Avoiding the False Negative Results in LC Method Robustness Testing by Modifications of the Algorithm of Dong and Dummy Factor Effects Approach

The algorithm of Dong and error estimation based on a priori declared negligible effects (dummy factor effects approach) were evaluated for testing robustness, in case they provide contradictory results. Robustness of LC method for separation of ropinirole and its impurity was determined. Plackett–Burman design was applied to unravel the significant/influential factors. Four selected responses (retention factor of ropinirole and impurity, selectivity and resolution) were analyzed by the standard algorithm of Dong and dummy factor effects approach. The interpretation of the results for retention factor of ropinirole and resolution was inconclusive, since the two applied approaches identified different significant factors. The potential false negative or false positive results were avoided reanalyzing the results by the modified approaches. Modification of the dummy factor effects approach included omitting the large dummy effects values, and modification of the algorithm of Dong included calculating the margin of error values for all different number of factors included, and then selecting the lowest one to be the critical effect. The applied reanalysis allowed final important factor identification and non-significant intervals for significant effects calculation.     

Metal-to-Metal Distance Modulation by Ligand Design: A Case Study of Structure-Property Correlation in Planar Chiral Cyclophanyl Metal Complexes

Multinuclear metal complexes have seen tremendous progress in synthetic advances, their versatile structural features, and emerging applications. Here, we conceptualize Metal-to-Metal distance modulation in cyclophanyl metal complexes by bridging ligand design employing the co-facially stacked cyclophanyl-derived pseudo-geminal, -ortho, -meta, and -para constitutional isomers grafted with N-, O-, and P- containing chelates that allow the installation of diverse (hetero)metallic moieties in a distance-defined and spatially-oriented relation to one another. Metal-to-Metal distance modulation and innate transannular “through-space” π–π electronic interactions via the co-facially stacked benzene rings in cyclophanyl-derived complexes as well as their specific stereochemical structural features (element of planar chirality) are crucial factors that contribute to the tuning of structure-property relationships, which stand at the very center from the perspective of cooperative effects in catalysis as well as emerging material applications.     

Subsystem‐Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies

The absorption properties of chromophores in biomolecular systems are subject to several fine‐tuning mechanisms. Specific interactions with the surrounding protein environment often lead to significant changes in the excitation energies, but bulk dielectric effects can also play an important role. Moreover, strong excitonic interactions can occur in systems with several chromophores at close distances. For interpretation purposes, it is often desirable to distinguish different types of environmental effects, such as geometrical, electrostatic, polarization, and response (or differential polarization) effects. Methods that can be applied for theoretical analyses of such effects are reviewed herein, ranging from continuum and point‐charge models to explicit quantum chemical subsystem methods for environmental effects. Connections to physical model theories are also outlined. Prototypical applications to optical spectra and excited states of fluorescent proteins, biomolecular photoreceptors, and photosynthetic protein complexes are discussed.     

New method for the computation of ionic distribution around rod-like polyelectrolytes with the helical distribution of charges. I. General approach and a nonlinearized Poisson–Boltzmann equation

This article is a first step in an attempt to reevaluate the relative role of different contributions to the energetics of DNA in salt solutions. To identify individual terms yielding such contributions a new derivation is given of the generalized Poisson–Boltzmann equation, which includes correlation effects, and explicitly shows terms ignored in the regular Poisson–Boltzmann approach. A general method based on the Boundary Element Technique is discussed, which can be used to evaluate these terms in the next steps of the reevaluation. An implementation of this method for the solution of the nonlinear Poisson–Boltzmann equation is described in detail, and is used to compute the ionic atmosphere around DNAs modeled as cylinders with helical distributions of charges. In the B-type DNA models, it is found that the ion densities in the minor and major grooves near the DNA surface differ by up to threefold. This difference is ca. 10-fold for Z-type DNA models. There are 20–25% differences in the magnitude of the maximum ionic charge density between DNA models of the same type. The addition of excess salt (up to 0.15 M) changes this maximum by only 10–15%. This change is not proportional to the concentration of excess salt. The contributions of different factors to the stabilization of alternative forms of DNA are evaluated. These factors are: (1) interactions between the phosphates, (2) interactions of phosphates with water, (3) interactions of phosphates with the ionic cloud, (4) interactions within the ionic cloud, (5) entropy of the ionic cloud. It is found that regardless of large variations in the counterion distributions around different DNAs, energetic contributions from these distributions are similar (?12.65 ± 0.6 kcal/mol · cell). The calculated change in stabilization per unit cell of models of B and Z-type DNAs due to 0.15 M excess NaCl is only ?0.56 ± 0.02 kcal/mol, indicating no tendency toward B-Z transition in this concentration range. Significantly larger variations of the order of 10 kcal/mol per unit cell can result from factors 1–2. Possible effects of the realistic DNA-solvent boundaries on the energetics of DNA solutions are discussed.     

