SimLabel: a graphical user interface to simulate continuous wave EPR spectra from site‐directed spin labeling experiments

Site‐directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the residue level, structural transitions in proteins. SDSL‐EPR is based on the selective grafting of a paramagnetic label on the protein under study, followed by cw EPR analysis. To extract valuable quantitative information from SDSL‐EPR spectra and thus give reliable interpretation on biological system dynamics, numerical simulations of the spectra are required. Such spectral simulations can be carried out by coding in MATLAB using functions from the EasySpin toolbox. For non‐expert users of MATLAB, this could be a complex task or even impede the use of such simulation tool. We developed a graphical user interface called SimLabel dedicated to run cw EPR spectra simulations particularly coming from SDSL‐EPR experiments. Simlabel provides an intuitive way to visualize, simulate, and fit such cw EPR spectra. An example of SDSL‐EPR spectra simulation concerning the study of an intrinsically disordered region undergoing a local induced folding is described and discussed. We believe that this new tool will help the users to rapidly obtain reliable simulated spectra and hence facilitate the interpretation of their results. Copyright © 2017 John Wiley & Sons, Ltd.     

MoCalc: a new graphical user interface for molecular calculations

A new computer program called MoCalc (Molecular Calculations) has been designed to help the computational chemistry practitioner in the task of performing and analyzing molecular calculations. MoCalc is a graphical user interface for the MO calculation programs Gamess and Mopac, and uses Rasmol and Babel for molecule display and file conversion, respectively. In its initial version, MoCalc can execute the following operations: (a) create and handle Gamess and Mopac input files; (b) import any kind of molecular geometry supported by Babel and paste it as Cartesian, internal, or Gaussian-type coordinates on the input file; (c) convert Gamess and Mopac output files to inputs of both programs; (d) edit and validate the keywords that control the Gamess and Mopac calculation procedure; (e) display the input (Mopac) and output (Gamess and Mopac) molecular geometries; (f) run single or multiple (batch) calculations, either interactively or in background; (g) automatically open the output files as soon as the calculation finishes; (h) extract results from the output files, such as energy, charges, dipole, population analysis, wave function, bond orders, and valence analysis, and display them in spreadsheets; (i) calculate reactivity indices derived from the frontier orbital theory and the root-mean-square (rms) deviation of input and output geometries. All the results generated by MoCalc can be promptly transferred to text editors and electronic spreadsheets, which facilitate a detailed subsequent analysis and the publication of the results. MoCalc can also perform graphical and numerical comparative analysis of the some results when more than one output file is loaded. The program was coded in Visual Basic and runs in Windows 95/98/NT4/ME/2000/XP environments.     

Implementation of a graphical user interface for the virtual multifrequency spectrometer: The VMS‐Draw tool

This article presents the setup and implementation of a graphical user interface (VMS‐Draw) for a virtual multifrequency spectrometer. Special attention is paid to ease of use, generality and robustness for a panel of spectroscopic techniques and quantum mechanical approaches. Depending on the kind of data to be analyzed, VMS‐Draw produces different types of graphical representations, including two‐dimensional or three‐dimesional (3D) plots, bar charts, or heat maps. Among other integrated features, one may quote the convolution of stick spectra to obtain realistic line‐shapes. It is also possible to analyze and visualize, together with the structure, the molecular orbitals and/or the vibrational motions of molecular systems thanks to 3D interactive tools. On these grounds, VMS‐Draw could represent a useful additional tool for spectroscopic studies integrating measurements and computer simulations. © 2014 Wiley Periodicals, Inc.     

