Metamorphosis of a transition state into a stable species.

Medium variations usually affect the shape of the bimolecular nucleophilic reaction profile at the reactants' and products' ends and, to a much lesser extent, the shape around the transition state. In water, the reactions of extended allylic systems such as F(-) + H-(CH=CH)n-CH2-F → F-CH2-(CH=CH)n-H + F(-) have been computationally shown (for n = 2) to have a single transition state. As the polarity is decreased the transition state is gradually transformed into a double-humped profile that then changes smoothly through a triple-well profile into a single-well profile where the symmetric structure of the transition state is retained. The depth of the well is ca. 16 kcal/mol for n = 2 and reaches 40 kcal/mol for n = 7, resembling the stability of a weak chemical bond. This is traced to electrostatic effects as well as to the effect of an intermediate VB configuration. In the analogous polyynes, a stable adduct is already formed at n = 1. This is attributed to the formation of the relatively stable vinylic carbanion. As the number of acetylene units increases, the vinylic geometry (a CCC angle of 123°) is gradually lost until at n = 5 the adduct attains a linear geometry.

Nucleophilic and electrophilic reactions of polyynes catalyzed by an electric field: toward barcoding of carbon nanotubes like long homogeneous substrates.

Computational studies at the B3LYP/6-31+G* level were carried out on the addition of pyridine to polyynes (C6-C18) and on the protonation of polyynes by methyl ammonium fluoride under electric fields of 2.5 and 5 MV/cm. The electric field in each case was oriented along the polyyne axis in a direction that enhances the reaction by stabilizing the incipient dipole. It was found that the reaction of pyridine addition is endothermic with a late transition state. The longer the polyynes and the stronger the field, the electric field catalysis was more efficient. Extrapolation of the data to long polyynes shows that at 1000 nm an electric field of 50 000 V/cm will reduce the barrier by 10 kcal/mol. This reduction is equivalent to 7 orders of magnitude in rate enhancement. A similar barrier reduction could be achieved with a 2.5 MV/cm field at a polyyne length of 20 nm. Protonation reactions were found to be much more affected by the electric field. A reduction of the reaction barrier by 10 kcal/mol using a 2.5 MV/cm electric field could be achieved at a polyyne length of 10 nm. Thus the electric field along the long axis of a substrate could induce a gradient of reactivity which could, in principle, enable the barcoding of substrates by using a sequence of reactants having different reactivities.

Conjugation in polyyne rods: to what extent is charge delocalization coupled to geometrical changes?

Ab initio methods were used to calculate the geometry and the charge distribution (natural bond orbital) in end-protonated polyynes. The geometry obtained is practically identical to that of the corresponding anion and the neutral radical. Thus, the geometry is not much dependent on charge dispersal. Moreover, it is shown that regardless of whether the imposed geometry is that of a cumulenic structure which localizes the charge at one end or that of the neutral molecule which localizes the charge at the other end, the same amount of charge is delocalized to the remote end of the protonated molecule regardless of the imposed structure. The same phenomenon is observed also for polyenes. It is interesting to note that regardless of the charge or its absence, as in the case of the radical, the optimal geometry is obtained as the arithmetic sum of the main resonance structures. Thus, it is concluded that, in these cases, the wave function is only weakly coupled to the geometry of the molecule.

Strain energy release and intrinsic barriers in internal nucleophilic reactions.

This paper reports computational data for the energetics of internal attacks, both in ring-opening reactions (eq 3) where strain energy is released and in model, strain-free systems (eq 4). A comparison is drawn with the corresponding bimolecular processes. The exothermicity of three-membered ring-opening reactions is significantly larger than that of the four-membered ring systems. However, using the Marcus equation, it is shown that the higher reactivity of the three-membered rings is intrinsic to the system and does not stem only from a higher thermodynamic driving force. The intrinsic barriers for the strain-free reactions are shown to be dominated by the position of the nucleophilic and nucleofugic atoms in the periodic table, as in the bimolecular SN2 reactions, although a pi rather than a sigma bond is formed in these reactions.

Reaction of H2 with a Binuclear Zirconium Dinitrogen Complex - Evaluation of Theoretical Models and Hybrid Approaches.

