Mechanism and theory of d-glucopyranose homogeneous acid catalysis in the aqueous solution phase.

A detailed systematic theoretical study of the mechanism of the homogeneous Brønsted-acid catalysis of d-glucose in aqueous solution phase ("acid hydrolysis") is reported. G4MP2 with the SMD solvation model at B3LYP/6-31G(2df,p) are employed to compute the free energies of the molecular and ionic species pertaining to the isomerization, protonation, hydrogen cation transfer and decomposition processes of d-glucopyranose in aqueous solution phase. This information is used to hypothesise a reaction mechanism that is of improved accuracy and completeness from the existing art. It is found that rotation of the d-glucose alkyl carbon-carbon bond is a facile process and is very important to the subsequent catalytic mechanism. This rotation produces two rotameric isomers which are of notably different thermodynamic stability and reactivity, even with regard to the products of this acid catalysis. As a low energy process (ΔG‡ = ∼3.8-6.7 kcal mol-1), the alkyl carbon-carbon bond may rotate toward the hydroxyl group at the adjacent "4" position reducing the energy required to protonate that position by 3.0-7.2 kcal mol-1 (or 15-30%). The combination of two rotomeric isomers with the six structural isomers owing to the oxygen atoms, means that protonated d-glucose cations embark on a complex competition of interconversion and decomposition that is both thermodynamically and kinetically influenced. The calculations support the hypothesis that the acid-catalysed hydrolysis of d-glucose may yield a number of platform chemicals that have not previously been suggested. These include the prospect of three isomers of 5-hydroxymethylfurfural (HMF); 5-(hydroxymethyl)furan-2-carbaldehyde, 5-(hydroxymethyl)furan-3-carbaldehyde and 5-(hydroxymethyl)furan-4-carbaldehyde. Vibrational spectra of these HMF isomers are also computed and compared to experimentally determined infrared spectra of "humins". On this basis, it is cautiously speculated that the alternative HMF isomers, may be monomeric constituent of the polymeric "humins".

Like-charge ion pairs of hydronium and hydroxide in aqueous solution?

The like-charge ion pairings of hydronium and hydroxide were investigated using both ab initio cluster calculations and QM/MM-MD aqueous simulations. While only a two-water-bridged H3O(+)(H2O)2H3O(+) is found in hydronium cluster calculations, three clusters of HO(-)(H2O)2HO(-), HO(-)(H2O)3HO(-) and HO(-)(H2O)4HO(-) are stable dihydroxide aggregates. In addition, an interesting yet very stable parallelogram structure of [O-H···H-O](2-) without any bridging water was also discovered using QM/MM-MD simulations. According to our analysis, its unique structure reduces the electrostatic repulsion and allows stable coordination with solvents at the same time. In conclusion, hydroxide can form stronger like-ion pairs than hydronium in aqueous solution mostly due to its versatile coordination ability with solvents.

A priori prediction of heats of vaporization and sublimation by EFP2-MD.

New theoretical procedures were proposed for the heats of vaporization (ΔHvap) and sublimation (ΔHsub) predictions by adopting effective fragment potential version 2-molecular dynamics (EFP2-MD) simulations. The particular EFP2, as generated by HF/6-31++G(2d,2p), yielded excellent results in the predictions of ΔHvap, where mean absolute deviation (MAD) and root-mean-square deviation (RMSD) for 16 molecules were 0.34 and 0.44 kcal/mol, respectively. By introducing a uniform scaling factor, we further derived a prediction procedure for ΔHsub, where its MAD and RMSD were 0.76 and 0.90 kcal/mol, respectively. Because EFP2-MD does not require any ab initio computations during simulation, computational overhead of our procedures is minimal. We believe that our new procedures for the ΔHvap and ΔHsub predictions could be widely applicable in the areas where accurate chemical information for virtual molecules is critical.

Which hydrogen atom of toluene protonates PAH molecules in (+)-mode APPI MS analysis?

