Calculated Energy Profiles Research Articles

Chiral Adsorption Structures of Styrene on Ge(001): A First-Principles Study

We investigated the chiral adsorption structures of styrene on the Ge(001) surface by first-principles density functional calculations within the generalized gradient approximation. Our calculated energy profile for the reaction pathways shows that styrene adsorbs not only on top of a single dimer but also across the ends of two adjacent dimers in the same dimer row. In the latter adsorption configuration (termed the configuration), we predict the existence of two different structures where two unsaturated Ge atoms within the two adjacent dimers are differently displaced up and down or down and up. Additional styrene adsorption on these two different end-bridge structures proceeds to formation of the cis- and trans-paired end-bridge (PEB) structures. The relative stability of the two different end-bridge structures provides an explanation for a recent scanning tunneling microscopy observation that the populations of the cis-PEB and trans-PEB structures are different from each other.

Influence of charge state on the reaction of [formula omitted] with carbon monoxide

A combined experimental and theoretical study shows that highly oxidized iron clusters are able to readily effect the oxidation of CO to CO 2 at ambient temperature. Calculated energy profiles of the reaction demonstrate that the oxidation efficiency is governed by the strength of oxygen binding to the iron atom. Results for FeO 3 + / - are presented and reveal that cation clusters are more efficient than the corresponding anion clusters at effecting the oxidation reaction due to different oxygen bond energies resulting from charge distribution.

The Reductive Elimination of Methane from ansa‐Hydrido(methyl)metallocenes of Molybdenum and Tungsten: Application of Hammond’s Postulate to Two‐State Reactions

AbstractThe energetic profile of the methane reductive elimination from a selected number of hydrido(methyl)molybdenocene and ‐tungstenocene derivatives has been calculated by DFT methods. The calculations were carried out for the CH2(C5H4)2M (a‐M), SiH2(C5H4)2M (a‐H2Si–M), and SiMe2(C5Me4)2M (a‐Me2Si–M*) ansa‐metallocene systems for M = Mo, W. They include the full optimization of minima [the hydrido(methyl) starting complexes, M(H)(CH3), the intermediate methane complexes, M(CH4), and the metallocene products in the singlet and triplet configurations, (3M and 1M)], transition states (for the methyl hydride reductive elimination, M–TSins, and for the hydrogen exchange, M–TSexch), and the minimum energy crossing point (M–MECP) leading from the singlet methane complexes to the corresponding triplet metallocenes. The results are compared with those previously obtained for the simpler (C5H5)2M (Cp2M) systems (J. C. Green, J. N. Harvey, and R. Poli, J. Chem. Soc., Dalton Trans. 2002, 1861). The calculated energy profiles, notably the relative energies of M–TSins and M–MECP, are in agreement with available experimental observations for the a‐Me2Si–M* systems. The comparison of the energies and geometries of the rate‐determining M–TSins and M–MECP structures with those of the thermodynamically relevant minima for the various systems show the applicability of Hammond’s postulate to two‐state reactions. However, one notable exception serves to show that the principle is only quantitatively reliable when all the potential energy surfaces for the set of analogous reactions have similar shapes. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

Participation of Multioxidants in the pH Dependence of the Reactivity of Ferrate(VI)

Alcohol oxidation by ferrate (FeO(4)(2)(-)) in water is investigated from B3LYP density functional theory calculations in the framework of polarizable continuum model. The oxidizing power of three species, nonprotonated, monoprotonated, and diprotonated ferrates, was evaluated. The LUMO energy levels of nonprotonated and monoprotonated ferrates are greatly reduced by solvent effects, and as a result the oxidizing power of these two species is increased enough to effectively mediate a hydrogen-atom abstraction from the C-H and O-H bonds of methanol. The oxidizing power of these oxidants increases in the order nonprotonated ferrate < monoprotonated ferrate < diprotonated ferrate. The reaction pathway is initiated by C-H bond activation, followed by the formation of a hydroxymethyl radical intermediate or an organometallic intermediate with an Fe-C bond. Kinetic aspects of this reaction are analyzed from calculated energy profiles and experimentally known pK(a) values. The pH dependence of this reaction in water is explained well in terms of a multioxidant scheme.

