A computational study of tetrahedrene: strained alkene or dicarbene?

A computational study of tetrahedrene at the RCCD/cc-pVDZ level led to a singlet-state structure with a lowest energy vibrational mode of 660 cm(-1). The corresponding triplet state was found to be ca. 37 kcal/mol lower in energy than the singlet state. The heat of formation of the singlet state was estimated to be 270 kcal/mol. An isomeric singlet bicyclic dicarbene bis-bicyclo[1.1.0]cyclobutylidene was found to be approximately 94 kcal/mol lower in energy than tetrahedrene.     

Do spin state changes matter in organometallic chemistry? A computational study

Spin changes occur often in organometallic chemistry, and their effect on kinetics is not well understood. We report computations on the singlet and triplet potential energy surfaces of several processes of this type and show that the topology of the individual surfaces, as well as of the crossing regions between them, can be used to rationalize the observed reactivity in all cases. In particular, the slow addition of dihydrogen to W[N(CH(2)CH(2)NSiMe(3))(3)]H (Schrock, R. R.; Shih, K. Y.; Dobbs, D. A.; Davis, W. M. J. Am. Chem. Soc. 1995, 117, 6609) is shown to be a "spin-blocked" reaction with a high barrier due to the crossing between reactant triplet and product singlet surfaces. In contrast, addition of CO to TpCo(CO) (Detrich, J. L.; Reinaud, O. M.; Rheingold, A. L.; Theopold, K. H. J. Am. Chem. Soc. 1995, 117, 11745) is fast because the triplet and singlet surfaces cross at low energy. Particular care is taken to use DFT methods which are in adequate agreement with experimental and high-level computational energetics for these systems.     

Stepwise diels-alder: more than just an oddity? A computational mechanistic study

We have employed hybrid DFT and SCS-MP2 calculations at the SMD-PCM-6-311++G(2d,2p)//6-31+G(d) level to investigate the relationship between three possible channels for forming a Diels-Alder adduct from a highly nucleophilic diene and moderately to highly electrophilic dienophiles. We discuss geometries optimized using the B3LYP and M06-2X functionals with the 6-31+(d) basis set. The transition states and intermediates are characterized on the basis of geometric and electronic properties, and we also address the possibility of predicting detectability of a zwitterionic intermediate based on its relative stability. Our results show that a conventional Diels-Alder transition state conformation yields intermediates in all four investigated cases, but that these are too short-lived to be detected experimentally for the less activated reactants. The stepwise trans pathway, beginning with a conjugate addition-like transition state, becomes increasingly competitive with more activated reactants and is indeed favored for the most electrophilic dienophiles. Addition of a trans diene leads to a dead-end as the trans intermediates have insurmountable rotation barriers that prohibit formation of the second bond, unless another, heterocyclic intermediate is formed. We also show that introduction of a hydrogen bond donating catalyst favors a stepwise pathway even for less activated dienophiles.     

Is the Beckmann rearrangement a concerted or stepwise reaction? A computational study

[reaction: see text] RB3LYP calculations were performed on the Beckman rearrangement by the use of three substrates, acetone oxime (1), acetophenone oxime (2), and cyclohexanone oxime (3). Acidic solvents were modeled by H+ (CH3COOH)3 and H3O+ (H2O)6, and reaction paths were determined precisely. For 1, a two-step process involving a sigma-type cationic complex was obtained. For 2, a three-step process with pi- and sigma-type complexes was found in H+ (CH3COOH)3 and a two-step process involving a sigma-type cationic complex was obtained in H3O+ (H2O)6. However, for 3, a concerted process without pi and sigma complexes was calculated, which leads to the product, epsilon-caprolactam. Three different mechanisms were explained in terms of FMO theory.     

How does the nickel pincer complex catalyze the conversion of CO2 to a methanol derivative? A computational mechanistic study