Aligning retention time shifts in HPLC three‐dimensional spectra by icoshift approach combined with data arrangement methods and the release of a graphical user interface

High‐performance liquid chromatography coupled with photodiode array detection has been extensively applied in many fields and the peaks among the analyzed samples can be shifted due to the variations of instrumental and experimental conditions. In multivariate analysis, retention time alignment is an important pretreatment step. Hence, the shifted peaks in high‐performance liquid chromatography coupled with photodiode array detection three‐dimensional spectra should be aligned for further analysis. Being motivated by this purpose, the interval correlated shifting method combined with the proposed data arrangement methods are recommended and employed on high‐performance liquid chromatography coupled with photodiode array detection data as a demonstration. We validate the alignment performance of the proposed method through comparison the consistency of the retention time before and after alignment. The obtained results demonstrated that the proposed method is capable of successful aligning the employed data. Additionally, the interval correlated shifting method combined with the data arrangement modes is implemented in an easy‐to‐use graphical user interface environment and so can be operated easily by users not familiar with programming languages.     

Grcarma: A fully automated task‐oriented interface for the analysis of molecular dynamics trajectories

We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules. It is a cross‐platform, Perl/Tk‐based front‐end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user‐friendly and intuitive design. Particular emphasis was given to the automation of several tedious tasks, such as extraction of clusters of structures based on dihedral and Cartesian principal component analysis, secondary structure analysis, calculation and display of root‐mean‐square deviation (RMSD) matrices, calculation of entropy, calculation and analysis of variance–covariance matrices, calculation of the fraction of native contacts, etc. The program is free‐open source software available immediately for download. © 2013 Wiley Periodicals, Inc.     

EPR spectra of V(IV) complexes and the structure of oil porphyrins

For natural bitumoids, the effects of the structure of vanadyl-porphyrin complexes on the EPR spectra were investigated. The ambiguity of the hyperfine structure (its presence or absence) corresponding to four nitrogen atoms in the spectra of oil vanadyl porphyrins correlates with the changes in the second coordination sphere of the nearest environment of the metal ion, namely, in methine bridges.     

Catalytic olefination of carbonyl compounds. A new versatile method for the synthesis of alkenes

The review is devoted to a new catalytic olefination reaction (COR) discovered by the authors. This is the reaction between N-unsubstituted hydrazones of carbonyl compounds with dihalides CHal₂XY in the presence of copper(i) chloride to give substituted alkenes. Catalytic olefination is versatile. Variation of the carbonyl and olefinating components opens up the way for the synthesis of various classes of unsaturated compounds including those containing functional groups. The reaction mechanism is discussed and a catalytic cycle describing the process is proposed. A model for estimating and predicting the reactivity of halogen-containing compounds in the COR is developed. The relationship between the structure of the carbonyl substrates and their behavior in the title reaction is elucidated.     

Quantification of the trans influence in d8 square planar and d6 octahedral complexes: a database study

A systematic search of the Cambridge structural database was undertaken to quantify the trans influence in square planar and octahedral transition metal compounds. For square planar geometry, d⁸ metal centers were studied, while octahedral searches focused on low-spin d⁶ complexes. Two probe ligands (PL) were used to measure the effect of the trans ligand (TL), chloride, and triphenylphosphine (PPh₃). For the TLs O=CX₂, NR₃, pyridine, and Cl^? (X?=?any non-metal, R?=?H or hydrocarbon), the effects on the metal–probe ligand (M–PL) distance were statistically equal and were taken as essentially no trans influence. The other ligands studied showed significant decrease in the mean M–PL bond order, relative to the above ligands: SR₂?=?0.941; S=CX₂?=?0.887; PPh₃?=?0.825; phenyl?=?0.743; CR₃?=?0.719; hydride?=?0.685. Some variation in the trans influence is observed, based on the geometry of the metal center and the PL. In general, electron-donating, σ-bonding ligands lead to a larger trans influence, but π-bonding effects can also be important, particularly when the probe ligand also has π-bonding properties.     

On the long-range corrections to computer simulation results for the Lennard-Jones vapor-liquid interface

The long-range corrections (LRCs) to the configurational energy have been taken into consideration in the Monte Carlo simulation of the vapor-liquid interface for a pure Lennard-Jones (LJ) fluid. The simulated bulk densities agree satisfactorily with those obtained from the Gibbs ensemble method, and the simulated surface tension values agree reasonably well with those reported in the literature for a larger number of molecules and a larger cut-off distance. To compare the influence of the potential forms on the simulation results, a truncated LJ potential, and a shifted and truncated LJ potential have been examined. Although the bulk densities and surface tensions calculated for different model fluids are strongly affected by the LRC, the different potentials essentially lead to similar density values and similar surface tension values when the respective calculated values are compared on the basis of a reduced temperature scale.     