Molecular orbital and hybrid ONIOM (both IMOMO and IMOMM) calculations have been carried out on the important reaction of H2 with a binuclear zirconium dinitrogen complex to test the efficacy of several structural models of the ancillary ligand. The complete experimental ligand, PhP(CH2SiMe2NSiMe2CH2)2PPh, in the zirconium complex has been treated at the IMOMM level, while two smaller approximations of the ligand, HP(CH2SiH2NSiH2CH2)2PH and (PH3)2(NH2)2, have received the full molecular orbital treatment. The mechanism of dihydrogen addition has been compared with our earlier study (Basch, Musaev, and Morokuma J. Am. Chem. Soc. 1999, 121, 5754-5761). We find that the substituent effects do cause some small changes in both the structures of the complexes studied and the activation energies of the transition structures. However for the most part the potential energy profiles are very similar to our earlier study and lend support to our use of simple theoretical models to represent moderately large experimental structures.

Binding at molecule/gold transport interfaces. V. Comparison of different metals and molecular bridges.

The geometric and electronic structural properties of symmetric and asymmetric metal cluster-molecule-cluster' complexes have been explored. The metals include Au, Ag, Pd, and Al, and both benzenedithiol and the three isometric forms of dicyanobenzene are included as bridging molecules. Calculated properties such as cluster-molecule interface geometry, electronic state, degree of metal --> molecule charge transfer, metal-molecule mixing in the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy region, the HOMO-LUMO gap, cluster --> cluster' charge transfer as a function of external field strength and direction, and the form of the potential profile across such complexes have been examined. Attempts are made to correlate charge transport with the characteristics of the cluster-complex systems. Indications of rectification in complexes that are asymmetric in the molecule, clusters, and molecule-cluster interfaces are discussed. The results obtained here are only suggestive because of the limitations of the cluster-complex model as it relates to charge transport.

Molecular binding at gold transport interfaces. III. Field dependence of electronic properties.

The behavior of the electronic structure in a metal/molecular/metal junction as a function of the applied electric field is studied using density functional methods. Although the calculations reported here do not include the electrode bulk, or intermolecular interactions, and do not permit actual transport to occur, nevertheless they illuminate the charging, energy shift, polarization and orbital occupation changes in the molecular junction upon the application of a static electric field. Specifically, external electric fields generally induce polarization localization on the two cluster ends. The HOMO/LUMO gap usually decreases and, for large enough fields, energy levels can cross, which presages a change of electronic state and, if found in molecular electronic circuits, a change in transmission. The calculations also show changes in the geometry both of the molecule and the molecule/cluster interface upon application of the electric field. These effects should be anticipated in whole circuit studies.

Molecular binding at gold transport interfaces. IV. Thiol chemisorption.

Alkene thiol/coinage metal molecular interfaces are relatively easy to make, and can result in well-ordered self-assembled monolayer films. The energetics of such formation is complex-differing experimental and theoretical accounts have focused on the nature of the binding, the energetics via different pathways (thiol radical, thiol or thiolate) and the geometry of binding. We report density functional theory calculations on a four atom gold cluster interacting with different (alkane, alkene, alkyne) thiolates. We find thiolate addition to be strongly exoergic, thiol radical to be roughly half as favorable, and thiol to be slightly favorable. We also find that the S-H bond can remain when the thiol attaches to the gold cluster, formally resulting in increased coordination on the sulfur atom.

Relative reactivity of three and four membered rings--the absence of charge effect.

Radical (neutral) and electrophilic (cationic) ring opening reactions were studied computationally in order to probe the difference in reactivity between three and four membered rings. Using the Marcus equation we have shown that the activation energy for the four membered ring opening is close to the Marcus predicted barrier whereas three membered rings display much higher reactivity than that predicted by the Marcus equation. Thus, the reactivity of the three membered rings is enhanced, in addition to the strain release, by another factor which is not operative in the four membered rings. It is clear also that this factor is not charge dependent. The possible origin of this effect is discussed.

Reduced basis set for the gold atom in cluster complexes.

To extend the metal cluster size used in interfacing between bulk metals and molecules in ab initio studies of molecular electronics and chemisorption, a reduced size atomic orbital basis set for the gold atom has been generated. Based on the SKBJ relativistic effective core potential set, the three component 5d Gaussian orbital basis set is completely contracted. Comparisons between the full and reduced basis set in Au atom clusters and cluster complexes for geometry, bond distances, dipole moments, atomic charges, spin, bond dissociation energies, lowest energy harmonic frequencies, electron affinities, ionization energies, and density of states distributions show the contracted set to be a viable replacement for the full basis set. This result is obtained using both the B3LYP and BPW91 exchange-correlation potentials in density functional theory.