Theoretical study of excited states of DNA base dimers and tetramers using optimally tuned range‐separated density functional theory

Excited states of various DNA base dimers and tetramers including Watson‐Crick H‐bonding and stacking interactions have been investigated by time‐dependent density functional theory using nonempirically tuned range‐separated exchange (RSE) functionals. Significant improvements are found in the prediction of excitation energies and oscillator strengths, with results comparable to those of high‐level coupled‐cluster (CC) models (RI‐CC2 and EOM‐CCSD(T)). The optimally‐tuned RSE functional significantly outperforms its non‐tuned (default) version and widely‐used B3LYP functional. Compared to those high‐level CC benchmarks, the large mean absolute deviations of conventional functionals can be attributed to their inappropriate amount of exact exchange and large delocalization errors which can be greatly eliminated by tuning approach. Furthermore, the impacts of H‐bonding and π‐stacking interactions in various DNA dimers and tetramers are analyzed through peak shift of simulated absorption spectra as well as corresponding change of absorption intensity. The result indicates the stacking interaction in DNA tetramers mainly contributes to the hypochromicity effect. The present work provides an efficient theoretical tool for accurate prediction of optical properties and excited states of nucleobase and other biological systems. © 2015 Wiley Periodicals, Inc.     

Quantum electrodynamic effects in atomic structure

Summary In high-Z atoms, quantum electrodynamic (QED) corrections are an important component in the theoretical prediction of atomic energy levels. The main QED effects in electronic atoms are the one-electron self-energy and vacuum-polarization corrections which are well known. At the next level of precision, estimates of the effect of electron interactions on the self energy and higher-order effects in two exchanged photon corrections are necessary. These corrections can be evaluated within the framework of QED in the bound interaction picture. For high-Z few-electron atoms, this approach provides a rapidly converging series in 1/Z for the corrections, which is the generalization of the well-known relativistic 1/Z expansion methods. This paper describes recent work on the effect of electron interactions on the self energy. The QED effects are particularly important for the theory for lithiumlike uranium where an accurate measurement of the Lamb shift has been made, as well as for numerous other cases where systematic differences appear between theory that does not include these QED effects and experiment.     

Solid-State nuclear magnetic resonance: performance of point-charge distributions to model intermolecular effects in 19F chemical shifts

This contribution presents results from applying two different charge models to take into account intermolecular interactions to model the solid-state effects on the ¹⁹F NMR chemical-shift tensors. The density functional theory approach with the B3LYP gradient-corrected exchange correlation functional has been used because it includes electron correlation effects at a reasonable cost and is able to reproduce chemical shifts for a great variety of nuclei with reasonable accuracy. The results obtained with the charge models are compared with experimental data and with results obtained from employing the cluster model, which explicitly includes neighboring molecular fragments. The results show that the point-charge models offer similar accuracy to the cluster model with a lower cost. Received: 3 October 1999 / Accepted: 3 February 2000 / Published online: 5 June 2000     

Charge transfer processes and environmental degrees of freedom: cooperativity and non-linearity

To investigate supramolecular effects in samples with high concentration of push-pull chromophores, we propose a model for interacting polar and polarizable molecules. Each molecule is described in terms of the same two-state picture successfully adopted to model solvated chromophores and electrostatic interactions among different chromophores are introduced. Important supramolecular effects are observed even at the lowest mean-field level, showing up the possibility of tuning molecular polarity from the neutral to the zwitterionic regime or vice versa. Supramolecular effects in excitation spectra are more complex. Here we demonstrate large supramolecular effects beyond mean-field in static optical responses.     

