Reaction Path Calculations Research Articles

The geochemistry of trace elements in geothermal fluids, Iceland

Trace element geochemistry was studied in geothermal fluids in Iceland. The major and trace element compositions of hot springs, sub-boiling, and two-phase (liquid and vapor) wells from 10 geothermal areas were used to reconstruct the fluid composition in the aquifers at depth. Aquifer fluid temperatures ranged from 4 to 300°C, pH values between 4.5 and 9.3, and fluids typically contained total dissolved solids <1000ppm, except in geothermal areas that have seawater and seawater-meteoric water mixtures. Trace alkali elements Li, Rb and Cs are among the most mobile elements in aquifer fluids, with concentrations in the range of <1ppb to 3.49ppm Li, <0.01 to 57ppb Cs, and <1ppb to 3.77ppm Rb. Their chemistry is thought to be dominated by rock leaching and partitioning into Na- and K-containing major alteration minerals. Arsenic, Sb, Mo and W are typically present in concentrations in the range of 1–100ppb. They are relatively mobile, yet Mo may be limited by molybdenite solubility. The alkaline earth elements Ba and Sr are quite immobile with concentrations in the range of <0.1–10ppb Ba and <1–100ppb Sr in the dilute fluids, but up to 5.9ppm Ba and 8.2ppm Sr in saline fluids. These elements show a systematic relationship with Ca, possibly due to substitution for Ca in Ca-containing major alteration minerals like calcite, epidote and anhydrite. Incorporation into major Ca-minerals may also be important for Mn. Many metals including Fe, Cr, Ni, Zn, Cu, Co, Pb and Ag have low mobility and concentrations, typically <1ppb for Ag, Cd, Co, Cr, Cu, Ni, and Pb, <10ppb for Zn and<100ppb for Fe, although for some metals higher concentrations are associated with saline fluids. Based on the metals assessed, saturation is approached with respect to many sulfide minerals and in some cases oxide minerals but Cu, Ni and Pb minerals are slightly but systematically undersaturated, and Ag phases significantly undersaturated. Evaluation of mineral-fluid equilibria for these metals is problematic due to their low concentrations, problems associated with assessing the aqueous species distribution by thermodynamic calculations, and uncertainties concerning the exact minerals possibly involved in such reactions. Reaction path calculations, poor comparison of concentrations measured in the samples collected at the wellhead and published downhole data as well as boiling, cooling and mass precipitation calculations suggest removal of many metals due to changes upon depressurization boiling and conductive cooling of the aquifer fluids as they ascend in wells. These results imply that processes such as mass precipitation upon fluid ascent may be highly important and emphasize the importance of considering mass movement in geothermal systems.

Major hydrogeochemical processes in an Acid Mine Drainage affected estuary

This study provides geochemical data with the aim of identifying and quantifying the main processes occurring in an Acid Mine Drainage (AMD) affected estuary. With that purpose, water samples of the Huelva estuary were collected during a tidal half-cycle and ion–ion plots and geochemical modeling were performed to obtain a general conceptual model. Modeling results indicated that the main processes responsible for the hydrochemical evolution of the waters are: (i) the mixing of acid fluvial water with alkaline ocean water; (ii) precipitation of Fe oxyhydroxysulfates (schwertmannite) and hydroxides (ferrihydrite); (iii) precipitation of Al hydroxysulfates (jurbanite) and hydroxides (amorphous Al(OH)3); (iv) dissolution of calcite; and (v) dissolution of gypsum. All these processes, thermodynamically feasible in the light of their calculated saturation states, were quantified by mass-balance calculations and validated by reaction-path calculations. In addition, sorption processes were deduced by the non-conservative behavior of some elements (e.g., Cu and Zn).

