New insight into the electrochemical desorption of alkanethiol SAMs on gold

A combination of Polarization Modulation Infrared Reflection Absorption Spectroscopy (PMIRRAS) under electrochemical control, Electrochemical Scanning Tunneling Microscopy (ECSTM) and Molecular Dynamics (MD) simulations has been used to shed light on the reductive desorption process of dodecanethiol (C12) and octadecanethiol (C18) SAMs on gold in aqueous electrolytes. Experimental PMIRRAS, ECSTM and MD simulations data for C12 desorption are consistent with formation of randomly distributed micellar aggregates stabilized by Na(+) ions, coexisting with a lying-down phase of molecules. The analysis of pit and Au island coverage before and after desorption is consistent with the thiolate-Au adatoms models. On the other hand, PMIRRAS and MD data for C18 indicate that the desorbed alkanethiolates adopt a Na(+) ion-stabilized bilayer of interdigitated alkanethiolates, with no evidence of lying down molecules. MD simulations also show that both the degree of order and tilt angle of the desorbed alkanethiolates change with the surface charge on the metal, going from bilayers to micelles. These results demonstrate the complexity of the alkanethiol desorption in the presence of water and the fact that chain length and counterions play a key role in a complex structure.     

Ferromagnetic bonding: high spin copper clusters (n+1)Cu(n); n = 2-14) devoid of electron pairs but possessing strong bonding

Density functional theoretic studies are performed for the high-spin copper clusters (n)(+1)Cu(n) (n = 2-14), which are devoid of electron pairs shared between atoms, hence no-pair clusters (J. Phys. Chem. 1988, 92, 1352; Isr. J. Chem. 1993, 33, 455; J. Am. Chem. Soc. 1999, 121, 3165). Despite the lack of electron pairing, it is found that the bond dissociation energy per atom (BDE/n) is significant and converges (to within 1 kcal mol(-1)), around a cluster size (11)Cu(10), to a value of BDE/n = 19 kcal mol(-1). This is a very large bonding energy, much larger than has previously been obtained for no-pair clusters of lithium, BDE/n = 12 kcal mol(-1), or sodium clusters, BDE/n = 3 kcal mol(-1). This bonding, so-called ferromagnetic bonding (FM-bonding) is analyzed using a valence bond (VB) model (J. Phys. Chem. A 2002, 106, 4961; Phys. Chem. Chem. Phys. 2003, 5, 158). As such, FM-bonding in no-pair clusters is described as an ionic fluctuation, of the triplet pair, that spreads over all the close neighbors of a given atom in the clusters. Thus, if we refer to each triplet pair and its ionic fluctuations as a local FM-bond, we can regard the electronic structure of a given (n)(+1)M(n) cluster as a resonance hybrid of all the local FM-bonds between close neighbors. The model shows how a weak interaction in the diatomic triplet molecule can become a remarkably strong binding force that binds together mono-valent atoms without even a single electron pair. This is achieved because the growing number of VB structures exerts a cumulative effect of stabilization that is maximized when the cluster has a compact structure with an optimal coordination number for the atoms.     

Barriers of hydrogen abstraction vs halogen exchange: an experimental manifestation of charge-shift bonding

This paper shows that the differences between the barriers of the halogen exchange reactions, in the H + XH systems, and the hydrogen abstraction reactions, in the X + HX systems (X = F, Cl, Br), measure the covalent-ionic resonance energies of the corresponding X-H bonds. These processes are investigated using CCSD(T) calculations as well as the breathing-orbital valence bond (BOVB) method. Thus, the VB analysis shows that (i) at the level of covalent structures the barriers are the same for the two series and (ii) the higher barriers for halogen exchange processes originate solely from the less efficient mixing of the ionic structures into the respective covalent structures. The barrier differences, in the HXH vs XHX series, which decrease as X is varied from F to I, can be estimated as one-quarter of the covalent-ionic resonance energy of the H-X bond. The largest difference (22 kcal/mol) is calculated for X = F in accord with the finding that the H-F bond possesses the largest covalent-ionic resonance energy, 87 kcal/mol, which constitutes the major part of the bonding energy. The H-F bond belongs to the class of "charge-shift" bonds (Shaik, S.; Danovich, D.; Silvi, B.; Lauvergnat, D. L.; Hiberty, P. C. Chem. Eur. J. 2005, 21, 6358), which are all typified by dominant covalent-ionic resonance energies. Since the barrier difference between the two series is an experimental measure of the resonance energy quantity, in the particular case of X = F, the unusually high barrier for the fluorine exchange reaction emerges as an experimental manifestation of charge-shift bonding.     

