A perturbation-based super-CI approach for the orbital optimization of a CASSCF wave function

A perturbation theory-based algorithm for the iterative orbital update in complete active space self-consistent-field (CASSCF) calculations is presented. Following Angeli et al. (J. Chem. Phys. 2002, 117, 10525), the first-order contribution of singly excited configurations to the CASSCF wave function is evaluated using the Dyall Hamiltonian for the determination of a zeroth-order Hamiltonian. These authors employ an iterative diagonalization of the first-order density matrix including the first-order correction arising from single excitations, whereas the present approach uses the single-excitation amplitudes directly for the construction of the exponential of an anti-Hermitian matrix resulting in a unitary matrix which can be used for the orbital update. At convergence, the single-excitation amplitudes vanish as a consequence of the generalized Brillouin's theorem. It is shown that this approach in combination with direct inversion of the iterative subspace (DIIS) leads to very rapid convergence of the CASSCF iteration procedure. © 2019 Wiley Periodicals, Inc.     

Propagation of Scalar Fields in a Plane Symmetric Spacetime

The present article deals with solutions for a minimally coupled scalar field propagating in a static plane symmetric spacetime. The considered metric describes the curvature outside a massive infinity plate and exhibits an intrinsic naked singularity (a singular plane) that makes the accessible universe finite in extension. This solution can be interpreted as describing the spacetime of static domain walls. In this context, a first solution is given in terms of zero order Bessel functions of the first and second kind and presents a stationary pattern which is interpreted as a result of the reflection of the scalar waves at the singular plane. This is an evidence, at least for the massless scalar field, of an old interpretation given by Amundsen and Grøn regarding the behaviour of test particles near the singularity. A second solution is obtained in the limit of a weak gravitational field which is valid only far from the singularity. In this limit, it was possible to find out an analytic solution for the scalar field in terms of the Kummer and Tricomi confluent hypergeometric functions.     

A multireference perturbation theory study on the vertical electronic spectrum of thiophene

The vertical electronic spectrum of the thiophene molecule is investigated by means of second and third order multireference perturbation theory (NEVPT). Single-state and quasi-degenerate NEVPT calculations of more than 25 singlet excited states have been performed. The study is addressed to the theoretical characterization of the four lowest-energy valence states, as well as the 3s, 3p and 3d Rydberg states. In addition, the excitation energies of two and valence states are also reported. For almost all the excited states, coupled cluster calculations (CCSD and CCSDR(3)) have been also carried out, using the same geometry and basis set used for the NEVPT ones, in order to make the comparison between the results of the two methods meaningful. A remarkable accordance between the NEVPT and CC excitation energies is found. The present results, over all, confirm the experimental assignments but, above all, represent an important contribution to the assignments of some low-energy states, valence and Rydberg, for which a firm interpretation is not available in the literature.     

Effects of alkyl groups in the rate determining step of the Baeyer-Villiger reaction of phenyl alkyl ketones: a quantum chemistry study

In this work, we have studied the substituent effect of several alkyl groups in the rate-determining step of the catalyzed Baeyer-Villiger (BV) reaction of phenyl alkyl ketones with performic (PFA) and trifluoroperacetic (TFPAA) acids, using quantum chemistry methods. Our results reveal that the substituent effect is more pronounced in the migration step barriers than in the corresponding addition step; that could change the rate-determining step (RDS) of the reaction, as observed in the oxidation of phenyl tert-butyl ketone with both peracids. In addition, the effect of the acid/peracid pairs used is also analyzed. We have demonstrated that the addition step is less susceptible to the acid/peracid nature since the acid strength and the nucleophilicity of the peracid have opposite effects. The effect of the acid/peracid pair is much more pronounced in the migration step because it only depends on the leaving ability of the acid, which in turn depends on its strength. These observations are relevant for understanding the effects of the substrate, the peracid, and the catalyst on the switching of the RDS in the BV reaction.     