Initial Stages of Oxygen Chemisorption on the Ge(001) Surface

There is currently considerable interest in processes associated with the modification of germanium surfaces due to their potential application in electronic components such as MOSFETs. In this work, we combine first-principles total energy and reaction path calculations to study the initial stages of the oxidation of the Ge(001) surface due to the adsorption of both atomic and molecular oxygen. The obtained results provide real insights regarding several outstanding issues in the literature, including the identification of key features observed in the experimental studies. Three new structures for oxygen adsorption on Ge(001) have been examined, at least one of which is predicted to be likely to occur. Scanning Tunnelling Microscopy (STM) images have also been simulated for comparison with the experimental data.

Dynamic structural disorder in supported nanoscale catalysts

We investigate the origin and physical effects of "dynamic structural disorder" (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale.

Hydroxide-ion induced degradation pathway for dimethylimidazolium groups in anion exchange membranes

The alkaline stability of imidazolium-based anion exchange membranes was studied by FT-IR and 13C solid state NMR. Imidazolium groups are susceptible to attack by hydroxide ions and undergo degradation in alkaline conditions through a ring-opening mechanism. Density functional theory (DFT) studies were performed to better understand the degradation pathway and the relative stability of imidazolium cations on exposure to hydroxide. The ring-opening degradation pathway follows the following three steps: (a) a nucleophilic reaction, (b) a ring-opening reaction, and (c) a rearrangement reaction. The structural changes induced in the imidazole ring were studied using a model of the dimethylimidazolium cation ([DMIM]+). The energy changes along the degradation pathway were obtained from reaction path calculations. The effect of hydroxide ion concentration and dielectric constant of surrounding medium on reaction energy barriers were studied. The hydroxide-ion induced degradation of the dimethylimidazolium cation was found to be more facile in high-pH environments. Good solvation of the dimethylimidazolium cation and the hydroxide ion was helpful in minimizing the degradation and enhancing the chemical stability of anion exchange membranes based on these cations.

New Delhi Metallo-β-Lactamase I: Substrate Binding and Catalytic Mechanism

Metallo-β-lactamases can hydrolyze and deactivate lactam-containing antibiotics, which is the major mechanism for causing drug resistance in the treatment of bacterial infections. This has become a global concern because of the lack of clinically approved inhibitors so far. The emergence of New Delhi metallo-β-lactamase I (NDM-1) makes the situation even more serious. In this work, first, the structure of NDM-1 in complex with the inhibitor molecule l-captopril is investigated by both density functional theory (DFT) and hybrid quantum mechanical/molecular mechanical (QM/MM) methods, and the theoretical results are in good agreement with the X-ray structure. The Michaelis structure with an antibiotic compound (ampicillin) bound in the active site is constructed from a recent X-ray structure of the NDM-1 enzyme with hydrolyzed ampicillin. It is further simulated using a QM/MM molecular dynamics method. One of the interesting binding features of ampicillin in the NDM-1 active site is that the conserved C3 carboxylate group is not ligated with Zn2 but rather is only hydrogen-bonded with N220 and K211. A bridging hydroxide ion is suggested to connect two zinc cofactors. This hydroxide ion is also hydrogen-bonded with D124. Subsequent reaction path calculations indicate that the initial step of lactam ring-opening occurs through a concerted step in which the cleavage of the C-N bond and the transfer of the hydrogen bond to D124 are nearly concerted. The ligand bond between Zn2 and the C3 carboxylate group forms after the first step of nucleophilic addition. The calculated activation energy barrier height is about 19.4 kcal/mol for the hydrolysis of ampicillin, which can be compared with the experimental value of 15.8 kcal/mol derived from kcat = 15 s(-1). The overall mechanism is finally confirmed by a subsequent DFT study of a truncated active-site model.

Including Torsional Anharmonicity in Canonical and Microcanonical Reaction Path Calculations.

