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Wybren Jan Buma

Publications and source records attributed to Wybren Jan Buma.

7 recordsLinked to original sources
PubMed2006

Combined experimental-theoretical study of the lower excited singlet states of paravinyl phenol, an analog of the paracoumaric acid chromophore.

The low-lying excited singlet states of paravinyl phenol (pVP) are investigated experimentally and theoretically paying attention to their similarity to excited states of paracoumaric acid, the chromophore of the photoactive yellow protein (PYP). Resonance enhanced multiphoton ionization and laser induced fluorescence spectroscopic techniques are employed to obtain supersonically cooled, vibrationally resolved excitation and emission spectra related to the lowest (1)A'(V') excited state of pVP. Comprehensive analyses of the spectral structures are carried out by means of the equation-of-motion coupled cluster singles and doubles and time dependent density functional theory methods in combination with the linear vibronic coupling model and Franck-Condon calculations. The assignments of the spectral patterns are given, mostly in terms of excitations of totally symmetric modes. Weak activity of the non-totally-symmetric modes indicates low probability of photochemical processes in the Franck-Condon region of the (1)A'(V') state. The second (1)A'(V) and third (1)A" (Ryd) excited states of pVP are characterized with regard to their electronic structure, properties, and effects of geometry relaxations. The lengthening of the double bond relevant to the trans-cis isomerization of the PYP chromophore is found for the (1)A'(V) state. A possibility of photochemical processes and strong vibronic interactions in this state can be expected. The theoretical results for the (1)A"(Ryd) state predict that dissociation with respect to the O-H bond is possible.

Computer Simulation↗
PubMed2006

Femtosecond studies of charge-transfer mediated proton transfer in 2-butylamino-6-methyl-4-nitropyridine N-oxide.

We have unraveled the effects of an amino substituent in the ortho position on the excited-state dynamics of 4-nitropyridine N-oxide by studying the picosecond fluorescence kinetics and femtosecond transient absorption of a newly synthesized compound, 2-butylamino-6-methyl-4-nitropyridine N-oxide, and by quantum chemical calculations. Similar to the parent compound, the S(1) state of the target molecule has significant charge-transfer character and shows a large (approximately 8000 cm(-1)) static Stokes shift in acetonitrile. Analysis of the experimental and the theoretical results leads, however, to a new scenario in which this intramolecular charge transfer triggers in polar, aprotic solvents an ultrafast (around 100 fs) intramolecular proton transfer between the amino and the N-O group. The electronically excited N-OH tautomer is subsequently subject to solvent relaxation and decays with a lifetime of approximately 150 ps to the ground state.

Computer Simulation↗
PubMed2005

Probing the structure of a rotaxane with two-dimensional infrared spectroscopy.

Femtosecond 2D-IR spectroscopy has been used to study the structure of a [2]rotaxane composed of a benzylic amide macrocycle that is mechanically interlocked onto a succinamide-based thread. Both the macrocycle and the thread contain carbonyl groups, and by determining the coupling between the stretching modes of these groups from the cross-peaks in the 2D-IR spectrum, the structure of the macrocycle-thread system has been probed. Our results demonstrate that 2D-IR spectroscopy can be used to observe structural changes in molecular devices on a picosecond time scale.

Amides↗
PubMed2005

Ionization potentials of fluoroindoles and the origin of nonexponential tryptophan fluorescence decay in proteins.

This work reports an explanation for the unusual monoexponential fluorescence decay of 5-fluorotryptophan (5FTrp) in single-Trp mutant proteins [Broos, J.; Maddalena, F.; Hesp, B. H. J. Am. Chem. Soc. 2004, 126, 22-23] and substantially clarifies the origin of the ubiquitous nonexponential fluorescence decay of tryptophan in proteins. Our results strongly suggest that the extent of nonexponential fluorescence decay is governed primarily by the efficiency of electron transfer (ET) quenching by a nearby amide group in the peptide bond. Fluoro substitution increases the ionization potential (IP) of indole, thereby suppressing the ET rate, leading to a longer average lifetime and therefore a more homogeneous decay. We report experimental IPs for a number of substituted indoles including 5-fluoroindole, 5-fluoro-3-methylindole, and 6-fluoroindole, along with accurate ab initio calculations of the IPs for these and 20 related molecules. The results predict the IP of 5-fluorotryptophan to be 0.19 eV higher than that of tryptophan. 5-Fluoro substitution does not measurably alter the excitation-induced change in permanent dipole moment nor does it change the fluorescent state from 1La to 1Lb. In combination with electronic structure information this argues that the increased IP and the decreased excitation energy of the 1La state, together 0.3 eV, are solely responsible for the strong reduction of electron transfer quenching. 6-Fluoro substitution is predicted to increase the IP by a mere 0.09 eV. In agreement with our conclusions, the fluorescence decay curves of 6-fluorotryptophan-containing proteins are well fit using only two decay times compared to three required for Trp.

Electrochemistry↗
PubMed2002

Structure and photophysics of an old, new molecule: 1,3,6,8-tetraazatricyclo[4.4.1.1(3,8)]dodecane.

More than a century after its initial synthesis, the static and dynamic geometry of 1,3,6,8-tetraazatricyclo [4.4.1.1(3,8)]dodecane (TTD), a fully saturated cage-like molecule, is finally established. Detection and modeling of the supersonic jet fluorescence excitation and emission spectra show that the molecule undergoes interconversion between two S(4) symmetry minima. The barrier at the D(2d) symmetric conformation is only 105 cm(-1), i.e., approximately 0.3 kcal mol(-1), and is overcome along a carbon-carbon torsional mode of a(2) symmetry. The presence of an S(4) conformation is corroborated by a Raman investigation. When excited to the first excited singlet state, the 3s Rydberg state, the molecule adopts a geometry with D(2d) symmetry. The satisfactory description of the spectroscopy of TTD obtained by a combination of quantum chemical and quantum mechanical models is discussed, and the apparent conflict between the present results and nuclear magnetic resonance and X-ray diffraction experiments is solved. Because of the close analogy between a Rydberg state and the ground state of the radical cation regarding geometry and spectroscopic properties, it is concluded that the radical cation is also of D(2d) symmetry.

Journal Article↗