Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field

All-atom molecular dynamics computer simulations were used to blindly predict the hydration free energies of a range of chloro-organic compounds as part of the SAMPL3 challenge. All compounds were parameterized within the framework of the OPLS-AA force field, using an established protocol to compute the absolute hydration free energy via a windowed free energy perturbation approach and thermodynamic integration. Three different approaches to deriving partial charge parameters were pursued: (1) using existing OPLS-AA atom types and charges with minor adjustments of partial charges on equivalent connecting atoms; (2) calculation of quantum mechanical charges via geometry optimization, followed by electrostatic potential (ESP) fitting, using Jaguar at the LMP2/cc-pVTZ(-F) level; and (3) via geometry optimization and CHelpG charges (Gaussian03 at the HF/6-31G* level), followed by two-stage RESP fitting. Protocol 3 generated the most accurate predictions with a root mean square (RMS) error of 1.2 kcal mol(-1) for the entire data set. It was found that the deficiency of the standard OPLS-AA parameters, protocol 1 (RMS error 2.4 kcal mol(-1) overall), was mostly due to compounds with more than three chlorine substituents on an aromatic ring. For this latter subset, the RMS errors were 1.4 kcal mol(-1) (protocol 3) and 4.3 kcal mol(-1) (protocol 1), respectively. We propose new OPLS-AA atom types for aromatic carbon and chlorine atoms in rings with ≥4 Cl-substituents that perform better than the best QM-based approach, resulting in an RMS error of 1.2 kcal mol(-1) for these difficult compounds.     

Kinetics of the sulfur oxidation on palladium: a combined in situ x-ray photoelectron spectroscopy and density-functional study

We studied the reaction kinetics of sulfur oxidation on the Pd(100) surface by in situ high resolution x-ray photoelectron spectroscopy and ab initio density functional calculations. Isothermal oxidation experiments were performed between 400 and 500 K for small amounts (~0.02 ML) of preadsorbed sulfur, with oxygen in large excess. The main stable reaction intermediate found on the surface is SO(4), with SO(2) and SO(3) being only present in minor amounts. Density-functional calculations depict a reaction energy profile, which explains the sequential formation of SO(2), SO(3), and eventually SO(4), also highlighting that the in-plane formation of SO from S and O adatoms is the rate limiting step. From the experiments we determined the activation energy of the rate limiting step to be 85 ± 6 kJ mol(-1) by Arrhenius analysis, matching the calculated endothermicity of the SO formation.     

Direct measurement of Criegee intermediate (CH2OO) reactions with acetone, acetaldehyde, and hexafluoroacetone

Criegee biradicals, i.e., carbonyl oxides, are critical intermediates in ozonolysis and have been implicated in autoignition chemistry and other hydrocarbon oxidation systems, but until recently the direct measurement of their gas-phase kinetics has not been feasible. Indirect determinations of Criegee intermediate kinetics often rely on the introduction of a scavenger molecule into an ozonolysis system and analysis of the effects of the scavenger on yields of products associated with Criegee intermediate reactions. Carbonyl species, in particular hexafluoroacetone (CF(3)COCF(3)), have often been used as scavengers. In this work, the reactions of the simplest Criegee intermediate, CH(2)OO (formaldehyde oxide), with three carbonyl species have been measured by laser photolysis/tunable synchrotron photoionization mass spectrometry. Diiodomethane photolysis produces CH(2)I radicals, which react with O(2) to yield CH(2)OO + I. The formaldehyde oxide is reacted with a large excess of a carbonyl reactant and both the disappearance of CH(2)OO and the formation of reaction products are monitored. The rate coefficient for CH(2)OO + hexafluoroacetone is k(1) = (3.0 ± 0.3) × 10(-11) cm(3) molecule(-1) s(-1), supporting the use of hexafluoroacetone as a Criegee-intermediate scavenger. The reactions with acetaldehyde, k(2) = (9.5 ± 0.7) × 10(-13) cm(3) molecule(-1) s(-1), and with acetone, k(3) = (2.3 ± 0.3) × 10(-13) cm(3) molecule(-1) s(-1), are substantially slower. Secondary ozonides and products of ozonide isomerization are observed from the reactions of CH(2)OO with acetone and hexafluoroacetone. Their photoionization spectra are interpreted with the aid of quantum-chemical and Franck-Condon-factor calculations. No secondary ozonide was observable in the reaction of CH(2)OO with acetaldehyde, but acetic acid was identified as a product under the conditions used (4 Torr and 293 K).     