Dissociative adsorption of vinyl bromide on Si(001): A first-principles study

The adsorption of vinyl bromide on the Si(001) surface is investigated by first-principles density-functional calculations within the generalized gradient approximation. We find that the formation of the two adsorption configurations (i.e., the di-$\ensuremath{\sigma}$ structure on top of a Si dimer and the end-bridge structure across the ends of two adjacent Si dimers) takes place with no barrier. Both chemisorption states proceed to undergo $\mathrm{C}\mathrm{Br}$ dissociation over an energy barrier of $\ensuremath{\sim}0.30\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$. Our results do not support the conclusion drawn from a recent high-resolution electron energy loss spectroscopy (HREELS), where the formation of the di-$\ensuremath{\sigma}$ structure would occur via a strongly bound precursor state with an activation energy of $0.283\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$. Our calculated energy profiles for the reaction pathways indicate that the precursor and chemisorption states proposed by the HREELS experiment should be reinterpreted in terms of the chemisorption and dissociative states, respectively.

Catalytic Roles of Active-Site Amino Acid Residues of Coenzyme B12-Dependent Diol Dehydratase: Protonation State of Histidine and Pull Effect of Glutamate

The hydrogen abstraction and the OH migration processes catalyzed by diol dehydratase are discussed by means of a quantum mechanical/molecular mechanical method. To evaluate the push effect of His143 and the pull effect of Glu170, we considered three kinds of whole-enzyme model, the protonated and two unprotonated His143 models. A calculated activation energy for the hydrogen abstraction by the adenosyl radical is 15.6 (13.6) kcal/mol in the protonated (unprotonated) His143 model. QM/MM calculational results show that the mechanism of the OH migration is significantly changed by the protonation of His143. In the protonated His143 model, the OH group migration triggered by the full proton donation from the imidazolium to the migrating OH group occurs by a stepwise OH abstraction/re-addition process in which the water production reduces the barrier for the C-O bond cleavage. On the other hand, the OH migration in the unprotonated His143 model proceeds in a concerted manner, as we previously proposed using a simple model including only K+ ion and substrate. The latter mechanism seems to be kinetically more favorable from the calculated energy profiles and is consistent with experimental results. The activation barrier of the OH group migration step is only 1.6 kcal/mol reduced by the hydrogen-bonding interaction between the O2 of the substrate and unprotonated His143. Thus, it is predicted that His143 is not protonated, and therefore the main active-site amino acid residue that lowers the energy of the transition state for the OH group migration is determined to be Glu170.

Self-directed growth of benzonitrile line on H-terminated Si(001) surface

Using first-principles density-functional calculations we predict a self-directed growth of benzonitrile molecular line on a H-terminated Si(001) surface. The C[triple bond]N bond of benzonitrile reacts with a single Si dangling bond which can be generated by the removal of a H atom, forming one Si-N bond and one C radical. Subsequently, the produced C radical can be stabilized by abstracting a H atom from a neighboring Si dimer, creating another H-empty site. This H-abstraction process whose activation barrier is 0.65 eV sets off a chain reaction to grow one-dimensional benzonitrile line along the Si dimer row. Our calculated energy profile for formation of the benzonitrile line shows its relatively easier formation compared with previously reported styrene and vinylferrocene lines.

An unusually fast nucleophilic aromatic displacement reaction: the gas-phase reaction of fluoride ions with nitrobenzene.

Quick reactions: The gas-phase nucleophilic displacement reaction of fluoride ions with nitrobenzene proceeds with a rate constant close to the collision limit. The calculated energy profile indicates that the reaction proceeds by an out-of-plane attack, with the Meisenheimer complex being the local transition state for the reaction (see picture).

Quantum mechanical/molecular mechanical investigation of the mechanism of C-H hydroxylation of camphor by cytochrome P450cam: theory supports a two-state rebound mechanism.

