Improved Description of Chemical Barriers with Generalized Gradient Approximations (GGAs) and Meta-GGAs

Ambident Nucleophilic Substitution: Understanding Non-HSAB Behavior through Activation Strain and Conceptual DFT Analyses

The ability to understand and predict ambident reactivity is key to the rational design of organic syntheses. An approach to understand trends in ambident reactivity is the hard and soft acids and bases (HSAB) principle. The recent controversy over the general validity of this principle prompted us to investigate the competing gas-phase SN 2 reaction channels of archetypal ambident nucleophiles CN- , OCN- , and SCN- with CH3 Cl (SN 2@C) and SiH3 Cl (SN 2@Si), using DFT calculations. Our combined analyses highlight the inability of the HSAB principle to correctly predict the reactivity trends of these simple, model reactions. Instead, we have successfully traced reactivity trends to the canonical orbital-interaction mechanism and the resulting nucleophile-substrate interaction energy. The HOMO-LUMO orbital interactions set the trend in both SN 2@C and SN 2@Si reactions. We provide simple rules for predicting the ambident reactivity of nucleophiles based on our Kohn-Sham molecular orbital analysis.

Activation Strain Analyses of Counterion and Solvent Effects on the Ion-Pair SN 2 Reaction of NH 2 - and CH3 Cl

We have computationally studied the bimolecular nucleophilic substitution (S_N 2) reactions of M_n NH₂ ^(n-1) + CH₃ Cl (M⁺  = Li⁺ , Na⁺ , K⁺ , and MgCl⁺ ; n = 0, 1) in the gas phase and in tetrahydrofuran solution at OLYP/6-31++G(d,p) using polarizable continuum model implicit solvation. We wish to explore and understand the effect of the metal counterion M⁺ and of solvation on the reaction profile and the stereochemical preference, that is, backside (S_N 2-b) versus frontside attack (S_N 2-f). The results were compared to the corresponding ion-pair S_N 2 reactions involving F^- and OH^- nucleophiles. Our analyses with an extended activation strain model of chemical reactivity uncover and explain various trends in S_N 2 reactivity along the nucleophiles F^- , OH^- , and NH 2 - , including solvent and counterion effects. © 2019 Wiley Periodicals, Inc.

Nucleophilic Substitution (SN 2): Dependence on Nucleophile, Leaving Group, Central Atom, Substituents, and Solvent

The reaction potential energy surface (PES), and thus the mechanism of bimolecular nucleophilic substitution (SN 2), depends profoundly on the nature of the nucleophile and leaving group, but also on the central, electrophilic atom, its substituents, as well as on the medium in which the reaction takes place. Here, we provide an overview of recent studies and demonstrate how changes in any one of the aforementioned factors affect the SN 2 mechanism. One of the most striking effects is the transition from a double-well to a single-well PES when the central atom is changed from a second-period (e. g. carbon) to a higher-period element (e.g, silicon, germanium). Variations in nucleophilicity, leaving group ability, and bulky substituents around a second-row element central atom can then be exploited to change the single-well PES back into a double-well. Reversely, these variations can also be used to produce a single-well PES for second-period elements, for example, a stable pentavalent carbon species.

Ion-Pair SN 2 Reaction of OH- and CH3 Cl: Activation Strain Analyses of Counterion and Solvent Effects

We have theoretically studied the non-identity S_N 2 reactions of M_n OH^(n-1) +CH₃ Cl (M⁺ =Li⁺ , Na⁺ , K⁺ , and MgCl⁺ ; n=0, 1) in the gas phase and in THF solution at the OLYP/6-31++G(d,p) level using polarizable continuum model (PCM) implicit solvation. We want to explore and understand the effect of the metal counterion M⁺ and solvation on the reaction profile and the stereoselectivity of these processes. To this end, we have explored the potential energy surfaces of the backside (S_N 2-b) and frontside (S_N 2-f) pathways. To explain the computed trends, we have carried out analyses with an extended activation strain model (ASM) of chemical reactivity that includes the treatment of solvation effects.

