Do orientation effects contribute to the molecular weight dependence of the free solution mobility of DNA?

The free solution mobility of DNA increases with increasing molecular weight and then levels off and becomes constant at molecular weights above approximately 400 bp (Stellwagen, N. C., Gelfi, C., Righetti, P. G., Biopolymers 1997,42, 687-703). To investigate whether the increase in mobility could be attributed to an increased orientation of the larger DNA molecules in the electric field, the free solution mobility of DNA was measured by capillary electrophoresis as a function of electric field strength. Mixtures containing 20-, 118- and 422-bp DNA molecules, and 20-, 422- and 2116-bp DNAs, were studied. If the larger DNA molecules in each mixture were oriented by the electric field, their mobilities should increase with electric field strength faster than the mobility of the 20-bp oligomer, which is too small to be oriented by the electric fields used in this study. Instead, the ratios of the mobilities of the 118-, 422- and 2116-bp fragments to the mobility of the 20-bp oligomer were independent of electric field strength. Hence, orientation effects are not important for DNA molecules up to 2 kbp in size, in electric fields up to 500 V/cm in amplitude. An explanation is suggested.     

Is the rate constant of chain propagation kp in radical polymerization really chain-length independent?

A careful investigation of the k_p data obtained from pulsed-laser polymerization at different pulse separations t₀ in a lot of systems has revealed that k_p exhibits a slight but significant decrease when t₀ is increased, corresponding to an about 20% decrease of k_p extending over several hundreds in degree of polymerization. Transformation of this integral effect to individual chain-lengths reduces this range, of course, but still shows more than one hundred propagation steps to be concerned. This is interpreted in terms of a decrease of the monomer concentration at the site of propagation caused by the segments already added to the growing chain.     

Electronic and steric effects on the photo-induced C→E ring-opening of structurally modified furylfulgides

The ultrafast C→E ring-opening reactions of four selectively modified furylfulgides have been studied by means of ultrafast broadband transient absorption spectroscopy after femtosecond laser excitation at λ = 500 nm. A large difference in the dynamics was found in the case of benzannulation at the furyl moiety as an example for an electronic effect by extension of the conjugated π-electron system compared to furylfulgides carrying sterically different alkyl substituents at the central cyclohexadiene (CHD) ring. The measured very similar spectro-temporal absorption maps for the furylfulgides with a methyl or isopropyl group at the CHD ring or an intramolecular alkyl bridge from the CHD to the furyl moiety showed two distinctive excited-state absorptions with slightly different decay times. The first time constant (τ(1) = 0.39-0.57 ps) was assigned to the rapid departure of the excited wavepacket from the Franck-Condon region. The slightly longer second decay time of τ(2) = 0.66-0.92 ps, depending on the compound, was attributed to the electronic deactivation and ring-opening through a conical intersection to the S(0) state. In contrast, the benzannulation at the furyl moiety was found to lead to a bi-phasic excited-state decay with τ(2) = 4.7 ps and a much slower additional contribution of τ(3) = 17.4 ps, ≈25 times longer compared to the normal furylfulgides. The drastic change is attributed to a trapping of excited molecules in a local potential energy minimum en route to the conical intersection.     

Is the ion-linear quadrupole capture rate constant anisotropic with respect to the sign of the product of the charge on the ion and the quadrupole moment of the molecule?

The sign of the charge-quadrupole moment product is shown to affect the rate of ion-linear quadrupole capture.

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What are the relative steric demands of carboxyl and methyl groups?

The relative steric demands of carboxyl and methyl groups are compared by contrasting the difference quantity H _f ^o (g, ArCOOH) — H _f ^o (g, ArCH₃) for a collection of alkylated benzoic acids and toluenes with the value for Ar=C₆H₅, the archetypical (i.e., unsubstituted) benzoic acid and toluene. We conclude that carboxyl and methyl groups are nearly the same size.     

Is the stereomutation of methane possible?

