Addition of sulfenic acids to monosubstituted acetylenes: a theoretical and experimental study

The reaction of benzenesulfenic acid, generated in situ by thermal decomposition of 3‐(phenylsulfinyl)propanenitrile, with monosubstituted acetylenes was experimentally and theoretically investigated at the DFT level using the MPW1B95 density functional. A computational model based on the Hard Soft Acid Base (HSAB) principle was evaluated for its ability to qualitatively and quantitatively predict the regioselectivity, while kinetics and thermodynamics of the reaction were studied through the analysis of the reaction paths leading to the possible regioisomers. Copyright © 2009 John Wiley & Sons, Ltd.     

Mechanism and regioselectivity of the 1,3‐dipolar cycloaddition of thiocarbonyl S‐imide with cyclopent‐3‐ene‐1,2‐dione and methoxyethene: a density functional theory approach

A theoretical study on the regioselectivity of 1,3‐dipolar cycloaddition reaction between an uncommon dipole (thiocarbonyl S‐imide) with cyclopent‐3‐ene‐1,2‐dione (DPh1) and methoxyethene (DPh2) has been carried out by means of several theoretical approaches, namely, activation energy, Houk's rule based on the frontier molecular orbital theory and density functional theory (DFT) reactivity indices. The calculations were performed at the DFT‐B3LYP/6‐31G(d) level of theory using GAUSSIAN 09. The present analysis shows that the 1,3‐dipolar cycloaddition of thiocarbonyl S‐imide with DPh1 and DPh2 has normal‐electron demand and inverse‐electron demand character, respectively. Moreover, the results obtained from energetic point view are in agreement with electronic approaches, and the Houk's rule is capable to predict true regioselectivity. Copyright © 2012 John Wiley & Sons, Ltd.     

Regioselectivity and stereoselectivity of Diels–Alder reaction: a DFT study on the functionalization of organic semiconductor crystals

Diels–Alder (DA) reaction is one of the most commonly tools in functionalizing organic semiconductor crystals. The DA reactions of two organic semiconductors, i.e. tetracene ( 1 ) and rubrene ( 2 ), to several dienophiles ( 3 to 7 ) were performed experimentally recently. But the kinetics and mechanism of stereoselectivity and regioselectivity remain unknown. In the current study, all related 20 DA reactions (totally 32 possible pathways) were investigated by density functional theory. It was found that the reaction of 7 and a–b position of 1 is the most favorable one. The c–d position of 2 is more reactive than its a–b position when 2 combines with 3 , but is less reactive when combines with 4 to 7 . The endo and exo pathways have similar activation barriers in each reaction. The rate coefficients were calculated using the canonical variational transition state theory and their Arrhenius expressions were fitted. The theoretical conclusion agrees with the experimental observations and is of general importance for similar reactions. Solvent has a slight effect on these reactions. Copyright © 2016 John Wiley & Sons, Ltd.     

Metal‐assisted regioselectivity in nucleophilic substitutions: a study by Raman spectroscopy and density functional theory calculations

A series of complexes (Fe^II, Cu^II and Ni^II) of the N,O bidentate ligand 6,7‐dichloroquinoline‐5,8‐dione in water was investigated by using Raman spectroscopy, and the experimental peaks were assigned with the help of computed spectra by density functional theory (DFT) calculations. A strong shift to lower wavenumbers was observed for the vibration of the CO group involved in chelation, depending on the type of metal ion. When each complex was used in the substitution reaction by the nucleophilic reagent piperidine, two products having the same molecular composition but showing the substituent in different regions of the molecule were obtained, and moreover their regioselective formation was in agreement with the size of the Raman shifts previously observed for the complexes. This example confirms the potential of the approach involving Raman spectroscopy combined with DFT calculations in the characterization of metal complexes as key intermediates in organic reactions, with the possibility of predicting the metal system capable to achieve the highest selectivity. Copyright © 2010 John Wiley & Sons, Ltd.     

Theoretical insights into the regioselectivity of a Pictet‐Spengler reaction: Transition state structures leading to salsolinol and isosalsolinol

The mechanism of the cyclization step of the Pictet‐Spengler reaction between acetaldehyde and dopamine to give salsolinol and isosalsolinol was studied computationally, using density functional theory. The preferential formation in acidic media of salsolinol, the product of para‐cyclization, and the requirement of a neutral pH for the formation of the ortho‐cyclized isosalsolinol are explained in terms of 2 different mechanistic routes with an iminium ion or a phenolate‐iminium zwitterion as starting reactants.     

