Reaction Path Calculations Research Articles

First-Principles Periodic Density Functional Study of the Hydrogenation of Maleic Anhydride to Succinic Anhydride over Palladium(111)

Gradient-corrected periodic density functional (DFT) calculations were carried out in order to examine the hydrogenation of maleic anhydride to succinic anhydride via a Horiuti-Polanyi like mechanism on the well-defined Pd(111) surface. Reaction path calculations were performed at a surface coverage of maleic anhydride corresponding to 0.11 monolayer. The hydrogenation of maleic anhydride to the maleic anhydryl surface intermediate was found to have the highest intrinsic barrier (+95 kJ/mol) on Pd(111), of all the elementary steps involved in the hydrogenation of the olefinic group of maleic anhydride. This step is endothermic by 17 kJ/mol. Calculations indicate that the second step in the mechanism, the hydrogenation of maleic anhydryl to succinic anhydride, has a slightly lower barrier (+89 kJ/mol) and is exothermic by 37 kJ/mol. In an effort to understand the effect of change in the electronic properties of the metal on the intrinsic barrier for maleic anhydride hydrogenation, the C−H bond formation re...

Conical intersections induced by repulsive 1πσ * states in planar organic molecules: malonaldehyde, pyrrole and chlorobenzene as photochemical model systems

Ab initio calculations of reaction paths and potential-energy profiles of excited states are reported for the model systems malonaldehyde, pyrrole and chlorobenzene. In all three cases, optically dark singlet states of πσ * character have been found, which are repulsive with respect to an appropriate reaction coordinate. The resulting surface crossings with 1ππ * states and/or the electronic ground state, which are symmetry allowed for the planar systems, are converted into conical intersections by out-of-plane modes of appropriate symmetry. It is argued that conical intersections of this type are a common phenomenon in planar organic molecules with heteroatoms and may dominate the photochemistry of these systems.

Distinguishing ultramafic‐from basalt‐hosted submarine hydrothermal systems by comparing calculated vent fluid compositions

Submarine hydrothermal vent fluid compositions may be controlled by peridotite‐seawater or basalt‐seawater reactions. Previous studies of slow‐spreading ridges indicate that in addition to basalts, peridotites often play a prominent role in the construction of upper oceanic crust. Therefore the surface outcrop at a submarine hydrothermal vent field may not reveal the composition of the rock that hosts the reaction zone. We can, however, predict the compositional differences between ultramafic‐ and basalt‐hosted vent fluids by using theoretical reaction path calculations. These calculations determine equilibrium fluid compositions and mineral assemblages, yielding synthetic hydrothermal vent fluid compositions that can be compared to analytical measurements. Synthetic vent fluid compositions created from basalt and seawater reactants at 350° or 400°C and 500 bars are in close agreement with analytical measurements of end‐member vent fluids from mid‐ocean ridges. Twenty simulations at a 1:1 water to rock ratio using basalt compositions spanning the range of geochemical variability observed amongst mid‐ocean ridge basalts yield vent fluid compositions with <20% variation in major element concentrations. We also performed 15 ultramafic‐seawater simulations using dunite, lherzolite, and harzburgite compositions found in oceanic crust. All produced aqueous SiO2, K, and H2 concentrations that are distinct from the basalt‐seawater calculations. These differing concentrations can be used to attribute analytical measurements of vent fluid compositions to ultramafic or basaltic reaction zones.

Ammonia synthesis at low temperatures

Density functional theory (DFT) calculations of reaction paths and energies for the industrial and the biological catalytic ammonia synthesis processes are compared. The industrial catalyst is modeled by a ruthenium surface, while the active part of the enzyme is modeled by a MoFe6S9 complex. In contrast to the biological process, the industrial process requires high temperatures and pressures to proceed, and an explanation of this important difference is discussed. The possibility of a metal surface catalyzed process running at low temperatures and pressures is addressed, and DFT calculations have been carried out to evaluate its feasibility. The calculations suggest that it might be possible to catalytically produce ammonia from molecular nitrogen at low temperatures and pressures, in particular if energy is fed into the process electrochemically.

