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The ionic density profiles and corresponding integrated charge distribution close to an aqueous interface carrying charged functional groups of different valences exposed to mixed-salt solutions of 1:1 and 3:1 electrolytes were computed by use of extensive Monte Carlo simulations within the framework of the primitive model. The influence of varying ion sizes on charge inversion was analyzed, along with the crucial role of electrostatic images arising from dielectric discontinuities. For small sizes of charged species, it was found that charge inversion is enhanced by the presence of multivalent interfacial groups. Moreover, dielectric images further intensify the degree of charge inversion despite strong depletion effects. In particular, the onset of charge inversion shifts closer to the nonaqueous phase if the surface charge density is sufficiently low. These observations are opposite to the general belief of image repulsion. When large-sized ions were considered, the degree of charge inversion was found to be independent of the structure of interfacial groups and to remain widely unaffected in the absence and presence of dielectric images. Overall, our results show that interionic excluded-volume interactions are an overwhelming factor in determining counterion condensation. In addition, the inclusion of ionic size asymmetry at weakly charged interface results in surface charge amplification, which becomes more pronounced with increasing valence of the interfacial groups. Our work emphasizes the fact that surface equilibria mainly result from a subtle balance between steric and charge correlations. [ABSTRACT FROM AUTHOR]

The reaction pathways for 5′-hydroxylation and N-demethylation of nicotine catalyzed by cytochrome P450 were investigated by performing a series of first-principle electronic structure calculations on a catalytic reaction model system. The computational results indicate that 5′-hydroxylation of nicotine occurs through a two-state stepwise process, that is, an initial hydrogen atom transfer from nicotine to Cpd I (i.e., the HAT step) followed by a recombination of the nicotine moiety with the iron-bound hydroxyl group (i.e., the rebound step) on both the high-spin (HS) quartet and low-spin (LS) doublet states. The HAT step is the rate-determining one. This finding represents the first case that exhibits genuine rebound transition state species on both the HS and the LS states for Cα-H hydroxylation of amines. N-Demethylation of nicotine involves a N-methylhydroxylation to form N-(hydroxymethyl)nornicotine, followed by N-(hydroxymethyl)nornicotine decomposition to nornicotine and formaldehyde. The N-methylhydroxylation step is similar to 5′-hydroxylation, namely, a rate-determining HAT step followed by a rebound step. The decomposition process occurs on the deprotonated state of N-(hydroxymethyl)nornicotine assisted by a water molecule, and the energy barrier is significantly lower than that of the N-methylhydroxylation process. Comparison of the rate-determining free energy barriers for the two reaction pathways predicts a preponderance of 5′-hydroxylation over the N-demethylation by roughly a factor of 18:1, which is in excellent agreement with the factor of 19:1 derived from available experimental data. [ABSTRACT FROM AUTHOR]

The hydrogen bond acceptor capability of halogens has long been underappreciated in the field of biology. In this work, we have surveyed structures of protein complexes with halogenated ligands to characterize geometrical preferences of C−X···H contacts and contributions of such interactions to protein−ligand binding affinity. Notably, F···H interactions in biomolecules exhibit a remarkably different behavior as compared to three other kinds of X···H (X = Cl, Br, I) interactions, which has been rationalized by means of ab initio calculations using simple model systems. The C−X···H contacts in biological systems are characterized as weak hydrogen bonding interactions. Furthermore, the electrophile “head on” and nucleophile “side on” interactions of halogens have been extensively investigated through the examination of interactions in protein structures and a two-layer ONIOM-based QM/MM method. In biomolecular systems, C−X···H contacts are recognized as secondary interaction contributions to C−X···O halogen bonds that play important roles in conferring specificity and affinity for halogenated ligands. The results presented here are within the context of their potential applications in drug design, including relevance to the development of accurate force fields for halogens. [ABSTRACT FROM AUTHOR]

The blue-shifted C−D stretching vibrations (νCD) of deuteriated dimethyl sulfoxide (DMSO-d6) in mixtures of DMSO-d6/ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([Bmim][BF4]) were carefully investigated and compared with those in DMSO-d6/water. Results from FTIR studies indicate that the direct interaction of C−D···F between DMSO-d6and the anion [BF4−] plays a minor role in the blue-shift of νCDin the mixtures of DMSO-d6/IL. They also show that the indirect influence of the hydrogen bond formed by the nearby functional group SO with C2−H of the cation significantly contributes to the blue-shift of νCD, as can be inferred from the significant differences of the blue-shift in [Bmim][BF4] and 1-butyl-2,3-dimethylimidazolium tetrafluoroborate ([Bm2im][BF4]). In contrast, in the case of DMSO-d6/water mixtures, direct hydration of C−H···O between the methyl groups of DMSO-d6with the oxygen atom of water is mainly responsible for the blue shift of νCD. Furthermore, theoretical calculations revealed that charge migrations as well as rehybridization have a dominant effect on the blue-shift in both mixtures. [ABSTRACT FROM AUTHOR]

