Àngels González-Lafont

Interpolated variational transition-state theory: Practical methods for estimating variational transition-state properties and tunneling contributions to chemical reaction rates from electronic structure calculations

In many cases, variational transition states for a chemical reaction are significantly displaced from a saddle point because of zero‐point and entropic effects that depend on the reaction coordinate. Such displacements are often controlled by the competition between the potential energy along the minimum‐energy reaction path and the energy requirements of one or more vibrational modes whose frequencies show a large variation along the reaction path. In calculating reaction rates from potential‐energy functions we need to take account of these factors and—especially at lower temperatures—to include tunneling contributions, which also depend on the variation of vibrational frequencies along a reaction path. To include these effects requires more information about the activated complex region of the potential‐energy surface than is required for conventional transition‐state theory. In the present article we show how the vibrational and entropic effects of variational transition‐state theory and the effective potentials and effective masses needed to calculate tunneling probabilities can be estimated with a minimum of electronic structure information, thereby allowing their computation at a higher level of theory than would otherwise be possible. As examples, we consider the reactions OH+H2, CH3+H2, and Cl+CH4 and some of their isotopic analogs. We find for Cl+CH4→HCl+CH3 that the reaction rate is greatly enhanced by tunneling under conditions of interest for atmospheric chemistry.

MORATE: a program for direct dynamics calculations of chemical reaction rates by semiempirical molecular orbital theory

Abstract We present a computer program, MORATE (Molecular Orbital RATE calculations), for direct dynamics calculations of unimolecular and bimolecular rate constants of gas-phase chemical reactions involving atoms, diatoms, or polyatomic species. The potential energies, gradients, and higher derivatives of the potential are calculated whenever needed by semiempirical molecular orbital theory without the intermediary of a global or semiglobal fit. The dynamical methods used are conventional or variational transition state theory and multidimensional semiclassical approximations for tunneling and nonclassical reflection. The computer program is conveniently interfaced package consisting of the POLYRATE program, version 4.5.1, for dynamical rate calculations, and the MOPAC program, version 5.03, for semiempirical electronic structure computations. All semiempirical methods available in MOPAC, in particular MINDO/3, MNDO, AM1, and PM3, can be called on to calculate the potential and gradient. Higher derivatives of the potential are obtained by numerical derivatives of the gradient. Variational transition states are found by a one-dimensional search of generalized-transition-state dividing surfaces perpendicular to the minimum-energy path, and tunneling probabilities are evaluated by numerical quadrature.

Testing electronic structure methods for describing intermolecular H · · · H interactions in supramolecular chemistry

In this article a wide variety of computational approaches (molecular mechanics force fields, semiempirical formalisms, and hybrid methods, namely ONIOM calculations) have been used to calculate the energy and geometry of the supramolecular system 2‐(2′‐hydroxyphenyl)‐4‐methyloxazole (HPMO) encapsulated in β‐cyclodextrin (β‐CD). The main objective of the present study has been to examine the performance of these computational methods when describing the short range H · · · H intermolecular interactions between guest (HPMO) and host (β‐CD) molecules. The analyzed molecular mechanics methods do not provide unphysical short H · · · H contacts, but it is obvious that their applicability to the study of supramolecular systems is rather limited. For the semiempirical methods, MNDO is found to generate more reliable geometries than AM1, PM3 and the two recently developed schemes PDDG/MNDO and PDDG/PM3. MNDO results only give one slightly short H · · · H distance, whereas the NDDO formalisms with modifications of the Core Repulsion Function (CRF) via Gaussians exhibit a large number of short to very short and unphysical H · · · H intermolecular distances. In contrast, the PM5 method, which is the successor to PM3, gives very promising results. Our ONIOM calculations indicate that the unphysical optimized geometries from PM3 are retained when this semiempirical method is used as the low level layer in a QM:QM formulation. On the other hand, ab initio methods involving good enough basis sets, at least for the high level layer in a hybrid ONIOM calculation, behave well, but they may be too expensive in practice for most supramolecular chemistry applications. Finally, the performance of the evaluated computational methods has also been tested by evaluating the energetic difference between the two most stable conformations of the host(β‐CD)‐guest(HPMO) system.

