Unusual structure-energy correlations in intramolecular Diels–Alder reaction transition states

Detailed analysis of calculated data from an experimental/computational study of intramolecular furan Diels–Alder reactions has led to the unusual discovery that the mean contraction of the newly forming C-C σ-bonds from the transition state to the product shows a linear correlation with both reaction Gibbs free energies and reverse energy barriers. There is evidence for a similar correlation in other intramolecular Diels–Alder reactions involving non-aromatic dienes. No such correlation is found for intermolecular Diels–Alder reactions

Dynamic Arrest in Polymer Melts: Competition between Packing and Intramolecular Barriers

We present molecular dynamics simulations of a simple model for polymer melts with intramolecular barriers. We investigate structural relaxation as a function of the barrier strength. Dynamic correlators can be consistently analyzed within the framework of the Mode Coupling Theory (MCT) of the glass transition. Control parameters are tuned in order to induce a competition between general packing effects and polymer-specific intramolecular barriers as mechanisms for dynamic arrest. This competition yields unusually large values of the so-called MCT exponent parameter and rationalize qualitatively different observations for simple bead-spring and realistic polymers. The systematic study of the effect of intramolecular barriers presented here also establishes a fundamental difference between the nature of the glass transition in polymers and in simple glass-formers.Comment: 4 pages, 3 figures, 2 table

Atomic force microscopy shows that vaccinia topoisomerase IB generates filaments on DNA in a cooperative fashion

Type IB DNA topoisomerases cleave and rejoin one strand of the DNA duplex, allowing for the removal of supercoils generated during replication and transcription. In addition, electron microscopy of cellular and viral TopIB–DNA complexes has suggested that the enzyme promotes long-range DNA–DNA crossovers and synapses. Here, we have used the atomic force microscope to visualize and quantify the interaction between vaccinia topoisomerase IB (vTopIB) and DNA. vTopIB was found to form filaments on nicked-circular DNA by intramolecular synapsis of two segments of a single DNA molecule. Measuring the filament length as a function of protein concentration showed that synapsis is a highly cooperative process. At high protein:DNA ratios, synapses between distinct DNA molecules were observed, which led to the formation of large vTopIB-induced DNA clusters. These clusters were observed in the presence of Mg(2+), Ca(2+) or Mn(2+), suggesting that the formation of intermolecular vTopIB-mediated DNA synapsis is favored by screening of the DNA charge

Role of Internal Motions and Molecular Geometry on the NMR Relaxation of Hydrocarbons

The role of internal motions and molecular geometry on $^1$H NMR relaxation times $T_{1,2}$ in hydrocarbons is investigated using MD (molecular dynamics) simulations of the autocorrelation functions for in{\it tra}molecular $G_R(t)$ and in{\it ter}molecular $G_T(t)$ $^1$H-$^1$H dipole-dipole interactions arising from rotational ($R$) and translational ($T$) diffusion, respectively. We show that molecules with increased molecular symmetry such as neopentane, benzene, and isooctane show better agreement with traditional hard-sphere models than their corresponding straight-chain $n$-alkane, and furthermore that spherically-symmetric neopentane agrees well with the Stokes-Einstein theory. The influence of internal motions on the dynamics and $T_{1,2}$ relaxation of $n$-alkanes are investigated by simulating rigid $n$-alkanes and comparing with flexible (i.e. non-rigid) $n$-alkanes. Internal motions cause the rotational and translational correlation-times $\tau_{R,T}$ to get significantly shorter and the relaxation times $T_{1,2}$ to get significantly longer, especially for longer-chain $n$-alkanes. Site-by-site simulations of $^1$H's along the chains indicate significant variations in $\tau_{R,T}$ and $T_{1,2}$ across the chain, especially for longer-chain $n$-alkanes. The extent of the stretched (i.e. multi-exponential) decay in the autocorrelation functions $G_{R,T}(t)$ are quantified using inverse Laplace transforms, for both rigid and flexible molecules, and on a site-by-site bases. Comparison of $T_{1,2}$ measurements with the site-by-site simulations indicate that cross-relaxation (partially) averages-out the variations in $\tau_{R,T}$ and $T_{1,2}$ across the chain of long-chain $n$-alkanes. This work also has implications on the role of nano-pore confinement on the NMR relaxation of fluids in the organic-matter pores of kerogen and bitumen

First-principles description of van der Waals-bonded spin-polarized systems using vdW-DF+U+U method---application to solid oxygen at low pressure

