The correspondence problem for metabonomics datasets

In metabonomics it is difficult to tell which peak is which in datasets with many samples. This is known as the correspondence problem. Data from different samples are not synchronised, i.e., the peak from one metabolite does not appear in exactly the same place in all samples. For datasets with many samples, this problem is nontrivial, because each sample contains hundreds to thousands of peaks that shift and are identified ambiguously. Statistical analysis of the data assumes that peaks from one metabolite are found in one column of a data table. For every error in the data table, the statistical analysis loses power and the risk of missing a biomarker increases. It is therefore important to solve the correspondence problem by synchronising samples and there is no method that solves it once and for all. In this review, we analyse the correspondence problem, discuss current state-of-the-art methods for synchronising samples, and predict the properties of future methods.     

A general <Emphasis Type="Italic">Z</Emphasis>-scan theory

A novel Z-scan theory based on the solution of the nonlinear paraxial wave equation, completed by the Huygens–Fresnel principle is introduced. This theory is valid for the general case, i.e. for thick samples and large nonlinearities including both nonlinear refraction and absorption. In both limiting cases of thin sample and weak nonlinearity, predictions of this model are in good agreement with theories not using parabolic approximation for the beam profile. It is shown that the widely used parabolic approximation leads to inadequate results when evaluating Z-scan measurements.     

Retro‐Brook Rearrangement of Ferrocene‐Derived Silyl Ethers

An intramolecular Li–Si exchange was observed on various lithiated ferrocenylbenzyl silyl ethers. The thermodynamically more stable C‐silylated isomers were isolated in good yields and fully characterized. The reaction mechanism of the [1,4] retro‐Brook rearrangement was investigated by DFT calculations. Two distinct reaction routes were proposed and a possible stabilization effect of the ferrocenyl fragment on the C‐silylated isomers was described. The diastereoselective rearrangement of the trimethylsilyl group to the ortho position of the ferrocenyl cyclopentadienyl ring was also accomplished and the absolute configuration of the product was determined.     

A second-quantization framework for the unified treatment of relativistic and nonrelativistic molecular perturbations by response theory

A formalism is presented for the calculation of relativistic corrections to molecular electronic energies and properties. After a discussion of the Dirac and Breit equations and their first-order Foldy-Wouthuysen [Phys. Rev. 78, 29 (1950)] transformation, we construct a second-quantization electronic Hamiltonian, valid for all values of the fine-structure constant alpha. The resulting alpha-dependent Hamiltonian is then used to set up a perturbation theory in orders of alpha(2), using the general framework of time-independent response theory, in the same manner as for geometrical and magnetic perturbations. Explicit expressions are given to second order in alpha(2) for the Hartree-Fock model. However, since all relativistic considerations are contained in the alpha-dependent Hamiltonian operator rather than in the wave function, the same approach may be used for other wave-function models, following the general procedure of response theory. In particular, by constructing a variational Lagrangian using the alpha-dependent electronic Hamiltonian, relativistic corrections can be calculated for nonvariational methods as well.     

Stanley–Reisner resolution of constant weight linear codes

Given a constant weight linear code, we investigate its weight hierarchy and the Stanley–Reisner resolution of its associated matroid regarded as a simplicial complex. We also exhibit conditions on the higher weights sufficient to conclude that the code is of constant weight.     

Time, Mode and Perceptual Content

Francois Recanati has recently argued that each perceptual state has two distinct kinds of content, complete and explicit content. According to Recanati, the former is a function of the latter and the psychological mode of perception. Furthermore, he has argued that explicit content is temporally neutral and that time-consciousness is a feature of psychological mode. In this paper it is argued, pace Recanati, that explicit content is not temporally neutral. Recanati??s position is initially presented. Three desiderata for a theory of time-consciousness are subsequently introduced. It is then argued that a theory locating time-consciousness as a feature of psychological mode will fail to satisfy these desiderata. In the last section the intentionality of memories is discussed. Using the notion of shiftable indexical, it is argued that memories have the same explicit content as perceptions, but that they nevertheless can have different conditions of satisfaction since they are entertained in different modes.     

Excited states from range-separated density-functional perturbation theory

We explore the possibility of calculating electronic excited states by using perturbation theory along a range-separated adiabatic connection. Starting from the energies of a partially interacting Hamiltonian, a first-order correction is defined with two variants of perturbation theory: a straightforward perturbation theory and an extension of the Görling–Levy one that has the advantage of keeping the ground-state density constant at each order in the perturbation. Only the first, simpler, variant is tested here on the helium and beryllium atoms and on the hydrogen molecule. The first-order correction within this perturbation theory improves significantly the total ground- and excited-state energies of the different systems. However, the excitation energies mostly deteriorate with respect to the zeroth-order ones, which may be explained by the fact that the ionisation energy is no longer correct for all interaction strengths. The second (Görling–Levy) variant of the perturbation theory should improve these results but has not been tested yet along the range-separated adiabatic connection.     

Molecular properties in the Tamm–Dancoff approximation: indirect nuclear spin–spin coupling constants

The Tamm–Dancoff approximation (TDA) can be applied to the computation of excitation energies using time-dependent Hartree–Fock (TD-HF) and time-dependent density-functional theory (TD-DFT). In addition to simplifying the resulting response equations, the TDA has been shown to significantly improve the calculation of triplet excitation energies in these theories, largely overcoming issues associated with triplet instabilities of the underlying reference wave functions. Here, we examine the application of the TDA to the calculation of another response property involving triplet perturbations, namely the indirect nuclear spin–spin coupling constant. Particular attention is paid to the accuracy of the triplet spin–dipole and Fermi-contact components. The application of the TDA in HF calculations leads to vastly improved results. For DFT calculations, the TDA delivers improved stability with respect to geometrical variations but does not deliver higher accuracy close to equilibrium geometries. These observations are rationalised in terms of the ground- and excited-state potential energy surfaces and, in particular, the severity of the triplet instabilities associated with each method. A notable feature of the DFT results within the TDA is their similarity across a wide range of different functionals. The uniformity of the TDA results suggests that some conventional evaluations may exploit error cancellations between approximations in the functional forms and those arising from triplet instabilities. The importance of an accurate treatment of correlation for evaluating spin–spin coupling constants is highlighted by this comparison.     

Simple derivation of the potential energy gradient for an arbitrary electronic wave function

The magnitude of reorganization energies in the photoelectron (PE ) spectra of various transition metal compounds with Mn, Fe, and Ni as 3d center is studied by means of a variable INDO Hamiltonian. The Koopmans defects are analyzed as a function of the one-electron resonance integral β and as function of the one- and two-center electron–electron interaction integrals. β has the property of an inverse coupling constant; reorganization effects are enlarged with reduced β values. In the limit of very small resonance integrals a reduction of the calculated Koopmans defects due to modified localization properties of the orbital wave function is encountered. The two-center electron-electron interaction integrals γ have been calculated via an exponential formula with a variable range parameter. In the limit of long-range potentials with flattened γ; gradients a significant reduction of relaxation and correlation is diagnozed; large defects are predicted in the short-range limit with steep gradients in the repulsion potential. The one-center Coulomb and exchange integrals (γ, K) have been modified by a multiplicative factor. With enlarged one-center integrals enhanced Koopmans defects are encountered. The reorganization energies are determined by means of a Green's function approach with a renormalized approximation for the self-energy part.