We reformulate multistructural variational transition state theory by removing the approximation of calculating torsional anharmonicity only at stationary points. The multistructural method with torsional anharmonicity is applied to calculate the reaction-path free energy of the hydrogen abstraction from the carbon-1 position in isobutanol by OH radical. The torsional potential anharmonicity along the reaction path is taken into account by a coupled torsional potential. The calculations show that it can be critical to include torsional anharmonicity in searching for canonical and microcanonical variational transition states. The harmonic-oscillator approximation fails to yield reasonable free energy curves along the reaction path.

Chrysotile dissolution rates: Implications for carbon sequestration

Serpentine minerals (e.g., chrysotile) are a potentially important medium for sequestration of CO2 via carbonation reactions. The goals of this study are to report a steady-state, far from equilibrium chrysotile dissolution rate law and to better define what role serpentine dissolution kinetics will have in constraining rates of carbon sequestration via serpentine carbonation. The steady-state dissolution rate of chrysotile in 0.1m NaCl solutions was measured at 22°C and pH ranging from 2 to 8. Dissolution experiments were performed in a continuously stirred flow-through reactor with the input solutions pre-equilibrated with atmospheric CO2. Both Mg and Si steady-state fluxes from the chrysotile surface, and the overall chrysotile flux were regressed and the following empirical relationships were obtained: FMg=-0.22pH-10.02;FSi=-0.19pH-10.37;Fchrysotile=-0.21pH-10.57 where FMg, FSi, and Fchrysotile are the log10 Mg, Si, and molar chrysotile fluxes in mol/m2/s, respectively. Element fluxes were used in reaction-path calculations to constrain the rate of CO2 sequestration in two geological environments that have been proposed as potential sinks for anthropogenic CO2. Carbon sequestration in chrysotile tailings at 10°C is approximately an order of magnitude faster than carbon sequestration in a serpentinite-hosted aquifer at 60°C on a per kilogram of water basis. A serpentinite-hosted aquifer, however, provides a larger sequestration capacity. The chrysotile dissolution rate law determined in this study has important implications for constraining potential rates of sequestration in serpentinite-hosted aquifers and under accelerated sequestration scenarios in mine tailings.

One- and Two-Dimensional Translational Energy Distributions in the Iodine-Loss Dissociation of 1,2-C2H4I2+ and 1,3-C3H6I2+: What Does This Mean?

Threshold photoelectron photoion coincidence (TPEPICO) has been used to study the sequential photodissociation reaction of internal energy selected 1,2-diiodoethane cations: C(2)H(4)I(2)(+) → C(2)H(4)I(+) + I → C(2)H(3)(+) + I + HI. In the first I-loss reaction, the excess energy is partitioned between the internal energy of the fragment ion C(2)H(4)I(+) and the translational energy. The breakdown diagram of C(2)H(4)I(+) to C(2)H(3)(+), i.e., the fractional ion abundances below and above the second dissociation barrier as a function of the photon energy, yields the internal energy distribution of the first daughter, whereas the time-of-flight peak widths yield the released translational energy in the laboratory frame directly. Both methods indicate that the kinetic energy release in the I-loss step is inconsistent with the phase space theory (PST) predicted two translational degrees of freedom, but is well-described assuming only one translational degree of freedom. Reaction path calculations partly confirm this and show that the reaction coordinate changes character in the dissociation, and it is, thus, highly anisotropic. For comparison, data for the dissociative photoionization of 1,3-diiodopropane are also presented and discussed. Here, the reaction coordinate is expected to be more isotropic, and indeed the two degrees of freedom assumption holds. Characterizing kinetic energy release distributions beyond PST is crucial in deriving accurate dissociative photoionization onset energies in sequential reactions. On the basis of both experimental and theoretical grounds, we also suggest a significant revision of the 298 K heat of formation of 1,2-C(2)H(4)I(2)(g) to 64.5 ± 2.5 kJ mol(-1) and that of CH(2)I(2)(g) to 113.5 ± 2 kJ mol(-1) at 298 K.