Further insights in the ability of classical nonadditive potentials to model actinide ion–water interactions

Pursuing our efforts on the development of accurate classical models to simulate radionuclides in complex environments (Réal et al., J. Phys. Chem. A 2010, 114, 15913; Trumm et al. J. Chem. Phys. 2012, 136, 044509), this article places a large emphasis on the discussion of the influence of models/parameters uncertainties on the computed structural, dynamical, and temporal properties. Two actinide test cases, trivalent curium and tetravalent thorium, have been studied with three different potential energy functions, which allow us to account for the polarization and charge‐transfer effects occurring in hydrated actinide ion systems. The first type of models considers only an additive energy term for modeling ion/water charge‐transfer effects, whereas the other two treat cooperative charge‐transfer interactions with two different analytical expressions. Model parameters are assigned to reproduce high‐level ab initio data concerning only hydrated ion species in gas phase. For the two types of cooperative charge‐transfer models, we define two sets of parameters allowing or not to cancel out possible errors inherent to the force field used to model water/water interactions at the ion vicinity. We define thus five different models to characterize the solvation of each ion. For both ions, our cooperative charge‐transfer models lead to close results in terms of structure in solution: the coordination number is included within 8 and 9, and the mean ion/water oxygen distances are 2.45 and 2.49 Å, respectively, for Th(IV) and Cm(III). © 2012 Wiley Periodicals, Inc.     

Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II

The mechanism of color tuning in the rhodopsin family of proteins has been studied by comparing the optical properties of the light-driven proton pump bacteriorhodopsin (bR) and the light detector sensory rhodopsin II (sRII). Despite a high structural similarity, the maximal absorption is blue-shifted from 568 nm in bR to 497 nm in sRII. The molecular mechanism of this shift is still a matter of debate, and its clarification sheds light onto the general mechanisms of color tuning in retinal proteins. The calculations employ a combined quantum mechanical/molecular mechanical (QM/MM) technique, using a DFT-based method for ground state properties and the semiempirical OM2/MRCI method and ab initio SORCI method for excited state calculations. The high efficiency of the methodology has allowed us to study a wide variety of aspects including dynamical effects. The absorption shift as well as various mutation experiments and vibrational properties have been successfully reproduced. Our results indicate that several sources contribute to the spectral shift between bR and sRII. The main factors are the counterion region at the extracellular side of retinal and the amino acid composition of the binding pocket. Our analysis allows a distinction and identification of the different effects in detail and leads to a clear picture of the mechanism of color tuning, which is in good agreement with available experimental data.     

Distortion-Controlled Redshift of Organic Dye Molecules

It is shown, quantum chemically, how structural distortion of an aromatic dye molecule can be leveraged to rationally tune its optoelectronic properties. By using a quantitative Kohn–Sham molecular orbital (KS-MO) approach, in combination with time-dependent DFT (TD-DFT), the influence of various structural and electronic tuning parameters on the HOMO–LUMO gap of a benzenoid model dye have been investigated. These parameters include 1) out-of-plane bending of the aromatic core, 2) bending of the bridge with respect to the core, 3) the nature of the bridge itself, and 4) π–π stacking. The study reveals the coupling of multiple structural distortions as a function of bridge length and number of bridges in benzene to be chiefly responsible for a decreased HOMO–LUMO gap, and consequently, red-shifting of the absorption wavelength associated with the lowest singlet excitation (λ≈560 nm) in the model cyclophane systems. These physical insights together with a rational approach for tuning the oscillator strength were leveraged for the proof-of-concept design of an intense near-infrared (NIR) absorbing cyclophane dye at λ=785 nm. This design may contribute to a new class of distortion-controlled NIR absorbing organic dye molecules.     

Interplay of intrinsic, environmental, and dynamic effects in tuning the EPR parameters of nitroxides: further insights from an integrated computational approach

The role of stereoelectronic, environmental, and short-time dynamic effects in tuning the hyperfine and gyromagnetic tensors of a prototypical nitroxide spin probe has been investigated by an integrated computational approach based on extended Lagrangian molecular dynamics and discrete-continuum solvent models. Trajectories were generated in two protic solvents as well as in the gas phase for reference; structural analysis of the dynamics, and comparison with optimized solute-solvent clusters, allowed for the identification of the prevailing solute-solvent hydrogen-bonding patterns and helped to define the strategy for the computation of magnetic parameters. This was performed in a separate step, on a large number of frames, by a high-level DFT approach coupling the PBE0 hybrid functional with a tailored basis set and with proper account of specific and bulk solvent effects. Remarkable changes in solvation networks are found on going from aqueous to methanol solution, thus providing a rationalization of indirect experimentally available evidence. The computed magnetic parameters are in satisfactory agreement with the available measured values and allow for an unbiased evaluation of the role of different effects in tuning the overall EPR observables. Apart from their intrinsic interest, our results pave the route toward the development of tunable detection protocols based on specific spectroscopic signatures.     

