Linear-scaling implementation of molecular electronic self-consistent field theory

A linear-scaling implementation of Hartree-Fock and Kohn-Sham self-consistent field (SCF) theories is presented and illustrated with applications to molecules consisting of more than 1000 atoms. The diagonalization bottleneck of traditional SCF methods is avoided by carrying out a minimization of the Roothaan-Hall (RH) energy function and solving the Newton equations using the preconditioned conjugate-gradient (PCG) method. For rapid PCG convergence, the Lowdin orthogonal atomic orbital basis is used. The resulting linear-scaling trust-region Roothaan-Hall (LS-TRRH) method works by the introduction of a level-shift parameter in the RH Newton equations. A great advantage of the LS-TRRH method is that the optimal level shift can be determined at no extra cost, ensuring fast and robust convergence of both the SCF iterations and the level-shifted Newton equations. For density averaging, the authors use the trust-region density-subspace minimization (TRDSM) method, which, unlike the traditional direct inversion in the iterative subspace (DIIS) scheme, is firmly based on the principle of energy minimization. When combined with a linear-scaling evaluation of the Fock/Kohn-Sham matrix (including a boxed fitting of the electron density), LS-TRRH and TRDSM methods constitute the linear-scaling trust-region SCF (LS-TRSCF) method. The LS-TRSCF method compares favorably with the traditional SCF/DIIS scheme, converging smoothly and reliably in cases where the latter method fails. In one case where the LS-TRSCF method converges smoothly to a minimum, the SCF/DIIS method converges to a saddle point.     

Supercritical fluid chromatography of metoprolol and analogues on aminopropyl and ethylpyridine silica without any additives

Metoprolol and a number of related amino alcohols and similar analytes have been chromatographed on aminopropyl (APS) and ethylpyridine (EPS) silica columns. The mobile phase was carbon dioxide with methanol as modifier and no amine additive was present. Optimal isocratic conditions for the selectivity were evaluated based on experiments using design of experiments. A central composite circumscribed model for each column was used. Factors were column temperature, back-pressure and % (v/v) of modifier. The responses were retention and selectivity versus metoprolol. The % of modifier mainly controlled the retention on both columns but pressure and temperature could also be important for optimizing the selectivity between the amino alcohols. The compounds could be divided into four and five groups on both columns, with respect to the selectivity. Furthermore, on the aminopropyl silica the analytes were more spread out whereas on the ethylpyridine silica, due to its aromaticity, retention and selectivity were closer. For optimal conditions the column temperature and back-pressure should be high and the modifier concentration low. A comparison of the selectivity using optimized conditions show a few switches of retention order between the two columns. On aminopropyl silica an aldehyde failed to be eluted owing to Schiff-base formation. Peak symmetry and column efficiency were briefly studied for some structurally close analogues. This revealed some activity from the columns that affected analytes that had less protected amino groups, a methyl group instead of isopropyl. The tailing was more marked with the ethylpyridine column even with the more bulky alkyl substituents. Plate number N was a better measure than the asymmetry factor since some analyte peaks broadened without serious deterioration of symmetry compared to homologues.     

Long-range deuterium isotope effects on (13)C chemical shifts of intramolecularly hydrogen-bonded N-substituted 3-(cycloamine)thiopropionamides or amides: a case of electric field effects

A series of intramolecularly hydrogen-bonded N-substituted 3-(piperidine, morpholine, N-methylpiperazine)thiopropionamides and some corresponding amides have been studied with special emphasis on hydrogen bonding. The compounds have been selected in order to vary and to minimize the N...N distance. Geometries, charge distributions, and chemical shifts of these compounds are obtained from DFT-type BP3LYP calculations. 1H and 13C 1D and 2D NMR experiments were performed to obtain H,H coupling constants, 13C chemical shifts assignments, and deuterium isotope effects on13C chemical shifts. Variable-temperature NMR studies and 2D exchange NMR spectra have been used to describe the rather complicated conformational behavior mainly governed by the ring flipping of the piperidine (morpholine) rings and intramolecular hydrogen bonding. Unusual long-range deuterium isotope effects on 13C chemical shifts are observed over as far as eight bonds away from the site of deuteriation. The isotope effects are related to the N...N distances, thus being related to the hydrogen bonding and polarization of the N-H bond. Arguments are presented showing that the deuterium isotope effects on 13C chemical shifts originate in electric field effects.     

Evaluation of sample fractionation using micro-scale liquid-phase isoelectric focusing on mass spectrometric identification and quantitation of proteins in a SILAC experiment

Mass spectrometric methods based on stable isotopes have shown great promise for identification and quantitation of complex mixtures. Stable isotope labelling by amino acids in cell culture (SILAC) is a straightforward and accurate procedure for quantitation of proteins from cell lines, that are cultured in media containing the natural amino acid or its isotopically labelled analogue, giving rise to either 'light' or 'heavy' proteins. The two cell populations are pooled and treated as a single sample, which allows the use of various protein purification methods without introducing errors into the quantitative analysis. The quantitation of the proteins is based on the intensities of the light and heavy peptides. The increased number of peptides in a quantitative experiment arising from peptide pairs implies that prefractionation is critical prior to liquid chromatography/mass spectrometric (LC/MS) analysis to minimise signal suppression effects and errors in measurements of the intensity ratios. In this study, the effect of a prefractionation step on identification and quantitation of proteins in a SILAC experiment was evaluated. We show that micro-scale liquid-phase isoelectric focusing in the Micro Rotofor separates proteins into well-defined fractions and reduces the sample complexity. Furthermore, the fractionation enhanced the number of identified proteins and improved their quantitation.     