Heterobimetallic Cuprates Consisting of a Redox‐Switchable,Silicon‐Based Metalloligand: Synthesis,Structures, and Electronic Properties

A series of bimetallic silyl halido cuprates consisting of the new tripodal silicon‐based metalloligand [κ³N‐Si(3,5‐Me₂pz)₃Mo(CO)₃]^? is presented (pz=pyrazolyl). This metalloligand is straightforwardly accessible by reacting the ambidentate ligand tris(3,5‐dimethylpyrazolyl)silanide ({Si(3,5‐Me₂pz)₃}^?) with [Mo(CO)₃(η⁶‐toluene)]. The compound features a fac‐coordinated tripodal chelating ligand and an outward pointing, “free” pyramidal silyl donor, which is easily accessible for a secondary coordination to other metal centers. Several bimetallic silyl halido cuprates of the general formula [CuX{μ‐κ¹Si:κ³N‐Si(3,5‐Me₂pz)₃Mo(CO)₃}]^? (X=Cl, Br, I) have been synthesized. The electronic and structural properties of these complexes were probed in detail by X‐ray diffraction analysis, electrospray mass spectrometry, infrared‐induced multiphoton dissociation studies, cyclic voltammetry, spectroelectrochemistry, gas‐phase photoelectron spectroscopy, as well as UV/Vis and fluorescence spectroscopy. The heterobimetallic complexes contain linear two‐coordinate copper(I) entities with the shortest silicon–copper distances reported so far. Oxidation of the anionic complexes in methylene chloride and acetonitrile solutions at ${E{{0\hfill \atop 1/2\hfill}}}$ =?0.60 and ?0.44 V (vs. ferrocene/ferrocenium (Fc/Fc⁺)), respectively, shows substantial reversibility. Based on various results obtained from different characterization methods, as well as density functional theory calculations, these oxidation events were attributed to the Mo⁰/Mo^I redox couple.     

Concise Synthesis and X-Ray Crystal Structure of N-Benzyl-2-(pyrimidin-4′-ylamino)-thiazole-4-carboxamide (Thiazovivin), a Small-Molecule Tool for Stem Cell Research

Stem cell research is one of the most promising fields of modern biomedical research and regenerative medicine. Limited availability and ethical concerns suggest the renouncement of embryonic stem cells (ESCs), thus raising the need for more efficient procedures for the generation of stem cells, ideally through reprogramming of mammalian cells. The small molecule N-benzyl-2-(pyrimidin-4′-ylamino)-thiazole-4-carboxamide (thiazovivin) is known to improve the generation of human induced pluripotent stem cells (iPSCs) from human fibroblasts. We herein describe a highly efficient procedure for the synthesis of thiazovivin over just five steps, which should be suitable for a large-scale application, and the first x-ray crystal structure of the target compound.

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource: Full experimental and spectral details.]     

Structure and cooperativity of the hydrogen bonds in sodium dihydrogen triacetate

Geometry and energetics of low energy conformers of sodium dihydrogen triacetate (SDHTA) and its anion are studied using density functional theory (DFT) at the Becke, Lee‐Yang‐Parr hybrid functional (BLYP) and Becke, three‐parameter, Lee‐Yang‐Parr hybrid functional (B3LYP) levels. For both cases, two structures of comparable energy are found, which have different symmetry with respect to the two hydrogen bonds (HBs). DFT‐based Born–Oppenheimer molecular dynamics simulations are performed for SDHTA, which show that both structures are visited at room temperature conditions. The trajectory analysis further reveals that the two HBs behave anticooperative, that is, on average elongation of one HB is accompanied by a compression of the other one. This is in accord with nuclear magnetic resonance (NMR) experimental studies for a similar counter ion–dihydrogen triacetate complex. © 2012 Wiley Periodicals, Inc.