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Bern Kohler

Publications and source records attributed to Bern Kohler.

10 recordsLinked to original sources
PubMed2006

Internal conversion to the electronic ground state occurs via two distinct pathways for pyrimidine bases in aqueous solution.

The femtosecond transient absorption technique was used to study the relaxation of excited electronic states created by absorption of 267-nm light in all of the naturally occurring pyrimidine DNA and RNA bases in aqueous solution. The results reveal a surprising bifurcation of the initial excited-state population in <1 ps to two nonradiative decay channels within the manifold of singlet states. The first is the subpicosecond internal conversion channel first characterized in 2000. The second channel involves passage through a dark intermediate state assigned to a lowest-energy (1)npi* state. Approximately 10-50% of all photoexcited pyrimidine bases decay via the (1)npi* state, which has a lifetime of 10-150 ps. Three- to 6-fold-longer lifetimes are seen for pyrimidine nucleotides and nucleosides than for the corresponding free bases, revealing an unprecedented effect of ribosyl substitution on electronic energy relaxation. A small fraction of the (1)npi* population is proposed to undergo intersystem crossing to the lowest triplet state in competition with vibrational cooling, explaining the higher triplet yields observed for pyrimidine versus purine bases at room temperature. Some simple correlations exist between yields of the (1)npi* state and yields of some pyrimidine photoproducts, but more work is needed before the photochemical consequences of this state can be definitively determined. These findings lead to a dramatically different picture of electronic energy relaxation in single pyrimidine bases with important ramifications for understanding DNA photostability.

Photochemistry↗
PubMed2006

Solvent-dependent photophysics of 1-cyclohexyluracil: ultrafast branching in the initial bright state leads nonradiatively to the electronic ground state and a long-lived 1npi* state.

The modified nucleic acid base, 1-cyclohexyluracil, was studied by femtosecond transient absorption spectroscopy in protic and aprotic solvents of varying polarity. UV excitation at 267 nm populates the lowest-energy bright state, a (1)pipi* state, which has a lifetime of 120-270 fs, depending on the solvent. In all solvents, this initial bright state population bifurcates with approximately 60% undergoing subpicosecond nonradiative decay to the electronic ground state and the remaining population branching to a singlet dark state. The latter absorbs between 340 and 450 nm. The latter state is assigned to the lowest-energy (1)npi* state. It decays to the electronic ground state with a lifetime that varies from 26 ps in water to at least several nanoseconds in aprotic solvents. The results suggest that the two nonradiative decay pathways identified for photoexcited uracil in recent quantum chemical calculations (Matsika, S. J. Phys. Chem. A. 2004, 108, 7584) are simultaneously operative in a wide variety of solvent environments. The lowest-energy triplet state was also detected by transient absorption. The triplet population appears in a few picoseconds and is not formed from the thermalized (1)npi* state. It is suggested that high spin-orbit coupling is found only along initial segments of the nonradiative decay pathways. Efficient intersystem crossing prior to vibrational cooling offers a possible explanation for the wavelength-dependent triplet yields seen in single DNA bases.

Absorption↗
PubMed2005

Base stacking controls excited-state dynamics in A.T DNA.

Solar ultraviolet light creates excited electronic states in DNA that can decay to mutagenic photoproducts. This vulnerability is compensated for in all organisms by enzymatic repair of photodamaged DNA. As repair is energetically costly, DNA is intrinsically photostable. Single bases eliminate electronic energy non-radiatively on a subpicosecond timescale, but base stacking and base pairing mediate the decay of excess electronic energy in the double helix in poorly understood ways. In the past, considerable attention has been paid to excited base pairs. Recent reports have suggested that light-triggered motion of a proton in one of the hydrogen bonds of an isolated base pair initiates non-radiative decay to the electronic ground state. Here we show that vertical base stacking, and not base pairing, determines the fate of excited singlet electronic states in single- and double-stranded oligonucleotides composed of adenine (A) and thymine (T) bases. Intrastrand excimer states with lifetimes of 50-150 ps are formed in high yields whenever A is stacked with itself or with T. Excimers limit excitation energy to one strand at a time in the B-form double helix, enabling repair using the undamaged strand as a template.

AT Rich Sequence↗
PubMed2005

Singlet excited-state dynamics of 5-fluorocytosine and Cytosine: an experimental and computational study.