The mechanistic details of nickel-catalyzed reduction of CO(2) with catecholborane (HBcat) have been studied by DFT calculations. The nickel pincer hydride complex ({2,6-C(6)H(3)(OP(t)Bu(2))(2)}NiH = [Ni]H) has been shown to catalyze the sequential reduction from CO(2) to HCOOBcat, then to CH(2)O, and finally to CH(3)OBcat. Each process is accomplished by a two-step sequence at the nickel center: the insertion of a C═O bond into [Ni]H, followed by the reaction of the insertion product with HBcat. Calculations have predicted the difficulties of observing the possible intermediates such as [Ni]OCH(2)OBcat, [Ni]OBcat, and [Ni]OCH(3), based on the low kinetic barriers and favorable thermodynamics for the decomposition of [Ni]OCH(2)OBcat, as well as the reactions of [Ni]OBcat and [Ni]OCH(3) with HBcat. Compared to the uncatalyzed reactions of HBcat with CO(2), HCOOBcat, and CH(2)O, the nickel hydride catalyst accelerates the H(δ-) transfer by lowering the barriers by 30.1, 12.4, and 19.6 kcal/mol, respectively. In general, the catalytic role of the nickel hydride is similar to that of N-heterocyclic carbene (NHC) catalyst in the hydrosilylation of CO(2). However, the H(δ-) transfer mechanisms used by the two catalysts are completely different. The H(δ-) transfer catalyzed by [Ni]H can be described as hydrogen being shuttled from HBcat to nickel center and then to the C═O bond, and the catalyst changes its integrity during catalysis. In contrast, the NHC catalyst simply exerts an electronic influence to activate either the silane or CO(2), and the integrity of the catalyst remains intact throughout the catalytic cycle. The comparison between [Ni]H and Cp(2)Zr(H)Cl in the stoichiometric reduction of CO(2) has suggested that ligand sterics and metal electronic properties play critical roles in controlling the outcome of the reaction. A bridging methylene diolate complex has been previously observed in the zirconium system, whereas the analogous [Ni]OCH(2)O[Ni] is not a viable intermediate, both kinetically and thermodynamically. Replacing HBcat with PhSiH(3) in the nickel-catalyzed reduction of CO(2) results in a high kinetic barrier for the reaction of [Ni]OOCH with PhSiH(3). Switching silanes to HBcat in NHC-catalyzed reduction of CO(2) generates a very stable NHC adduct of HCOOBcat, which makes the release of NHC less favorable.     

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 random are intrinsically disordered proteins? A small angle scattering perspective

While the crucial role of intrinsically disordered proteins (IDPs) in the cell cycle is now recognized, deciphering their molecular mode of action at the structural level still remains highly challenging and requires a combination of many biophysical approaches. Among them, small angle X-ray scattering (SAXS) has been extremely successful in the last decade and has become an indispensable technique for addressing many of the fundamental questions regarding the activities of IDPs. After introducing some experimental issues specific to IDPs and in relation to the latest technical developments, this article presents the interest of the theory of polymer physics to evaluate the flexibility of fully disordered proteins. The different strategies to obtain 3-dimensional models of IDPs, free in solution and associated in a complex, are then reviewed. Indeed, recent computational advances have made it possible to readily extract maximum information from the scattering curve with a special emphasis on highly flexible systems, such as multidomain proteins and IDPs. Furthermore, integrated computational approaches now enable the generation of ensembles of conformers to translate the unique flexible characteristics of IDPs by taking into consideration the constraints of more and more various complementary experiment. In particular, a combination of SAXS with high-resolution techniques, such as x-ray crystallography and NMR, allows us to provide reliable models and to gain unique structural insights about the protein over multiple structural scales. The latest neutron scattering experiments also promise new advances in the study of the conformational changes of macromolecules involving more complex systems.     

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 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 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 are the ready and unready states of nickel-iron hydrogenase activated by H2? A density functional theory study

We have explored possible mechanisms for the formation of the catalytically active Ni(a)-S state of the enzyme, nickel iron hydrogenase, from the Ni*(r) (ready) or Ni*(u) (unready) state, by reaction with H(2), using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an -OH bridge, the rate determining step is the cleavage of H(2) at the Ni(3+) centre with a barrier of approximately 15 kcal mol(-1). We take the unready state to have a -OOH bridge, and find that reaction with H(2) to form the Ni(r)-S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of approximately 19 kcal mol(-1). The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment.     

Are insertion compounds of CH2CHF and the rare gases stable? A computational study

Ab initio calculations, using second-order M?ller-Plesset perturbation theory with a 6-311+ +G(2d,2p) basis set, predict the stability of two novel compounds of monofluoroethene, CH2CHF, with the rare-gas atoms Ar and Kr. The dissociation energies to the lowest-energy fragmentation products, CH2CHF + Rg (Rg = Ar,Kr), were computed to be -528 and -449 kJ mol(-1), respectively, at the coupled-cluster singles, doubles, and triples level of theory. Possible transition states (at second-order M?ller-Plesset theory) via a C-Rg-F bending mode for these fragmentation reactions were also located with barrier heights of about 76 and 106 kJ mol(-1), for the Ar- and Kr-containing species, respectively. However, the Ar-containing species may not exist at all as it is less stable than the fragments CH2CH + F + Ar at the higher level of theory and may possibly dissociate via this route.     

