The kinetics of biomolecular isomerization processes, such as protein folding, is governed by a free-energy surface of high dimensionality and complexity. As an alternative to projections into one or two dimensions, the free-energy surface can be mapped into a weighted network where nodes and links are configurations and direct transitions among them, respectively. In this work, the free-energy...

The vibrational spectrum of HCP ~phosphaethyne! is studied and analyzed in terms of a 1:2 resonance effective Hamiltonian. The parameters of the model Hamiltonian are determined by fitting 361 out of the first 370 energy levels obtained from diagonalization of the full Hamiltonian, which is based on a newly calculated potential-energy surface with near spectroscopic accuracy. It is demonstrated...

Oxazinane rings can undergo isomerization or transformation to 5-membered tuned by the anomeric effect.

Fatty acid compositions in growing and resting cells of several strains of Pseudomonas putida (P8, NCTC 10936, and KT 2440) were studied, with a focus on alterations of the saturation degree, cis-trans isomerization, and cyclopropane formation. The fatty acid compositions of the strains were very similar under comparable growth conditions, but surprisingly, and contrary to earlier reports, tran...

The dissociation of the hydroxymethyl radical, CH(2)OH, and its isotopolog, CD(2)OH, following excitation in the 4ν(1) region (OH stretch overtone, near 13,600 cm(-1)) was studied using sliced velocity map imaging. A new vibrational band near 13,660 cm(-1) arising from interaction with the antisymmetric CH stretch was discovered for CH(2)OH. In CD(2)OH dissociation, D atom products (correlated ...

To understand how the protein achieves fluorescence, the isomerization mechanism of the HcRed chromophore is studied both under vacuum and in the solvated red fluorescent protein. Quantum mechanical (QM) and quantum mechanical/molecular mechanical (QM/MM) methods are applied both for the ground and the first excited state. The photoinduced processes in the chromophore mainly involve torsions ar...

The lifetimes of methyl 4-hydroxycinnamate (OMpCA) and its mono-hydrated complex (OMpCA-H(2)O) in the S(1) state have been measured by picosecond pump-probe spectroscopy in a supersonic beam. For OMpCA, the lifetime of the S(1)-S(0) origin is 8-9 ps. On the other hand, the lifetime of the OMpCA-H(2)O complex at the origin is 930 ps, which is ∼100 times longer than that of OMpCA. Furthermore, in...

The enzymatic conversion of the carcinogenic arylhydroxamic acid, N-hydroxy-2-fluorenylacetamide, to the o-amidophenols, N-(1-hydroxy-2-fluorenyl)acetamide and N-(3-hydroxy-2-fluorenyl)acetamide, referred to as the isomerization of N-hydroxy-2-fluorenylacetamide, by cell fractions of rat liver has been studied. Cell fractions prepared from the livers of normal rats were unable to perform the re...

This work is a study of the competition between the two unimolecular reaction channels available to the vinoxy radical (CH(2)CHO), C-H fission to form H+ketene, and isomerization to the acetyl radical (CH(3)CO) followed by C-C fission to form CH(3) + CO. Chloroacetaldehyde (CH(2)ClCHO) was used as a photolytic precursor to the vinoxy radical in its ground state; photodissociation of chloroaceta...