Ion-Pair SN 2 Substitution: Activation Strain Analyses of Counter-Ion and Solvent Effects

The ion-pair SN 2 reactions of model systems MnF(n-1) +CH3Cl(M(+) =Li(+), Na(+), K(+), and MgCl(+); n=0, 1) have been quantum chemically explored by using DFT at the OLYP/6-31++G(d,p) level. The purpose of this study is threefold: 1) to elucidate how the counterion M(+) modifies ion-pair SN 2 reactivity relative to the parent reaction F(-) +CH3Cl; 2) to determine how this influences stereochemical competition between the backside and frontside attacks; and 3) to examine the effect of solvation on these ion-pair SN2 pathways. Trends in reactivity are analyzed and explained by using the activation strain model (ASM) of chemical reactivity. The ASM has been extended to treat reactivity in solution. These findings contribute to a more rational design of tailor-made substitution reactions.

Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions

The hybrid meta density functionals M05-2X and M06-2X have been shown to provide broad accuracy for main group chemistry. In the present article we make the functional form more flexible and improve the self-interaction term in the correlation functional to improve its self-consistent-field convergence. We also explore the constraint of enforcing the exact forms of the exchange and correlation functionals through second order (SO) in the reduced density gradient. This yields two new functionals called M08-HX and M08-SO, with different exact constraints. The new functionals are optimized against 267 diverse main-group energetic data consisting of atomization energies, ionization potentials, electron affinities, proton affinities, dissociation energies, isomerization energies, barrier heights, noncovalent complexation energies, and atomic energies. Then the M08-HX, M08-SO, M05-2X, and M06-2X functionals and the popular B3LYP functional are tested against 250 data that were not part of the original training data for any of the functionals, in particular 164 main-group energetic data in 7 databases, 39 bond lengths, 38 vibrational frequencies, and 9 multiplicity-changing electronic transition energies. These tests include a variety of new challenges for complex systems, including large-molecule atomization energies, organic isomerization energies, interaction energies in uracil trimers, and bond distances in crowded molecules (in particular, cyclophanes). The M08-HX functional performs slightly better than M08-SO and M06-2X on average, significantly better than M05-2X, and much better than B3LYP for a combination of main-group thermochemistry, kinetics, noncovalent interactions, and electronic spectroscopy. More important than the slight improvement in accuracy afforded by M08-HX is the conformation that the optimization procedure works well for data outside the training set. Problems for which the accuracy is especially improved by the new M08-HX functional include large-molecule atomization energies, noncovalent interaction energies, conformational energies in aromatic peptides, barrier heights, multiplicity-changing excitation energies, and bond lengths in crowded molecules.

Isomerism and structural fluxionality in the Au26 and Au26(-) nanoclusters

Using the minima hopping global optimization method at the density functional level, we found low-energy nanostructures for neutral Au26 and its anion. The local-density and a generalized gradient approximation of the exchange–correlation functional predict different nanoscale motifs. We found a vast number of isomers within a small energy range above the respective putative global minima with each method. Photoelectron spectroscopy of Au26(-) under different experimental conditions revealed definitive evidence of the presence of multiple isomers, consistent with the theoretical predictions. Comparison between the experimental and simulated photoelectron spectra suggests that the photoelectron spectra of Au26(-) contain a mixture of three isomers, all of which are low-symmetry core–shell-type nanoclusters with a single internal Au atom. We present a disconnectivity graph for Au26(-) that has been computed completely at the density functional level. The transition states used to build this disconnectivity graph are complete enough to predict Au26(-) to have a possible fluxional shell, which facilitates the understanding of its catalytic activity.

Simulation studies of the Cl- + CH3I SN2 nucleophilic substitution reaction: comparison with ion imaging experiments