A computational study of C?S bond dissociation enthalpies in petroleum chemistry

High‐level theoretical methods (BMK, B3LYP, B98, B3P86, B3PW91, PBE1PBE, PBE1KIS, MPWPW91, MPW1KCIS, TPSS1KCIS, G3, G3//BMK, and CBS‐Q) were utilized to study the carbon–sulfur bond dissociation enthalpies (BDEs) of hydrocarbons in petroleum chemistry. The performance of these methods was evaluated on the basis of a training set including the available experimental BDEs, and it was found that the BMK (Boese‐Martin for Kinetics) method had the best agreement with experimental values. By using the BMK method to calculate C S BDEs of saturated hydrocarbon, the main factors, which determine the changing trend of BDE values, were discussed. Results revealed that the repulsive energies played an important role in determining a change in the trend of BDEs as well as the radical effect. Good agreements were obtained between further calculated BDEs and the experimental ones for C S and C O bonds. Moreover, the same calculation method was applied to predict C S BDEs for which the experimental values were still unavailable. A range of predicted bond dissociation enthalpy values were provided according to the calculations. © 2010 Wiley Periodicals, Inc. Heteroatom Chem 22:97–105, 2011; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.20662     

How computational methods and relativistic effects influence the study of chemical reactions involving Ru‐NO complexes?

Two treatments of relativistic effects, namely effective core potentials (ECP) and all‐electron scalar relativistic effects (DKH2), are used to obtain geometries and chemical reaction energies for a series of ruthenium complexes in B3LYP/def2‐TZVP calculations. Specifically, the reaction energies of reduction ( A ‐ F ), isomerization ( G‐I ), and Cl⁻ negative trans influence in relation to NH₃ ( J ‐ L ) are considered. The ECP and DKH2 approaches provided geometric parameters close to experimental data and the same ordering for energy changes of reactions A ‐ L . From geometries optimized with ECP, the electronic energies are also determined by means of the same ECP and basis set combined with the computational methods: MP2, M06, BP86, and its derivatives, so as B2PLYP, LC‐wPBE, and CCSD(T) (reference method). For reactions A ‐ I , B2PLYP provides the best agreement with CCSD(T) results. Additionally, B3LYP gave the smallest error for the energies of reactions J ‐ L . © 2017 Wiley Periodicals, Inc.     

How deeply are core electrons perturbed when valence electrons are spin polarized? The case study of transition metal compounds

The ferromagnetic and antiferromagnetic wave functions of the KMnF₃ perovskite have been evaluated quantum-mechanically by using an all electron approach and, for comparison, pseudopotentials on the transition metal and the fluorine ions. It is shown that the different number of α and β electrons in the d shell of Mn perturbs the inner shells, with shifts between the α and β eigenvalues that can be as large as 6 eV for the 3s level, and is far from negligible also for the 2s and 2p states. The valence electrons of F are polarized by the majority spin electrons of Mn, and in turn, spin polarize their 1s electrons. When a pseudopotential is used, such a spin polarization of the core functions of Mn and F can obviously not take place. The importance of such a spin polarization can be appreciated by comparing (i) the spin density at the Mn and F nuclear position, and then the Fermi contact constant, a crucial quantity for the hyperfine coupling, and (ii) the ferromagnetic–antiferromagnetic energy difference, when obtained with an all electron or a pseudopotential scheme, and exploring how the latter varies with pressure. This difference is as large as 50% of the all electron datum, and is mainly due to the rigid treatment of the F ion core. The effect of five different functionals on the core spin polarization is documented.     

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 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 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 do azoles inhibit cytochrome P450 enzymes? A density functional study

To examine how azole inhibitors interact with the heme active site of the cytochrome P450 enzymes, we have performed a series of density functional theory studies on azole binding. These are the first density functional studies on azole interactions with a heme center and give fundamental insight into how azoles inhibit the catalytic function of P450 enzymes. Since azoles come in many varieties, we tested three typical azole motifs representing a broad range of azole and azole-type inhibitors: methylimidazolate, methyltriazolate, and pyridine. These structural motifs represent typical azoles, such as econazole, fluconazole, and metyrapone. The calculations show that azole binding is a stepwise mechanism whereby first the water molecule from the resting state of P450 is released from the sixth binding site of the heme to create a pentacoordinated active site followed by coordination of the azole nitrogen to the heme iron. This process leads to the breaking of a hydrogen bond between the resting state water molecule and the approaching inhibitor molecule. Although, formally, the water molecule is released in the first step of the reaction mechanism and a pentacoordinated heme is created, this does not lead to an observed spin state crossing. Thus, we show that release of a water molecule from the resting state of P450 enzymes to create a pentacoordinated heme will lead to a doublet to quartet spin state crossing at an Fe-OH(2) distance of approximately 3.0 A, while the azole substitution process takes place at shorter distances. Azoles bind heme with significantly stronger binding energies than a water molecule, so that these inhibitors block the catalytic cycle of the enzyme and prevent oxygen binding and the catalysis of substrate oxidation. Perturbations within the active site (e.g., a polarized environment) have little effect on the relative energies of azole binding. Studies with an extra hydrogen-bonded ethanol molecule in the model, mimicking the active site of the CYP121 P450, show that the resting state and azole binding structures are close in energy, which may lead to chemical equilibrium between the two structures, as indeed observed with recent protein structural studies that have demonstrated two distinct azole binding mechanisms to P450 heme.