Oxidative Alteration of Spent Fuel in a Silica-Rich Environment: SEM/AEM Investigation and Geochemical Modeling

Correctly identifying the possible alteration products and accurately predicting their occurrence in a repository-relevant environment are the key for source-term calculations in a repository performance assessment. Uraninite in uranium deposits has long been used as a natural analog to spent fuel in a repository because of their chemical and structural similarity. In this paper, a SEM/AEM investigation has been conducted on a partially alterated uraninite sample from a uranium ore deposit of Shinkolobwe of Congo. The mineral formation sequences were identified: uraninite → uranyl hydrates → uranyl silicates → Ca-uranyl silicates or uraninite → uranyl silicates → Ca-uranyl silicates. Reaction-path calculations were conducted for the oxidative dissolution of spent fuel in a representative Yucca Mountain groundwater. The predicted sequence is in general consistent with the SEM observations. The calculations also show that uranium carbonate minerals are unlikely to become major solubility-controlling mineral phases in a Yucca Mountain environment. Some discrepancies between model predictions and field observations are observed. Those discrepancies may result from poorly constrained thermodynamic data for uranyl silicate minerals.

Biodegradable cross-linked prodrug of the bronchial dilator Vephylline ®. 2. Kinetics and quantum chemical studies on the release mechanism

Experimental thermodynamics studies and quantum chemical reaction path calculations on the hydrolytic degradation of Poly-vephyllinemalate microspheres in acidic and basic media were performed. It was possible to make a conclusion on the release mechanism of free Vephylline ® as follows: a hydrolytic cleavage of the ester bonds between molecular fragments of R, S-malic acid takes place and leads to a soluble oligoester fraction. Then, further hydrolysis of the ester bonds between the xanthine fragment and R, S-malic acid leads to the release of Vephylline ® as free base. The hydrolytic process takes place in acidic solution with rapid degradation of the ester bonds between the malic acid monomers and by far slower degradation of the ester bonds between the malic acid and Vephylline ®. In basic solution both steps of the hydrolysis are fast processes leading to a complete release of free Vephylline ® within 1 h. The process of Vephylline ® release is under entropic control. The experimental results are well correlated to the results obtained after kinetics investigation and after AM1 quantum chemically calculated energy barriers in the reaction path leading to the tetrahedral intermediates of the hydrolytic reactions. This conclusion is in good accordance with an indirect study on the release mechanism of Vephylline ® from its polymeric prodrug, paying attention to the biological response, reported previously.

Chemistry of Unique Chiral Olefins. 4. Theoretical Studies of the Racemization Mechanism of trans- and cis-1,1',2,2',3,3',4,4'-Octahydro-4,4'-biphenanthrylidenes.

The minimum energy conformations and racemization barriers for the chiral sterically overcrowded helical alkenes, trans- and cis-1,1',2,2',3,3',4,4'-octahydro-4,4'-biphenanthrylidenes (1 and 2), are reported. The trans-1 and cis-2 isomers can each adapt three different conformations, (P,P) and (M,M) (an enantiomeric pair) and an achiral (P,M) meso form, of which only the chiral isomers were obtained by synthesis. The conformations and heats of formation of (M,M)-(E)-1, (P,M)-(E)-1, (M,M)-(Z)-2, and (P,M)-(Z)-2 isomers were determined by MOPAC AM1 calculations. The racemization process for both the trans- and cis- isomers is postulated to occur via the (P,M) isomers by two successive inversions of the cyclohexenyl ring; (M,M) <--> (P,M) <--> (P,P). The (M,M) --> (P,M) and reverse (P,M) --> (M,M) isomerizations were simulated by reaction path calculations, providing the molecular structure and the activation energy of the transition state for each isomerization. For each racemization process, the activation enthalpy (DeltaH()) was calculated as 23.9 and 19.9 kcal mol(-)(1) for trans-olefin 1 and cis-olefin 2, respectively. These values reasonably agree with the experimental values obtained by temperature-dependent circular dichroism, optical rotation, and (1)H NMR magnetization transfer measurements: DeltaH() = 24.6 and 20.8 kcal mol(-)(1) for trans-olefin 1 and cis-olefin 2, respectively. While the racemization of cis-isomer 2 is controlled by the steric interaction of H5 with C4'a and C4'b, the surprisingly high barrier for trans-olefin 1 is due to the severe steric interaction between H5 and H3'alpha and/or H3'beta protons.