The photophysics of singlet excited 5-fluorocytosine (5FC) was studied in steady-state and time-resolved experiments and theoretically by quantum chemical calculations. Femtosecond transient absorption measurements show that replacement of the C5 hydrogen of cytosine by fluorine increases the excited-state lifetime by 2 orders of magnitude from 720 fs to 73 +/- 4 ps. Experimental evidence indicates that emission in both compounds originates from a single tautomeric form. The lifetime of 5FC is the same within experimental uncertainty in the solvents ethanol and dimethyl sulfoxide. The insensitivity of the S(1) lifetime to the protic nature of the solvent suggests that proton transfer is not the principal quenching mechanism for the excited state. Excited-state calculations were carried out for the amino-keto tautomer of 5FC, the dominant species in polar environments, in order to understand its longer excited-state lifetime. CASSCF and CAS-PT2 calculations of the excited states show that the minimum energy path connecting the minimum of the (1)pi,pi state with the conical intersection responsible for internal conversion has essentially the same energetics for cytosine and 5FC, suggesting that both bases decay nonradiatively by the same mechanism. The dramatic difference in lifetimes may be due to subtle changes along the decay coordinate. A possible reason may be differences in the intramolecular vibrational redistribution rate from the Franck-Condon active, in-plane modes to the out-of-plane modes that must be activated to reach the conical intersection region.

Absorption↗
PubMed2004

Strickler-Berg analysis of excited singlet state dynamics in DNA and RNA nucleosides.

The excited singlet state lifetime of the ribonucleoside uridine was found to be 210+/-30 fs by femtosecond transient absorption spectroscopy. This value is considerably shorter than all previous time-domain measurements. This result and our previous lifetime measurements [see J.-M. L. Pecourt, J. Peon and B. Kohler, J. Am. Chem. Soc., 2001, 123, 10 370] for the other common nucleosides are compared with lifetimes calculated from available photophysical data using the Strickler-Berg (SB) equation. The calculated lifetimes for pyrimidine nucleosides are 10-25% lower than the lifetimes measured in femtosecond transient absorption experiments. For the purine nucleosides, guanosine and adenosine, consideration of just the lowest 1pi --> pi* transition led to predicted lifetimes that are three times greater than experimental ones. On the other hand, inclusion of both of the lowest energy 1pi --> pi* absorption bands in the SB equation resulted in much better agreement with the experimental values. This suggests that both 1pi pi* states of the purine nucleosides contribute to their emission. Decay by the bright 1pi pi* state (or states, in the case of the purines) is believed to be responsible for the experimentally observed lifetimes.

DNA↗
PubMed2003

Ultrafast excited-state dynamics of adenine and monomethylated adenines in solution: implications for the nonradiative decay mechanism.

The DNA base adenine and four monomethylated adenines were studied in solution at room temperature by femtosecond pump-probe spectroscopy. Transient absorption at visible probe wavelengths was used to directly observe relaxation of the lowest excited singlet state (S(1) state) populated by a UV pump pulse. In H(2)O, transient absorption signals from adenine decay biexponentially with lifetimes of 0.18 +/- 0.03 ps and 8.8 +/- 1.2 ps. In contrast, signals from monomethylated adenines decay monoexponentially. The S(1) lifetimes of 1-, 3-, and 9-methyladenine are similar to one another and are all below 300 fs, while 7-methyladenine has a significantly longer lifetime (tau = 4.23 +/- 0.13 ps). On this basis, the biexponential signal of adenine is assigned to an equilibrium mixture of the 7H- and 9H-amino tautomers. Excited-state absorption (ESA) by 9-methyladenine is 50% stronger than by 7-methyladenine. Assuming that ESA by the corresponding tautomers of adenine is unchanged, we estimate the population of 7H-adenine in H(2)O at room temperature to be 22 +/- 4% (estimated standard deviation). To understand how the environment affects nonradiative decay, we performed the first solvent-dependent study of nucleobase dynamics on the ultrafast time scale. In acetonitrile, both lowest energy tautomers of adenine are present in roughly similar proportions as in water. The lifetimes of the 9-substituted adenines depend somewhat more sensitively on the solvent than those of the 7-substituted adenines. Transient signals for adenine in H(2)O and D(2)O are identical. These solvent effects strongly suggest that excited-state tautomerization is not an important nonradiative decay pathway. Instead, the data are most consistent with electronic energy relaxation due to state crossings between the optically prepared (1)pipi* state and one or more (1)npi* states and the electronic ground state. The pattern of lifetimes measured for the monomethylated adenines suggests a special role for the (1)npi* state associated with the N7 electron lone pair.

Adenine↗
PubMed2003

Singlet excited-state lifetimes of cytosine derivatives measured by femtosecond transient absorption.