In the previous work of Mikosch et al. [Science 319, 183 (2008)], ion imaging experiments were used to study the Cl(-) + CH3I → ClCH3 + I(-) reaction at collision energies E(rel) of 0.39, 0.76, 1.07, and 1.9 eV. For the work reported here MP2(fc)/ECP/d direct dynamics simulations were performed to obtain an atomistic understanding of the experiments. There is good agreement with the experimental product energy and scattering angle distributions for the highest three E(rel), and at these energies 80% or more of the reaction is direct, primarily occurring by a rebound mechanism with backward scattering. At 0.76 eV there is a small indirect component, with isotropic scattering, involving formation of the pre- and post-reaction complexes. All of the reaction is direct at 1.07 eV. Increasing E(rel) to 1.9 eV opens up a new indirect pathway, the roundabout mechanism. The product energy is primarily partitioned into relative translation for the direct reactions, but to CH3Cl internal energy for the indirect reactions. The roundabout mechanism transfers substantial energy to CH3Cl rotation. At E(rel) = 0.39 eV both the experimental product energy partitioning and scattering are statistical, suggesting the reaction is primarily indirect with formation of the pre- and post-reaction complexes. However, neither MP2 nor BhandH/ECP/d simulations agree with experiment and, instead, give reaction dominated by direct processes as found for the higher collision energies. Decreasing the simulation E(rel) to 0.20 eV results in product energy partitioning and scattering which agree with the 0.39 eV experiment. The sharp transition from a dominant direct to indirect reaction as E(rel) is lowered from 0.39 to 0.20 eV is striking. The lack of agreement between the simulations and experiment for E(rel) = 0.39 eV may result from a distribution of collision energies in the experiment and/or a shortcoming in both the MP2 and BhandH simulations. Increasing the reactant rotational temperature from 75 to 300 K for the 1.9 eV collisions, results in more rotational energy in the CH3Cl product and a larger fraction of roundabout trajectories. Even though a ClCH3-I(-) post-reaction complex is not formed and the mechanistic dynamics are not statistical, the roundabout mechanism gives product energy partitioning in approximate agreement with phase space theory.

SIX-DIMENSIONAL DYNAMICS OF DISSOCIATIVE CHEMISORPTION OF H2 ON METAL SURFACES

The theory of time-dependent quantum dynamics of dissociative chemisorption of hydrogen on metal surfaces is reviewed, in the framework of electronically adiabatic scattering from static surfaces. Four implementations of the time-dependent wave packet (TDWP) method are discussed. In the direct product pseudo-spectral and the spherical harmonics pseudo-spectral methods, no use is made of the symmetry associated with the surface unit cell. This symmetry is exploited by the symmetry adapted wave packet and the symmetry adapted pseudo-spectral (SAPS) method, which are efficient for scattering at normal incidence. The SAPS method can be employed for potential energy surfaces of general form.

Comparison to experiment shows that the TDWP method yields good, but not yet excellent, quantitative accuracy for dissociation of (ν = 0, j = 0) H 2 if the calculations are based on accurately fitted density functional theory calculations that are performed using the generalized gradient approximation. The influence of the molecule's vibration (rotation) is well (reasonably well) described. The theory does not yet yield quantitatively accurate results for rovibrationally inelastic scattering. The theory has helped with the interpretation of existing experimental results, for instance, by solving a parodox regarding the corrugation of Pt(111) as seen by reacting and scattering H 2. The theory has also provided some exciting new predictions, for instance, concerning where on the surface of Cu(100) H2 reacts depending on its vibrational state. Future theoretical studies of H 2 reacting on metal surfaces will likely be aimed at validating GGAs for molecule-surface interactions, and understanding trends in collisions of H 2 with complex metal surfaces.

Introduction to theory/modeling methods in photosynthesis

Theory and molecular modeling play an increasingly important role in complementing the experimental findings and supporting the interpretation of the data. Owing to the increase in computational power combined with the development of more efficient methods, computer simulations and modeling have emerged as primary ingredients of modern scientific inquiry. Here, we introduce the methods that in our view bring the largest promises in photosynthesis research, indicate how they have already contributed, and can in the near future assume a significant role in this field. Particular emphasis is given to density functional theory and its combination with molecular dynamics simulations. We point out the need for a multi-scale approach in facing the challenging task of describing processes which cover several orders of magnitude both in the time scale and in the size of the systems of interest.

Frontside versus Backside S(N)2 substitution at group 14 atoms: origin of reaction barriers and reasons for their absence

We have theoretically studied the gas-phase nucleophilic substitution at group-14 atoms (S(N)2@A) in the model reactions of Cl(-)+AH(3)Cl (A=C, Si, Ge, Sn, and Pb) using relativistic density functional theory (DFT) at ZORA-OLYP/TZ2P. Firstly, we wish to explore and understand how the reaction coordinate zeta, and potential energy surfaces (PES) along zeta, vary as the center of nucleophilic attack changes from carbon to the heavier group-14 atoms. Secondly, a comparison between the more common backside reaction (S(N)2-b) and the frontside pathway (S(N)2-f) is performed. The S(N)2-b reaction is found to have a central barrier for A=C, but none for the other group-14 atoms, A=Si-Pb. Relativistic effects destabilize reactant complexes and transition species by up to 10 kcal mol(-1) (for S(N)2-f@Pb), but they do not change relative heights of barriers. We also address the nature of the transformation in the frontside S(N)2-f reactions in terms of turnstile rotation versus Berry-pseudorotation mechanism.