Multireference perturbation CI IV. Selection procedure for one-electron properties

We present in this paper a modification of the selection procedure, within the CIPSI algorithm, specifically intended for the calculation of one-electron properties. In this new procedure the determinants are selected following their contribution to a certain one-electron property. As test cases we report the calculation of the electric dipole of carbon monoxide and of the hyperfine coupling constants of the CH₃ radical. Received: 20 August 2000 / Accepted: 2 October 2000 / Published online: 21 December 2000     

Synthesis of a new catechin-pyrylium derived pigment

A new catechin-pyrylium derived pigment compound was synthesised from the reaction of catechin with sinapaldehyde in acidic conditions and its structure has been characterised by UV-vis, MS and NMR spectroscopy. Similar compounds could be expected to be formed in wines and contribute to changes in colour and astringency during ageing.     

Ranking docking poses by graph matching of protein–ligand interactions: lessons learned from the D3R Grand Challenge 2

A novel docking challenge has been set by the Drug Design Data Resource (D3R) in order to predict the pose and affinity ranking of a set of Farnesoid X receptor (FXR) agonists, prior to the public release of their bound X-ray structures and potencies. In a first phase, 36 agonists were docked to 26 Protein Data Bank (PDB) structures of the FXR receptor, and next rescored using the in-house developed GRIM method. GRIM aligns protein–ligand interaction patterns of docked poses to those of available PDB templates for the target protein, and rescore poses by a graph matching method. In agreement with results obtained during the previous 2015 docking challenge, we clearly show that GRIM rescoring improves the overall quality of top-ranked poses by prioritizing interaction patterns already visited in the PDB. Importantly, this challenge enables us to refine the applicability domain of the method by better defining the conditions of its success. We notably show that rescoring apolar ligands in hydrophobic pockets leads to frequent GRIM failures. In the second phase, 102 FXR agonists were ranked by decreasing affinity according to the Gibbs free energy of the corresponding GRIM-selected poses, computed by the HYDE scoring function. Interestingly, this fast and simple rescoring scheme provided the third most accurate ranking method among 57 contributions. Although the obtained ranking is still unsuitable for hit to lead optimization, the GRIM–HYDE scoring scheme is accurate and fast enough to post-process virtual screening data.     

Epicatechin,procyanidins, and phenolic microbial metabolites after cocoa intake in humans and rats

Proanthocyanidins, flavonoids exhibiting cardiovascular protection, constitute a major fraction of the flavonoid ingested in the human diet. Although they are poorly absorbed, they are metabolized by the intestinal microbiota into various phenolic acids. An analytical method, based on an optimized 96-well plate solid-phase extraction (SPE) procedure and liquid chromatography tandem mass spectrometry (SPE-LC-MS/MS) for the analysis of 19 phenolic microbial metabolites and monomeric and dimeric flavanols in urine samples, was developed and validated. Human urine samples were obtained before and after ingestion of an acute consumption of 40 g of soluble cocoa powder and rat urines before and after the prolonged administration (2 weeks) of different diets composed of natural cocoa powder. The mean recovery of analytes using the new SPE-LC-MS/MS method ranged from 87% to 109%. Accuracy ranged from 87.5% to 113.8%, and precision met acceptance criteria (<15% relative standard deviation). Procyanidin B2 has been detected and quantified for the first time in human and rat urine after cocoa consumption. Changes in human and rat urinary levels of microbial phenolic acids and flavanols were in the range of 0.001–59.43 nmol/mg creatinine and of 0.004–181.56 nmol/mg creatinine, respectively. Major advantages of the method developed include reduction of laboratory work in the sample preparation step by the use of 96-well SPE plates and the sensitive measurement of a large number of metabolites in a very short run time, which makes it ideal for use in epidemiological studies. ^a INGENIO-CONSOLIDER Program, Fun-c-food CSD2007-063 ^b CIBER 06003 Physiopathology of Obesity and Nutrition (CIBEROBN), and RETICS RD06/0045/0003, Instituto de Salud Carlos III