Lifetimes of the lowest excited singlet (S1) electronic states of various derivatives of the pyrimidine nucleobase cytosine (Cyt) were measured by the femtosecond transient absorption technique. The bases were excited in room-temperature aqueous solution at 265 nm using approximately 200 fs pump pulses from a titanium-sapphire laser system. The decay of excited-state absorption (ESA) at visible probe wavelengths was used to determine the S1 lifetimes of a variety of modified Cyt compounds at different pH values by global fitting. Identical lifetimes were observed for Cyt and cytidine (Cyd) within experimental uncertainty, but ESA by the ribonucleoside was considerably stronger, suggesting that the ribose group increases the oscillator strength of the S1 --> SN transition. The S1 lifetime of the important minor base 5-methylcytosine (m5Cyt) is 7.2 +/- 0.4 ps at pH 6.8. The same lifetime was measured for the ribonucleoside 5-methylcytidine, but sugar substitution again increased the strength of the ESA signal. Protonation of Cyd and m5Cyt at low pH led to a modest decrease in their S1 lifetimes. On the other hand, deprotonation of Cyt and m5Cyt significantly increased the lifetime of their respective S1 states. These trends support the intermediacy of the n,pi* state localized on the carbonyl oxygen in the nonradiative decay mechanism of Cyt. Longer S1 lifetimes were observed for 5-fluorocytosine and N4-acetylcytosine. Collectively, these results illustrate the great potential of femtosecond laser spectroscopy for investigating excited-state dynamics in DNA and DNA components.

Cytosine↗
PubMed2002

Ultrafast decay of electronically excited singlet cytosine via a pi,pi* to n(O),pi* state switch.

Singlet fluorescence lifetimes of adenosine, cytidine, guanosine, and thymidine, determined by femtosecond pump-probe spectroscopy (Pecourt, J.-M. L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2000, 122, 9348. Pecourt, J.-M. L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2001, 123, 10370), show that the excited states produced by 263 nm light in these nucleosides decay in the subpicosecond range (290-720 fs). Ultrafast radiationless decay to the ground state greatly reduces the probability of photochemical damage. In this work we present a theoretical study of isolated cytosine, the chromophore of cytidine. The experimental lifetime of 720 fs indicates that there must be an ultrafast decay channel for this species. We have documented the possible decay channels and approximate energetics, using a valence-bond derived analysis to rationalize the structural details of the paths. The mechanism favored by our calculations and the experimental data involves (1) a two-mode decay coordinate composed of initial bond length inversion followed by internal vibrational energy redistribution (IVR) to populate a carbon pyramidalization mode, (2) a state switch between the pi,pi* and nO,pi* (excitation from oxygen lone pair) excited states, and (3) decay to the ground state through a conical intersention. A second decay path through the nN,pi* state (excitation from the nitrogen lone pair), with a higher barrier, involves out-of-plane bending of the amino substituent.

Cytosine↗
PubMed2002

Solvent reorganization controls the rate of proton transfer from neat alcohol solvents to singlet diphenylcarbene.

Femtosecond transient absorption spectroscopy was used to study singlet diphenylcarbene generated by photodissociation of diphenyldiazomethane with a UV pulse at 266 nm. Absorption by singlet diphenylcarbene was detected and characterized for the first time. Similar band shapes were observed in acetonitrile and in cyclohexane with lambda(max) approximately 370 nm. The singlet absorption decays by intersystem crossing to triplet diphenylcarbene at rates that agree with previous measurements. The singlet absorption band is completely formed 1 ps after the pump pulse. It is preceded by a strong and broad absorption band, which is tentatively assigned to excited-state absorption by a singlet diazo excited state. In neat alcohol solvents the growth and decay of the diphenylmethyl cation was observed. This species is formed by proton transfer from an alcohol molecule to singlet diphenylcarbene. Since a shell of solvent molecules surrounds each nascent carbene, the intrinsic rate of protonation in the absence of diffusion could be measured. In methanol, proton transfer occurs with a time constant of 9.0 ps, making this the fastest known intermolecular proton-transfer reaction to carbon. In O-deuterated methanol proton transfer occurs in 15.0 ps. Slower rates were observed in the longer alcohols. The protonation times correlate reasonably well with solvation times in these alcohols, suggesting that solvent fluctuations are the rate-limiting step. In all alcohols studied, the carbocations decay on a somewhat slower time scale to yield diphenylalkyl ethers. In methanol and ethanol the rate of decay is determined by reaction with neutral solvent nucleophiles. There is evidence in 2-propanol that geminate reaction within the initial ion pair is faster than reaction with solvent. No isotope effect was observed for the reaction of the diphenylmethyl carbocation in methanol. Using comparative actinometry the quantum yield of protonation was measured. In methanol, the quantum yield of carbocations reaches a maximum value of 0.18 approximately 18 ps after the pump pulse. According to our analysis, 30% of the photoexcited diazo precursor molecules are eventually protonated. Somewhat lower protonation efficiencies are observed in the other alcohols. Because the primary quantum yield for formation of singlet diphenylcarbene is still unknown, the importance of reaction channels that might exist in addition to protonation cannot be determined at present. Singlet carbenes are powerful, photogenerated bases that open new possibilities for fundamental studies of proton transfer in solution.

Journal Article↗