Stepwise walden inversion in nucleophilic substitution at phosphorus

We have studied the mechanism of S(N)2@P reactions in the model systems X(-) + PMe(2)Y and X(-) + POR(2)Y (with R=Me, OH, OMe; and X, Y=Cl, OH, MeO) using density functional theory at OLYP/TZ2P. Our main purpose is to analyze the nature of the Walden inversion in our model nucleophilic substitution reactions. Walden inversion is well-known to proceed, in general, as a concerted umbrella motion of the substituents at the central atom. Interestingly, we find here that, in certain model reactions, Walden inversion can also proceed in a stepwise fashion in which the individual substituents of the umbrella flip, consecutively, from the educt to the product conformation via separate barriers on the reaction profile. We also examine how variation in nucleophile and leaving group may tune the pentavalent transition structure between labile transition state (TS) and stable transition complex (TC). Furthermore, we explore the various competing multistep pathways in the symmetric (X=Y) and asymmetric (X not equal Y) substitution reactions in our model reaction systems.

Hartree-Fock orbitals significantly improve the reaction barrier heights predicted by semilocal density functionals

Semilocal density functional theory predictions for the barrier heights of representative hydrogen transfer, heavy-atom transfer, and nucleophilic substitution reactions are significantly improved in non-self-consistent calculations using Hartree-Fock orbitals. Orbitals from hybrid calculations yield related improvements. These results provide insight into compensating for one-electron self-interaction error in semilocal density functional theory.

Nucleophilicity and leaving-group ability in frontside and backside S(N)2 reactions

Nucleophilic substitution is ubiquitous in chemistry and well studied. Nucleophilicity and leaving-group ability have been related to various reactant properties, such as electronegativity, size, polarizability, and others. Yet, the state-of-the-art is to some extent still phenomenological. Here, we try to arrive at a straightforward, causal relationship between the reactants' electronic structure and their S(N)2 reactivity. To this end, we have explored the potential energy surfaces of the backside as well as frontside S(N)2 reactions of X(-) + CH3Y with X, Y = F, Cl, Br, and I, using relativistic density functional theory (DFT) at ZORA-OLYP/TZ2P. These explorations provide us with a consistent overview of trends, over a wide range of reactivities and pathways, which were analyzed using the activation strain model of chemical reactivity. A clear picture emerges from these analyses: nucleophilicity is determined by the electron-donor capability of the nucleophile (i.e., energy and shape of the X(-) np atomic orbital), and leaving-group ability derives directly from carbon-leaving group (C-Y) bond strength.

QUILD: QUantum-regions interconnected by local descriptions

A new program for multilevel (QM/QM and/or QM/MM) approaches is presented that is able to combine different computational descriptions for different regions in a transparent and flexible manner. This program, designated QUILD (for QUantum-regions Interconnected by Local Descriptions), uses adapted delocalized coordinates (Int J Quantum Chem 2006, 106, 2536) for efficient geometry optimizations of equilibrium and transition-state structures, where both weak and strong coordinates may be present. The Amsterdam Density Functional (ADF) program is used for providing density functional theory and MM energies and gradients, while an interface to the ORCA program is available for including RHF, MP2, or semiempirical descriptions. The QUILD optimization setup reduces the number of geometry steps needed for the Baker test-set of 30 organic molecules by approximately 30% and for a weakly-bound test-set of 18 molecules by approximately 75% compared with the old-style optimizer in ADF, i.e., a speedup of roughly a factor four. We report two examples of using geometry optimizations with numerical gradients, for spin-orbit relativistic ZORA and for excited-state geometries. Finally, we show examples of its multilevel capabilities for a number of systems, including the multilevel boundary region of amino acid residues, an S(N)2 reaction in the gas-phase and in solvent, and a DNA duplex.