Large basis set ab initio calculations at correlated levels, including MP2, single reference, as well as multireference configuration interaction, carried out on the methane potential energy surface, have located and characterized a transition structure for stereomutation (one imaginary frequency). This structure is best described as a pyramidal complex between singlet methylene and a side-on hydrogen molecule with C_s symmetry. At the single reference CI level, it lies 105 kcal/mol above the methane T_d-ground state but is stable relative to dissociation into CH₂(¹A₁) and H₂ by 13 kcal/mol at 0 K (with harmonic zero point energy (ZPE) corrections for all structures). Dissociation of the transition state into triplet methylene and hydrogen also is endothermic (by 4 kcal/mol), but single bond rupture to give CH and H^. is 3 kcal/mol exothermic. Thus, it does not appear likely that methane can undergo stereomutation classically beneath the dissociation limit. Confirming earlier conclusions, side-on insertion of ¹A₁ CH₂ into H₂ in a perpendicular geometry occurs without activation energy. Planar (D_4h) methane (130.5 kcal/mol) has four imaginary frequencies. Two of these are degenerate and lead to equivalent planar C_2v structures with one three-center, two-electron bond and two two-electron bonds and two imaginary frequencies. The remaining imaginary frequencies of the D_4h form lead to tetrahedral (T_d) and pyramidal (C_4v) methane. The latter has three negative eigenvalues in the force-constant matrix; one of these leads to the T_d global minimum and the other to the C_s (parallel) stereomutation transition structure. Multireference CI calculations with a large atomic natural orbitals basis set produce similar results, with the electronic energy of the C_s stereomutation transition state 0.7 ± 0.5 kcal/mol higher than that of CH + H^. dissociation products, and a ZPE-corrected energy which is 5 ± 1 kcal/mol higher. Also considered are photochemical pathways for stereomutation and the possible effects of nuclear spin, inversion tunneling, and the parity-violating weak nuclear interaction on the possibility of an experimental detection of stereomutation in methane. © 1995 by John Wiley & Sons, Inc.     

Are the solvent effects critical in the modeling of polyoxoanions?

DFT calculations were driven for a set of differently charged polyoxoanions in the gas phase and in solution. We have calculated and analyzed their geometries and orbital energies to trace simple rules of behavior regarding the modeling of anions in isolated form. We discuss the quality of the results depending on the molecular charge, q, and the size of the cluster in terms of the number of metal centers, m. When the q/m ratio reaches a value of approximately 0.8, DFT calculations for the isolated anion fail to describe the gap between the band of occupied oxo orbitals and the set of unoccupied orbitals delocalized among the metal atoms. In these cases the incorporation of the stabilizing external fields generated by the solvent through continuum models improves the geometries and orbital energies.     

What Is the Structure of Pterodonoic Acid?

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Effect of steric factors on the keto-cis-trans-enol equilibrium of α-acetylcycloalkaneacetic esters

Summary With the aid of atomic models the structures of -acetylcyclohexane-, -acetylcyclopentane-, and -acetyl-cyclobutane-acetic esters were examined, and an explanation is proposed for the observed proportions of the tautomeric forms.     

Suzuki–Miyaura reactions of the bis(triflates) of 1,3- and 1,4-dihydroxythioxanthone. Electronic and steric effects on the site-selectivity

The palladium(0)-catalyzed Suzuki cross-coupling reactions of the bis(triflates) of 1,3- and 1,4-dihydroxythioxanthone afforded various aryl-substituted thioxanthones. While the Suzuki reactions of the bis(triflate) derived from 1,3-dihydroxythioxanthone proceeded by site-selective attack in favor of position 3, the reactions of the bis(triflate) of 1,4-dihydroxythioxanthone proceeded in favor of position 1. The site-selectivity is controlled by steric and electronic parameters.     

Congested molecules. Where is the steric repulsion? An analysis of the electron density by the method of interacting quantum atoms

The computed electron density of several congested saturated hydrocarbons and halogenated derivatives has been analyzed by the method of interacting quantum atoms (IQA). For all the molecules studied, the calculations show the existence of a bond path between the congested atoms and which, according to the Quantum Theory of Atoms in Molecules, indicates that there is a stabilizing interaction between these atoms. The bond path is found to exist up to interatomic distances well‐beyond the sum of the van der Waals radii. The IQA results indicate that steric hindrance is not a repulsive force between the congested atoms but that is the result of an increase in the intra‐atomic or self‐energy of the congested atoms. This increase in self‐energy is caused by the deformation of the atomic basin of the congested atoms. © 2013 Wiley Periodicals, Inc.     

Mechanism of the acid-promoted intramolecular schmidt reaction: theoretical assessment of the importance of lone pair-cation, cation-π, and steric effects in controlling regioselectivity

The mechanism of the acid-catalyzed intramolecular Schmidt reaction of 2-azidopropylcyclohexanones was studied using density functional theory (primarily M06-2X). The reaction was found to proceed through rapid formation of azidohydrin intermediates followed by rate-determining concerted N(2)-loss/shift of the alkyl group antiperiplanar to the N(2) leaving group. For cases where steric, lone pair-cation, and cation-π effects have been invoked previously as regiocontrol elements, the origins and magnitudes of these effects have been examined theoretically.     

Evaluation of the steric interactions responsible for the enantioselective photodeconjugation of α,β-unsaturated esters

A model is proposed to explain the configuration and the proportion of the preponderant enantiomer in the enantioselective photodeconjugation of α,β-unsaturated esters. The major interactions in the transition state are developed between the inductor and the β-carbon of the intermediate dienol.     

