Multiquantum vibrational excitation of NO scattered from Au(111): quantitative comparison of benchmark data to ab initio theories of nonadiabatic molecule-surface interactions

Surface phenomena: measurements of absolute probabilities are reported for the vibrational excitation of NO(v=0→1,2) molecules scattered from a Au(111) surface. These measurements were quantitatively compared to calculations based on ab?initio theoretical approaches to electronically nonadiabatic molecule-surface interactions. Good agreement was found between theory and experiment (see picture; T(s) =surface temperature, P=excitation probability, and E=incidence energy of translation).     

Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

Preceding NMR experiments show that the conformation of tandem GA base pairs, an important recurrent non-canonical building block in RNA duplexes, is context dependent. The GA base pairs adopt "sheared" N3(G)-N6(A), N2(G)-N7(A) geometry in the r(CGAG)(2) and r(iGGAiC)(2) contexts while switching to "imino" N1(G)-N1(A), O6(G)-N6(A) geometry in the r(GGAC)(2) and r(iCGAiG)(2) contexts (iC and iG stand for isocytosine and isoguanine, respectively). As base stacking is likely to be one of the key sources of the context dependence of the conformation of GA base pairs, we calculated base stacking energies in duplexes containing such base pairs, to see if this dependence can be predicted by stacking energy calculations. When investigating the context dependence of the GA geometry two different conformations of the same duplex were compared (imino vs. sheared). The geometries were generated via explicit solvent MD simulations of the respective RNA duplexes, while the subsequent QM energy calculations focused on base stacking interactions of the four internal base pairs. Geometrical relaxation of nucleobase atoms prior to the stacking energy computations has a non-negligible effect on the results. The stacking energies were derived at the DFT-D/6-311++G(3df,3pd) level. We show a rather good correspondence between the intrinsic gas-phase stacking energies and the NMR-determined GA geometries. The conformation with more favorable gas-phase stacking is in most cases the one observed in experiments. This correlation is not improved when including solvent effects via the COSMO method. On the other side, the stacking calculations do not predict the relative thermodynamic stability of duplex formation for different sequences.     

Solubility of NaCl in water by molecular simulation revisited

In this paper, the solubility of NaCl in water is evaluated by using computer simulations for three different force fields. The condition of chemical equilibrium (i.e., equal chemical potential of the salt in the solid and in the solution) is obtained at room temperature and pressure to determine the solubility of the salt. We used the same methodology that was described in our previous work [E. Sanz and C. Vega, J. Chem. Phys. 126, 014507 (2007)] although several modifications were introduced to improve the accuracy of the calculations. It is found that the predictions of the solubility are quite sensitive to the details of the force field used. Certain force fields underestimate the experimental solubility of NaCl in water by a factor of four, whereas the predictions of other force fields are within 20% of the experimental value. Direct coexistence molecular dynamic simulations were also performed to determine the solubility of the salt. Reasonable agreement was found between the solubility obtained from free energy calculations and that obtained from direct coexistence simulations. This work shows that the evaluation of the solubility of salts in water can now be performed in computer simulations. The solubility depends on the ion-ion, ion-water, and water-water interactions. For this reason, the prediction of the solubility can be quite useful in future work to develop force fields for ions in water.     

Photodissociation dynamics of gaseous CpCo(CO)2 and ligand exchange reactions of CpCoH2 with C3H4, C3H6, and NH3

The photodissociation dynamics of CpCo(CO)(2) was studied in a molecular beam using photofragment translational energy spectroscopy with 157 nm photoionization detection of the metallic products. At 532 and 355 nm excitation, the dominant one-photon channel involved loss of a single CO ligand producing CpCoCO. The product angular distributions were isotropic, and a large fraction of excess energy appeared as product vibrational excitation. Production of CpCO + 2CO resulted from two-photon absorption processes. The two-photon dissociation of mixtures containing CpCo(CO)(2) and H(2) at the orifice of a pulsed nozzle was used to produce a novel 16-electron unsaturated species, CpCoH(2). Transition metal ligand exchange reactions, CpCoH(2) + L → CpCoL + H(2) (L = propyne, propene, or ammonia), were studied under single-collision conditions for the first time. In all cases, ligand exchange occurred via 18-electron association complexes with lifetimes comparable to their rotational periods. Although ligand exchange reactions were not detected from CpCoH(2) collisions with methane or propane (L = CH(4) or C(3)H(8)), a molecular beam containing CpCoCH(4) was produced by photolysis of mixtures containing CpCo(CO)(2) and CH(4).     