Nucleophilic substitution at phosphorus centers (SN2@p)

We have studied the characteristics of archetypal model systems for bimolecular nucleophilic substitution at phosphorus (SN2@P) and, for comparison, at carbon (SN2@C) and silicon (SN2@Si) centers. In our studies, we applied the generalized gradient approximation (GGA) of density functional theory (DFT) at the OLYP/TZ2P level. Our model systems cover nucleophilic substitution at carbon in X(-)+CH3Y (SN2@C), at silicon in X(-)+SiH3Y (SN2@Si), at tricoordinate phosphorus in X(-)+PH2Y (SN2@P3), and at tetracoordinate phosphorus in X(-)+POH2Y (SN2@P4). The main feature of going from SN2@C to SN2@P is the loss of the characteristic double-well potential energy surface (PES) involving a transition state [X--CH3--Y]- and the occurrence of a single-well PES with a stable transition complex, namely, [X--PH2--Y]- or [X--POH2--Y](-). The differences between SN2@P3 and SN2@P4 are relatively small. We explored both the symmetric and asymmetric (i.e. X, Y=Cl, OH) SN2 reactions in our model systems, the competition between backside and frontside pathways, and the dependence of the reactions on the conformation of the reactants. Furthermore, we studied the effect, on the symmetric and asymmetric SN2@P3 and S(N)2@P4 reactions, of replacing hydrogen substituents at the phosphorus centers by chlorine and fluorine in the model systems X(-)+PR2Y and X(-)+POR2Y, with R=Cl, F. An interesting phenomenon is the occurrence of a triple-well PES not only in the symmetric, but also in the asymmetric SN2@P4 reactions of X(-)+POCl2--Y.

Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods

Mechanistic studies on the hydrolytic dehalogenation catalyzed by haloalkane dehalogenases are of importance for environmental and industrial applications. Here, Car-Parrinello (CP) and ONIOM hybrid quantum-mechanical/molecular mechanics (QM/MM) are used investigate the second reaction step of the catalytic cycle, which comprises a general base-catalyzed hydrolysis of an ester intermediate (EI) to alcohol and free enzyme. We focus on the enzyme LinB from Sphingomonas paucimobilis UT26, for which the X-ray structure at atomic resolution is available. In agreement with previous proposals, our calculations suggest that a histidine residue (His272), polarized by glutamate (Glu132), acts as a base, accepting a proton from the catalytic water molecule and transferring it to an alcoholate ion. The reaction proceeds through a metastable tetrahedral intermediate, which shows an easily reversed reaction to the EI. In the formation of the products, the protonated aspartic acid (Asp108) can easily adopt conformation of the relaxed state found in the free enzyme. The overall free energy barrier of the reaction calculated by potential of the mean force integration using CP-QM/MM calculations is equal to 19.5 +/- 2 kcal . mol(-1). The lowering of the energy barrier of catalyzed reaction with respect to the water reaction is caused by strong stabilization of the reaction intermediate and transition state and their preorganization by electrostatic field of the enzyme.

Comparison of density functionals for reactions of sulfur ylides with aldehydes and olefins

The reactions of a model sulfur ylide with formaldehyde and 1,1-dicianoethylene, leading to the formation of an epoxyde and a cyclopropane, respectively, have been studied using different computational methods, and the results have been compared to those obtained with the CBS-QB3 method. The second step of these reactions presents transition states similar to that of an SN2 reaction. Depending on the degree of electron delocalization at the transition state, a different amount of exact exchange is necessary in the exchange functional to obtain accurate energy barriers. This amount is larger for the reaction of formaldehyde, in which the transition state is more delocalized, than for the reaction of 1,1-dicianoethylene. Similar results have been obtained for symmetric and non-symmetric SN2 reactions. The calculation of the reaction path has shown that the error relative to CBS-QB3 tends to increase when approaching the transition state. Among the different computational methods, PBE1PBE is the one to provide the most accurate energy barriers and reaction energies, whereas BB1K leads to the best results for the reaction path before the transition state.

Gas-Phase Ionic Syntheses of Amino Acids: β versus α

Both theoretical and experimental studies are reported for the gas-phase reactions of protonated hydroxylamine with acetic and propanoic acids which yield protonated glycine and alanine, GlyH+ and AlaH+, respectively. The key step for these reactions is an insertion of the amino group into a C-H bond. For the formation of AlaH+, the reaction barrier for insertion into a Cbeta-H bond is ca. 5 kcal.mol-1 lower than that for the insertion into a Calpha-H bond; the product beta-AlaH+ is ca. 6 kcal mol-1 lower in energy than alpha-AlaH+. Thus, both kinetics and thermodynamics favor formation of the beta-form. The energetic preference for the beta-form is due to more efficient hydrogen bonding between the amino group and the carbonyl oxygen in the limiting transition structure and in the beta-AlaH+ product. These theoretical results are in excellent accord with selected ion flow tube measurements of the gas-phase synthesis which show striking specificity for the beta-isomer according to multi-collision-induced dissociation of the AlaH+ product ion. The results suggest that Gly and beta-Ala found in carbonaceous chondrite meteorites are products of interstellar chemistry.