Microstructure Evolution and Weathering Reactions of Synroc Samples Crystallized from CaZrTi2O7 melts: TEM/AEM investigation and geochemical modeling

AbstractScanning electron microscopy (SEM), transmission electron microscopy (TEM), and analytical electron microscopy (AEM) studies have been conducted on samples crystallized from a melt with a composition of zirconolite {(Ca0.9Gd0.1)Zr(Ti1.9Al0.1)2, O7}. The formationof a whole suite of Synroc minerals (zirconia, ZrTiO4, zirconolite, perovskite, and rutile) has been observed. The formation of these minerals follows the crystallization sequence of Ti-bearing zirconia → ZrTiO4 phase → Zr-rich zirconolite → Zr-poor zirconolite → rutile/perovskite. This sequence is induced by a fractional crystallization process, in which Zr-rich mineral phases tend to crystallize first, resulting in continuous depletion of Zr in melt. Consistent with this melt compositional evolution, Zr content in the zirconolite decreases from the area next to ZrTiO4 phase to the area next to rutile or perovskite. High-resolution TEM images show that there are no glassy phases at the grain boundary between zirconolite and perovskite. The fractional crystallization-induced textural heterogeneity may have a significant impact on the incorporation of radionuclides into crystalline phases and the resistance of radioniclides to leaching processes. Exsolution lamellae and multiple twinning result from the phase transition from tetragonal zirconia to monoclinic zirconia may decrease durability of the Synroc. Fast cooling of melt may produce more zirconolite phase and relatively uniform texture. In general, however, a Synroc prepared by a through-melt method is less uniform in texture than that prepared by a through-sol-gel method. The reaction path calculation for the alteration of U-bearing zirconolite in an oxidizing fluid shows that zirconolite is first altered into a perovskite-like phase (CaZrO3), followed by rutile (TiO2 ), and U6+ -bearing phases of soddyite [(UO2)2SiO42H20] and haiweeite [Ca(U02)2Si6O15·5H2O].

Theoretical studies of heterogeneous reaction mechanisms relevant for stratospheric ozone depletion

Aspects of the heterogeneous reaction HCl+ClONO2→Cl2+HNO3 on ice and N2O5+H2O→2 HNO3 on supercooled water are modeled via electronic-structure calculations involving reactant–water cluster systems. Reaction-path calculations for a HCl⋅ClONO2⋅(H2O)9 system indicate a coupled proton-transfer (PT)/nucleophilic attack (SN2) process, in which the ice lattice is an active participant. Analysis of the N2O5⋅(H2O)4 reaction system geometry and charge distribution suggests that a similar coupled PT/SN2 mechanism could occur in a larger system. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 683–692, 1999

Theoretical studies of heterogeneous reaction mechanisms relevant for stratospheric ozone depletion

Aspects of the heterogeneous reaction HCl+ClONO2→Cl2+HNO3 on ice and N2O5+H2O→2 HNO3 on supercooled water are modeled via electronic-structure calculations involving reactant–water cluster systems. Reaction-path calculations for a HCl⋅ClONO2⋅(H2O)9 system indicate a coupled proton-transfer (PT)/nucleophilic attack (SN2) process, in which the ice lattice is an active participant. Analysis of the N2O5⋅(H2O)4 reaction system geometry and charge distribution suggests that a similar coupled PT/SN2 mechanism could occur in a larger system. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 683–692, 1999

GEOSURF: a computer program for modeling adsorption on mineral surfaces from aqueous solution

A new program, GEOSURF, has been developed for calculating aqueous and surface speciation consistent with the triple-layer model of surface complexation. GEOSURF is an extension of the original programs MINEQL, MICROQL and HYDRAQL. We present, here, the basic algorithm of GEOSURF along with a description of the new features implemented. GEOSURF is linked to internally consistent data bases for surface species (SURFK.DAT) and for aqueous species (AQSOL.DAT). SURFK.DAT contains properties of minerals such as site densities, and equilibrium constants for adsorption of aqueous protons and electrolyte ions on a variety of oxides and hydroxides. The Helgeson, Kirkham and Flowers version of the extended Debye-Huckel Equation for 1:1 electrolytes is implemented for calculating aqueous activity coefficients. This permits the calculation of speciation at ionic strengths greater than 0.5 M. The activity of water is computed explicitly from the osmotic coefficient of the solution, and the total amount of electrolyte cation (or anion) is adjusted to satisfy the electroneutrality condition. Finally, the use of standard symbols for chemical species rather than species identification numbers is included to facilitate use of the program. One of the main limitations of GEOSURF is that aqueous and surface speciation can only be calculated at fixed pH and at fixed concentration of total adsorbate. Thus, the program cannot perform reaction-path calculations: it cannot determine whether or not a solution is over- or under-saturated with respect to one or more solid phases. To check the proper running of GEOSURF, we have compared results generated by GEOSURF with those from two other programs, HYDRAQL and EQ3. The Davies equation and the “bdot” equation, respectively, are used in the latter two programs for calculating aqueous activity coefficients. An example of the model fit to experimental data for rutile in 0.001 M–2.0 M NaNO 3 is included.

Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease.

Two different structures of ligand-free HIV protease have been determined by X-ray crystallography. These structures differ in the position of two 12 residue, beta-hairpin regions (or "flaps") which cap the active site. The movements of the flaps must be involved in the binding of substrates since, in either conformation, the flaps block the binding site. One of these structures is similar to structures of the ligand-bound enzyme; however, the importance of both structures to enzyme function is unclear. This transformation takes place on a time scale too long for conventional molecular dynamics simulations, so the process was studied by first identifying a reaction path between the two structures and then calculating the free energy along this path using umbrella sampling. For the ligand-free enzyme, it is found that the two structures are nearly equally stable, with the ligand-bound-type structure being less stable, consistent with X-ray crystallography data. The more stable open structure does not have a lower potential energy, but is stabilized by entropy. The transition occurs through a collapse and reformation of the beta-sheet structure of the conformationally flexible, glycine-rich flap ends. Additionally, some problems in studying conformational changes in proteins through the use of a single reaction path are addressed.

Ettringite solubility and geochemistry of the Ca(OH) 2–Al 2(SO 4) 3–H 2O system at 1 atm pressure and 298 K

The solubility and weathering reactions of ettringite, (Ca 6Al 2(SO 4) 3(OH) 12·26H 2O), were used to study the geochemical equilibria of the Ca(OH) 2–Al 2(SO 4) 3–H 2O system at environmental pH conditions. Ettringite is a stable mineral above a pH of 10.7 and dissolved congruently with a log K sp of −111.6 (±0.8). Between pH 10.7 and 9.5, ettringite underwent incongruent dissolution to gypsum and Al-hydroxides and controlled Ca 2+, Al 3+, and SO 4 2− activities. At near neutral pH, Al-hydroxy sulfates precipitated in addition to gypsum and Al-hydroxide. These Al-hydroxy sulfate phases exhibited prismatic and anhedral shapes and had variable Al/S ratios. In addition, some new poorly crystalline Ca–Al-hydroxy sulfate phases were identified in microscopic studies when the pH was acidic (pH∼5). The activities of Ca 2+, Al 3+, and SO 4 2− suggest that the geochemistry of the Ca(OH) 2–Al 2(SO 4) 3–H 2O system in the pH range of 7 to 10 is simple and its component Ca(OH) 2–SO 3–H 2O and Al 2(SO 4) 3–H 2O systems behave independently of each other. The precipitation of Al-hydroxy sulfates below pH 7.0 significantly influenced Ca 2+ and SO 4 2− activities. This effect was pronounced when Ca–Al-hydroxy sulfate phases started precipitating (pH<5.0). The lack of thermodynamic data on the newly identified Al, and Ca–Al-hydroxy sulfates makes it difficult to interpret the geochemistry of Ca(OH) 2–Al 2(SO 4) 3–H 2O system for pH≤5.0. Reaction path calculations conducted using the EQ6 computer code predicted ion activities close to the experimental values above pH 5.0. The observed differences between thermodynamic modelling and actual experimental data below this pH can be explained by the formation of Al–/Ca–Al-hydroxy sulfate phases in the system, as detected by electron microscopy and X-ray elemental analysis. These reactions are relevant and useful to the prediction of Al, and Ca geochemistry in natural systems.

Rotation of Structural Water inside a Protein: Calculation of the Rate and Vibrational Entropy of Activation

Water molecules buried inside a protein are often considered as an integral part of the structure and are increasingly used as NMR probes to study the dynamics of proteins (Denisov, V.; Peters, J.; Horlein, H. D.; Halle, B. Nat. Struct. Biol. 1996, 3, 505). The present calculations give new insights into the mobility of such structural water. Reaction path calculations using conjugate peak refinement (Fischer, S.; Karplus, M. Chem. Phys. Lett. 1992, 194, 252) are carried out to compute the transition state and activation energy (9.7 kcal mol-1) for the rotation of a water molecule buried in the protein bovine pancreatic trypsin inhibitor. These are compared to the values calculated (10−12.3 kcal mol-1) for the same process in ice, for which the experimental value has been determined (12.8 ± 0.9 kcal mol-1). The process, which results in the interchange of the two water hydrogens, is similar in both systems. It is not a simple C2-flip of the buried water, but a complex motion involving two successive rotat...