Quantum Mechanical/Molecular Mechanical Study on the Mechanism of the Enzymatic Baeyer–Villiger Reaction

We report a combined quantum mechanical/molecular mechanical (QM/MM) study on the mechanism of the enzymatic Baeyer-Villiger reaction catalyzed by cyclohexanone monooxygenase (CHMO). In QM/MM geometry optimizations and reaction path calculations, density functional theory (B3LYP/TZVP) is used to describe the QM region consisting of the substrate (cyclohexanone), the isoalloxazine ring of C4a-peroxyflavin, the side chain of Arg-329, and the nicotinamide ring and the adjacent ribose of NADP(+), while the remainder of the enzyme is represented by the CHARMM force field. QM/MM molecular dynamics simulations and free energy calculations at the semiempirical OM3/CHARMM level employ the same QM/MM partitioning. According to the QM/MM calculations, the enzyme-reactant complex contains an anionic deprotonated C4a-peroxyflavin that is stabilized by strong hydrogen bonds with the Arg-329 residue and the NADP(+) cofactor. The CHMO-catalyzed reaction proceeds via a Criegee intermediate having pronounced anionic character. The initial addition reaction has to overcome an energy barrier of about 9 kcal/mol. The formed Criegee intermediate occupies a shallow minimum on the QM/MM potential energy surface and can undergo fragmentation to the lactone product by surmounting a second energy barrier of about 7 kcal/mol. The transition state for the latter migration step is the highest point on the QM/MM energy profile. Gas-phase reoptimizations of the QM region lead to higher barriers and confirm the crucial role of the Arg-329 residue and the NADP(+) cofactor for the catalytic efficiency of CHMO. QM/MM calculations for the CHMO-catalyzed oxidation of 4-methylcyclohexanone reproduce and rationalize the experimentally observed (S)-enantioselectivity for this substrate, which is governed by the conformational preferences of the corresponding Criegee intermediate and the subsequent transition state for the migration step.

Modelling groundwater processes in a carbonate catchment: A case study from the Madonie area (Northern Sicily)

Abstract This study reports on the results of a hydrogeochemical survey carried out in the Madonie area, a carbonate massif located in Palermo Province, Northern Sicily. The large dataset (226 collected sites) is used to highlight the processes controlling the distribution of dissolved chemicals in groundwaters; and, more importantly, to develop a general model (based on reaction-path modelling, and using the EQ3/6 code) of rock–water reactions in a carbonate environment. The investigated groundwater samples have conductivity between 31.7 and 8220 μS/cm; their total dissolved solids (TDS) content is higher near the coast area, where the seawater contribution becomes important. Calcium and HCO 3 - excess concentrations in groundwaters, with respect to the meteoric water–seawater mixing line, suggest that water–rock interactions in carbonate aquifers play a major role on water chemistry. Using the dataset, reaction-path modelling is used to simulate the evolution of groundwaters upon interaction with carbonate rocks. Model simulations are performed in time mode, taking into account the mineralogical composition of Madonie carbonate rocks, and the different dissolution rates of each dissolving mineral. The model results of reaction path calculations are in fair agreement with analytical data for natural waters, demonstrating the likelihood of model assumptions, and supporting further the relevance of carbonate dissolution in determining the chemistry of fluids in the investigated area. The developed model is useful for low-temperature weathering of carbonate mineral in general, and is thus likely to apply in a variety of geological contexts.

Steepest descent reaction path integration using a first-order predictor–corrector method

The theoretical treatment of chemical reactions inevitably includes the integration of reaction pathways. After reactant, transition structure, and product stationary points on the potential energy surface are located, steepest descent reaction path following provides a means for verifying reaction mechanisms. Accurately integrated paths are also needed when evaluating reaction rates using variational transition state theory or reaction path Hamiltonian models. In this work an Euler-based predictor-corrector integrator is presented and tested using one analytic model surface and five chemical reactions. The use of Hessian updating, as a means for reducing the overall computational cost of the reaction path calculation, is also discussed.

