Research applications of the Cambridge Structural Database (CSD)

Crystal structure data are of fundamental importance in a wide spectrum of scientific activities. This tutorial review summarises the principal application areas, so far, for the data from more than 300,000 crystal structures of small organic and metal-organic compounds that are stored in the Cambridge Structural Database (CSD). Direct use of the accumulated data is valuable in establishing standard molecular dimensions, determining conformational preferences and in the study of intermolecular interactions, all of which are crucial in structural chemistry and rational drug design. More recently, information derived from the CSD has been used to construct two dynamic libraries of structural knowledge: Mogul, which stores intramolecular information, and IsoStar, which stores information about intermolecular interactions. These electronic libraries provide information "at the touch of a button". In their turn, the libraries also serve as sources of structural knowledge for applications software that address specific problems in small-molecule and biological chemistry.     

Substitution-Inert Metal Complex Mobile Phases in Non-Suppressed Cation Chromatography

Substitution-inert metal complexes, [Co(edda)(H₂O)₂]⁺, (Co(edda)(en)]⁺, [Co(edda)(dmen)]⁺, [Co(en)₂-(gly)]²⁺, [Co(en)₂(acac)]²⁺, and [Co(trien)(gly)]²⁺ in their nitrate salt solutions are used as eluents in nonsuppressed cation chromatography (where edda = ethylenediamine-N,N′-diacetic acid, en = ethylenediamine, dmen = N,N′-dime-thylethylenediamine, gly = glycine, acac = acetylacetone, and trien = triethylenetetraamine). It is found that all the mono- and di-valent charged complexes can be used to separate alkali and alkaline earth metal cations, respectively. The separations for monovalent cations are sometimes comparable to those using ultrapure HNO₃ solutions. However, the divalent Ca²⁺ and Sr²⁺ ions cannot be resolved using the metal complex eluents. On the other hand, a selected, direct non-suppressed IC separation of zinc(II) and cadmium(II) ions is demonstrated for the first time using a substitution-inert metal complex eluent and a conductivity detector. Comparisons of these eluents with those reported previously, i. e. HNO₃ and ethylenediammonium salt solution are made and explanations are proposed to account for the different selectivities observed where possible. The future development of this technique is also briefly discussed.     

EVENTS SURROUNDING THE EARLY DEVELOPMENT OF EUGLENA CHLOROPLASTS. 12. SPECTROSCOPIC EXAMINATION OF THE PROTOCHLOROPHYLL(IDE) PHOTOTRANSFORMATION IN INTACT CELLS*

Abstract— Absorption measurements in the 600–720 nm region of dark-grown cells of Euglena gracilis Klebs var. bacillaris Cori were made in vivo at room temperature using computer-assisted spectrophotometry. Dark-grown wild-type cells have a prominent absorption maximum at 634 nm due to protochlorophyll(ide) absorption. Upon illumination, the absorption at 634nm decreases and a peak appears at 674nm, representing the phototransformation of protochlorophyll(ide) to chlorophyll(ide). Using difference spectroscopy, the resynthesis in the dark of protochlorophyll(ide) by previously-illuminated wild-type dark-grown cells was found to begin at about 10min after illumination and reached completion by about 25 min, the amount of protochlorophyll(ide) resynthesized being equivalent to that of dark-grown cells. Resynthesis of protochlorophyll(ide) following a second illumination follows the same kinetics, indicating that protochlorophyll(ide) resynthesis is under tight regulation, possibly via feedback control. Cells of dark-grown wild-type and W₃BUL, a mutant lacking protochlorophyll(ide) contain a component absorbing at 658 nm which does not undergo phototransformation when examined by difference spectroscopy at room and liquid N₂ temperatures. Following the phototransformation of protochlorophyll(ide) 634 to chlorophyll(ide) 674, the chlorophyll(ide) 674 shifts to shorter wavelengths, ultimately to 671 nm. Possible relationships among the various spectroscopic forms of protochlorophyll(ide) and chlorophyll(ide) at room temperature and liquid N₂ temperature in Euglena and higher plants are presented. It is concluded that Euglena, unlike older, etiolated higher plants, contains only protochlorophyll(ide) 634, making it an excellent system in which to examine the phototransformation of this pigment species in the absence of other forms.     

Photochemistry and photopolymerization activity of novel perester derivatives of fluorenone: a conventional and laser flash photolysis study