Energy landscapes of nucleophilic substitution reactions: A comparison of density functional theory and coupled cluster methods

We have carried out a detailed evaluation of the performance of all classes of density functional theory (DFT) for describing the potential energy surface (PES) of a wide range of nucleophilic substitution (SN2) reactions involving, amongst others, nucleophilic attack at carbon, nitrogen, silicon, and sulfur. In particular, we investigate the ability of the local density approximation (LDA), generalized gradient approximation (GGA), meta-GGA as well as hybrid DFT to reproduce high-level coupled cluster (CCSD(T)) benchmarks that are close to the basis set limit. The most accurate GGA, meta-GGA, and hybrid functionals yield mean absolute deviations of about 2 kcal/mol relative to the coupled cluster data, for reactant complexation, central barriers, overall barriers as well as reaction energies. For the three nonlocal DFT classes, the best functionals are found to be OPBE (GGA), OLAP3 (meta-GGA), and mPBE0KCIS (hybrid DFT). The popular B3LYP functional is not bad but performs significantly worse than the best GGA functionals. Furthermore, we have compared the geometries from several density functionals with the reference CCSD(T) data. The same GGA functionals that perform best for the energies (OPBE, OLYP), also perform best for the geometries with average absolute deviations in bond lengths of 0.06 A and 0.6 degrees, even better than the best meta-GGA and hybrid functionals. In view of the reduced computational effort of GGAs with respect to meta-GGAs and hybrid functionals, let alone coupled cluster, we recommend the use of accurate GGAs such as OPBE or OLYP for the study of SN2 reactions.

Nucleophilic Substitution at Silicon (SN2@Si) via a Central Reaction Barrier

It is textbook knowledge that nucleophilic substitution at carbon (SN2@C) proceeds via a central reaction barrier which disappears in the corresponding nucleophilic substitution reaction at silicon (SN2@Si). Here, we address the question why the central barrier disappears from SN2@C to SN2@Si despite the fact that these processes are isostructural and isoelectronic. To this end, we have explored and analyzed the potential energy surfaces (PES) of various Cl-+CR3Cl (R=H, CH3) and Cl-+SiR3Cl model reactions (R=H, CH3, C2H5, and OCH3). Our results show that the nature of the SN2 reaction barrier is in essence steric, but that it can be modulated by electronic factors. Thus, simply by increasing the steric demand of the substituents R around the silicon atom, the SN2@Si mechanism changes from its regular single-well PES (with a stable intermediate transition complex, TC), via a triple-well PES (with a pre- and a post-TS before and after the central TC), to a double-well PES (with a TS; R=OCH3), which is normally encountered for SN2@C reactions.

Assessment of the exchange-correlation functionals for the physical description of spin transition phenomena by density functional theory methods: All the same?

This study aims to assess present day density functionals in the description of spin crossover iron(II) complexes. Two recently synthesized spin crossover complexes were considered. Theoretical calculations were made using 53 of the most popular exchange-correlation density functionals with triple zeta plus polarization quality basis sets. The present work shows that even though different density functionals can lead to different energy gaps between spin states, most of them are very similar for these two compounds when a comparison between energy gaps is sought. The present work shows that even though different exchange correlations can lead to different energy gaps between spin states, the difference between these gaps calculated at different geometries and that calculated at a given reference geometry is surprisingly independent of the choice of functional. The reasons for the similarities and the differences among exchange and correlation functional combinations are discussed.

