How coordinating are non-coordinating anions?

Electrochemistry of (p-CH₃PhNC)₆Cr⁺³ and optical spectroscopy of [1,2-(9-fluorenyl)₂C₂H₄]ZrMe⁺ have been used to craft scales of coordinating ability of various anions. Coordinating ability also influences the barriers to intramolecular rearrangement in (RCp)₂ZrMe⁺ as well as activity of zirconocenium ions as polymerization catalysts.     

How big are atoms in crystals?

Atoms and bonds are central concepts in structural chemistry, but neither are concepts that arise naturally from the physics of condensed phases. It is ironic that the internuclear distances in crystals that are readily measured depend on the sizes of atoms, but since atoms in crystals can be defined in many different ways, all of them arbitrary and often incompatible, there is no natural way to express atomic size. I propose a simple coherent picture of Atoms-in-Crystals which combines properties selected from three different physically sound definitions of atoms and bonds. The charge density of the free atom that is used to construct the procrystal is represented by a sphere of constant charge density having the quantum theory of atoms in molecules (QTAIM) bonded radius. The sum of these radii is equal to the bond length that correlates with the bond flux (bond valence) in the flux theory of the bond. The use of this model is illustrated by answering the question: How big are atoms in crystals? The QTAIM bonded radii are shown to be simple functions of two properties, the number of quantum shells in the atomic core and the flux of the bond that links neighbouring atoms. Various radii can be defined. The univalent bonded radius measures the intrinsic size of the atom and is the same for all cations in a given row of the periodic table, but the observed bonded radius depends also on the bond flux that reflects the chemical environment.     

How many amorphous ices are there?

Many acronyms are used in the literature for describing different kinds of amorphous ice, mainly because many different preparation routes and many different sample histories need to be distinguished. We here introduce these amorphous ices and discuss the question of how many of these forms are of relevance in the context of polyamorphism. We employ the criterion of reversible transitions between amorphous "states" in finite intervals of pressure and temperature to discriminate between independent metastable amorphous "states" and between "substates" of the same amorphous "state". We argue that the experimental evidence suggests we should consider there to be three polyamorphic "states" of ice, namely low-(LDA), high-(HDA) and very high-density amorphous ice (VHDA). In addition to the realization of reversible transitions between them, they differ in terms of their properties, e.g., compressibility, or number of "interstitial" water molecules. Thus they cannot be regarded as structurally relaxed variants of each other and so we suggest considering them as three distinct megabasins in an energy landscape visualization.     

How different are two chemical structures?

We extend the scope of a recent method for superimposing two molecules ( J. Chem. Phys. 2009, 131, 124126-1-124126-10 ) to include the identification of chiral structures. This methodology is tested by applying it to several organic molecules and water clusters that were subjected to geometry optimization. The accuracy of four simpler, non-superimposing approaches is then analyzed by comparing pairs of structures for argon and water clusters. The structures considered in this work were obtained by a Markovian walk in the coordinate space. First, a random geometry is generated, and then, the iterative application of a mutation operator ensures the creation of increasingly dissimilar structures. The discriminating power of the non-superimposing approaches is tested by comparing the corresponding dissimilarity measures with the root-mean-square distance obtained from the superimposing method. Finally, we showcase the application of those methods to characterize the diversity of solutions in global geometry optimization by evolutionary algorithms.     

How reliable are estimates of hydrolysis constants?

The equilibrium constant for the first hydrolysis reaction of tetravalent plutonium is surrounded by uncertainty. A new method illustrates criteria by which the reliabilities of the numerical estimates can be judged. The new formulas are simple, the method is easy to apply, and the results are easy to compare.     

How useful are direct alpha-measurements of fecal ash? What are their limits?

The Cogema Radiotoxicology Laboratory at La Hague carries out more than 40 000 analyses per year. This figure includes approximately 12 000 systematic detections of actinides in urine and more than 400 analyses of actinides in feces performed following suspicion of an internal contamination incident. The radiochemical analysis of feces, which involves fractionated separation, is a difficult and time-consuming technique which is poorly suited to emergency detections of artificial radioelements. With feces that may contain artificial activity, the laboratory, therefore, uses a feces screening method consisting in a global count of the fecal ash. This method requires the preliminary determination of the background of the natural environmental radioactivity. This prompted our laboratory to carry out a global -count of the fecal ash of 30 people that both work on the site and live in the region but who are not exposed to artificial radioelements. A threshold value of 0.2 Bq/g of natural uranium and its derivatives in fecal ash was established.     

How easy are the syntheses of allenes?

Allenes have proven themselves to be valuable building blocks toward complex molecular targets, revealing novel applications in natural product synthesis, pharmaceutical chemistry and materials science. The ongoing interest in allene chemistry results in a variety of new methodologies and pathways for the synthesis of allenes. This feature article highlights some of the recent important developments on the synthesis of allenes and the applications on the synthesis of allenic natural products and allenic-based optoelectronic materials.     

