Localized molecular orbitals for polyatomic molecules

Molecular wavefunctions have been generated by the PRDDO (Partial Retention of Diatomic Differential Overlap) method for the monocyclic aromatic rings containing six π-electrons (C₄H ₄ ^?2 , C₅H ₅ ^? , C₆H₆, C₇H ₇ ⁺ , and C₈H ₈ ⁺² ) and ten π-electron species (C₈H ₈ ^?2 , C₉H ₉ ^? , C₁₀H₁₀). The eigenvalue spectra of the canonical molecular orbitals are presented. Localized molecular orbitals (LMO's) generated using the Boys criterion are reported for localizations involving all occupied molecular orbitals (complete localizations) and localizations of the π orbitals only. We find evidence for σ-π separation in the complete localizations for some of these molecules even though the Boys criterion is often biased against such results. We demonstrate for C₆H₆ and find for the other molecules that the π-orbital localizations are indeterminate (i.e. there are an infinite number of equally satisfactory LMO structures between two limiting extremes). This result may be viewed as a corollary of Hückel's (4n+2) rule for aromaticity.     

Near-IR MCD of the nonheme ferrous active site in naphthalene 1,2-dioxygenase: correlation to crystallography and structural insight into the mechanism of Rieske dioxygenases

Near-IR MCD and variable temperature, variable field (VTVH) MCD have been applied to naphthalene 1,2-dioxygenase (NDO) to describe the coordination geometry and electronic structure of the mononuclear nonheme ferrous catalytic site in the resting and substrate-bound forms with the Rieske 2Fe2S cluster oxidized and reduced. The structural results are correlated with the crystallographic studies of NDO and other related Rieske nonheme iron oxygenases to develop molecular level insights into the structure/function correlation for this class of enzymes. The MCD data for resting NDO with the Rieske center oxidized indicate the presence of a six-coordinate high-spin ferrous site with a weak axial ligand which becomes more tightly coordinated when the Rieske center is reduced. Binding of naphthalene to resting NDO (Rieske oxidized and reduced) converts the six-coordinate sites into five-coordinate (5c) sites with elimination of a water ligand. In the Rieske oxidized form the 5c sites are square pyramidal but transform to a 1:2 mixture of trigonal bipyramial/square pyramidal sites when the Rieske center is reduced. Thus the geometric and electronic structure of the catalytic site in the presence of substrate can be significantly affected by the redox state of the Rieske center. The catalytic ferrous site is primed for the O2 reaction when substrate is bound in the active site in the presence of the reduced Rieske site. These structural changes ensure that two electrons and the substrate are present before the binding and activation of O2, which avoids the uncontrolled formation and release of reactive oxygen species.     

Effect of substitution on the optical properties and HOMO-LUMO gap of oligomeric paraphenylenes

A series of dialkyl amino benzophenone dimers with various alkyl chain lengths is presented. Gaussian B3LYP/6-31G(d) calculations show that the band gap decreases within the dimer series as a function of the donor group efficiency. Theoretical calculations show that the interaction between phenyl-phenyl rings is more important than simple donor-acceptor effects. We report the experimental and electro-optical properties of one of these dimers, N,N-(dibutyl)-4-amino-benzophenone. The experimental and theoretical results enabled us to design a new dimer. Altogether, side chain substituents reported herein tune the theoretical band gap of paraphenylene based dimers by over 8.86 eV.     

Theoretical study of carbonic anhydrase-catalyzed hydration of co2: A brief review

Quantum mechanical calculations have been used to study the reaction mechanism of human carbonic anhydrase-catalyzed hydration of CO₂. This reaction is responsible for fast metabolism of CO₂ in the human body. For each of the reaction steps, possible catalytic effects of active site residues are examined. The pertinent results are as follows. (1) For CO₂ binding, the experimentally observed 2.5 cm^?1 frequency shift of the asymmetic stretching frequency between measurements taken in the aqueous solution and in the enzyme is reproduced in our theoretical calculations. Our results suggest that CO₂ binds to the zinc ion within the hydrophobic pocket. (2) No energy barrier is found for the nucleophilic attack from Zn²⁺?bound OH^? to C of CO₂ to form Zn²⁺?bound HCO₃^?. (3) For the internal proton transfer within zinc-bound HCO₃^?, the barrier of 35.6 kcal/mol for the direct internal proton transfer is reduced to 3.5 and 1.4 kcal/mol, respectively, when one or two water molecules are included for proton relay. (4) Displacement of Zn²⁺?bound HCO₃^? by H₂O is facilitated by the presence of the negatively charged Glu 106-Thr 199 chain and by the association and the subsequent ionization of a fifth water ligand. (5) For the intramolecular proton transfer between Zn²⁺-bound H₂O and His 64, the Zn²⁺ ion lowers the pK_a of Zn²⁺?bound water and repels the proton. His 64, or a similar proton receptor with a larger proton affinity than H₂O, functions as proton receiver; and the active site water molecules visualized by x-ray crystallography are important for the proton relay function. In summary, it is demonstrated that in order to achieve effective catalysis, a sequence of precisely coordinated catalytic events among all participating catalytic elements in the enzyme's active site is essential.     

Modulation of substrate binding to naphthalene 1,2-dioxygenase by rieske cluster reduction/oxidation

The active site of the oxygenase component of naphthalene 1,2-dioxygenase (NDO) contains a Rieske Fe-S cluster and a mononuclear non-heme iron, which are contributed by different alpha-subunits in the (alphabeta)(3) structure. The enzyme catalyzes cis-dihydroxylation of aromatic substrates in addition to numerous other adventitious oxidation reactions. High-resolution Mims (2)H-ENDOR spectra have been recorded for the NO-ferrous center of NDO bound with d(8)-naphthalene and d(2)-naphthalene; spectra were collected for the enzyme with the Rieske diiron center both in its oxidized and in its reduced states. A sharp quartet ENDOR pattern from a nearby deuteron of substrate was detected for each substrate. Examination of the sample prepared with 1,4-dideutero-naphthalene shows that the signal arises from D1. The ENDOR data place D1 at a distance of ca. 4.4 A from the mononuclear Fe and with the Fe-D vector being roughly along the Fe-N(O) direction. Because reduction of the Rieske cluster is required for O(2) binding and subsequent catalysis, the effect of its oxidation state on substrate binding was examined. The spectra from the NDO-naphthalene complex reveal two different binding conformations, which change in relative population when the oxidation state of the Rieske cluster is changed. This shift, and the conformational coupling it implies, may hold the key to both oxygen gating and oxygen reactivity for Rieske aromatic dioxygenases.