A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation

For applying to a number of theoretical methodologies based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics method connecting AMBER9 with GAUSSIAN03, we have developed an AMBER-GAUSSIAN interface (AG-IF), which can be one of the simplest architectures. In the AG-IF, only a few subroutines addition is necessary to retrieve the QM/MM energy and forces, obtained by GAUSSIAN, for solving a set of Newtonian equations of motion in AMBER. It is, therefore, easy to be modified for individual applications since AG-IF utilizes most of those functions originally equipped not only in AMBER but also in GAUSSIAN. In the present minimal implementation, only AMBER is modified, whereas GAUSSIAN is left unchanged. Moreover, a different method of calculating electrostatic forces of MM atoms interacting with QM region is proposed. Using the AG-IF, we also demonstrate three examples of application: (i) the QM versus MM comparison in the radial distribution function, (ii) the free energy gradient method, and (iii) the charge from interaction energy and forces.     

Terminal end-on coordination of dinitrogen versus isoelectronic CO: A comparison using the charge displacement analysis

The metal dinitrogen bonding in a wide series of terminal end-on dinitrogen complexes is investigated with the charge displacement analysis based on natural orbitals of chemical valence (CD-NOCV). The effect of the σ donation and π backdonation on the N N bond are discussed and compared with the observations for a series of carbonyl complexes, published in 2016 by Tarantelli et al. The σ donation is relative invariant over the series of dinitrogen complexes and has no significant effect on the N N bond strength, whereas the π backdonation causes a considerable elongation of the N N bond. Some uncommon examples of weakly bound dinitrogen with blue-shifted stretching frequency compared to free N₂ (ν = 2330 cm⁻¹) are known. The dinitrogen bonding in these complexes is simulated with a point charge. Apparently, electrostatics account for the shortened N─N bond in these systems.     

Modeling the solvation shell of complexes in solution for quantum chemical calculations of electronic spectra

A procedure that allows for solvation effects is suggested; it is designed for quantum chemical calculations of the electronic spectra of complex compounds. Based on Monte Carlo (MC) simulation of the solvation shell one can calculate the electrostatic potential created by the solvation shell at the sites of all atoms of the complex; appropriate corrections are added to the diagonal elements of the Fock matrix and to the matrix elements of the Hamiltonian in the configuration interaction method. The method suggested has been implemented based on the semiempirical (CINDO) version of the CI (configuration interaction) technique and tested on the following compounds: [Ru(NH₃)₅(py)]²⁺, [Ru(NH₃)₅(pyz)]²⁺, [Ru(bpy)(CN)₄]^2?, [Ru(NO)(py)₄-NC-Ru(py)₄(CN)]³⁺.     

Modification of immobilized metal complexes toward the design and synthesis of functional materials for nitric oxide delivery

Functional polymeric materials containing immobilized metal complexes with the potential to bind nitric oxide (NO) are described. The materials were synthesized using template copolymerization techniques and contain immobilized metalloporphyrin and metallosalen (N,N′‐bis(salicylidene)‐1,2‐ethylenediaminato(2‐)) sites where NO binding occurs. A potential drawback of current materials designed for NO‐delivery is the rebinding of NO to the material after release. To minimize this undesirable rebinding event, materials were prepared in which immobilized sites contain additional covalently‐linked functional groups that can bind to the metal centers after NO dissociation. A model system with a covalently attached Co^IIsalen complex and pyridine groups confirmed that the immobilized sites bind NO in the presence of the additional ligands. Attempts to immobilize an iron porphyrin, containing two axial imidazole ligands, were unsuccessful because the lability of the iron center prevented the formation of a stable template. Instead, the desired material was achieved by selecting Co^III porphyrin with axially coordinated imidazole ligands as the template complex. Once immobilized, a procedure was developed to remove the cobalt ions and incorporate iron into the sites. The site structure of these new immobilized sites was examined spectroscopically. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 2282–2292, 2006     