The stereospecific cytochrome P450-catalyzed hydroxylation of the C(5)-H((5-exo)) bond in camphor has been studied theoretically by a combined quantum mechanical/molecular mechanical (QM/MM) approach. Density functional theory is employed to treat the electronic structure of the active site (40-100 atoms), while the protein and solvent environment (ca. 24,000 atoms) is described by the CHARMM force field. The calculated energy profile of the hydrogen-abstraction oxygen-rebound mechanism indicates that the reaction takes place in two spin states (doublet and quartet), as has been suggested earlier on the basis of calculations on simpler models ("two-state reactivity"). While the reaction on the doublet potential energy surface is nonsynchronous, yet effectively concerted, the quartet pathway is truly stepwise, including formation of a distinct intermediate substrate radical and a hydroxo-iron complex. Comparative calculations in the gas phase demonstrate the effect of the protein environment on the geometry and relative stability of intermediates (in terms of spin states and redox electromers) through steric constraints and electronic polarization.

Adsorption kinetics of acetylene and ethylene on Si(001)

The reaction of acetylene and ethylene on the Si(001) surface is investigated by first-principles density-functional calculations within the generalized-gradient approximation. We have identified the two different reaction pathways that result in adsorptions on top of a single dimer and across the ends of two adjacent dimers in the same dimer row. Our calculated energy profile of the reaction path shows that ${\mathrm{C}}_{2}{\mathrm{H}}_{2}$ easily occupies both configurations because the difference between their reaction barriers is small, whereas ${\mathrm{C}}_{2}{\mathrm{H}}_{4}$ occupies mainly the former configuration because of a relatively larger barrier for formation of the latter configuration. This result provides an explanation for a subtle difference in the adsorption structures of ${\mathrm{C}}_{2}{\mathrm{H}}_{2}$ and ${\mathrm{C}}_{2}{\mathrm{H}}_{4}.$

First-principles study of the adsorption and reaction of cyclopentene on Ge(001)

The adsorption and reaction of cyclopentene on the Ge(001) surface is investigated by first-principles density-functional calculations within the generalized gradient approximation. Surprisingly, a recent cluster calculation for adsorbed cyclopentene on Ge(001) obtained an adsorption energy of 2.10 eV. which is larger than the same cluster result (1.65 eV) on Si(001). However, our calculated adsorption energy for 0.5(1)-monolayer cyclopentene on Ge(001) is 0.79(0.51)eV, comparable with an observed activation energy of 0.7 eV for desorption. In addition we find that the energy barriers for the adsorption of cyclopentene on Ge(001) and Si(001) not only depend on cyclopentene coverage but also quantitatively differ from each other. Based on the calculated energy profile for the reaction we discuss the experimental observations of the difference between cyclopentene sticking on the Ge(001) and Si(001) surfaces.

2+2] versus [3+2] addition of metal oxides across C=C double bonds: toward an understanding of the surprising chemo- and periselectivity of transition-metal-oxide additions to ketene.

The peri-, chemo-, stereo-, and regioselectivity of the addition of the transition-metal oxides OsO4 and LReO3 (L = O-, H3PN, Me, Cp) to ketene were systematically investigated using density-functional methods. While metal-oxide additions to ethylene have recently been reported to follow a [3+2] mechanism only, the calculations reveal a strong influence of the metal on the periselectivity of the ketene addition: OsO4 again prefers a [3+2] pathway across the C=C moiety whereas, for the rhenium oxides LReO3, the [2+2] barriers are lowest. Furthermore, a divergent chemoselectivity arising from the ligand L was found: ReO4- and (H3PN)ReO3 add across the C=O bond while MeReO3 and CpReO3 favor the addition across the C=C moiety. The calculated energy profile for the MeReO3 additions differs from the CpReO3 energy profile by up to 45 kcal/mol due to the stereoelectronic flexibility of the Cp ligand adopting eta5, eta3, and eta1 bonding modes. The selectivity of the cycloadditions was rationalized by the analysis of donor-acceptor interactions in the transition states. In contrast, metal-oxide additions to diphenylketene probably follow a different mechanism: We give theoretical evidence for a zwitterionic intermediate that is formed by nucleophilic attack at the carbonyl moiety and undergoes a subsequent cyclization yielding the thermodynamically favored product. This two-step pathway is in agreement with the results of recent experimental work.