Molecular modeling of solvation. Cl−(D2O)

The isotopic fractionation factor in the monohydrated gas‐phase cluster Cl−(H2O), i.e., the equilibrium constant for Cl−(H2O)(g)+D2O(g)⇄Cl−(D2O)(g) +H2O(g), is used to test models used for solution‐phase simulations and to test semiempirical and ab initio molecular orbital theory for their detailed structural and vibrational predictions for both the solute–solvent bond properties and the interaction‐induced intramolecular changes in water itself. The isotope effect is studied at a consistent level of vibration–rotation theory, i.e., the harmonic‐oscillator‐rigid‐rotator approximation, using four different kinds of approach, namely extended‐basis‐set ab initio electronic structure calculations, both (i) with and (ii) without electron correlation, (iii) semiempirical molecular orbital theory at the level of neglect of diatomic differential overlap, and (iv) analytic force fields based on site–site interactions. The calculations of type (i) show good convergence and are compared both to experiment, which pre...

The nucleophilic aromatic photosubstitutions of 4,5-dinitroveratrole with amines. Photoreductions of aromatic dinitrocompounds

Abstract 4,5-Dinitroveratrole is effectively photosubstituted by amines with relatively high ionization potential such as methylamine, n-butylamine and ethyl glycinate, but is mainly photoreduced when amines with relatively low ionization potential, such as dimethyl or trimethylamine are used. The photoreduction of several aromatic dinitrocompounds by triethylamine gives nitroanilines. A mechanistic scheme is proposed embracing our photosubstitutions and photoreductions, based on our experimental results and on MINDO/3 calculations of the ground states and the more likely intermediates.

Theoretical study of the mechanism of the hydride transfer between ferredoxin-NADP+ reductase and NADP+: the role of Tyr303.

During photosynthesis, ferredoxin-NADP(+) reductase (FNR) catalyzes the electron transfer from ferredoxin to NADP(+) via its FAD cofactor. The final hydride transfer event between FNR and the nucleotide is a reversible process. Two different transient charge-transfer complexes form prior to and upon hydride transfer, FNR(rd)-NADP(+) and FNR(ox)-NADPH, regardless of the hydride transfer direction. Experimental structures of the FNR(ox):NADP(+) interaction have suggested a series of conformational rearrangements that might contribute to attaining the catalytically competent complex, but to date, no direct experimental information about the structure of this complex is available. Recently, a molecular dynamics (MD) theoretical approach was used to provide a putative organization of the active site that might represent a structure close to the transient catalytically competent interaction of Anabaena FNR with its coenzyme, NADP(+). Using this structure, we performed fully microscopic simulations of the hydride transfer processes between Anabaena FNR(rd)/FNR(ox) and NADP(+)/H, accounting also for the solvation. A dual-level QM/MM hybrid approach was used to describe the potential energy surface of the whole system. MD calculations using the finite-temperature string method combined with the WHAM method provided the potential of mean force for the hydride transfer processes. The results confirmed that the structural model of the reactants evolves to a catalytically competent transition state through very similar free energy barriers for both the forward and reverse reactions, in good agreement with the experimental hydride transfer rate constants reported for this system. This theoretical approach additionally provides subtle structural details of the mechanism in wild-type FNR and provides an explanation why Tyr303 makes possible the photosynthetic reaction, a process that cannot occur when this Tyr is replaced by a Ser.

The reactions CHnD4−n+OH→P and CH4+OD→CH3+HOD as a test of current direct dynamics computational methods to determine variational transition-state rate constants. I.