A previous study (Ahmed, A. et al., Anal. Chem. 84, 1146-1151( 2012) reported that toluene used as a solvent was the proton source for polyaromatic hydrocarbon compounds (PAHs) that were subjected to (+)-mode atmospheric-pressure photoionization. In the current study, the exact position of the hydrogen atom in the toluene molecule (either a methyl hydrogen or an aromatic ring hydrogen) involved in the formation of protonated PAH ions was investigated. Experimental analyses of benzene and anisole demonstrated that although the aromatic hydrogen atom of toluene did not contribute to the formation of protonated anthracene, it did contribute to the formation of protonated acridine. Thermochemical data and quantum mechanical calculations showed that the protonation of anthracene by an aromatic ring hydrogen atom of toluene is endothermic, while protonation by a methyl hydrogen atom is exothermic. However, protonation of acridine by either an aromatic ring hydrogen or a methyl hydrogen atom of toluene is exothermic. The different behavior of acridine and anthracene was attributed to differences in gas-phase basicity. It was concluded that both types of hydrogen in toluene can be used for protonation of PAH compounds, but a methyl hydrogen atom is preferred, especially for non-basic compounds.

Hydrophobic and hydrophilic associations of a methanol pair in aqueous solution.

The association dynamics of a methanol pair in aqueous solution were theoretically studied with QM/EFP-MD and quantum mechanical methods. Stable contact pairs and solvent separated configurations (SS) were found from simulations with a free energy barrier of 2 kcal/mol, revealing the strong tendency of methanol association. The stable contact pairs were further identified as the hydrophobic (CP(A)) and hydrophilic (CP(B)) species, with the CP(A) having a larger population. Although the free energy difference between the CP(A) and CP(B) is negligible with virtually no associated free energy barrier, the slow isomerization dynamics of intermolecular rotations ensures their individual identity. Further mechanistic analysis revealed that only the CP(A) has a direct path to the SS, showing that hydrophobic attraction initiates the association process. A subsequent intermolecular hydrophilic attraction isomerizes CP(A) and CP(B). Therefore, our results show that both the hydrophobic and hydrophilic attractions between methanol molecules play important roles in the association dynamics. The former operates on the longer intermolecular distance, while the latter is effective in contact pairs.

Direct simulations of anharmonic infrared spectra using quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD): methanol in water.

One of the most stringent tests for chemical accuracy of a hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation method would be to directly compare the calculated vibrational spectra with the corresponding experimental results. Here, the applicability of hybrid QM/effective fragment potential (EFP) to the simulations of methanol infrared spectra is investigated in detail. It is demonstrated that the QM/EFP simulations in combination with time correlation function theory yield not only the fundamental transition bands but also the major overtone and combination bands of methanol dissolved in water in both mid- and near-IR regions. This clearly indicates that the QM/EFP-molecular dynamics can be a viable way of obtaining an anharmonic infrared spectrum that provides information on solvatochromic frequency shifts and fluctuations, solute-solvent interaction-induced dephasing, and anharmonic coupling effects on vibrational spectra of aqueous solutions. We anticipate that the computational protocol developed here can be effectively used to simulate both one- and two-dimensional vibrational spectra of biomolecules and chemically reactive systems in condensed phases.

Adsorption mechanisms of isoxazole and oxazole on Si(100)-2 × 1 surface: Si-N dative bond addition vs. [4+2] cycloaddition.

The surface reaction pathways of isoxazole and oxazole on Si(100)-2 × 1 surface were theoretically investigated. They both form a weakly bound Si-N dative bond adduct on Si(100)-2 × 1 surface. In the case of isoxazole, the barrierlessly formed Si-N adduct is the most important surface product, that cannot be easily converted into other species. On the other hand, a facile concerted [4+2](CC) cycloaddition without involving the initial Si-N dative bond adduct was also found in the case of oxazole adsorption. The existence of Diels-Alder reactions is attributed to the particular arrangement of the two heteroatoms of oxazole in such a way that the two Si-C σ-bonds can be formed in a [4+2] fashion. In short, the unique geometric arrangements and electronegativity of these similar heteroatomic molecules yielded distinctively different surface reaction characteristics.