Ab Initio Molecular Orbital Study of the Oxidation Mechanism of Hypophosphite Ion as a Reductant for an Electroless Deposition Process

The oxidation (electron emission) mechanism of a hypophosphite ion (H2PO2, which is a representative reducing agent for an electroless deposition process, was studied by an ab initio molecular orbital method. Two types of reaction pathways were examined; namely, the pathway via three-coordinate compound obtained by primary dehydrogenation, and the one via five-coordinate compound by primary addition of OH-. The calculated energy profile showed that the oxidation reaction occurs via five-coordinate compounds. The solvation effect is clarified to make the reaction endothermic, indicating that the reaction preferably proceeds at the solid/liquid interface, i.e., the surface of the deposits, rather than in the solution bulk. The catalytic activity of the metal surface, which is one of the most significant factors for the electroless deposition process, was also investigated using Pdn (n = 4−7) clusters as a model surface. It was found that one of the most important characters determine the catalytic activity of the deposited metal is the electron-accepting ability from the reductant.

Adducts ofo-Silaborane With Water and Methanol

The synthesis of alkoxide adducts of o-silaborane [(TMPDAH)2][(Me2Si2B10H10)2O] (3) and [TMPDAH][(Me2Si2B10H10)OMe] (4) are presented (TMPDA = tetramethylpropylenediamine). For both silaborate clusters 3 and 4 the results of the NMR spectroscopic investigations together with the X-ray single crystal structure determinations are discussed. The geometries of ab initio calculations (HF and B3LYP methods) on the hydroxide adduct [Si2B10H12(OH)]– are compared with the structures of 3 and 4. The dynamic behaviour of the adducts 3 and 4 in solution is discussed with respect to the calculated energy profile for the rotation of the HSi(OH) group.

Polarizable continuum model for lithium interface transitions between a liquid electrolyte and an intercalation electrode

A model is described and used to calculate the energy of lithium when crossing the interface between a liquid electrolyte and an electrode surface. The model is based on a classical treatment of the solute–solvent interactions in terms of a polarizable continuum model (PCM), and of the lithium crystal interactions by electrostatic (Madelung) energy calculations including short-range closed shell repulsion. In addition, the coupling of Li + with the charge compensating electron on a neighbour Mn 4+ site is taken into account. A first application of the model to the Li–Mn 2 O 4 (spinel) system shows that diffusion of Li from the surface to bulk of the electrode requires an activation energy, which is higher than the one for bulk diffusion. Surface charges, as deduced from electronegativity calculations are strongly reduced compared to the bulk ones. As a result, a barrier is also formed for the solvent to the surface Li + diffusion. On the basis of the calculated energy profiles we conclude that for Li/Mn 2 O 4 bulk diffusion is considerably faster than lattice incorporation. Our results are in qualitative agreement with fits of equivalent circuits to alternating current impedance measurements for Li + intercalation in cubic and layered TiS 2 and NiO 2 and potential jump kinetic experiments on Mn 2 O 4 :Li.

Interaction of Methane with a [Li]0 Center on MgO(100): HF, Post-HF, and DFT Cluster Model Studies

We investigate the interaction between methane and a [Li]0 center on MgO(100) using ab initio cluster methodology. We focus on the catalytic activation of the C−H bond, an essential reaction step in the oxidative coupling of methane (OCM). In the first part of the study we use a simple embedded cluster model that allows us to compare different levels of theory and to study the influence of electron correlation on the calculated energy profile for the H abstraction reaction. Hartree−Fock (HF) calculations are compared to results obtained from post-HF (Møller−Plesset perturbation theory) and gradient-corrected density functional theory (DFT) computational schemes. We show that the use of the density functional exchange potential without self-interaction corrections leads to an inadequate potential energy surface for the hydrogen abstraction reaction at the [Li]0 center. The second part of the study is devoted to substrate relaxation effects, employing a much larger cluster model. The geometry of the lattice around the [Li]0 cener is optimized for key stages along the reaction path. Comparison with previous studies shows the importance of including extensive relaxation if accurate geometries about the surface defect sites are to be calculated.

