Rate constants from the reaction path Hamiltonian. I. Reactive flux simulations for dynamically correct rates

As ab initio electronic structure calculations become more accurate, inherent sources of error in classical transition state theory such as barrier recrossing and tunneling may become major sources of error in calculating rate constants. This paper introduces a general method for diabatically constructing the transverse eigensystem of a reaction path Hamiltonian in systems with many degenerate transverse frequencies. The diabatically constructed reaction path Hamiltonian yields smoothly varying coupling constants that, in turn, facilitate reactive flux calculations. As an example we compute the dynamically corrected rate constant for the chair to boat interconversion of cyclohexane, a system with 48 degrees of freedom and a number of degenerate frequencies. The transmission coefficients obtained from the reactive flux simulations agree with previous results that have been calculated using an empirical potential. Furthermore, the calculated rate constants agree with experimental values. Comparison to variational transition state theory shows that, despite finding the true bottleneck along the reaction pathway, variational transition state theory only accounts for half of the rate constant reduction due to recrossing trajectories.     

Structure and conformational isomerism of the major dimer of 2,3-naphthoquinodimethane

The major product from 2,3-naphthoquinodimethane formed by cyclisation of $\text{o}$-dipropadienylbenzene was found to be the dimer 5 containing an eight-membered ring, for which the inversion barrier was determined by dynamic ¹H NMR spectrometry, ΔG3 = 18 kcal/mole.     

Synthesis of substituted 3-amino[6,5-b]triazinoindoles

4-[(9-Methyl-as-triazino[6,5-b]indol-3-yl)amino]-2-methyl-2-butanol ( 13 ) and the corresponding 2-methyl-3-imino derivative 12 were synthesized and tested in vitro against Rhino 2 virus. The two compounds were more active than the known triazino[5,6-b]indole 4 . 2,9-Dimethyl-3-methoxy-9H-as-triazino[6,5-b]indolium tosylate ( 21 ) and the related 3-methylthio compound 9 were prepared. Quaternary 21 formed a pseudo base, 22a , whereas quaternary 9 did not form a pseudo base.     

Photochlorination of tetramethylsilane and hexamethyldisilane in the gas phase

Preliminary studies of the reaction of chlorine with tetramethylsilane and hexamethyldisilane in the gas phase show that the photochlorination of tetramethylsilane is complex, giving different products from the corresponding reaction in solution and having an explosion boundary. At pressures below the explosion boundary the main products are ethylene, hydrogen chloride, dimethylchlorosilane, and more highly chlorinated methylsilanes. Above the explosion boundary main products after explosion are methane, acetylene, ethylene, hydrogen chloride, and silicon tetrachloride. Hexamethyldisilane reacts rapidly with chlorine in the dark, as it does in solution, forming mainly trimethylchlorosilane along with similar products to those found with tetramethylsilane. Subsequent photochlorination of trimethylchlorosilane follows a similar course to that of tetramethylsilane in the gas phase. Tentative mechanisms involving “hot” molecules are suggested.     

Modular fluorescence sensors for saccharides

Modular and modular polymer supported fluorescence photoinduced electron transfer (PET) sensors 2 and 3 with two boronic acid receptor units, a pyren-1-yl fluorophore, and hexamethylene linker show selective saccharide binding in aqueous methanolic solution at pH 8.21.     

Gradient of the ZAPT2 energy

 An explicit expression for the analytical first derivative of the Z-averaged perturbation theory taken to second order energy, due to Lee and Jayatilaka, is presented for application to high-spin systems described by a restricted open-shell Hartree–Fock wavefunction. The use of frozen core orbitals is incorporated into the derivation. Received: 23 April 2001 / Accepted: 31 August 2001 / Published online: 9 January 2002     

Acid-Catalyzed Amine-Borane Reduction of Nitrite

The rate of reduction of nitrite by trimethylamine-borane was followed by observing the decrease in nitrite absorbance under pseudo-first-order conditions. The reaction is acid-catalyzed and exhibits a first-order dependence on both amine-borane and total nitrite concentration. The molar equivalence of NaNO(2) to (CH(3))(3)NBH(3) = 2:1. Equimolar amounts of hydrogen and nitrous oxide are formed, and the molar ratio of nitrite reacted to N(2)O produced is 2:1. In concentrated HCl or H(2)SO(4), a correlation of rate with the Hammett acidity function, h(o), is observed. The reaction is subject to a pronounced inversesolvent isotope effect (k(D)()2(O)/k(H)()2(O) approximately 2.7) and a modest normal substrate effect (k((CH)()3())()3(N.BH)()3/k((CH)()3())()3(N.BD)()3 approximately 1.4). The reaction is first-order in H(3)O(+) in the region pH 0.7-2.7, but a second-order dependence is observed above pH 4 with the transition occurring at pH approximately pK(a) for HNO(2). Results are consistent with a mechanistic model involving preequilibration protonation of molecular nitrous acid followed by rate-limiting hydride attack on H(2)ONO(+) or free NO(+) to produce nitrosyl hydride as a reactive intermediate.     

Polyaromatic amines. Part 3: Synthesis of poly(diarylamino)styrenes and related compounds

The title compounds were synthesised and characterised as part of a study into new aromatic amines for charge transporting materials. Compounds 12-16, 20-24 and 27-34 are alkene linked triarylamines, compounds 35-36 are hydrazone derivatives and compounds 38-41 are pyrrole substituted triarylamines. Each compound was characterised by cyclic voltammetry.     

Transfection mediated by gemini surfactants: engineered escape from the endosomal compartment

The structure of the lipoplex formed from DNA and the sugar-based cationic gemini surfactant 1, which exhibits excellent transfection efficiency, has been investigated in the pH range 8.8-3.0 utilizing small-angle X-ray scattering (SAXS) and cryo-electron microscopy (cryo-TEM). Uniquely, three well-defined morphologies of the lipoplex were observed upon gradual acidification: a lamellar phase, a condensed lamellar phase, and an inverted hexagonal (H(II)) columnar phase. Using molecular modeling, we link the observed lipoplex morphologies and physical behavior to specific structural features in the individual surfactant, illuminating key factors in future surfactant design, viz., a spacer of six methylene groups, the presence of two nitrogens that can be protonated in the physiological pH range, two unsaturated alkyl tails, and hydrophilic sugar headgroups. Assuming that the mechanism of transfection by synthetic cationic surfactants involves endocytosis, we contend that the efficacy of gemini surfactant 1 as a gene delivery vehicle can be explained by the unprecedented observation of a pH-induced formation of the inverted hexagonal phase of the lipoplex in the endosomal pH range. This change in morphology leads to destabilization of the endosome through fusion of the lipoplex with the endosomal wall, resulting in release of DNA into the cytoplasm.