Biomedical subjects

Manuela Merchán

Publications and source records attributed to Manuela Merchán.

15 recordsLinked to original sources

PubMed2006

Unified model for the ultrafast decay of pyrimidine nucleobases.

Ultrafast decay processes detected after absorption of UV radiation in gas-phase pyrimidine nucleobases uracil, thymine, and cytosine are ascribed to the barrierless character of the pathway along the low-lying 1(pipi*) hypersurface connecting the Franck-Condon region with an out-of-plane distorted ethene-like conical intersection with the ground state. Longer lifetime decays and low quantum yield emission are on the other hand related to the presence of a 1(pipi*) state planar minimum on the S1 surface and the barriers to access other conical intersections. A unified model for the three systems is established on the basis of accurate multiconfigurational CASPT2 calculations, whereas the effect of the different levels of theory on the results is carefully analyzed.

Models, Chemical↗

PubMed2006

Theoretical insight into the spectroscopy and photochemistry of isoalloxazine, the flavin core ring.

The electronic singlet-singlet and singlet-triplet electronic transitions of the isoalloxazine ring of the flavin core are studied using second-order perturbation theory within the framework of the CASPT2//CASSCF protocol. The main features of the absorption spectrum are computed at 3.09, 4.28, 4.69, 5.00, and 5.37 eV. The lowest singlet (S1) and triplet (T1) excited states are found to be both of pi character with a singlet-triplet splitting of 0.57 eV. On the basis of the analysis of the computed spin-orbit couplings and the potential energy hypersurfaces built for the relevant excited states, the intrinsic mechanism for photoinduced population of T1 is discussed. Upon light absorption, evolution of the lowest singlet excited state along the relaxation pathway leads ultimately to the population of the lowest triplet state, which is mediated by a singlet-triplet crossing with a state of npi* type. Subsequently a radiationless decay toward T1 through a conical intersection takes place. The intersystem crossing mechanism and the internal conversion processes documented here provide a plausible route to access the lowest triplet state, which has a key role in the photochemistry of the flavin core ring and is mainly responsible for the reactivity of the system.

Flavins↗

PubMed2006

Toward the understanding of DNA fluorescence: the singlet excimer of cytosine.

By using the multiconfigurational second-order perturbation method CASPT2, including corrections for the basis set superposition error, the lowest-singlet excited state of the face-to-face pi-stacked cytosine homodimer is revealed to be bound by about half an eV, being the source of an emissive feature consistent with the observed redshifted fluorescence.

Chemistry, Physical↗

PubMed2006

Ab initio determination of the ionization potentials of DNA and RNA nucleobases.

Quantum chemical high level ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated. The present results represent a systematic compendium of these magnitudes, establishing theoretical reference values at a level not reported before, calibrating computational strategies, and guiding the assignment of the features in the experimental photoelectron spectra.

Adenine↗

PubMed2006

A three-state model for the photophysics of adenine.

An ab initio theoretical study at the CASPT2 level is reported on minimum energy reaction paths, state minima, transition states, reaction barriers, and conical intersections on the potential energy hypersurfaces of two tautomers of adenine: 9H- and 7H-adenine. The obtained results led to a complete interpretation of the photophysics of adenine and derivatives, both under jet-cooled conditions and in solution, within a three-state model. The ultrafast subpicosecond fluorescence decay measured in adenine is attributed to the low-lying conical intersection (gs/pipi* La)(CI), reached from the initially populated 1(pipi* La) state along a path which is found to be barrierless only in 9H-adenine, while for the 7H tautomer the presence of an intermediate plateau corresponding to an NH2-twisted conformation may explain the absence of ultrafast decay in 7-substituted compounds. A secondary picosecond decay is assigned to a path involving switches towards two other states, 1(pipi* Lb) and 1(npi*), ultimately leading to another conical intersection with the ground state, (gs/npi*), with a perpendicular disposition of the amino group. The topology of the hypersurfaces and the state properties explain the absence of secondary decay in 9-substituted adenines in water in terms of the higher position of the 1(npi*) state and also that the 1(pipi* Lb) state of 7H-adenine is responsible for the observed fluorescence in water. A detailed discussion comparing recent experimental and theoretical findings is given. As for other nucleobases, the predominant role of a pipi*-type state in the ultrafast deactivation of adenine is confirmed.

Adenine↗

PubMed2006

Adenine and 2-aminopurine: paradigms of modern theoretical photochemistry.