The photochemistry of three novel t-butylperester derivatives of fluorenone was examined and compared with unsubstituted fluorenone and a mono-t-butylperester of benzophenone using both conventional microsecond and nanosecond laser flash photolysis. On conventional microsecond flash photolysis in 2-propanol, all four fluorenone compounds gave transient absorption in the region 300–400 nm due to a ketyl radical formed from the abstraction of a hydrogen atom from the solvent by the upper excited triplet n—π* state of the fluorenone chromophore. This assignment was confirmed by a pH-dependent study on the transient absorption spectra. The nitro-t-butylperester derivative of fluorenone gave additional absorption above 400 nm due to species associated with the nitro group. No evidence for benzoyloxy radical formation could be found in non-hydrogen-atom-donating solvents with microsecond flash photolysis which is associated with homolysis of the perester groups. On nanosecond laser flash photolysis of the fluorenone compounds at 355 nm excitation in acetonitrile and hexa-fluorobenzene, transient absorptions were observed in the region 320–640 nm due to the corresponding triplet states. All the t-butylperester derivatives showed residual absorbances at longer time delays which were tentatively assigned to the corresponding benzoyloxy radicals produced by homolysis of the perester groups. In contrast, the mono-t-butylperester of benzophenone, included for comparison only, showed very weak transient absorption in the region 320–640 nm compared with that of the strong triplet of benzophenone under the same excitation conditions. The triplet absorptions and lifetimes of the fluorenone compounds were correlated with their photopolymerization activities in bulk methylmethacrylate monomer. In oxygenated solutions, the triplet absorptions of fluorenone and benzophenone were effectively quenched; however, long-lived transient growths were observed for all the t-butylperester derivatives. The intensities of these novel transient absorptions appear to correlate with the total number of t-butylperester groups in the fluorenone molecule and tentative assignments are discussed.     

Analysis of methoxypyrazines in wine using headspace solid phase microextraction with isotope dilution and comprehensive two-dimensional gas chromatography

This study reports an optimized headspace-solid phase microextraction (HS-SPME) method for the determination of methoxypyrazines in wine. Analysis was performed by using comprehensive two-dimensional gas chromatography with novel detection capabilities, including nitrogen phosphorus detection (GC x GC-NPD) and time-of-flight mass spectrometry (GC x GC-TOFMS). In the latter, stable isotope dilution was performed for the quantitation of 2-methoxy-3-(2-methylpropyl) pyrazine (IBMP), using labelled 2-(2H3)methoxy-3-(2-methylpropyl)pyrazine (d3-IBMP) as the internal standard, and resolution of the two analogues was facilitated using the deconvolution capabilities of the TOFMS. This research represents the first report of HS-SPME with isotope dilution and GC x GC-TOFMS (GC x GC-IDTOFMS). Analysis by GC x GC-NPD enabled detection limits of 0.5 ng/L for the quantitation of IBMP, which was superior to that obtained using GC x GC-IDTOFMS (1.95 ng/L). Nevertheless, both methods were adequately sensitive for real wine analysis, yielding highly comparable IBMP concentrations of 26.1 and 27.8 ng/L, respectively, from a Sauvignon blanc wine. The complexity of the real wine headspace was simplified as a result of selective detection using GC x GC-NPD and, in the case of GC x GC-IDTOFMS, the use of extracted ion chromatograms (EICs).     

Anomalous Stereochemistry in the Wittig Reaction Induced by Nucleophilic Groups in the Phosphonium Ylide

Abstract

Reaction of ylides from 3–9 with benzaldehyde show that carboxylate and oxido functionalities proximate to the ylide center promote anomalously high E stereoselectivity in alkene formation. Through the use of α-deuterated ylides 12–14, an internal “trans-selective Wittig” mechanism was ruled out as a principal source of exaggerated E alkene production.     

Food structure: Roles of mechanical properties and oral processing in determining sensory texture of soft materials

There is a desire to alter food composition to make foods healthier and at the same time not diminish sensory quality. This requires an understanding of key elements of food structure associated with texture perception. Texture, in part, is perceived during oral processing of food. Knowledge of structure–oral processing–texture interrelations could be utilized to develop or prevent specified textural attributes. Overall, the investigation of structure–oral processing–texture interrelations is just starting as a research focus. Factors including non-universal and inconsistent sensory terminology, omission of consideration for structural changes incurred by oral processes, and the lack of cross-disciplinary investigations hamper progress in this field. Consideration of these factors in future investigations on sensory texture will increase the applicability of their findings and bring us closer to understanding the contribution of food structure to sensory texture.     

A Simple Approach for Multi‐fidelity Experimentation Applied to Financial Engineering

In practical applications, information about the accuracy or ‘fidelity’ of alternative surrogate systems may be ambiguous and difficult to determine. To address this problem, we propose to treat surrogate system fidelity level as a categorical factor in optimal response surface design. To design the associated experiments, we apply the Expected Integrated Mean Squared Error optimal design criterion, which takes into account both variance and bias errors. The performance of the proposed design was compared using three test cases to four types of alternatives using the Empirical Integrated Squared Error. Because of its ability to foster relatively accurate predictions, the proposed design is recommended in fidelity experimental design, particularly when the experimenters lack sufficient information about the fidelity levels of surrogate systems. The method was applied to the case of intraday trading optimization in which data were collected from the Taiwan Futures Exchange. We also calculated the implied volatility from the Merton's Jump‐diffusion model via the fast Fourier transform algorithm with three different models of varying fidelity levels. Copyright © 2014 John Wiley & Sons, Ltd.     

Titanocene-catalyzed metallation of propargylic acetates in homopropargyl alcohol synthesis

The titanium-catalyzed metallation and subsequent carbonyl addition of propargylic acetates enable the direct formation of homopropargylic alcohols in good yields. The corresponding products were obtained as single regioisomers without the corresponding allene adducts observed.     

Integrating open‐source software applications to build molecular dynamics systems

Three open‐source applications, NanoEngineer‐1, packmol, and mis2lmp are integrated using an open‐source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open‐source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol‐a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real‐world research requirements and integrated to create a new capability. © 2014 Wiley Periodicals, Inc.