How accurate are DFT treatments of organic energies?

Increasing awareness that popular functionals fail to describe many energies accurately has ended expectations of black-box DFT usage. The performance of nine density functionals, compared by computing the bond separation energies of 72 illustrative hydrocarbons with available experimental data, reveals that only Zhao and Truhlar's recently proposed M05-2X functional, with a 2.13 kcal/mol average deviation from experiment, performs satisfactorily. B3LYP and other functionals show larger deviations.     

How rigid are conjugated non-ladder and ladder polymers?

Persistence length is commonly used to quantitatively describe the chain rigidity of macromolecules, which represents an important structural parameter governing many physical properties of polymers. Although the mathematical models and experimental measurements on the chain rigidity of conventional single stranded polymers have been well explored and documented, those of the more rigid yet highly intriguing multiple stranded polymers, especially conjugated ladder polymers, are yet not well established. This article introduces the fundamental concepts on macromolecular chain rigidity, as well as the corresponding experimental methods, models, and simulations. Subsequently, representative examples of works done on the chain rigidity of nonladder conjugated polymers and conjugated ladder polymers are reviewed. Last but not least, it provides outlooks on the challenges with respect to the less-investigated chain rigidity of conjugated ladder polymers, including new models to describe and predict chain conformation, synthetic control on structural defects, and insights into the correlation of rigidity and applications.     

How flexible are fleximer nucleobases? A computational study

Density functional theory was used to study the potential energy surface for rotation about the carbon-carbon bonds in a variety of guanosine, adenosine, and inosine fleximers, which are modified purines with the imidazole and pyrimidine rings separated by a single carbon-carbon bond. Various connectivities between C4 or C5 of the imidazole ring and C5' or C6' of the pyrimidine ring were considered. Calculations on fleximer nucleobases in the absence of the ribose moiety suggest that a planar relative arrangement of the imidazole and pyrimidine rings is favored, and that all fleximers are indeed very flexible with regards to rotation about the carbon-carbon bond, where calculated barriers are generally less than 40 kJ mol(-1). Furthermore, calculated binding energies of fleximer-pyrimidine pairs indicate that the hydrogen-bonding properties of these modified nucleobases mimic those of the corresponding natural purine. Inclusion of the sugar moiety often leads to a favored nonplanar orientation of the two rings, and either a reduction in the rotational barrier height or small changes in the rotational surface depending on the connectivity and nucleobase considered. It is concluded that several connectivities may have favorable properties for biochemical applications where flexible nucleobases would be beneficial.     

How important are temperature effects for cluster polarizabilities?

State-of-the-art first-principle all-electron density functional theory calculations on small sodium clusters are performed to study the temperature dependency of their polarizabilities. For this purpose Born-Oppenheimer molecular dynamics simulations with more than 100,000 time steps (>200 ps) are recorded employing gradient corrected functionals in combination with a double-zeta valence polarization basis set. For each cluster 18 trajectories between 50 and 900 K are collected. The cluster polarizabilities are then calculated along these trajectories employing a triple-zeta valence polarization basis set augmented with field-induced polarization functions. The analysis of these calculations shows that the temperature dependency of the sodium cluster polarizabilities varies strongly with cluster size. For several clusters characteristic changes in the polarizability per atom as a function of temperature are observed. It is shown that the inclusion of finite temperature effects resolves the long-standing mismatch between calculated and measured sodium cluster polarizabilities.     

How many Langmuirs are required for monolayer formation?

In the present work, we provide the exact answer to the title question employing a probabilistic approach. The average number of Langmuirs L required for monolayer formation was found to be equal to (1/i), i.e., the armonic series up to the nth term, where n is the number of adsorption sites. This result is particularly useful when a reduced number of adsorption sites is considered, such as adsorption on small terraces of nanoscopic dimensions where the value of n could be in the range of a few thousands sites. In this case, the use of integrated equations derived from the mean-field approach would provide completely misleading results.     

How accurate are electronic structure methods for actinoid chemistry?

The CASPT2, CCSD, and CCSD(T) levels of wave function theory and seven density functionals were tested against experiment for predicting the ionization potentials and bond dissociation energies of actinoid monoxides and dioxides with their cations. The goal is to guide future work by enabling the choice of an appropriate method when performing calculations on actinoid-containing systems. We found that four density functionals, namely MPW3LYP, B3LYP, M05, and M06, and three levels of wave function theory, namely CASPT2, CCSD, and CCSD(T), give similar mean unsigned errors for actinoid?Coxygen bond energies and for ionization potentials of actinoid oxides and their cations.     

How accurate are continuum solvation models for drug-like molecules?