The Role of Binary and Many-centre Molecular Interactions in Spin Crossover in the Solid State. Part I. Equation for Free Energy

Summary. A formalism has been developed that describes spin crossover equilibrium in the solid state by taking into account the effects of n nearest neighbours of a given molecule on its partition function. In this way binary and many-body interactions of the order n + 1 are included into the theoretical model and represented by non-ideality parameters connected with the splitting of free energy levels. Binary interactions are characterised by the main splittings whereas higher order interactions manifest themselves in asymmetries of splittings within multiplets. The contribution of molecular interactions can also be written in terms of formal excess free energies of the second, third, fourth and higher orders. Simple relationships between excess free energies and parameters of multiplets have been found for binary, ternary and quaternary interactions. This formalism is reduced to that of the model of binary interactions when effects of surroundings are additive leading to equidistant free energy multiplets. Higher order interactions may cause an abrupt spin crossover but in a limited range of compositions around the transition point. The regression of experimental transition curves of one-step spin crossover may yield estimates of excess energies up to the fifth order.     

The Role of Binary and Many-centre Molecular Interactions in Spin Crossover in the Solid State. Part I. Equation for Free Energy

A formalism has been developed that describes spin crossover equilibrium in the solid state by taking into account the effects of n nearest neighbours of a given molecule on its partition function. In this way binary and many-body interactions of the order n + 1 are included into the theoretical model and represented by non-ideality parameters connected with the splitting of free energy levels. Binary interactions are characterised by the main splittings whereas higher order interactions manifest themselves in asymmetries of splittings within multiplets. The contribution of molecular interactions can also be written in terms of formal excess free energies of the second, third, fourth and higher orders. Simple relationships between excess free energies and parameters of multiplets have been found for binary, ternary and quaternary interactions. This formalism is reduced to that of the model of binary interactions when effects of surroundings are additive leading to equidistant free energy multiplets. Higher order interactions may cause an abrupt spin crossover but in a limited range of compositions around the transition point. The regression of experimental transition curves of one-step spin crossover may yield estimates of excess energies up to the fifth order.     

Blood porphyrins in binary mixtures of N,N-dimethylformamide with 1-octanol and chloroform: The energetics of solvation, (solute + cosolvent) interactions and model calculations

This study provides the first accurate analysis of the energetics of solvation of blood porphyrins in binary solvents which are considered as appropriate models for a smooth transition from a polar protein-like phase to an apolar lipid-like environment. Our results do indicate that hematoporphyrin dimethylether dimethylester (HDEDE) and deuteroporphyrin dimethylether (DDE), as well as the model of their ester side-chains ethyl acetate (EtOAc), reveal more exothermic solvation in chloroform (CHCl₃) than in dimethylformamide (DMF) and, especially, in 1-octanol (OctOH). The energetics of pair interaction between dissolved species and cosolvent molecules both in a protein-like and a lipid-like environment are clearly associated with these solvation effects. The interaction between blood porphyrins and DMF in OctOH is accompanied by large negative enthalpy changes at both temperatures, whereas in chloroform, forming strong H-bonds with dissolved species, the interaction is strongly thermochemically repulsive. All solute molecules interact in the energetically unfavorable way with OctOH and CHCl₃ in DMF, the effect being much stronger pronounced for chloroform. The most significant result of this work is that it is possible to connect this pair interaction in a highly diluted solution with the solute behavior in the entire range of the binary mixture. The approach proposed is independent of a solute and solvent structure, it provides a good prediction of the energetics of solvation in mixed solvents and can be extended for a lot of other biologically active solutes.     

Partial least-squares regression on design variables as an alternative to analysis of variance

The partial least-squares (PLS) algorithm has become popular for explorative multivariate data analysis and for multivariate calibration. The same PLS algorithm can also be used for confirmatory data analysis. The discussion is limited to analysis of a single response variable. A close correspondence of PLS1 regression to classical analysis of variance (ANOVA) is demonstrated. The design of an experiment is described in terms of discrete design variables for main effects and simple interactions (dummy variables). These are used as regressors X = (x₁, x₂,…,) for modelling the response variable of the experiment, y. As in conventional use of PLS1 regression, the algorithm gives a concentrated model or diagram of the most important, y-relevant variability types in the X-data. In the present case, this gives the combination of design variables that models the variations in y. A simple plot of the resulting factor loadings immediately reveals the important design variables. Statistical tests and confidence regions in the PLS solution give additional safeguards against interpretation of spurious effects. The method is applied to two data sets. One concerns assessment of personal preference for blackcurrent juice, studied in a 2⁵ factorial experiment; these data are also studied with missing values and as fractional factorials. The other ceoncers spectrophotometric absorbance-based colour assessments of pigment in strawberry jam in a 3-factor design with 2, 2 and 3 levels in the respective factors.     