The periodic table and the intrinsic barrier in s(n)2 reactions.

The identity S(N)2 reactions on nitrogen (see eq 3) with nucleophiles having the general structure H(n)()X(-) where X belongs to the group of nonmetallic elements which do not border the line separating them from the metallic elements (X = F, Cl, Br, I, O, S, Se, N, P, and C) were studied at the G2+ level. The results show that, similarly to the previously observed phenomenon for S(N)2 reaction on carbon (J. Am. Chem. Soc. 1999, 121, 7724), the Periodic Table, through the valence of the element X, controls the intrinsic barrier for the reaction. The average intrinsic barriers obtained for nitrogen substrates were 20, 27, 39, and 57 kcal/mol for the mono-, di-, tri-, and tetravalent X's, respectively. It is also concluded that the intrinsic barriers are similar for N- and C-based substrates and dimethyl substitution on both raises the intrinsic barrier by ca. 10 kcal/mol.

Theoretical study of the mechanism of alkane hydroxylation and ethylene epoxidation reactions catalyzed by diiron bis-oxo complexes. The effect of substrate molecules.

The hybrid density functional method B3LYP was used to study the mechanism of the hydrocarbon (methane, ethane, methyl fluoride, and ethylene) oxidation reaction catalyzed by the complexes cis-(H(2)O)(NH(2))Fe(mu-O)(2)(eta(2)-HCOO)(2)Fe(NH(2))(H(2)O), I, and cis-(HCOO)(Imd)Fe(mu-O)(2)(eta(2)-HCOO)(2)Fe(Imd)(HCOO) (Imd = Imidazole), I_m, the "small" and "medium" model of compound Q of the methane monooxygenase (MMO). The improvement of the model from "small" to "medium" did not change the qualitative conclusions but significantly changed the calculated energetics. As in the case of methane oxidation reported by the authors previously, the reaction of all the substrates studied here is shown to start by coordination of the substrate molecule to the bridging oxygen atom, O(1) of I, an Fe(IV)-Fe(IV) complex, followed by the H-atom abstraction at the transition state III leading to the bound hydroxy alkyl intermediate IV of Fe(III)-Fe(IV) core. IV undergoes a very exothermic coupling of alkyl and hydroxy groups to give the alcohol complex VI of Fe(III)-Fe(III) core, from which alcohol dissociates. The H(b)-atom abstraction (or C-H bond activation) barrier at transition state III is found to be a few kcal/mol lower for C(2)H(6) and CH(3)F than for CH(4). The calculated trend in the H(b)-abstraction barrier, CH(4) (21.8 kcal/mol) > CH(3)F (18.8 kcal/mol) > or = C(2)H(6) (18.5 kcal/mol), is consistent with the C-H(b) bond strength in these substrates. Thus, the weaker the C-H(b) bond, the lower is the H(b)-abstraction barrier. It was shown that the replacement of a H-atom in a methane molecule with a more electronegative group tends to make the H(b)-abstraction transition state less "reactant-like". In contrast, the replacement of the H-atom in CH(4) with a less electronegative group makes the H(b)-abstraction transition state more "reactant-like". The epoxidation of ethylene by complex I is found to proceed without barrier and is a highly exothermic process. Thus, in the reaction of ethylene with complex I the only product is expected to be ethylene oxide, which is consistent with the experiment.

Computational studies of reaction mechanisms of methane monooxygenase and ribonucleotide reductase.

An overview of the computational efforts made by our group during the last few years in the field of nonheme diiron proteins is presented. Through application of ab initio methodology to a reasonable set of molecular models, significant progress is made in understanding how the soluble Methane Monooxygenase system achieves the hydroxylation of methane and how the catalytic cycle of Ribonucleotide Reductase is initiated. In particular, the current studies reveal in more detail (1) the nature of key intermediates in the reaction cycles of these two metalloenzymes, (2) details of how the iron centers regulate the systems, and (3) important aspects of how the carboxylate ligands in the active sites may tailor the enzymatic needs of the metalloprotein. This knowledge also leads to novel connections between the two enzymes. The coordinative unsaturation and carboxylate shifts investigated herein are two properties that are likely to be of more general impact in nonheme proteins. The control of the redox chemistry of the enzyme by the binuclear metal center, also analyzed here, should find common ground among other bimetallic systems as well.