The description of the molecular solid phase of O$_2$, especially its ground-state antiferromagnetic insulating phase, is known to be quite unsatisfactory within the conventional local and semilocal density functional approximations used in the Kohn-Sham formalism of density functional theory. The recently-developed van der Waals functionals that take into account nonlocal correlations have also shown subpar performance in this regard. The difficulty lies in the subtle balance between the van der Waals interactions and the exchange coupling between the antiferromagnetic and ferromagnetic molecule pairs in the molecular crystal. Here, we report that the DFT$+U$ approach used in combination with the vdW-DF functional performs surprisingly well in this regard, and discuss the reasoning behind this behavior. We also apply this approach to study the recently-reported magnetic field-induced $\theta$ phase of solid O$_2$.Comment: Final published versio

On the Theory of Intramolecular Energy Transfer

We consider the distinguishing features of two main types of classical anharmonic motion in molecules, their quantum parallels, and conditions that classical chaos also be sufficient for “quantum chaos”. Implications are considered for experimental reaction rates, R.R.K.M. theory, spectra and a possible type of system for intramolecular laser-selective chemistry. A theory of intramolecular energy transfer between two ligands of a heavy atom is described for a system which may contain many coordinates. It is partly statistical and, for the modes of each ligand which communicate through the heavy atom, dynamical

A perturbation density functional theory for the competition between inter and intramolecular association

Using the framework of Wertheim's thermodynamic perturbation theory we develop the first density functional theory which accounts for intramolecular association in chain molecules. To test the theory new Monte Carlo simulations are performed at a fluid solid interface for a 4 segment chain which can both intra and intermolecularly associate. The theory and simulation results are found to be in excellent agreement. It is shown that the inclusion of intramolecular association can have profound effects on interfacial properties such as interfacial tension and the partition coefficient

Picosecond-jet spectroscopy and photochemistry. Energy redistribution and its impact on coherence, isomerization, dissociation and solvation

The development of the picosecond-jet technique is presented. The applications of the technique to the studies of coherence (quantum beats), photodissociation, isomerization and partial solvation of molecules in supersonic-jet beams are detailed with emphasis on the role of intramolecular energy redistribution. Experimental evidence for intramolecular threshold effect for rates as a function of excess molecular energy is given and explained using simple theory for the redistribution of energy among certain modes. Comparison with R.R.K.M. calculation is also made to assess the nature of the statistical behaviour of the energy redistribution

Hydrogen bond based noncovalent association in the semi-fluorous solvent perfluorobutyl-methyl ether: Host-host and host-guest association of the host 1-(3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,10-Heptadecafluoro-decyl)-3-pyridin-2-yl-urea

A fluorous pyridyl-urea, 1-(3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,10-heptadecafluoro-decyl)-3-pyridin-2-yl-urea, was prepared to act as a host and analyzed by 1H NMR inCD2Cl2 and perfluorobutyl-methyl ether (HFE7100). Crystals were analyzed by X-ray diffraction. The host molecules were found to form pillar-like structures in the crystal. There is an intramolecular bond between the pyridyl nitrogen and one urea hydrogen. 1H NMR spectra demonstrated that the urea hydrogens’ positions shift as the concentration of the host changes. The dependence of the shifts on concentration are consistent with the formation of a trimer of hosts with a logKeq for formation of trimer from monomer approximately 6. Association of the host with guests octanoic acid, ethyl acetate, N-ethylacetamide, N,N-dimethylacetamide, and acetone, was analyzed by titration of the host with individual guests in HFE7100 solvent. Downfield or upfield shifts of the urea hydrogens were used to indicate hydrogen bond formation with the guest. Acetone and ethyl acetate were unable to overcome the self-association of the host and form host-guest complexes. Octanoic acid binding caused shifts in the 1H NMR spectra of one hydrogen of the urea group. N-ethylacetamide and N,N-dimethylacetamide induced shifts in both urea hydrogens. The results indicate that the host monomer’s favored conformation contains an intramolecular hydrogen bond. This bond is not broken upon association with octanoic acid, but it is broken upon association with the two acetamides

Excitation and characterization of long-lived hydrogenic Rydberg states of nitric oxide

High Rydberg states of nitric oxide (NO) with principal quantum numbers between 40 and 100 and lifetimes in excess of 10 $\mu$s have been prepared by resonance enhanced two-color two-photon laser excitation from the X $^2\Pi_{1/2}$ ground state through the A $^2\Sigma^+$ intermediate state. Molecules in these long-lived Rydberg states were detected and characterized 126 $\mu$s after laser photoexcitation by state-selective pulsed electric field ionization. The laser excitation and electric field ionization data were combined to construct two-dimensional spectral maps. These maps were used to identify the rotational states of the NO$^+$ ion core to which the observed series of long-lived hydrogenic Rydberg states converge. The results presented pave the way for Rydberg-Stark deceleration and electrostatic trapping experiments with NO, which are expected to shed further light on the decay dynamics of these long-lived excited states, and are of interest for studies of ion-molecule reactions at low temperatures.Comment: 12 pages, 10 figure