Photonic‐on‐a‐chip: a thermal actuated Mach‐Zehnder interferometer and a molecular thermometer based on a single di‐ureasil organic‐inorganic hybrid

An integrated photonic‐on‐a‐chip device based on a single organic‐inorganic di‐ureasil hybrid was fabricated for optical waveguide and temperature sensing. The device is composed by a thermal actuated Mach‐Zehnder (MZ) interferometer operating with a switching power of 0.011 W and a maximum temperature difference between branches of 0.89 ºC. The MZ interferometer is covered by a Eu³⁺/Tb³⁺ co‐doped di‐ureasil luminescent molecular thermometer with a temperature uncertainty of 0.1ºC and a spatial resolution of 13 µm. This is an uncommon example in which the same material (an organic‐inorganic hybrid) that is used to fabricate a particular device (a thermal‐actuated MZ interferometer) is also used to measure one of the device intrinsic properties (the operating temperature). The photonic‐on‐a‐chip example discussed here can be applied to sense temperature gradients with high resolution (10⁻³ ºC·µm⁻¹) in chip‐scale heat engines or refrigerators, magnetic nanocontacts and energy‐harvesting machines.     

Adsorption of 1,2,4‐triazole on a silver electrode: surface‐enhanced Raman spectroscopy and density functional theory studies

The pH‐dependent surface‐enhanced Raman scattering (SERS) of 1,2,4‐triazole adsorbed on silver electrode and normal Raman (NR) spectra of this compound in the aqueous solutions were investigated. The observed bands in the NR and SERS spectra were assigned with the help of density functional theory calculations for model molecules in the neutral, anionic, and cationic forms and their complexes with silver. The Raman wavenumbers and intensities were computed at the optimized molecular geometry. Vibrational assignments of the SERS and NR spectra are provided by calculated potential energy distributions. The combination of experimental SERS results and density functional theory calculations provide an insight into the molecular structure of adlayers formed by 1,2,4‐triazole on a silver surface at varying pH values and enable the determination of molecular orientation with respect to the surface. Copyright © 2012 John Wiley & Sons, Ltd.     

A DFT‐based exploration augmented by X‐ray and NMR of the stereoselectivity in the 1,3‐dipolar cycloaddition of 1‐pyrroline‐1‐oxide to methyl cinnamate and benzylidene acetophenone

A B3LYP/6–31G* study was carried out for the reactions of 1‐pyrroline‐1‐oxide (N1) with methyl cinnamate (E1) and benzylidene acetophenone (E2) for getting a quantitative rationalization of the experimental findings. The product ratios were determined by NMR studies of the crude reaction mixtures. The conformation and stereochemistry of the isolated cycloadducts were finally confirmed by 2D NMR and X‐ray diffraction. The endo/exo‐selectivities were predicted through the computation of activation parameters on the basis of assumed concerted mechanism. The regioselectivity and reactivity were amply predicted by local and global electrophilicity indices and were found to be in good agreement with the experimental findings which were supportive of polar character and of the direction of charge transfer (CT) accompanying the cycloaddition. It was found that the cycloaddition involving methyl cinnamate was endo‐selective, while that with benzylidene acetophenone produced the exo‐isomer as the major adduct. Copyright © 2010 John Wiley & Sons, Ltd.     

UV filter 2‐ethylhexyl 4‐methoxycinnamate: a structure,energetic and UV–vis spectral analysis based on density functional theory

2‐Ethylhexyl 4‐methoxycinnamate (EHMC) is a very commonly used UVB filter that is known to isomerize from the (E) to the (Z) isomer in the presence of light. In this study, we have performed high level quantum chemical calculations using density functional theory (DFT) with the B3LYP density functional and extended basis sets to study the gas‐phase molecular structure of EHMC and its energetic stability. Calculations were also performed for related smaller molecules cinnamic acid and 4‐methoxycinnamic acid. Charge delocalization has been analyzed using natural charges and Wiberg bond indexes within the natural bond orbital analysis and using nucleus independent chemical shifts. Density functional theory calculations reveal that the (E) isomer of EHMC is more stable than the (Z) by about 20 kJ mol^?1 in both the gas and aqueous phases. The enthalpy of formation in the gas phase of (E)‐EHMC was derived from an isodesmic bond separation reaction. Long‐range corrected DFT calculations in implicit water were made in order to understand the excited state properties of the (E) and (Z) isomers of EHMC. Copyright © 2013 John Wiley & Sons, Ltd.     