Electronic and steric effects controlling efficiencies of photoaddition reactions of fullerene C60 with N-α-trimethylsilyl-N-alkyl-N-benzylamines

Single electron transfer (SET)-promoted photoaddition reactions between fullerene C₆₀ and both various alkyl (Me, Et, i-Pr, t-Bu)- and para-substituted (p-Me, p-OMe, p-F, p-CF₃) arene ring containing, N-α-trimethylsilyl-N-alkyl-N-benzylamines were explored to gain information about photoproduct profiles and how the electronic and steric nature of the amine substrates influence reaction efficiencies. The results show that visible light (λ > 540 nm) irradiation of 10% EtOH-toluene solutions containing C₆₀ and N-α-trimethylsilyl-N-alkyl-N-benzylamines produce 1-aminomethyl-1,2-dihydrofullerenes as a sole photoproduct. In addition, SET-promoted photoaddition reactions of unsubstituted and para-electron donating group substituted arene ring containing N-α-trimethylsilyl-N-alkyl-N-benzylamines take place to give photoproducts more efficiently than those containing para-electron withdrawing group substituted arene rings. Moreover, although steric factors are less significant than the electronic nature of the amine substrates in governing reaction efficiencies, sterics do play a significant role in photoreactions of electron deficient amine substrates.     

Is the problem of molecular structure just the quantum measurement problem?

In a recent article entitled “The problem of molecular structure just is the measurement problem”, Alexander Franklin and Vanessa Seifert argue that insofar as the quantum measurement problem is solved, the problems of molecular structure are resolved as well. The purpose of the present article is to show that such a claim is too optimistic. Although the solution of the quantum measurement problem is relevant to how the problem of molecular structure is faced, such a solution is not sufficient to account for the structure of molecules as understood in the field of chemistry.

     

Is the bisphenol A biradical formed in the pyrolysis of polycarbonate?

An unknown species has been detected in the analysis of the products in a pyrolysis of polycarbonate using Li(+) ion-attachment mass spectrometry (IAMS). The mass spectra exhibited a Li(+) adduct peak at m/z 233 that was tentatively assigned to bisphenol A (BPA) biradical. Experimentally, this assignment was supported by the observation that the production rate increased under an inert nitrogen atmosphere. To further confirm the assignment, the stability of the BPA biradical to intramolecular rearrangement reactions as well as unimolecular decomposition has been analyzed via density functional theory calculations [B3LYP/6-311+G(3df,2p)]. The results show that the bisphenol A biradical is an open-shell biradical singlet that is stable to unimolecular decomposition. Although some of the proposed intramolecular rearrangement products have lower energies than those of the BPA diradical, these pathways have large reaction barriers and the kinetic lifetime of the radical is expected to be of the order of hours under the conditions of the experiment. The calculations also reveal that the bisphenol A diradical has large Li(+) affinities supporting the fact that these Li(+) complexes could be detected in the Li(+) ion attachment mass spectrometry. On the basis of these results the Li(+) adduct peak at m/z 233 detected in the pyrolysis of polycarbonate is assigned to the bisphenol A biradical.     

Assessment of solvent effects: do weak alignment media affect the structure of the solute?

Alignment media used for measuring residual dipolar couplings, such as solutions of filamentous phages, phospholipid mixtures, polyacrylamide gels and various lyotropic liquid crystalline systems were investigated with respect to solvent effects on molecular structure. Structural parameters of the small rigid model compound 13C-acetonitrile were calculated from dipolar couplings and variations from expectation values were used for assessment of solvent effects. Only minor solvent effects were observed for most of the media employed and the measured structural data are in good agreement with microwave data and theoretical predictions.     

Is the 3MLCT the only photoreactive state of polypyridyl complexes?

By means of Delta-SCF and time-dependent density functional theory (DFT) calculations on [Ru(LL)3]2+ (LL = bpy = 2,2'-bipyridyl or bpz = 2,2' -bipyrazyl) complexes, we have found that emission of these two complexes could originate from two metal-to-ligand charge-transfer triplet states (3MLCT) that are quasi-degenerate and whose symmetries are D3 and C2. These two states are true minima. Calculated absorption and emission energies are in good agreement with experiment; the largest error is 0.14 eV, which is about the expected accuracy of the DFT calculations. For the first time, an optimized geometry for the metal-centered (MC) state is proposed for both of these complexes, and their energies are found to be almost degenerate with their corresponding 3MLCT states. These [RuII(LL)(eta1-LL)2]2+ MC states have two vacant coordination sites on the metal, so they may react readily with their environment. If these MC states are able to de-excite by luminescence, the associated transition (ca. 1 eV) is found to be quite different from those of the 3MLCT states (ca. 2 eV).     

Do the electronic effects of sulfur indeed control the pi-selectivity of gamma-sulfenyl Enones? An investigation

The electronic effects of sulfur in gamma-sulfenyl enones are not transmitted to the carbonyl carbon through the pi bond as reported previously. The diastereoselectivity is rather controlled by a combination of several other factors. The steric effects arising from the substituents on the sulfur atom and the gamma-carbon and the bulk of the nucleophile constitute the major control elements.