Polysulfoximine: A Novel Sulfur-Based Polymer for High Performance Engineering Plastics

First polysulfoximine was synthesized and characterized. 4-Phenoxybenzenesulfonimidoyl chloride was prepared by the reaction of 4-phenoxybenzenesulfinyl chloride with anhydrous chloramine T. Acid-catalyzed polycondensation of the sulfonimidoyl chloride with 10% of anhydrous ferric chloride in nitrobenzene at 120°C for 48 h afforded 80% yield of polysulfoximine having tosyl group at the nitrogen atom (NTs derivative). The spectral characteristics of the NTs derivative suggested occurrence of the regioselective polycondenstion. The NTs derivative was treated with conc. sulfuric acid followed by neutralization with sodium hydroxide to give corresponding “free” polysulfoximine having hydrogen atom at the nitrogen atom (NH derivative) in 80% conversion. Benzylated derivative (NBz derivative) was obtained by benzylation of the NH derivative with benzyl chloride. Thermal properties of these polysulfoximines were examined.     

Electrochemical impedance simulation of a metal oxide heterostructure/electrolyte interface: A review

The results of an analysis of the literature data obtained when investigating processes of charge transfer at interfaces of heterostructures formed by various methods, including the high-energy methods, are presented in this paper. The performed investigation of oxide layers at the titanium surface, with use made of impedance spectroscopy data made it possible to reveal the nature and influence of some processes and factors on the charge transfer mechanism realized at a metal oxide heterostructure/electrolyte interface. Simulating an oxide/electrolyte interface gives one a chance to identify, in a spectrum, the responses that characterize the behavior of porous and poreless layers, as well as the responses that are due to the space-charge region formed in the oxide material and to the corrosion and diffusion processes.     

FI catalysts: new olefin polymerization catalysts for the creation of value-added polymers

This contribution reports the discovery and application of phenoxy-imine-based catalysts for olefin polymerization. Ligand-oriented catalyst design research has led to the discovery of remarkably active ethylene polymerization catalysts (FI Catalysts), which are based on electronically flexible phenoxy-imine chelate ligands combined with early transition metals. Upon activation with appropriate cocatalysts, FI Catalysts can exhibit unique polymerization catalysis (e.g., precise control of product molecular weights, highly isospecific and syndiospecific propylene polymerization, regio-irregular polymerization of higher alpha-olefins, highly controlled living polymerization of both ethylene and propylene at elevated temperatures, and precise control over polymer morphology) and thus provide extraordinary opportunities for the syntheses of value-added polymers with distinctive architectural characteristics. Many of the polymers that are available via the use of FI Catalysts were previously inaccessible through other means of polymerization. For example, FI Catalysts can form vinyl-terminated low molecular weight polyethylenes, ultra-high molecular weight amorphous ethylene-propylene copolymers and atactic polypropylenes, highly isotactic and syndiotactic polypropylenes with exceptionally high peak melting temperatures, well-defined and controlled multimodal polyethylenes, and high molecular weight regio-irregular poly(higher alpha-olefin)s. In addition, FI Catalysts combined with MgCl(2)-based compounds can produce polymers that exhibit desirable morphological features (e.g., very high bulk density polyethylenes and highly controlled particle-size polyethylenes) that are difficult to obtain with conventionally supported catalysts. In addition, FI Catalysts are capable of creating a large variety of living-polymerization-based polymers, including terminally functionalized polymers and block copolymers from ethylene, propylene, and higher alpha-olefins. Furthermore, some of the FI Catalysts can furnish living-polymerization-based polymers catalytically by combination with appropriate chain transfer agents. Therefore, the development of FI Catalysts has enabled some crucial advances in the fields of polymerization catalysis and polymer syntheses.