Structure and vibrational analysis of 1‐hydroxy naphthalene based on density functional theory calculations

The solid phase mid‐FTIR and FT‐Raman spectra of 1‐hydroxy naphthalene (HNP) were recorded in the regions 4000–400 and 4000–50 cm, respectively. The spectra were interpreted with the help of normal coordinate analysis following full structure optimization and force field calculations based on the density functional theory (DFT) using the standard B3LYP/6‐31G** method and basis set combination. The results of the calculations were applied to simulate infrared and Raman spectra of the title compound which showed excellent agreement with the observed spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Density functional theory and time‐dependent density functional theory study on a series of iridium complexes with tetraphenylimidodiphosphinate ligand

A series of heteroleptic cyclometalated Ir(III) complexes for organic light‐emitting diodes (OLEDs) application have been investigated theoretically to explore their electronic structures and spectroscopic properties. The geometries, the electronic structures, the lowest‐lying singlet absorptions and triplet emissions of Ir(dfppy)₂(tpip), Ir(tfmppy)₂(tpip), and theoretically designed models of Ir(ppy)₂(tpip) were investigated with the density functional theory (DFT)‐based approaches, where ppy = 2‐phenylpyridine, dfppy = 4,6‐difluorophenylpyridine, tfmppy = 4‐trifluoromethylphenylpyridine, and tpip = tetraphenylimidodiphosphinate. Their structures in the ground and their excited states have been optimized at the DFT/Becke 3‐parameter Lee Yang Parr (B3LYP)/Los Alamos National Laboratory 2‐double‐z (LANL2DZ) and time‐dependent DFT/B3LYP/LANL2DZ levels, and the lowest absorptions and emissions were evaluated at B3LYP and M062X level of theory, respectively. Furthermore, the energy transfer mechanism together with the advantage of low efficiency roll‐off for these complexes also can be analyzed here. Copyright © 2013 John Wiley & Sons, Ltd.     

Aza‐Diels–Alder reaction between cyclopentadiene and protonated N‐phenylethyliminoacetates of 8‐phenylmenthol and 8‐phenylneomenthol: a density functional theory study

The cycloaddition between glyoxylate imines possessing two chiral auxiliaries, N‐(R)‐ or N‐(S)‐1‐phenylethyl and 8‐phenylmenthyl or 8‐phenylneomenthyl, and cyclopentadiene is described. Computational calculations using density functional theory with the Becke, three‐parameter, Lee–Yang–Parr functional and the 6‐31G(d) basis set were performed to better understand the highly diastereoselective mechanism and the exo‐selectivity observed experimentally for these ionic aza‐Diels–Alder reactions. Copyright © 2011 John Wiley & Sons, Ltd.     

Analysis of structure and vibrational spectra of 2,5‐dihydroxybenzoicacid based on density functional theory calculations

The spectra of 2,5‐dihydroxybenzoic acid (DHBA) have been recorded using Fourier transform‐infrared spectroscopy (FT‐IR) and FT‐Raman measurements. The total energy calculations of DHBA were evaluated for various possible conformers. The spectra were interpreted with the help of normal coordinate analysis based on density functional theory (DFT) using standard B3LYP/6–31G* method for the most optimized geometry. The effect of intramolecular hydrogen bonding was discussed. Normal coordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors, yielding fairly good agreement between observed and calculated frequencies. On the basis of the comparison between calculated and experimental results, assignments of fundamental modes were examined. Copyright © 2009 John Wiley & Sons, Ltd.     