Distinct photophysical behavior of nucleobase adenine and its constitutional isomer, 2-aminopurine, has been studied by using quantum chemical methods, in particular an accurate ab initio multiconfigurational second-order perturbation theory. After light irradiation, the efficient, ultrafast energy dissipation observed for nonfluorescent 9H-adenine is explained here by the nonradiative internal conversion process taking place along a barrierless reaction path from the initially populated 1(pipi* La) excited state toward a low-lying conical intersection (CI) connected with the ground state. In contrast, the strong fluorescence recorded for 2-aminopurine at 4.0 eV with large decay lifetime is interpreted by the presence of a minimum in the 1(pipi* La) hypersurface lying below the lowest CI and the subsequent potential energy barrier required to reach the funnel to the ground state. Secondary deactivation channels were found in the two systems related to additional CIs involving the 1(pipi* Lb) and 1(npi*) states. Although in 9H-adenine a population switch between both states is proposed, in 7H-adenine this may be perturbed by a relatively larger barrier to access the 1(npi*) state, and, therefore, the 1(pipi* Lb) state becomes responsible for the weak fluorescence measured in aqueous adenine at approximately 4.5 eV. In contrast to previous models that explained fluorescence quenching in adenine, unlike in 2-aminopurine, on the basis of the vibronic coupling of the nearby 1(pipi*) and 1(npi*) states, the present results indicate that the 1(npi*) state does not contribute to the leading photophysical event and establish the prevalence of a model based on the CI concept in modern photochemistry.

2-Aminopurine↗

PubMed2006

A theoretical insight into the photophysics of psoralen.

Psoralen photophysics has been studied on quantum chemistry grounds using the multiconfigurational second-order perturbation method CASPT2. Absorption and emission spectra of the system have been rationalized by computing the energies and properties of the low-lying singlet and triplet excited states. The S1 pipi* state has been determined to be responsible of the lowest absorption and fluorescence bands and to initially carry the population in the photophysical processes related to the phototherapeutic properties of psoralen derivatives. The low-lying T1 pipi* state is, on the other hand, protagonist of the phosphorescence, and its prevalent role in the reactivity of psoralen is suggested to be related to the elongation of the pyrone ring C3-C4 bond, where the spin density is distributed on both carbon atoms. Analysis of energy gaps and spin-orbit coupling elements indicates that the efficient photophysical process leading to the population of the lowest triplet state does not take place at the Franck-Condon region but along the S1 relaxation path.

Absorption↗

PubMed2005

A theoretical study on the low-lying excited states of 2,2':5',2''-terthiophene and 2,2':5',2'':5'',2'''-quaterthiophene.

The nature and properties of the low-lying singlet and triplet valence excited states of 2,2':5',2''-terthiophene (terthiophene) and 2,2':5',2'':5'',2'''-quaterthiophene (tetrathiophene) are discussed on the basis of high-level ab initio computations. The spectroscopic features determined experimentally for short alpha-oligothiophenes are rationalised on theoretical grounds. Special attention is devoted to the nonradiative decay process through intersystem crossing (ISC) from the singlet to the triplet manifold, which is known to be relatively less efficient in tetrathiophene. Along the geometry relaxation of the S1 state of terthiophene, the S1 and T2 states become degenerate, which leads to a favourable situation for the occurrence of ISC. The parallel process is expected to be less favoured in tetrathiophene because of the less efficient spin-orbit coupling and the increase of the S1-T2 energy gap.

Journal Article↗

PubMed2005

Computation of conical intersections by using perturbation techniques.

Multiconfigurational second-order perturbation theory, both in its single-state multiconfigurational second-order perturbation theory (CASPT2) and multistate (MS-CASPT2) formulations, is used to search for minima on the crossing seams between different potential energy hypersurfaces of electronic states in several molecular systems. The performance of the procedures is tested and discussed, focusing on the problem of the nonorthogonality of the single-state perturbative solutions. In different cases the obtained structures and energy differences are compared with available complete active space self-consistent field and multireference configuration interaction solutions. Calculations on different state crossings in LiF, formaldehyde, the ethene dimer, and the penta-2,4-dieniminium cation illustrate the discussions. Practical procedures to validate the CASPT2 solutions in polyatomic systems are explored, while it is shown that the application of the MS-CASPT2 procedure is not straightforward and requires a careful analysis of the stability of the results with the quality of the reference wave functions, that is, the size of the active space.

Journal Article↗

PubMed2005

Triplet-state formation along the ultrafast decay of excited singlet cytosine.

We address the possibility of populating the lowest triplet state of cytosine by an "intrinsic"mechanism, namely, intersystem crossing (ISC) along the ultrafast internal conversion pathway of the electronically excited singlet species. For this purpose, we present a discussion of the ISC process and triplet-state reactivity based on theoretical analysis of the spin-orbit strength and the potential energy surfaces for the relevant singlet and triplet states of cytosine. High-level ab initio computations show that ISC is possible in wide regions of the singlet manifold along the reaction coordinate that controls the ultrafast internal conversion to the ground state. Thus, the ISC mechanism documented here provides a possibility to access the triplet state, which has a key role in the photochemistry of the nucleic acid bases.