An all-atom force field is developed using a combination of density functional theory calculations and OPLS force field parameter values for the 1,1,3,3-tetramethylguanidium lactate (TMG) lactic acid (LAC) ionic liquid (TMGL). The computed density of the TMGL is in good agreement with available experimental values. The internal energy components, cohesive energy density, and the self-diffusion constants are also discussed. Molecular dynamics simulations are then conducted to investigate the solubility of the SO2and CO2gases in the TMGL. The simulation results show strong organization of SO2about the TMG cation and the LAC anion, especially the LAC anion, but relatively weak organization of CO2about the cation and the anion of the TMGL, which explained well the selectivity of the TMGL toward the SO2and CO2. [ABSTRACT FROM AUTHOR]

The mechanism of N-demethylation of N,N-dimethylanilines (DMAs) by cytochrome P450, a highly debated topic in mechanistic bioinorganic chemistry (Karki, S. B.; Dinnocenczo, J. P.; Jones, J. P.; Korzekwa, K. R. J. Am. Chem. Soc.1995, 117, 3657), is studied here using DFT calculations of the reactions of the active species of the enzyme, Compound I (Cpd I), with four para-(H, Cl, CN, NO2) substituted DMAs. The calculations resolve mechanistic controversies, offer a consistent mechanistic view, and reveal the following features:  (a) the reaction pathways involve C−H hydroxylation by Cpd I followed by a nonenzymatic carbinolamine decomposition. (b) C−H hydroxylation is initiated by a hydrogen atom transfer (HAT) step that possesses a “polar” character. As such, the HAT energy barriers correlate with the energy level of the HOMO of the DMAs. (c) The series exhibits a switch from spin-selective reactivity for DMA and p-Cl-DMA to two-state reactivity, with low- and high-spin states, for p-CN-DMA and p-NO2-DMA. (d) The computed kinetic isotope effect profiles (KIEPs) for these scenarios match the experimentally determined KIEPs. Theory further shows that the KIEs and TS structures vary in a manner predicted by the Melander−Westheimer postulate:  as the substituent becomes more electron withdrawing, the TS is shifted to a later position along the H-transfer coordinate and the corresponding KIEs increases. (e) The generated carbinolaniline can readily dissociate from the heme and decomposes in a nonenzymatic environment, which involves water assisted proton shift. [ABSTRACT FROM AUTHOR]

The density functional theory (DFT) method has been used to investigate NO probe molecule adsorption on the stoichiometric (Mo16S32) and nonstoichiometric (Mo16S34and Mo16S29) clusters. The calculated adsorption energies indicate that the stoichiometric cluster has stronger NO affinity than the nonstoichiometric surfaces. It is also found that mononitrosyl adsorption is favored at low NO coverage, while dinitrosyl (germinal) and (NO)2dimer adsorption at high NO coverage are possible. Strong repulsive interaction has been found for the adsorbed dinitrosyl and (NO)2dimer species. In addition, the computed NO stretching frequencies for the mononitrosyl and dinitrosyl species agree well with the experimental data, while those of the dimer species are much lower than the suggested experimental data. [ABSTRACT FROM AUTHOR]

Recent experimental studies revealed that cytochrome P450 2E1 (CYP2E1) could metabolize not only ethanol but also its primary product, acetaldehyde, accompanying the well-known acetaldehyde dehydrogenases (ALDH) in the metabolism of acetaldehyde. Mechanistic aspects of acetaldehyde hydroxylation by Compound I model active species of CYP2E1 were investigated by means of B3LYP DFT calculations in the present paper. Our study results demonstrate that acetaldehyde hydroxylation by CYP2E1 is in accord with the effectively concerted mechanisms both on the high quartet spin state (U.) and on the low doublet spin state (LS). The rate-limiting step is H-abstraction, and the activation energy is about 11.7∼14.0 kcal/mol on the quartet (doublet) reaction route, which is about one-half to one-third of that needed by methane hydroxylation. The phenomenon that the U. and LS reaction routes are both effectively concerted was shown for the first time to occur in trans-2-phenyl-iso-propylcyclopropane hydroxylation by Kumar et al. (see Figure 7 in the paper of Kumar, D.; de Visser, S. P.; Sharma, P. K.; Cohen, S.; Shaik, S. J. Am. Chem. Soc.2004, 126, 1907) and was confirmed in our work of acetaldehyde hydroxylation by cytochrome P450. Theoretical exploration of the U. O-rebound barrier degradation is also presented in the present paper on the basis of Shaik's valence bond (VB) model. [ABSTRACT FROM AUTHOR]