Prediction of human cytochrome P450 2B6‐substrate interactions using hierarchical support vector regression approach

The human cytochrome P450 2B6 can metabolize a number of clinical drugs. Inhibition of CYP2B6 by coadministered multiple drugs may lead to drug–drug interactions and undesired drug toxicity. The aim of this investigation is to develop an in silico model to predict the interactions between P450 2B6 and novel inhibitors using a novel hierarchical support vector regression (HSVR) approach, which simultaneously takes into account the coverage of applicability domain (AD) and the level of predictivity. Thirty‐seven molecules were deliberately selected and rigorously scrutinized from the literature data, of which 26 and 11 molecules were treated as the training set and the test set to generate the models and to validate the generated models, respectively. The generated HSVR model gave rise to an r² value of 0.97 for observed versus predicted pK_m values for the training set, a q² value of 0.93 by the 10‐fold cross‐validation, and an r² value of 0.82 for the test set. Additionally, the predicted results show that the HSVR model outperformed the individual local models, the global model, and the consensus model. Thus, this HSVR model provides an accurate tool for the prediction of human cytochrome P450 2B6‐substrate interactions and can be utilized as a primary filter to eliminate the potential selective inhibitor of CYP2B6. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

Energy levels of paramagnetic ions: Algebra. IV. The case of fN ions in cubical symmetry

The symmetry-adapted formalism and the weak-field model described in the first three papers of this series are applied to the case of a configuration nf^N in octahedral symmetry. In this case, the latter weakfield model is restricted to a 30-parameter model which accounts for isotropic and anisotropic Coulomb (repulsion) interactions, isotropic and anisotropic spin-orbit interactions, and crystal-field interactions. A comparison between this 30-parameter weak-field model and a 33-parameter strong-field model is established. Equivalence between these two models requires three constraint relations to be satisfied for some strong-field parameters. The three relations are examined on various viewpoints.     

Heme protein oxygen affinity regulation exerted by proximal effects

Heme proteins are found in all living organisms and are capable of performing a wide variety of tasks, requiring in many cases the binding of diatomic ligands, namely, O(2), CO, and/or NO. Therefore, subtle regulation of these diatomic ligands' affinity is one of the key issues for determining a heme protein's function. This regulation is achieved through direct H-bond interactions between the bound ligand and the protein, and by subtle tuning of the intrinsic heme group reactivity. In this work, we present an investigation of the proximal regulation of oxygen affinity in Fe(II) histidine coordinated heme proteins by means of computer simulation. Density functional theory calculations on heme model systems are used to analyze three proximal effects: charge donation, rotational position, and distance to the heme porphyrin plane of the proximal histidine. In addition, hybrid quantum-classical (QM-MM) calculations were performed in two representative proteins: myoglobin and leghemoglobin. Our results show that all three effects are capable of tuning the Fe-O(2) bond strength in a cooperative way, consistently with the experimental data on oxygen affinity. The proximal effects described herein could operate in a large variety of O(2)-binding heme proteins-in combination with distal effects-and are essential to understand the factors determining a heme protein's O(2) affinity.     

Structure,energy spectra and magnetic properties of poly(m-aniline)s

The energy spectra and magnetic properties of a large class of one-dimensional poly(m-aniline)s (PMA) and further model polymers are investigated theoretically. The band structure of those PMA's which are aza-analogs of the alternant non-classical (non-Kekulé) hydrocarbons (polymers) is characterized by a wide gap in which there is a narrow half-filled band (HFB). The different contributions to the effective spin exchange between the unpaired electrons in the HFB: Coulomb (Hund), kinetic and indirect exchange interactions are calculated. While it has been shown earlier that PMA exhibits a net spin exchange of ferromagnetic nature, this approach enables a detailed understanding of the influence of substituents on the nitrogen centers and changes in the aromatic bridging unit. The ferromagnetic nature of the spin coupling in the singly bridged PMA models therebye prevails independent of the structural changes. The HFB width of those PMA's which are derivatives (aza-analogs) of ladder-type non-alternant hydrocarbons is very large and the Wannier functions are delocalized. For this group of polymers the delocalized, non-magnetic state is favored and, therefore, they may be good candidates for testing electrical conduction.