Biomedical subjects

Luis Serrano-Andrés

Publications and source records attributed to Luis Serrano-Andrés.

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

Ultrafast electron transfer in photosynthesis: reduced pheophytin and quinone interaction mediated by conical intersections.

The mechanism of electron transfer (ET) from reduced pheophytin (Pheo(-)) to the primary stable photosynthetic acceptor, a quinone (Q) molecule, is addressed by using high-level ab initio computations and realistic molecular models. The results reveal that the ET process involving the (Pheo(-) + Q) and (Pheo + Q(-)) oxidation states can be essentially seen as an ultrafast radiationless transition between the two hypersurfaces taking place via conical intersections (CIs). According to the present findings, an efficient ultrafast ET implies that the Pheo- and Q move toward each other in a given preferential parallel orientation, reaching the most effective arrangement for ET at intermolecular distances (R) around 5-3 Angstrom, where the lowest CIs are predicted. Favored donor/acceptor interactions are related to orientations with some overlap between the lowest occupied molecular orbitals (LUMO) of the two systems, and they lead to state-crossings at an earlier stage of the movement (larger R). Furthermore, when the topology of the interacting moieties does not make possible the LUMOs overlap, the corresponding diabatic potential energy curves do not intersect. Thus, it is anticipated that large scale motions, which are difficult to monitor experimentally, are actually occurring in the photosynthetic reaction centers of bacteria, algae, and higher plants, to fulfill the observed ultrafast ET processes.

Journal Article↗

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

Determination of the lowest-energy oxidation site in nucleotides: 2'-deoxythymidine 5'-monophosphate anion.

High level ab initio computations anticipate nucleobases as the most favorable sites for oxidation in nucleotides. At the CASPT2 level, the lowest ionization channel for the 2'-deoxythymidine 5'-monophosphate anion is related to a pi-orbital of the thymine base. The present findings lead to revision of the recent assignments of the photodetachment photoelectron spectra of mononucleotide anions in the gas phase and support the classical view of the nucleobase being the main actor in the oxidation process of both nucleosides and nucleotides.

Anions↗

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↗

PubMed2006

A computational study of the lowest singlet and triplet states of neutral and dianionic 1,2-substituted icosahedral and octahedral o-carboranes.

This work introduces a calibrated B3LYP/6-31G(d) study on the electronic structure of singlet and triplet neutral species of 1,2-substituted icosahedral 1,2-R(2)-1,2-C(2)B(10)H(10) and octahedral 1,2-R(2)-1,2-C(2)B(4)H(4) molecules with R = {H, OH, SH, NH(2), PH(2), CH(3), SiH(3)} and their respective dianions formed by proton removal on each R group. A variety of small adiabatic singlet-triplet gaps DeltaE(ST) are obtained from these systems ranging from 2.93 eV (R = NH(2)) <or= DeltaE(ST) <or= 3.98 eV (R = SiH(3)) for the icosahedral neutrals and 1.56 eV (R = NH(2)) <or= DeltaE(ST) <or= 4.13 eV (R = SiH(3)) for the octahedral neutrals, these gaps being globally smaller for the dianionic systems, ranging from 0.94 eV (R(-) = CH(2) (-)) <or= DeltaE(ST) <or= 2.01 (R(-) = e(-)) for the icosahedral dianions 1,2-(R(-))(2)-C(2)B(10)H(10) and 0.91 (R(-) = CH(2) (-)) <or= DeltaE(ST) <or= 2.41 (R = SiH(2) (-)) for the octahedral dianions 1,2-(R(-))(2)--C(2)B(4)H(4) (R(-) = e(-), O(-), S(-), NH(-), PH(-), CH(2) (-), PH(2) (-)). The different gaps lie within or in the neighborhood of the visible region of the electromagetic spectrum. The optimized geometries for the molecular cage remain similar in substituted icosahedral and octahedral singlet states, while a rich variety of different structures can be found for the optimized triplet states.

Algorithms↗

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

On the low-lying excited states of sym-triazine-based herbicides.

We report a joint computational and luminescence study on the low-lying excited states of sym-triazines, namely, 1,3,5-triazine (1) and the ubiquitous herbicides atrazine [6-chloro-N2-ethyl-N4-isopropyl-1,3,5-triazine-2,4-diamine (2)] and ametryn [6-methylthio-N2-ethyl-N4-isopropyl-1,3,5-triazine-2,4-diamine (3)]. Geometrical structures, energetics, and transition and state properties of I and 2 were computed at the TD-DFT, CASSCF, and CASPT2 levels of theory. The fluorescence and phosphorescence emission spectra, lifetimes, and fluorescence quantum yields were measured for the three compounds, and from these, the energies of the lowest excited states and their corresponding radiative rates were determined. The predictions from CASPT2 calculations are in good agreement with the experimental results obtained from the luminescence studies and allow the interpretation of different absorption and emission features.

Absorption↗

PubMed2004

Multiconfigurational second-order perturbation study of the decomposition of the radical anion of nitromethane.

The doublet potential energy surfaces involved in the decomposition of the nitromethane radical anion (CH(3)NO(2) (-)) have been studied by using the multistate extension of the multiconfigurational second-order perturbation method (MS-CASPT2) in conjunction with large atomic natural orbital-type basis sets. A very low energy barrier is found for the decomposition reaction: CH(3)NO(2) (-)-->[CH(3)NO(2)](-)-->CH(3)+NO(2) (-). No evidence has been obtained on the existence of an isomerization channel leading to the initial formation of the methylnitrite anion (CH(3)ONO(-)) which, in a subsequent reaction, would yield nitric oxide (NO). In contrast, it is suggested that NO is formed through the bimolecular reaction: CH(3)+NO(2) (-)-->[CH(3)O-N-O](-)-->CH(3)O(-)+NO. In particular, the CASSCF/MS-CASPT2 results indicate that the methylnitrite radical anion CH(3)ONO(-) does not represent a minimum energy structure, as concluded by using density functional theory (DFT) methodologies. The inverse symmetry breaking effect present in DFT is demonstrated to be responsible for such erroneous prediction.

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↗