Possible reaction pathways of nitroethylene with the Si(100)-2 × 1 surface have been investigated by unrestricted density functional theory. The facile occurrence of the studied reactions was demonstrated by the low activation energies of the rate-determining steps (1.07−5.23 kcal/mol). It was found that the [6b+ 2] cycloaddition reaction of nitroethylene is most kinetically favorable. The isomerization reactions of the addition products were also investigated. The [1b+ 2] cycloaddition product may further undergo a rearrangement by overcoming a 12.37 kcal/mol activation energy barrier into an isomer, with an oxygen atom of the nitryl group inserted between two silicon atoms of the Si(100) surface. [ABSTRACT FROM AUTHOR]

Spin-polarized density functional theory calculations have been performed to characterize the hydrogen adsorption and diffusion on the Fe(111) surface at 2/3-, 1-, and 2-monolayer (ML) coverages. It is found that the most favored adsorption site for atomic hydrogen (H) is the top-shallow bridge site (tsb), followed by the quasi 4-fold site (qff) with the energy difference of about 0.1 eV, while the top site (t) is not competitive. Furthermore, the adsorbed atomic hydrogen (H) has a high mobility, as indicated by the small diffusion barriers. The local density of state (LDOS) analysis reveals that the Fe−H (tsb or qff) bond involves mainly the Fe 4s and 4p and H 1s orbitals with less contribution of the Fe 3d orbital, while the Fe 4s, 4p, and 3d orbitals all participate in the Fe−H (top) bond. In addition, the coverage effects on the adsorption configurations and adsorption energies are addressed. [ABSTRACT FROM AUTHOR]

Two-dimensional vibrational spectroscopy is applied to investigate the dilution process of 1-ethyl-3-methyl-imidazolium tetrafluoroborate ([Emim][BF 4]) in water. With increasing water content in ionic liquid (IL)/water mixtures, the C−H stretching vibration of the imidazolium cation showed systematic blue-shifts, which reflect the weakening of the cohesion between the cation and anion of ILs. The two-dimensional IR results reveal that the ILs sense quite different environments during the whole dilution process. First, the three-dimensional network structure of pure ILs was destroyed gradually into ionic clusters, then the clusters were further dissociated into ionic pairs surrounded by water molecules, and finally the latter became the dominant form in bulk water. Within the concentration range we investigated (0.02 < XD2O< 0.90), the intruding water does not dissociate ILs into ions completely. The structure evolution of ILs can be clearly detected and visualized in the asynchronous spectrum. [ABSTRACT FROM AUTHOR]

Amide-based ionic liquids are receiving great enthusiasm recently. In this work, the structures of a kind of N,N-dimethylformamide-based (DMF-based) ionic liquid are investigated theoretically by means of density-functional theory methods. Enol and keto forms of the cation with anions are optimized. The enol form of the DMFHcation can form three stable configurations of ion pairs with the anion, while the cation of the keto form is unstable and the proton transfer occurs to form three kinds of neutral molecule pairs. Moreover, the neutral pairs are more stable than the ion pairs, and the ion pairs tend to tautomerize to neutral pairs without barriers. It is suggested that the transformation from the ion pairs to neutral pairs may be the first step for decomposition of DMF-based ionic liquids. [ABSTRACT FROM AUTHOR]

Density functional theory calculations have been carried out for CO adsorption on the Feoct2- and Fetet1-terminated Fe3O4(111) surfaces, which are considered as active catalysts in water-gas shift reaction. It is found that the on-top configurations are most stable on these two surfaces. Some bridge configurations are also stable in which the new C−O bond formed between the surface O atom and the C atom of CO. The adsorption on the Feoct2-termiated surface is more stable than on the Fetet1-terminated surface. The density of state reveals the binding mechanism of CO adsorption on the two surfaces. Our calculations have also shown that the absorbed CO can migrate from the on-top site to the bridge site or 3-fold site. The oxidation of CO via surface oxygen atoms is feasible, which is in good agreement with experimental results. [ABSTRACT FROM AUTHOR]