Description of Carbo-oxocarbons and Assessment of Exchange-Correlation Functionals for the DFT Description of Carbo-mers

Mono- and polycyclic valence isomers of carbo-[3]oxocarbon C(9)O(3) and carbo-[5]oxocarbon C(15)O(5) have been characterized on the singlet spin state potential energy surface. By contrast to their geometry, their relative stability is highly sensitive to the calculation level. The performance of LDA, GGA, meta-GGA, and hybrid functionals is compared to that of HF, post-HF, and multiconfigurational calculations. The results obtained for C(9)O(3) are compared to those obtained for hydrocarbon analogues such as &[3]pericyclyne C9(H2)3 and carbo-[3]radialene C9(CH2)3 and are analyzed on the basis of an energy decomposition scheme. The respective role of the exchange and correlation counterparts of the functional in the discrepancy of the results is discussed.

Nonradical mechanisms for the uncatalyzed thermal functionalization of silicon surfaces by alkenes and alkynes: a density functional study

We propose a new concerted mechanism for the uncatalyzed hydrosilylation of terminal alkenes and alkynes, alternative to the conventional radical-based mechanism. Density functional calculations have been carried out on these and on previously proposed alternative mechanisms for the hydrosilylation of ethylene and acetylene by suitable finite size clusters as models of the thermal functionalization of -SiH3, =SiH2, and [triple bound] SiH groups in flat Si(100) and Si(111) and porous silicon surfaces by alkenes and alkynes. For each step involved in the considered hydrosilylation pathways, we optimized the geometries of reactants and products and located the corresponding transition states. The calculated activation energies for the concerted pathways of ethylene and acetylene are, respectively, 57.6 and 60.9 kcal mol(-1) on -SiH3 and in the ranges 62-63 and 58-61 kcal mol-1 on =SiH2 and 64-66 and 56-61 kcal mol(-1) on SiH. These values are much lower than the activation energies calculated for the corresponding homolytic dissociation of the Si-H bond, which is the preliminary step in the radical path, 85.6, 82-83, and 79-81 kcal mol(-1), respectively, for -SiH3, =SiH2, and [triple bound] SiH groups. Our results thus suggest that the thermal hydrosilylation of alkenes and alkynes on silicon surfaces, for which a radical-based mechanism is currently accepted, may occur through a concerted mechanism.

Reactive and Nonreactive Scattering of H2 from a Metal Surface Is Electronically Adiabatic

The Born-Oppenheimer approximation of uncoupled electronic and nuclear motion is a standard tool of the computational chemist. However, its validity for molecule-metal surface reactions, which are important to heterogeneous catalysis, has been questioned because of the possibility of electron-hole pair excitations. We have performed experiments and calculations on the scattering of molecular hydrogen from a catalytically relevant metal surface, obtaining absolute probabilities for changes in the molecule's velocity parallel to the representative Pt(111) surface. The comparison for in-plane and out-of-plane scattering and results for dissociative chemisorption in the same system show that for hydrogen-metal systems, reaction and diffractive scattering can be accurately described using the Born-Oppenheimer approximation.

Ab initio and DFT benchmark study for nucleophilic substitution at carbon (SN2@C) and silicon (SN2@Si)

To obtain a set of consistent benchmark potential energy surfaces (PES) for the two archetypal nucleophilic substitution reactions of the chloride anion at carbon in chloromethane (S(N)2@C) and at silicon in chlorosilane (S(N)2@Si), we have explored these PESes using a hierarchical series of ab initio methods [HF, MP2, MP4SDQ, CCSD, CCSD(T)] in combination with a hierarchical series of six Gaussian-type basis sets, up to g polarization. Relative energies of stationary points are converged to within 0.01 to 0.56 kcal/mol as a function of the basis-set size. Our best estimate, at CCSD(T)/aug-cc-pVQZ, for the relative energies of the [Cl(-), CH(3)Cl] reactant complex, the [Cl-CH(3)-Cl](-) transition state and the stable [Cl-SiH(3)-Cl](-) transition complex is -10.42, +2.52, and -27.10 kcal/mol, respectively. Furthermore, we have investigated the performance for these reactions of four popular density functionals, namely, BP86, BLYP, B3LYP, and OLYP, in combination with a large doubly polarized Slater-type basis set of triple-zeta quality (TZ2P). Best overall agreement with our CCSD(T)/aug-cc-pVQZ benchmark is obtained with OLYP and B3LYP. However, OLYP performs better for the S(N)2@C overall and central barriers, which it underestimates by 2.65 and 4.05 kcal/mol, respectively. The other DFT approaches underestimate these barriers by some 4.8 (B3LYP) to 9.0 kcal/mol (BLYP).