Cytosine↗

PubMed2005

Theoretical study of the electronic excited states of tetracyanoethylene and its radical anion.

The low-lying electronic states of tetracyanoethylene (TCNE) and its radical anion were studied using multiconfigurational second-order perturbation theory (CASPT2) and extended atomic natural orbital (ANO) basis sets. The results obtained yield a full interpretation of the electronic absorption spectra, explain the spectral changes undergone upon reduction, give support to the occurrence of a bound excited state for the anionic species, and provide valuable information for the rationalization of the experimental data obtained with electron transmission spectroscopy.

Journal Article↗

PubMed2003

The low-lying excited states of 2,2'-bithiophene: a theoretical analysis.

The low-energy region of the singlet-->singlet, singlet-->triplet, and triplet-->triplet electronic spectra of 2,2'-bithiophene are studied using multiconfigurational second-order perturbation theory (CASPT2) and extended atomic natural orbitals (ANO) basis sets. The computed vertical, adiabatic, and emission transition energies are in agreement with the available experimental data. The two lowest singlet excited states, 1(1)Bu and 2(1)Bu, are computed to be degenerate, a novel feature of the system to be borne in mind during the rationalization of its photophysics. As regards the observed high triplet quantum yield of the molecule, it is concluded that the triplet states 2(3)Ag and 2(3)Bu, separated about 0.4 eV from the two lowest singlet excited states, can be populated by intersystem crossing from nonplanar singlet states.

Journal Article↗

PubMed2003

Ultrafast internal conversion of excited cytosine via the lowest pipi electronic singlet state.

Computational evidence at the CASPT2 level supports that the lowest excited state pipi* contributes to the S1/S0 crossing responsible for the ultrafast decay of singlet excited cytosine. The computed radiative lifetime, 33 ns, is consistent with the experimentally derived value, 40 ns. The nOpi* state does not play a direct role in the rapid repopulation of the ground state; it is involved in a S2/S1 crossing. Alternative mechanisms through excited states pisigma* or nNpi* are not competitive in cytosine.

Cytosine↗

PubMed2003

An Ab initio study on the mechanism of the atmospheric reaction NH2 + O3-->H2NO + O2.

The atmospheric reaction NH2 + O3-->H2NO + O2 has been investigated theoretically by using MP2, QCISD, QCISD(T), CCSD(T), CASSCF, and CASPT2 methods with various basis sets. At the MP2 level of theory, the hypersurface of the potential energy (HPES) shows a two step reaction mechanism. Therefore, the mechanism proceeds along two transition states (TS1 and TS2), separated by an intermediate designated as Int. However, when the single-reference higher correlated QCISD and the multiconfigurational CASSCF methodologies have been employed, the minimum structure Int and TS2 are not found on the HPES, which thus confirms a direct reaction mechanism. Single-reference high correlated and multiconfigurational methods consistently predict the barrier height of the reaction to be within the range of 3.9 to 6.6 kcal mol-1, which is somewhat higher than the experimental value. The calculated reaction enthalpy is -67.7 kcal mol-1.

Journal Article↗

PubMed2002

Cyclooctatetraene computational photo- and thermal chemistry: a reactivity model for conjugated hydrocarbons.

We use ab initio CASSCF and CASPT2 computations to construct the composite multistate relaxation path relevant to cycloocta-1,3,5,7-tetraene singlet photochemistry. The results show that an efficient population of the dark excited state (S(1)) takes place after ultrafast decay from the spectroscopic excited state (S(2)). A planar D(8)(h)-symmetric minimum represents the collecting point on S(1). Nonadiabatic transitions to S(0) appear to be controlled by two different tetraradical-type conical intersections, which are directly accessible from the S(1) minimum following specific excited-state reaction paths. The higher-energy conical intersection belongs to the same type of intersections previously documented in linear and cyclic conjugated hydrocarbons and features a triangular -(CH)(3)- kink. This point mediates both cis --> trans photoisomerization and cyclopropanation reactions. The lowest energy conical intersection has a boat-shaped structure. This intersection accounts for production of semibullvalene or for double-bond shifting. The mapping of both photochemical and thermal reaction paths (including also Cope rearrangements, valence isomerizations, ring inversions, and double-bond shifting) has allowed us to draw a comprehensive reactivity scheme for cyclooctatetraene, which rationalizes the experimental observations and documents the complex network of photochemical and thermal reaction path interconnections. The factors controlling the selection and accessibility of a number of conjugated hydrocarbon prototype conical intersections and ground-state relaxation channels are discussed.

Journal Article↗