CO2reforming of CH4on Ni(111) was investigated by using density functional theory. On the basis of thermodynamic analyses, the first step is CH4sequential dissociation into surface CH (CH4→ CH3→ CH2→ CH) and hydrogen, and CO2dissociation into surface CO and O (CO2→ CO O). The second step is CH oxygenation into CHO (CH O → CHO), which is more favored than dissociation into C and hydrogen (CH → C H). The third step is the dissociation of CHO into surface CO and H (CHO → CO H). This can explain the enhanced selectivity toward the formation of CO and H2on Ni catalysts. It is found that surface carbon formation by the Bouduard back reaction (2CO C(ads) CO2) is more favored than by CH4sequential dehydrogenation. The major problem of CO2reforming of CH4is the very strong CO adsorption on Ni(111), which results in the accumulation of CO on the surface and hinders the subsequent reactions and promotes carbon deposition. Therefore, promoting CO desorption should maintain the reactivity and stability of Ni catalysts. The computed energy barriers of the most favorable elementary reaction identify the CH4activation into CH3and H as the rate-determining step of CO2reforming of CH4on Ni(111), in agreement with the isotopic experimental results. [ABSTRACT FROM AUTHOR]

A systematic density functional theory study has been carried out on the structure and stability of triangular molybdenum sulfide (MoSx) models. On the basis of the structural and energetic comparison, the triangle Mo28S84 (VII) cluster has been identified as a reasonable structure for triangular MoSx model. Under reductive atmosphere, the most stable structure has bridging sulfur on edge sites and two H2S at each corner site. It is found that CO adsorption at the corner site represents the most stable conformation. Along with other stretching modes, the computed frequency at 2102 cm-1 for CO at the corner agrees perfectly with the experimental observation. [ABSTRACT FROM AUTHOR]

Water flow inside polyamide (PA) reverse osmosis (RO) membranes is studied by steady state nonequilibrium molecular dynamics (NEMD) simulations in this work. The PA RO membrane is constructed with the all-atom model, and the density and average pore size obtained thereby are consistent with the latest experimental results. To obtain the time-independent water flux, a steady state NEMD method is used under various pressure drops. The water flux in our simulations, which is calculated under higher pressure drops, is in a linear relation with the pressure drops. Hence, the water flux in lower pressure drops can be reliably estimated, which could be compared with the experimental results. The molecular details of water flowing inside the membrane are considered. The radial distribution function and residence time of water around various groups of polyamide are introduced to analyze the water velocities around these groups, and we find that water molecules flow faster around benzene rings than around carboxyl or amino groups in the membrane, which implies that the main resistance of mass transport of water molecules comes from the carboxyl or amino groups inside the membranes. This finding is in good consistency with experimental results and suggests that less free carboxyl or amino groups should be generated inside RO membranes to enhance water permeance. [ABSTRACT FROM AUTHOR]

AmtB is one of the ammonium transporter proteins facilitating the ammonium transport across the cellular membranes. Experimentally, the substrate used in in vitro studies is the radio labeled [14C]methylammonium, rather than ammonium itself. To explore the similarity and difference of the conduction mechanism of methylamine and ammonia molecules through AmtB, molecular dynamics simulations on 22 carefully designed systems were performed, which demonstrated that methylamine could be automatically transported in a very similar way to ammonia. The driving force for the conduction is mainly the hydrogen bond network comprising His168, His318, and Tyr32, working in coordination with NH−π interaction with residue Trp212. Then, Ser263 translocated the substrates from the exit gate into the cytoplasm by hydrogen bond interaction. The aromatic ring of Trp212 acted like a springboard to facilitate the translocation of the substrates from site Am2 to Am4 via NH−π interaction. Without the mediation of Trp212, further movement of substrate in the channel would be hampered by the strong hydrogen bonding from His168. In agreement with experimental results, the substrates could be transported by W212F mutant but not by W212A within the simulation time as long as 20 ns. In addition, we predicted that the mutants S263D and S263C remain the function of the transporter but S263A does not. The difference of transporting the two substrates is that methylamine involves more hydrophobic interactions than ammonia. In conclusion, methylamine molecule is a good mimic for investigating the translocation mechanism of ammonium transporter AmtB. [ABSTRACT FROM AUTHOR]