The effect of heme environment on the hydrogen abstraction reaction of camphor in P450cam catalysis: a QM/MM study

The discrepancies between the published QM/MM studies (Sch?neboom, J. C.; Cohen, S.; Lin, H.; Shaik, S.; Thiel, W. J. Am. Chem. Soc. 2004, 126, 4017; Guallar, V.; Friesner, R. A. J. Am. Chem. Soc. 2004, 126, 8501) on H-abstraction of camphor in P450cam have largely been resolved. The crystallographic water molecule 903 situated near the oxo atom of Compound I acts as a catalyst for H-abstraction, lowering the barrier by about 4 kcal/mol. Spin density at the A-propionate side chain of heme can occur in the case of incomplete screening but has no major effect on the computed barrier.     

Two-state reactivity, electromerism, tautomerism, and "surprise" isomers in the formation of compound II of the enzyme horseradish peroxidase from the principal species, compound I

QM and QM/MM calculations on Compound II, the enigmatic species in the catalytic cycle of the horseradish peroxidase enzyme, reveal six low-lying isomers. The principal isomer is the triplet oxo-ferryl form (PorFe(IV)=O) that yields the hydroxo-ferryl isomer (PorFe(IV)-OH+). These are the only forms observed in experimental studies. Theory shows, however, that these are the least stable isomers of Compound II. The two most stable forms are the singlet and triplet states of the Por+*Fe(III)-OH electromer. In addition, theory reveals species never considered in heme enzymes: the singlet and triplet states of the Por+*Fe(III)-OH2 electromer. The computational results reproduce the experimental features of the known isomers and enable us to draw relationships and make predictions regarding the missing ones. For example, while the "surprise" species, singlet and triplet Por+*Fe(III)-OH2, have never been considered in heme chemistry, the calculated Fe-O bond lengths indicate that these isomers may have, in fact, been observed in one of the two opposing EXAFS studies reported previously. Furthermore, these ferric-aqua complexes could be responsible for the reported 18O exchange with bulk water. It is clear, therefore, that the role of Compound II in the HRP cycle is considerably more multi-faceted than has been revealed so far. Our suggested multi-state reactivity scheme provides a paradigm for Compound II species. The calculated M?ssbauer parameters may be helpful toward eventual characterization of these missing isomers of Compound II.     

A combined kinetic-quantum mechanical model for assessment of catalytic cycles: application to cross-coupling and Heck reactions

The efficiency of catalytic cycles is measured by their turnover frequency (TOF). The degree of TOF control determines which states contribute most to the rate of the cycle, and thus indicates the steps that have the highest impact on the cycle. A kinetic model developed by Christiansen (Christiansen, J. A. Adv. Catal. 1953, 5, 311) for catalytic cycles is implemented here in a form that utilizes state energies. This enables one to assess the efficiency of quantum mechanically computed catalytic cycles like the palladium-catalyzed cross-coupling and Heck reactions, to test alternative hypotheses, and to make some predictions. This implementation can also account for effects such as Sabatier's volcano curve for heterogeneous catalysis. The model leads to a dependence of the TOF for any cycle on the "corrected" energy span quantity, deltaE, whose precise expression depends on the location of the summit and trough of the cycle in the step sequence of the cycle. Thus, knowing the highest energy transition state, the most abundant reaction intermediate, and the reaction energy enables one to make quick predictions about relative efficiency of cycles. At the same time, the degree of TOF control determines which states contribute most to the rate of reaction, and thus indicates the values to be included in the calculation of the energetic span and the steps that may be tinkered with to improve the cycle.     