CHIH-DFT determination of the molecular structure and infrared and ultraviolet spectra of gamma-solanine

Glycoalkaloids are toxic secondary plant metabolites found in potatoes, tomatoes, and eggplants and they are considered potential precursors of steroids for applications in bionanotechnology. In this work, we make use of a new model chemistry within density functional theory, which is called CHIH-DFT, to calculate the molecular structure of gamma-solanine, as well to predict its infrared (IR) and ultraviolet (UV-vis) spectra, and some other electronic parameters.     

Lactide Polymerisation with Air‐Stable and Highly Active Zinc Complexes with Guanidine–Pyridine Hybrid Ligands

New class of air‐stable catalysts for lactide polymerisation: Guanidine–pyridine hybrid ligands (picture, left) were used to prepare a series of zinc complexes (e.g., depicted cation [ZnL₂(CF₃SO₃)]⁺, where L is the quinoline‐containing ligand with R¹=R²=R³=R⁴=Me), in which the ligand binds through two different N‐donor atoms. The zinc complexes show high activity in ring‐opening polymerisation of d,l ‐lactide (right), giving polylactide with molecular masses up to 176 000 g mol^?1 and in high yield.

     

Highly Sensitive Magnetic Effects Induced by Hydrogen‐Bonding Interactions in a High‐Spin Metallosupramolecular Fe4II [2×2] Grid‐Type Complex

A sensitive magnetic nanoprobe : Hydrogen‐bonding interactions are reflected with great sensitivity in the ¹H NMR spectra of a high‐spin multinuclear Fe₄^II [2×2] grid‐type complex (see scheme) and the measured shifts can be used to evaluate the hydrogen‐bond donating ability. The grid complex also represents a prototype of a very sensitive magnetic nanoreceptor for the detection of very small changes around a magnetic center.

     

Chemo‐ and Regioselective Palladium‐Catalyzed Oxycyclization Reactions of Allendiols: Preparation of Five‐, Six‐, and Eight‐Membered Cycles

Positive discrimination : Chemo‐ and regioselective palladium‐catalyzed cycloetherification of allendiols, namely β,γ‐ and γ,δ‐allendiols, may occur by judicious choice of palladium‐catalyzed conditions owing to their potential ability to discriminate between both nucleophilic sites (see scheme).

     

Electronic Structure and Redox Properties of Metal Nitride Endohedral Fullerenes M3N@C2n (M=Sc,Y, La,and Gd; 2n=80, 84, 88, 92, 96)

An extensive study of the redox properties of metal nitride endohedral fullerenes (MNEFs) based on DFT computational calculations has been performed. The electronic structure of the singly oxidized and reduced MNEFs has been thoroughly analyzed and the first anodic and cathodic potentials, as well as the electrochemical gaps, have been predicted for a large number of M₃N@C_2n systems (M=Sc, Y, La, and Gd; 2n=80, 84, 88, 92, and 96). In particular, calculations that include thermal and entropic effects correctly predict the different anodic behavior of the two isomers (I_h and D_5h) of Sc₃N@C₈₀, which is the basis for their electrochemical separation. Important differences were found in the electronic structure of reduced M₃N@C₈₀ when M=Sc or when M is a more electropositive metal, such as Y or Gd. Moreover, the changes in the electrochemical gaps within the Gd₃N@C_2n series (2n=80, 84, and 88) have been rationalized and the use of Y‐based computational models to study the Gd‐based systems has been justified. The redox properties of the largest MNEFs characterized so far, La₃N@C_2n (2n=92 and 96), were also correctly predicted. Finally, the quality of these predictions and their usefulness in distinguishing the carbon cages for MNEFs with unknown structures is discussed.     

Dötz Benzannulation Reactions: Heteroatom and Substituent Effects in Chromium Fischer Carbene Complexes

We have carried out a theoretical investigation of the Dötz reaction between acetylene and a series of chromium Fischer‐type carbenes [(CO)₅Cr?C(X)R] with different representative substituents (R=CH?CH₂, Ph) and heteroatom ligands (X=OH, NH₂, OCH₃, N(CH₃)₂) by using density functional theory with the B3LYP functional. We have studied the Dötz and chromahexatriene mechanisms of benzannulation and also the reaction mechanism leading to cyclopentannulation. For the benzannulation, it was found that the most likely mechanism in the case of vinylcarbenes is the chromahexatriene route, whereas for phenylcarbenes, the Dötz route via a ketene intermediate is clearly the most favorable. The reactions leading to the cyclopentannulated and benzannulated products are more exothermic with vinylcarbenes than with phenylcarbenes and also more exothermic with alkoxycarbenes than with aminocarbenes. The relative stability of the cyclopentannulated products as compared with the benzannulated products increases for bulkier X substituents and on going from alkoxy‐ to aminocarbenes. The kinetic data concurs with the experimental product distribution found for vinylcarbenes, by which mainly benzannulated products are obtained, and dimethylaminophenylcarbenes, which lead exclusively to cyclopentannulated adducts.