Auxetics at the molecular level: a negative poisson's ratio in molecular rods.
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Biomedical subjects
Harold Basch
Publications and source records attributed to Harold Basch.
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.
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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.
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Harder than diamond: determining the cross-sectional area and Young's modulus of molecular rods.
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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.
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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.
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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.
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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.
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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.
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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.
Alkanes↗
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.
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