Application of reaction path concept in intramolecular proton transfer

Intramolecular proton transfer in the ground state and the first singlet excited state are investigated on ab initio level using 2(2′-hydroxyphenyl)-imidazoline as a model compound. The reaction-path concept is applied and new descriptions of the proton positions are proposed. The full calculations show surprising differences between the method using mass-weighted internals and mass-weighted Cartesian coordinates. In the simplified “static” approach the results are dependent on the choice of the reaction coordinate. If the choice is made with care, the results comparable with full intrinsic reaction coordinate search are obtained. The concerted reaction-path calculations are justified only in the vicinity of the transition state.

HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD simulation and reaction path calculations using a hybrid QM/MM potential

The cleavage mechanism of HIV-1 protease (HIV-PR) is investigated with classical molecular dynamics (MD) simulation and with methods incorporating a hybrid quantum mechanical and molecular mechanical (QM/MM) potential function. An X-ray structure of an HIV-PR/inhibitor complex was used to generate model HIV-PR/substrate and HIV-PR/intermediate complexes. Analysis of the feasibility of reaction is based on three hypothetical reaction mechanisms and a variety of possible starting conditions. The classical MD simulations were analyzed for conformations consistent with reaction initiation, as reported previously. It was concluded that Asp125 is the general acid in the first reaction step and transfers a proton to the carbonyl oxygen. Simulations suggest that water 301 stabilizes productive reactant and intermediate conformations but does not participate directly in the reaction. A lytic water, when present, is held very tightly in a position propitious for nucleophilic attack at the scissile carbon. For mechanisms consistent with the classical simulations, reaction barriers were calculated using a QM/MM potential. The QM/MM potential and a restrained energy minimization method for calculating reaction paths and barriers are described. Preliminary results identify reasonable barrier heights and transition state conformations and predict that the first reaction step follows a predominantly stepwise rather than concerted pathway.

Reaction-Path Dynamics in Redundant Internal Coordinates

This paper presents a general method for reaction-path calculations with redundant curvilinear internal coordinates. Following Pulay and Fogarasi, the generalized inverse of the Wilson &#x1d4a2; matrix is used to remove the redundancy of the curvilinear internal coordinates. An illustrative application to HBr + HCCH → H2CCHBr is presented, and the results with the new algorithm are compared to calculations with rectilinear coordinates.

The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature

An algorithm for the calculation of reaction paths between known reactant and product states in systems of low or high dimension is described. The optimal reaction path is defined as the path of maximum flux for a diffusive dynamics assuming isotropic friction. The resulting reaction path is temperature dependent and independent of the magnitude of the friction. Comparison is made with a number of algorithms designed for the calculation of minimum-energy reaction paths. Applications to two model potentials and an extended atom model of a dipeptide are presented. The applications demonstrate the ability of the algorithm to isolate a temperature-dependent optimal reaction path for a high dimensional molecular system.

Finding transition states using contangency curves

We present a new method for approximating reaction paths and transition states of conformational transitions in polyatomic systems. The method uses the quasi-harmonic properties of the metastable state to construct a bi-Gaussian model for the energy landscape. Its reaction path is approximated by the equipotential contour cotangency (contangency) curve which connects the two equilibrium states with the saddle point lying between them. Unlike the reaction path, the contangency curve has an explicit analytic definition which makes it a useful starting point for conventional reaction path calculations. The method is illustrated for the conformational transition between the chair and twisted-boat isomers of cyclohexane.

Analytical potential energy surface for the NH3+H↔NH2+H2 reaction: Application of variational transition-state theory and analysis of the equilibrium constants and kinetic isotope effects using curvilinear and rectilinear coordinates

The potential energy surface (PES) for the gas-phase NH3+H↔NH2+H2 reaction is constructed with suitable functional forms to represent the stretching and bending modes, and using as calibration criterion the reactant and product experimental properties and the ab initio saddle point properties. This surface is then used to calculate rate constants with variational transition-state theory over the temperature range 300–2000 K. While the forward rate constants agree with experimental results, the reverse ones are lower by factors of between 4 and 6. Since the same PES is used and these rates are related by detailed balance, this disagreement could indicate an uncertainty in the few available experimental studies for the reverse reaction. We also provide a detailed analysis of the equilibrium constants and of the kinetic isotope effects and compare the results of this analytical PES with earlier ab initio reaction-path calculations. Finally, for the vibrational frequency calculations, we analyze the consequences of the choice of different coordinate systems (curvilinear or rectilinear) on various kinetic magnitudes.