In the present work, we have theoretically calculated the rate constants and their temperature dependence for the reactions CHnD4−n+OH→P, and for the reaction of methane with OD, by means of variational transition-state theory plus multidimensional tunneling corrections, at the MP-SAC2//MP2/cc-pVTZ/// and CCSD(T)//MP2/cc-pVTZ/// electronic levels. Also, the newly developed single-point energy interpolation algorithm has been used at the CCSD(T)/aug-cc-pVTZ//MP2/cc-pVTZ and CCSD(T)-SAC//MP2/cc-pVTZ levels. For reactions with n=1, 2 or 3, the competitive canonical unified statistical theory has been applied as they involve more than one nonequivalent reaction channel. Variational effects and tunneling have been found to be very important. The proton shift classical energy barrier turns out to be 5.83 and 4.97 kcal/mol at the CCSD(T)/aug-cc-pVTZ//MP2/cc-pVTZ and CCSD(T)-SAC//MP2/cc-pVTZ levels, respectively. Even though we have used the highest ab initio electronic level reported up to now for dynamics calcu...

Understanding the activation energy trends for the C2H4+OH→C2H4OH reaction by using canonical variational transition state theory

The potential-energy hypersurface of the addition reaction OH+C2H4 was partially explored following two different approaches. First, the stationary points were located at the MP2(FULL)/6-31G(d,p) level and then the minimum energy path (MEP) was built starting from the MP2 saddle-point geometry. In order to improve the energetics along the MEP, single-point calculations were carried out at several higher levels, in particular, PMP2, MP4sdtq, PMP4sdtq, and QCIsd(t). In a different approach, the C–O bond length was assumed to provide an accurate parametrization of the reaction path in the vicinity of the transition state. The minimum energy structures at the MP4sdq/6-311+G(d,p) level for 16 points along the RC–O coordinate have been calculated, followed by a generalized normal-mode analysis at the MP2(FULL)/6-311+G(d,p) level for each point. The initial potential information from both approaches was used to calculate canonical variational transition state (CVT) association rate constants for the temperature ...

A Monte Carlo simulation of Fe2+ aqueous solvation

Abstract A Monte Carlo simulation of Fe 2+ aqueous solvation, at 298 K, including 100 water molecules, has been done using periodic boundary conditions under the minimum image conversion. The energy has been calculated in the pair-potential approach, employing the MCY potential for the H 2 OH 2 O interaction and an ab initio analytical potential generated by us for the Fe 2+ H 2 O interaction. The examination of interaction energies and of the radial distribution functions clearly show that the first hydration shell is formed by eight water molecules. By classifying the generated configurations into different significant structures of the solvent, it has been found that the eight water molecules of the first hydration shell are situated in a lightly distorted D 4d structure which maximizes the water—solute stabilization and minimizes the water—water repulsion. Finally, the validity of our theoretical predictions is discussed.

Electronic structure study of the initiation routes of the dimethyl sulfide oxidation by OH

In the present work the potential energy surface (PES) corresponding to the different initiation routes of the oxidation mechanism of DMS by hydroxyl radical in the absence of O2 has been studied, and connections among the different stationary points have been established. Single‐point high level electronic structure calculations at lower level optimized geometries have been shown to be necessary to assure convergence of energy barriers and reaction energies. Our results demonstrate that the oxidation of DMS by OH turns out to be initiated via three channels: a hydrogen abstraction channel that through a saddle point structure finally leads to CH3SCH2 + H2O, an addition‐elimination channel that firstly leads to an adduct complex (AD) and then via an elimination saddle point structure finally gives CH3SOH and CH3 products, and a third channel that through a concerted pathway leads to CH3OH and CH3S. The H‐abstraction and the addition‐elimination channels initiate by a common pathway that goes through the same reactant complex (RC). Our theoretical results agree quite well with the branching ratios experimentally assigned to the formation of the different products. Finally, the calculated equilibrium constants of the formation of the complex AD and the hexadeuterated complex AD from the corresponding reactants, as a function of the temperature, are in good accordance with the experimental values.