Effects of solid substrate on the SERS‐based immunoassay: a comparative study

A comparative study of the solid substrates used in surface‐enhanced Raman scattering (SERS) based immunoassay is made in this paper. Five different substrates were prepared and divided into two groups with and without SERS activity. They are (1) a poly‐L ‐lysine slide, (2) a glutaraldehyde (GA)‐aminosilane slide, (3) a substrate assembled with silver nanoparticles, (4) a substrate assembled with silver nanoparticles and functionalized with GA–aminosilane and (5) a substrate assembled with gold nanoparticles, of which the first two are substrates are without SERS activity and the latter three are with SERS activity because of the existence of the metallic nanoparticles. The SERS experimental results show that the immunoassay performed on an SERS‐active substrate is more effective than that employing the inactive substrate. Among the inactive substrates, the GA–aminosilane slide with a better ability for antibody immobilization leads to a more sensitive immunoassay than the poly‐L ‐lysine slide. Moreover, for SERS‐based immunoassay, the substrate with assembled silver nanoparticles has an advantage of higher SERS enhancement capacity over the substrate assembled with gold nanoparticles. This work indicates that SERS‐active substrates play important and positive roles in sensitive SERS‐based immunoassay. Copyright © 2010 John Wiley & Sons, Ltd.     

A note on medieval microfabrication: the visualization of a prayer nut by synchrotron‐based computer X‐ray tomography

One of the most fascinating objects in the Rijksmuseum (Amsterdam, The Netherlands) is an early 16th century prayer nut. This spherical wooden object measures 4 cm in diameter and consists of two hemispheres connected with a small hinge so that it can be opened. The interior of the nut holds wood carvings with scenes from the life of Christ. These miniature reliefs show an incredible degree of finish with carving details well beyond the millimetre scale. In the present paper it is shown how synchrotron‐based computer X‐ray tomography revealed the structure and fabrication method of the bead. The central part of the relief was cut from a single piece of wood, rather than assembled from multiple components, underlining the extraordinary manual dexterity of its maker. In addition, a piece of fibrous material contained in the inner structure of the bead is revealed. This may have served as a carrier for an odorous compound, which would be in line with the religious function of the prayer nut.     

Identification of Raman spectra through a case‐based reasoning system: application to artistic pigments

This paper presents a methodology conceived as a support system to identify unknown materials by means of the automatic recognition of their Raman spectra. Initially, the design and implementation of the system were framed in an artistic context where the Raman spectra analyzed belong to artistic pigments. The analysis of the pigmentation used in an artwork constitutes one of the most important contributions in its global study. This paper proposes a methodology to systematically identify Raman spectra, following the way analysts usually work in their laboratory but avoiding their assessment and subjectivity. It is a three‐phase methodology that automates the spectral comparison, which is based on one of the most powerful paradigms inmachine learning: the case‐based reasoning (CBR) systems. A CBR system is able to solve a problem by using specific knowledge of previous experiences (well‐known spectral library of patterns) and finding the most similar past cases (patterns), reusing and adapting them to the new problem situation (unknown spectrum). The system results in a global signal processing methodology that includes different phases such as reducing the Raman spectral expression by means of the principal component analysis, the definition of similarity measures to objectively quantify the spectral similarity and providing a final value obtained by a fuzzy logic system that will help the analyst to take a decision. The major benefit of a Raman spectral identification system lies in offering a decision‐support tool to those who are not experts or under difficult situations with respect to Raman spectroscopy. Copyright © 2011 John Wiley & Sons, Ltd.     

Radiation damage to protein specimens from electron beam imaging and diffraction: a mini‐review of anti‐damage approaches,with special reference to synchrotron X‐ray crystallography

Recent research progress using X‐ray cryo‐crystallography with the photon beams from third‐generation synchrotron sources has resulted in recognition that this intense radiation commonly damages protein samples even when they are held at 100 K. Other structural biologists examining thin protein crystals or single particle specimens encounter similar radiation damage problems during electron diffraction and imaging, but have developed some effective countermeasures. The aim of this concise review is to examine whether analogous approaches can be utilized to alleviate the X‐ray radiation damage problem in synchrotron macromolecular crystallography. The critical discussion of this question is preceded by presentation of background material on modern technical procedures with electron beam instruments using 300–400 kV accelerating voltage, low‐dose exposures for data recording, and protection of protein specimens by cryogenic cooling; these practical approaches to dealing with electron radiation damage currently permit best resolution levels of 6 Å (0.6 nm) for single particle specimens, and of 1.9 Å for two‐dimensional membrane protein crystals. Final determination of the potential effectiveness and practical value of using such new or unconventional ideas will necessitate showing, by experimental testing, that these produce significantly improved protection of three‐dimensional protein crystals during synchrotron X‐ray diffraction.     