Gold(III) six-membered N

The first six-membered gold(III) N^C^N pincer complex was obtained in good yield, under very mild conditions, by transmetalation of [Hg(κC-N^C^N)Cl] (N^CH^N = 1,3-bis(pyridin-2-ylmethyl)benzene, HL(1)) with Na[AuCl(4)]. The X-ray crystal structure of [Au(N^C^N)Cl][PF(6)] showed that the fused six-membered metallacycles each exist in a strongly puckered boat conformation. As shown by the (1)H NMR spectra in various solvents, the same structure is also retained in solution: no inversion of the six-membered metallacycles is observed in DMSO up to 95 °C. This correlates well with a reaction barrier of 17.5 kcal/mole, as determined by quantum chemical calculations. The reactivity of the present pincer complex is compared to that of the analogous 1,3-bis(2-pyridyl)benzene, HL(2), derivative, which has five-membered fused metallacycles. Sharp differences are found in the reactions with phosphines, such as PPh(3) and dppe (1,2-bis-diphenylphosphino-ethane), and with silver salts. Theoretical calculations were carried out on the two pincer complexes in order to try to understand these differences, and we found that the gold-chlorine bond is significantly stronger in the case of the complex containing five-membered metallacyclic rings.

Ping-pong at gold: proton jump between coordinated phenyl and eta1-benzene ligands, a computational study.

A DFT computational investigation predicts that the Au(III) complex (bpy)Au(C(6)H(5))(2+) reacts with benzene to furnish square planar (bpy)Au(C(6)H(5))(eta(1)-C(6)H(6))(2+). Intramolecular processes that occur within this species have been located, and the energetics of all processes have been quantified. The dynamic processes that have been identified are (1) benzene ring rotation with respect to Au, (2) direct hydrogen transfer from the benzene to the phenyl ligand, (3) hydrogen transfer from the ipso to the ortho positions in the coordinated benzene ligand, and (4) hydrogen transfer from the benzenium ligand formed by the ipso/ortho isomerization to the phenyl ligand. Similarities and differences are seen between the behavior of (bpy)Au(C(6)H(5))(eta(1)-C(6)H(6))(2+) and previously reported isoelectronic Pt(II) complexes. Preliminary experimental results related to this chemistry are reported, and possible consequences for C-H bond activation mediated by gold are discussed.

Adsorption reactions of dimethylaluminum isopropoxide and water on the H/Si(100)-2 x 1 surface: initial reactions for atomic layer deposition of Al2O3.

The surface reaction pathways of dimethylaluminum isopropoxide (DMAI) and water with the H/Si(100)-2 x 1 surface were theoretically investigated with SIMOMM:MP2/6-31G(d). The oxygen atom in DMAI stabilizes an initial complex, facilitating the approach of DMAI to the surface. The methane loss reaction, propane loss reaction, methylation, hydrogen loss reaction, and ring closing reaction channels of the DMAI-surface reactions were identified. Among these, the methane loss reaction depositing -Al(CH3)OCH(CH3)2 was found to be the major channel due to low barrier height and large exothermicity. The ring closing reaction is kinetically the second most accessible channel, even though it is not thermodynamically favorable. On the basis of these theoretical results, recent experimental data were reinterpreted such that the experimentally observed peaks of CH4 and CH(CH3)2OH are in fact the products of these two channels. The propane loss reaction is kinetically the third most probable channel. It produces the surface Si-O bond, which is a reaction unique to DMAI as compared to trimethylaluminum. In summary, the oxygen substitution not only affects the basic nature of the existing potential energy surfaces but also opens new possibilities.