QM/MM Studies of the Matrix Metalloproteinase 2 (MMP2) Inhibition Mechanism of (S)-SB-3CT and its Oxirane Analogue

SB-3CT, (4-phenoxyphenylsulfonyl)methylthiirane, is a potent, mechanism-based inhibitor of the gelatinase sub-class of the matrix metalloproteinase (MMP) family of zinc proteases. The gelatinase MMPs are unusual in that there are several examples where both enantiomers of a racemic inhibitor have comparable inhibitory abilities. SB-3CT is one such example. Here, the inhibition mechanism of the MMP2 gelatinase by the (S)-SB-3CT enantiomer and its oxirane analogue is examined computationally, and compared to the mechanism of (R)-SB-3CT. Inhibition of MMP2 by (R)-SB-3CT was shown previously to involve enzyme-catalyzed C-H deprotonation adjacent to the sulfone, with concomitant opening by β-elimination of the sulfur of the three-membered thiirane ring. Similarly to the R enantiomer, (S)-SB-3CT was docked into the active site of MMP2, followed by molecular dynamics simulation to prepare the complex for combined quantum mechanics and molecular mechanics (QM/MM) calculations. QM/MM calculations with B3LYP/6-311+G(d,p) for the QM part (46 atoms) and the AMBER force field for the MM part were used to compare the reaction of (S)-SB-3CT and its oxirane analogue in the active site of MMP2 (9208 atoms). These calculations show that the barrier for the proton abstraction coupled ring opening reaction of (S)-SB-3CT in the MMP2 active site is 4.4 kcal/mol lower than its oxirane analogue, and the ring opening reaction energy of (S)-SB-3CT is only 1.6 kcal/mol less exothermic than its oxirane analogue. Calculations also show that the protonation of the ring-opened products by water is thermodynamically much more favorable for the alkoxide obtained from the oxirane, than for the thiolate obtained from the thiirane. In contrast to (R)-SB-3CT and the R-oxirane analogue, the double bonds of the ring-opened products of (S)-SB-3CT and its S-oxirane analogue have the cis-configuration. Vibrational frequency and intrinsic reaction path calculations on a reduced size QM/MM model (2747 atoms) provide additional insight into the mechanism. These calculations yield 5.9 and 6.7 for the deuterium kinetic isotope effect for C-H bond cleavage in the transition state for the R and S enantiomers of SB-3CT, in good agreement with the experimental results.

Rapid estimation of activation enthalpies for cytochrome‐P450‐mediated hydroxylations

Cytochrome P450 (CYP) enzymes play a critical role in detoxication and bioactivation of xenobiotics; thus, the ability to predict the biotransformation rates and regioselectivity of CYP enzymes toward substrates is an important goal in toxicology and pharmacology. Here, we present the use of the semiempirical quantum chemistry method SAM1 to rapidly estimate relative activation enthalpies (ΔH(‡)) for the hydroxylation of aliphatic carbon centers of various substrates. The ΔH(‡) were determined via a reaction path calculation, in the reverse direction (RRP), using the iron-hydroxo-porphine intermediate and the substrate radical. The SAM1 ΔH(‡) were calculated via unrestricted Hartree-Fock (UHF) and configuration interaction (CI) formalisms for both the doublet and quartet spin states. The SAM1 RRP ΔH(‡), after subtracting a correction factor, were compared with density functional theory (DFT) B3LYP activation energies for two sets of substrates and showed R(2) ranging from 0.69 to 0.89, and mean absolute differences ranging from 1.2 ± 1.0 to 1.7 ± 1.5 kcal/mol. SAM1 UHF and CI RRP calculation times were, on average, more than 200 times faster than those for the corresponding forward reaction path DFT calculations. Certain key transition-state (TS) geometry measurements, such as the forming O···H bond length, showed good correlation with the DFT values. These results suggest that the SAM1 RRP approach can be used to rapidly estimate the DFT activation energy and some key TS geometry measurements and can potentially be applied to estimate substrate hydroxylation rates and regioselectivity by CYP enzymes.