Simulation of the enzyme reaction mechanism of malate dehydrogenase.

A hybrid numerical method, which employs molecular mechanics to describe the bulk of the solvent-protein matrix and a semiempirical quantum-mechanical treatment for atoms near the reactive site, was utilized to simulate the minimum energy surface and reaction pathway for the interconversion of malate and oxaloacetate catalyzed by the enzyme malate dehydrogenase (MDH). A reaction mechanism for proton and hydride transfers associated with MDH and cofactor nicotinamide adenine dinucleotide (NAD) is deduced from the topology of the calculated energy surface. The proposed mechanism consists of (1) a sequential reaction with proton transfer preceding hydride transfer (malate to oxaloacetate direction), (2) the existence of two transition states with energy barriers of approximately 7 and 15 kcal/mol for the proton and hydride transfers, respectively, and (3) reactant (malate) and product (oxaloacetate) states that are nearly isoenergetic. Simulation analysis of the calculated energy profile shows that solvent effects due to the protein matrix dramatically alter the intrinsic reactivity of the functional groups involved in the MDH reaction, resulting in energetics similar to that found in aqueous solution. An energy decomposition analysis indicates that specific MDH residues (Arg-81, Arg-87, Asn-119, Asp-150, and Arg-153) in the vicinity of the substrate make significant energetic contributions to the stabilization of proton transfer and destabilization of hydride transfer. This suggests that these amino acids play an important role in the catalytic properties of MDH.

An Extraordinarily Violent Molecular Dissociation: The Unprecedented Kinetic Energy Release in the Decomposition of HONF+, a Singly Charged Metastable Ion

2.68 + 0.10 eV, the largest value by far for the kinetic energy release (KER) in the decomposition of metastable, singly charged ions was detected by mass spectrometry for the fragmentation of HONF+. Thus, the exceptionally large KER predicted by a theoretical analysis of the potential energy surface (calculated energy profile shown on the right) was also confirmed experimentally.

Conformational Analysis of Open‐Chain 1,2:3,4‐Diepoxides: Comparison of crystal structures, NMR data, and molecular‐orbital calculations

AbstractSeveral pairs of diastereoisomeric open‐chain 1,2:3,4‐diepoxides with different substitution patterns were prepared (see 3–9). As far as possible, crystal structures were determined to corroborate the relative configurations and to give insight into the solid‐state conformations of these compounds. The comparison with our earlier molecular‐orbital calculations and with 1H‐NMR measurements shows that the solid‐state conformations of eight out of the nine open‐chain 1,2:3,4‐diepoxides, whose crystal structures had been determined, correspond to minima on the calculated energy profiles for these compounds or for closely related derivatives. In solution, highly substituted diepoxides of the erythro‐series (e‐6, e‐7, e‐9) seem to prefer the same conformation as in the crystal. The solution conformations of all other diepoxides differ from the arrangement in the solid state.

SINDO1 study of electronic structure and carbonyl fluxionality in Fe 3(CO) 12

The electronic structure and carbonyl fluxionality of Fe 3(CO) 12 have been investigated by the semiempirical MO method SINDO1. Based on the calculated bond valence indices, it is pointed out that the electronic structure, due to the different σ/π bonding capacities of bridging and terminal carbonyls and the number of direct MM bonds, is quite important besides the steric effects for the determination of the ligand geometry in M 3(CO) 12 type cluster compounds. The calculated energy profiles for three possible terminal-bridging carbonyl exchange mechanisms show that Cotton's mechanism is most probable for carbonyl exchange in solution and Johnson's mechanism is reasonable for solid state. The bond valence indices along these profiles have been studied as well.