Proton-shuffle mechanism of O-O activation for formation of a high-valent oxo-iron species of bleomycin

Bleomycins (BLMs) can utilize H2O2 to cleave DNA in the presence of ferric ions. DFT calculations were used to study the mechanism of O-O bond cleavage in the low-spin FeIII-hydroperoxo complex of BLM. The following alternative hypotheses were investigated using realistic structural models: (a) heterolytic cleavage of the O-O bond, generating a Compound I (Cpd I) like intermediate, formally BLM-FeV=O; (b) homolytic O-O cleavage, leading to a BLM-FeIV=O species and an OH* radical; and (c) a direct O-O cleavage/H-abstraction mechanism by ABLM. The calculations showed that (a) is a facile and viable mechanism; it involves acid-base proton reshuffle mediated by the side-chain linkers of BLM, causing thereby heterolytic cleavage of the O-O bond and generation of Cpd I. Formation of Cpd I is found to involve a barrier of 13.3 kcal/mol, which is lower than the barriers in the alternative mechanisms (b and c) that possess respective barriers of 31 and 17 kcal/mol. The so-formed Cpd I species with a radical on the side-chain linker, methylvalerate (V), adjacent to the BLM-FeIV=O complex, resembles the formation of the active species of cytochrome c peroxidase in the Poulos-Kraut proton-shuffle mechanism in heme peroxidases (Poulos, T. L.; Kraut, J. J. Biol. Chem. 1980, 255, 8199-8205). Experimental data are discussed and shown to be in accord with this proposal. It suggests that the high-valence Cpd I species of BLM participates in the DNA cleavage. This is an alternative mechanistic hypothesis to the exclusive reactivity scenario based on ABLM (FeIII-OOH).     

In silico design of a mutant of cytochrome P450 containing selenocysteine

A mutant of P450(cam), in which the cysteine ligand was replaced by selenocysteine, was designed theoretically using hybrid QM/MM (quantum mechanical/molecular mechanical) calculations. The calculations of the active species, Se-CpdI (selenocysteine-Compound I), of the mutant enzyme indicate that Se-Cpd I will be formed faster than the wild-type species and be consumed more slowly in C-H hydroxylation. As such, our calculations suggest that Se-Cpd I can be observed unlike the elusive species of the wild-type enzyme (Denisov, I. G.; Makris, T. M.; Sligar, S. G.; Schlichting, I. Chem. Rev. 2005, 105, 2253-2277). Spectral features of Se-Cpd I were calculated and may assist such eventual characterization. The observation of Se-Cpd I will resolve the major puzzle in the catalytic cycle of a key enzyme in nature.     

The ground and excited states of polyenyl radicals C2n-1H2n + 1 (n = 2-13): a valence bond study.

The semiempirical valence bond (VB) method, VBDFT(s), is applied to the ground states and the covalent excited states of polyenyl radicals C2n - 1H2n + 1 (n = 2-13). The method uses a single scalable parameter with a value that carries over from the study of the covalent excited states of polyenes (W. Wu, D. Danovich, A. Shurki, S. Shaik, J. Phys. Chem. A, 2000, 104, 8744). Whenever comparison is possible, the VB excitation energies are found to be in good accord with sophisticated molecular orbital (MO)-based methods like CASPT2. The symmetry-adapted Rumer structures are used to discuss the state-symmetry and VB constitution of the ground and excited states, and the expansion to VB determinants is used to gain insight on spin density patterns. The theory helps to understand in a coherent and lucid manner the properties of polyenyl radicals, such as the makeup of the various states, their geometries and energies, and the distribution of the unpaired electrons (the neutral solitons).