Mechanisms of nickel sorption by a bacteriogenic birnessite

Abstract A synergistic experimental–computational approach was used to study the molecular-scale mechanisms of Ni sorption at varying loadings and at pH 6–8 on the biogenic hexagonal birnessite produced by Pseudomonas putida GB-1. We found that Ni is scavenged effectively by bacterial biomass-birnessite assemblages. At surface excess values below 0.18 mol Ni kg −1 sorbent (0.13 mol Ni mol −1 Mn), the biomass component of the sorbent did not interfere with Ni sorption on mineral sites. Extended X-ray absorption fine structure (EXAFS) spectra showed two dominant coordination environments: Ni bound as a triple-corner-sharing (Ni-TCS) complex at vacancy sites and Ni incorporated (Ni-inc) into the MnO 2 sheet, with the latter form of Ni favored at high sorptive concentrations and decreased proton activity. In parallel to our spectral analysis, first-principles geometry optimizations based on density functional theory (DFT) were performed to investigate the structure of Ni surface complexes at vacancy sites. Excellent agreement was achieved between EXAFS- and DFT-derived structural parameters for Ni-TCS and Ni-inc. Reaction-path calculations revealed a pH-dependent energy barrier associated with the transition from Ni-TCS to Ni-inc. Our results are consistent with the rate-limited incorporation of Ni at vacancy sites in our sorption samples, but near-equilibrium state of Ni in birnessite phases found in nodule samples. This study thus provides direct and quantitative evidence of the factors governing the occurrence of Ni adsorption versus Ni incorporation in biogenic hexagonal birnessite, a key mineral in the terrestrial manganese cycle.

QM/MM Study on the Catalytic Mechanism of Cellulose Hydrolysis Catalyzed by Cellulase Cel5A from Acidothermus cellulolyticus

Cellulase Cel5A from Acidothermus cellulolyticus is an endoglucanase which features the retention mechanism for the cleavage of the beta-1,4-glycosidic bond. In this work, we investigated the detailed catalytic steps in the formation of two cellobiose units from the hydrolysis of a cellotetraose molecule using a combined QM/MM approach. The understanding of the catalysis process at the atomistic level may help further protein engineering research. Molecular dynamics, potentials of mean force (PMFs), and reaction path calculations confirmed that the hydrolysis of cellotetraose has a retention mechanism via oxocarbenium-like transition states for both the glycosylation and deglycosylation steps.

Hydrogeochemical modeling of a thermal system and lessons learned for CO 2 geologic storage

Geological storage of carbon dioxide is presently considered to be one of the main strategies to mitigate the impact of the emissions of this gas on global warming. Among the various alternatives considered for CO 2 geological storage, one of the main geological candidates for hosting injected CO 2 in the long term are deep porous reservoir rock formations saturated with brackish or saline solutions. Although valuable information on the expected hydrogeochemical processes involved in the CO 2 storage in such deep saline aquifers can be obtained in laboratory or modeling studies, the only direct source of information about the long-term behavior of geological storages for CO 2 in deep aquifers is natural analogues. In this work, a classical and simple geochemical methodology is successfully applied to the study of the features and hydrogeochemical processes determining the evolution of a Spanish thermal system (the Alhama–Jaraba complex), which can be considered as a natural analogue for deep geological CO 2 storage in carbonate rocks. The geology, structure, depth and hydrogeochemistry of the Alhama–Jaraba thermal system are very similar to the expected features of a potential CO 2 reservoir in carbonate materials. The processes determining the hydrogeochemical evolution in the Alhama–Jaraba thermal system have been successfully identified and quantified with the assistance of ion–ion plots, speciation–solubility calculations and mass-balance calculations. Furthermore, the feasibility of the proposed conceptual hydrogeochemical model for this system has been verified by using reaction-path calculations. Mass-balance calculation results have indicated that the observed hydrogeochemical evolution between springs is mainly due to halite dissolution and dedolomitization triggered by gypsum or anhydrite dissolution. CO 2(g) mass transfer has been estimated to be negligible, which suggests that the main processes responsible for the variation in the TIC and the CO 2(g) pressure during deep circulation are dissolution and precipitation reactions for carbonate minerals. All the processes identified in the Alhama–Jaraba thermal system are relevant for the long-term evolution of a deep CO 2 storage site hosted by carbonate rocks. As shown in this study, the application of classical geochemical tools provides an excellent starting point for understanding the behavior of prospective storage systems. Moreover, the existence of dedolomitization is very relevant for the hydraulic properties of carbonate aquifers potentially used for CO 2 geological storage because of the effects on porosity and, therefore, permeability during the long-term evolution of such systems. Furthermore, dedolomitization may represent a mechanism of mineral trapping for CO 2 sequestration under certain conditions.