Effect of low intensity laser interaction with human skin fibroblast cells using fiber-optic nano-probes

Over the past forty years, many efforts have been devoted to study low power laser light interactions with biological systems. Some of the investigations were performed in-vitro, on bulk cell populations. Our present work was undertaken to apply specially engineered fiber-optic based nano-probes for the precise delivery of laser light on to a single cell and to observe production of low power laser light induced reactive oxygen species (ROS). A normal human skin fibroblast (NHF) cell line was utilized in this investigation and the cells were irradiated under two different schemes of exposure: (1) an entire NHF cell population within a Petri dish using a fan beam methodology, and (2) through the precise delivery of laser energy on to a single NHF cell using fiber-optic nano-probe. Photobiostimulative studies were conducted through variation of laser intensity, exposure time, and the energy dose of exposure. Laser irradiation induced enhancement in the rate of cell proliferation was observed to be dependent on laser exposure parameters and the method of laser delivery. The total energy dose (fluence) had a greater influence on the enhancement in the rate of cellular proliferation than compared to laser intensity. The enhancement in the growth rate was observed to have a finite life-time of several days after the initial laser exposure. Fluorescent life-time imaging of ROS was performed during the nano-based single cell exposure method. The kinetics of ROS generation was found to depend strongly on the laser fluence and not on the laser intensity.     

Denting Nanospheres with a Short Peptide

Dented nanospheres show promising potential in drug delivery,nanomotors,etc.However,it is still challenging to prepare them by homopolymer self-assembly because of the strict structural requirements of the homopolymer.Herein,we propose a strategy for preparing dented nanospheres from homopolymers by co-assembly with a short peptide.They were co-assembled from poly(2-hydroxy-3-((4-(ethoxycarbonyl)phenyl)amino)propyl methacrylate) (PHBzoMA59) and (S)-2-((S)-2-((((gH-fluoren-9-yl)methoxy)carbonyl)amino)-3-phenylpro-panamido)-3-phenylpropanoic acid (Fmoc-FF-OH).PHBzoMA homopolymers can only self-assemble into nanospheres without dent,and the addition of a short peptide introduced hydrogen bonding and complementary π-π stacking interactions led to the final dented nanosphere morphology.The weight fractions of the short peptide can be adjusted to regulate the final morphology.It was confirmed that the radius of curvature of the dent on the surface was related to the organic bubble inside the protospheres prepared at critical aggregation concentration(CAC).The organic bubble can be adjusted by altering the kind of organic solvent and solution pH,which allowed control over the dented nanosphere dimension.The use of different organic solvents with various polarities allows adjustment of the interfacial tension,and hence the denting degree.This degree can also be controlled by manipulating the solution pH to (de)protonate the short peptide and homopolymer.Furthermore,the versatility of this method was highlighted by using a different homopolymer and the applicability of the resulting dented nanospheres was demonstrated by decoration with gold nanoparticles.Overall,this study provided important insights and a new simple strategy to prepare dented nanospheres in a controlled fashion.     

A Synthetic Strategy for Cofacial Porphyrin-Based Homo- and Heterobimetallic Complexes

We present a straightforward and generally applicable synthesis route for cofacially linked homo- and heterobimetallic porphyrin complexes. The protocol allows the synthesis of unsymmetrical aryl-based meso-meso as well as β-meso-linked porphyrins. Our method significantly increases the overall yield for the published compound known as o-phenylene-bisporphyrin (OBBP) by a factor of 6.8. Besides the synthesis of 16 novel homobimetallic complexes containing Mn^III, Fe^III, Ni^II, Cu^II, Zn^II, and Pd^II, we achieved the first single-crystal X-ray structure of an unsymmetrical cofacial benzene-linked porphyrin dimer containing both planar-chiral enantiomers of a Ni^II₂ complex. Additionally, this new methodology allows access to heterobimetallic complexes such as the Fe^III-Ni^II containing carbon monoxide dehydrogenase active site analogue. The isolated species were investigated by various techniques, including ion mobility spectrometry, DFT calculations, and UV/Vis spectroscopy. This allowed us to probe the influence of interplane distance on Soret band splitting.     

Causal Geometry

Information geometry has offered a way to formally study the efficacy of scientific models by quantifying the impact of model parameters on the predicted effects. However, there has been little formal investigation of causation in this framework, despite causal models being a fundamental part of science and explanation. Here, we introduce causal geometry, which formalizes not only how outcomes are impacted by parameters, but also how the parameters of a model can be intervened upon. Therefore, we introduce a geometric version of “effective information”—a known measure of the informativeness of a causal relationship. We show that it is given by the matching between the space of effects and the space of interventions, in the form of their geometric congruence. Therefore, given a fixed intervention capability, an effective causal model is one that is well matched to those interventions. This is a consequence of “causal emergence,” wherein macroscopic causal relationships may carry more information than “fundamental” microscopic ones. We thus argue that a coarse-grained model may, paradoxically, be more informative than the microscopic one, especially when it better matches the scale of accessible interventions—as we illustrate on toy examples.     

Robust optimization in spline regression models for multi-model regulatory networks under polyhedral uncertainty

In our study, we integrate the data uncertainty of real-world models into our regulatory systems and robustify them. We newly introduce and analyse robust time-discrete target–environment regulatory systems under polyhedral uncertainty through robust optimization. Robust optimization has reached a great importance as a modelling framework for immunizing against parametric uncertainties and the integration of uncertain data is of considerable importance for the model’s reliability of a highly interconnected system. Then, we present a numerical example to demonstrate the efficiency of our new robust regression method for regulatory networks. The results indicate that our approach can successfully approximate the target–environment interaction, based on the expression values of all targets and environmental factors.