The application of a new approach based on organic homo‐rank compounds and homologous compounds to the structure–property relationship study of mono‐substituted alkanes

The two conceptual systems of organic homologous compounds and homo‐rank compounds give insight into the influence of structures on the properties of mono‐substituted alkanes X_i–(CH₂)_j–H from the transverse (change of repeating unit number j of CH₂) and longitudinal (change of functional group X_i) perspectives, respectively. This paper aims to combine the organic homo‐rank compounds approach together with the homologous compounds approach to explore the property change rules of mono‐substituted alkanes involving various substituents. Firstly, based on the concept of organic homologous compounds, the properties of mono‐substituted straight‐chain alkane homologues were linearly correlated to the two‐thirds power of the number of carbon atoms (N^2/3) in alkyl, and regression equations such as Q = A + BN^2/3 were obtained. The regression coefficients A and B vary with different substituents X_i, so coefficients A and B were employed to characterize the structural information of substituent X_i. The structural features of alkyls (–(CH₂)_j–H, that is, –C_jH_2j+1) were described by the polarizability effect index (PEI_(R)) and vertex degree–distance index (VDI). Then based on four parameters A, B, PEI_(R), and VDI, quantitative structure–property relationship models were built for the boiling points (Bp) and refractive indexes (n_D) of each mono‐substituted alkane homo‐rank series, where j = 3–10 and the substituents X_i involve F, Cl, Br, I, NO₂, CN, NH₂, COOH, CHO, OH, SH, and NC. Good results indicate that the combination of an organic homo‐rank compounds method and a homologous compounds method has exhibited obvious advantages over traditional methods in the quantitative structure–property relationship study of mono‐substituted alkanes concerning various substituents. Copyright © 2015 John Wiley & Sons, Ltd.     

Influence of the chloro substituent position on the triplet reactivity of benzophenone derivatives: a time‐resolved resonance Raman and density functional theory study

A nanosecond time‐resolved resonance Raman (ns‐TR³) spectroscopic investigation of the photoreduction reactions and ability of several chloro‐substituted benzophenone (Cl‐BP) triplets is described. The TR³ results show that the 3‐chlorobenzophenone (3‐Cl‐BP), 4‐chlorobenzophenone (4‐Cl‐BP) and 4,4′‐dichlorobenzophenone (4,4′‐dichloro‐BP) triplets exhibit similar hydrogen abstraction ability with the parent BP triplet. In 2‐propanol, the 3‐Cl‐, 4‐Cl‐ and 4,4′‐dichloro‐diphenylketyl (DPK) radicals were observed and they appear to react with dimethylketyl radicals at the para‐position to form a light absorption transient species. These transient species were characterized with TR³ spectra, and identified with the help of results from density functional theory calculations. In an acetontitrile/water (MeCN:H₂O) 1:1 mixed solvent, these DPK radicals were also observed but with slower formation rates. However, the 2‐Cl‐DPK radical was observed to form with a lower yield and a significantly slower formation rate than the other chloro‐substituted benzophenones examined here in 2‐propanol under the same experimental conditions. These results reveal that the 2‐chloro substituent reduces the hydrogen abstraction ability of the substituted BP triplet, which was not as expected based on the assumption that the electron‐withdrawing group could increase its photoreduction ability. This unusual ortho effect of the chlorine substitution is briefly discussed. Copyright © 2011 John Wiley & Sons, Ltd.     

Blueprint XAS: a Matlab‐based toolbox for the fitting and analysis of XAS spectra

Blueprint XAS is a new Matlab‐based program developed to fit and analyse X‐ray absorption spectroscopy (XAS) data, most specifically in the near‐edge region of the spectrum. The program is based on a methodology that introduces a novel background model into the complete fit model and that is capable of generating any number of independent fits with minimal introduction of user bias [Delgado‐Jaime & Kennepohl (2010), J. Synchrotron Rad. 17 , 119–128]. The functions and settings on the five panels of its graphical user interface are designed to suit the needs of near‐edge XAS data analyzers. A batch function allows for the setting of multiple jobs to be run with Matlab in the background. A unique statistics panel allows the user to analyse a family of independent fits, to evaluate fit models and to draw statistically supported conclusions. The version introduced here (v0.2) is currently a toolbox for Matlab. Future stand‐alone versions of the program will also incorporate several other new features to create a full package of tools for XAS data processing.