and basis set dependence of zero-point vibrational corrections (ZPVCs) to nuclear magnetic resonance shielding constants and anisotropies has been investigated using water as a test system. A systematic comparison has been made using the Hartree–Fock, second-order Møller–Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)) and Kohn–Sham density functional theory with the B3LYP exchange-correlation functional methods in combination with the second-order vibrational perturbation theory (VPT2) approach for the vibrational corrections. As basis sets, the correlation consistent basis sets cc-pVXZ, aug-cc-pVXZ, cc-pCVXZ and aug-cc-pCVXZ with X = D, T, Q, 5, 6 and the polarisation consistent basis sets aug-pc-n and aug-pcS-n with n = 1, 2, 3, 4 were employed. Our results show that basis set convergence of the vibrational corrections is not monotonic and that very large basis sets are needed before a reasonable extrapolation to the basis set limit can be performed. Furthermore, our results suggest that coupled cluster methods and a decent basis set are required before the error of the electronic structure approach is lower than the inherent error of the VPT2 approximation.