Enzymatic Catalysis: The Emerging Role of Conceptual Density Functional Theory

Experimentalists and quantum chemists are living in a different world. A wealth of theoretical enzymology-related publications is hardly known by experimentalists, and vice versa. Our aim is to bring both worlds together and to show the powerful possibilities of a multidisciplinary approach to study subtle details of complicated enzymatic processes to a broad readership. MD simulations and QM/MM approaches often focus on the calculation of reaction paths based on activation energies, which is a time-consuming task. A valuable alternative is the reactivity descriptors founded in conceptual DFT like softness, electrophilicity, and the Fukui function, which describe the kinetic aspects of a reaction in terms of the response to perturbations in N and/or upsilon(r), typical for a chemical reaction, of the reagents in the ground state. As such, the relative energies at the beginning of the reaction predict a sequence of activation energies only based on the properties of the reactants (Figure 5 ). In 2003, Geerlings et al. published a key review giving a detailed description of the principles and concepts of conceptual DFT and highlighting its success to study generalized acid/base reactions including addition, substitution, and elimination reactions. Since the time that this review appeared, conceptual DFT has proven its strength in literally hundreds of papers with application to organic and inorganic reactions. Its role in unravelling enzymatic reaction mechanisms, in handling experimentally difficult accessible biochemical problems, and in the interpretation of biochemical experimental observations is emerging and very promising.

Nitric Acid Dissociation at an Aqueous Surface: Occurrence and Mechanism

AbstractHere we briefly review some highlights of our recent work on the acid dissociation of nitric acid HNO3 at an aqueous surface, a proton transfer reaction of interest not only from a fundamental perspective, but also in connection with heterogeneous chemistry in a wide range of atmospheric contexts. Two types of studies of the potential acid dissociation are discussed, quantum chemical reaction path calculations to assess the reaction free energy and Car‐Parrinello molecular dynamics simulations to assess the reaction feasibility. We discuss the agreement and disagreement between the predictions of these two calculations as a function of the initial location of the HNO3 molecule, ranging from a positioning on top of the aqueous surface to one several water layers below the surface. Special attention is given to the four key water solvent motions found to be necessary for the proton transfer reaction to occur. Finally, an Eigen cation, rather than a Zundel cation, is in all cases found to be predominant next to the nitrate ion in contact ion pairs produced in the acid dissociation. This predominance remains, although diminished, for solvent‐separated ion pairs.

Acetone on silicon (001): ambiphilic molecule meets ambiphilic surface

Using density functional theory, we report detailed reaction path calculations for the reaction of acetone with the silicon (001) surface. We identify the key reaction intermediates of dissociative adsorption and the transition states between them. This resolves the identity of the one-dimer intermediate observed in STM experiments and its role in the formation of several two-dimer-wide end products of dissociation. Key to the understanding of the dissociation mechanism is the ambiphilic character of the two reactants, that is the simultaneous expression of electrophilic and nucleophilic reactivities in both the surface and the acetone molecule.