We have estimated the hydration free energy for 20 neutral drug-like molecules, as well as for three series of 6–11 inhibitors to avidin, factor Xa, and galectin-3 with four different continuum solvent approaches (the polarised continuum method the Langevin dipole method, the finite-difference solution of the Poisson equation, and the generalised Born method), and several variants of each, giving in total 24 different methods. All four types of methods have been thoroughly calibrated for a number of experimentally known small organic molecules with a mean absolute deviation (MAD) of 1–6 kJ/mol for neutral molecules and 4–30 kJ/mol for ions. However, for the drug-like molecules, the accuracy seems to be appreciably worse. The reason for this is that drug-like molecules are more polar than small organic molecules and that the uncertainty of the methods is proportional to the size of the solvation energy. Therefore, the accuracy of continuum solvation methods should be discussed in relative, rather than absolute, terms. In fact, the mean unsigned relative deviations of the best solvation methods, 0.09 for neutral and 0.05 for ionic molecules, correspond to 2–20 kJ/mol absolute error for the drug-like molecules in this investigation, or 2–3,000 in terms of binding constants. Fortunately, the accuracy of all methods can be improved if only relative energies within a series of inhibitors are considered, especially if all of them have the same net charge. Then, all except two methods give MADs of 2–5 kJ/mol (corresponding to an uncertainty of a factor of 2–7 in the binding constant). Interestingly, the generalised Born methods typically give better results than the Poison–Boltzmann methods. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Solid-phase microextraction. How far are we from clinical practice?

The current review briefly discusses the future development of solid-phase microextraction (SPME) and its potential application in the field of clinical medicine, including pharmacokinetic studies, therapeutic drug monitoring, biomarker discovery, and targeted and untargeted metabolomics. We also discuss aspects of automation and high-throughput analysis as major requirements of daily clinical practice. We give examples of clinically-validated applications of SPME and point out the regulatory restrictions limiting some in-vivo SPME studies. We briefly review the current state of progress in this extraction technique in the context of its future application in medical research and laboratory testing, including new directions (i.e. personalized medicine).     

How Hot are Your Ions in TWAVE Ion Mobility Spectrometry?

Effective temperatures of ions during traveling wave ion mobility spectrometry (TWIMS) analysis were measured using singly protonated leucine enkephalin dimer as a chemical thermometer by monitoring dissociation of the dimer into monomer, as well as the subsequent dissociation of monomer into a-, b-, and y-ions, as a function of instrumental parameters. At fixed helium cell and TWIMS cell gas flow rates, the extent of dissociation does not vary significantly with either the wave velocity or wave height, except at low (<500 m/s) wave velocities that are not commonly used. Increasing the flow rate of nitrogen gas into the TWIMS cell and decreasing the flow rate of helium gas into the helium cell resulted in greater dissociation. However, the mobility distributions of the fragment ions formed by dissociation of the dimer upon injection into the TWIMS cell are nearly indistinguishable from those of fragment ions formed in the collision cell prior to TWIMS analysis for all TWIMS experiments. These results indicate that heating and dissociation occur when ions are injected into the TWIMS cell, and that the effective temperature subsequently decreases to a point at which no further dissociation is observed during the TWIMS analysis. An upper limit to the effective ion temperature of 449 K during TWIMS analysis is obtained at a helium flow rate of 180 mL/min, TWIMS flow rate of 80 mL/min, and traveling wave height of 40 V, which is well below previously reported values. Effects of ion heating in TWIMS on gas-phase protein conformation are presented.     

How accurate are TD-DFT excited-state geometries compared to DFT ground-state geometries?

In this work, we take a different angle to the benchmarking of time-dependent density functional theory (TD-DFT) for the calculation of excited-state geometries by extensively assessing how accurate such geometries are compared to ground-state geometries calculated with ordinary DFT. To this end, we consider 20 medium-sized aromatic organic compounds whose lowest singlet excited states are ideally suited for TD-DFT modeling and are very well described by the approximate coupled-cluster singles and doubles (CC2) method, and then use this method and six different density functionals (BP86, B3LYP, PBE0, M06-2X, CAM-B3LYP, and ωB97XD) to optimize the corresponding ground- and excited-state geometries. The results show that although each hybrid functional reproduces the CC2 excited-state bond lengths very satisfactorily, achieving an overall root mean square error of 0.011 Å for all 336 bonds in the 20 molecules, these errors are distinctly larger than those of only 0.004–0.006 Å with which the hybrid functionals reproduce the CC2 ground-state bond lengths. Furthermore, for each functional employed, the variation in the error relative to CC2 between different molecules is found to be much larger (by at least a factor of 3) for the excited-state geometries than for the ground-state geometries, despite the fact that the molecules/states under investigation have rather uniform chemical and spectroscopic character. Overall, the study finds that even in favorable circumstances, TD-DFT excited-state geometries appear intrinsically and comparatively less accurate than DFT ground-state ones.