0000000000177566
AUTHOR
Mercedes Rubio
DNA nucleobase properties and photoreactivity: Modeling environmental effects
Abstract The accurate ab initio quantum chemical (QM) method multiconfigurational second-order perturbation (CASSPT2)/complete active space self-consistent field (CASSCF) has been used in conjunction with molecular mechanics (MM) procedures to compute molecular properties and photoinduced reactivity of DNA/RNA nucleobases (NABs) in isolation and within a realistic environment, in which the double helix strand, the aqueous media, and the external counterions are included. It is illustrated that the use of an MM model is helpful both to account for short- and long-range effects of the system surrounding the QM molecular core and to provide the proper structural constraints that allow more acc…
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. Daniel.Roca@uv.es Mercedes.Rubio@uv.es Manuela.Merchan@uv.es Luis.Serrano@uv.es
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.
Electronic spectra of tetrathiafulvalene and its radical cation: analysis of the performance of the time-dependent DFT approach
Abstract The electronic spectra of tetrathiafulvalene and its radical cation have been studied within the framework of the time-dependent density functional theory by using a conventional hybrid functional. The behaviour of the method has been analyzed through the computed vertical excitation energies for the low-lying electronic excited states. Although the procedure provides a correct description of many of the features of the spectra, deviations in the range 0.4–0.7 eV have been obtained for several transitions, from which one can conclude misleading assignments.
On the chemiluminescence emission of luminol: protic and aprotic solvents and encapsulation to improve the properties in aqueous solution.
Luminol is a popular molecule that is currently gaining further interest due to its potential role for non-invasive cancer treatments. Design of more efficient derivatives in this context would benefit from a clear knowledge on the origin of the distinct intensity and spectroscopic properties in protic and aprotic solvents observed experimentally, which are still not rationalized. By efficiently combining molecular dynamics, quantum methodologies based on density functional theory and multiconfigurational quantum chemistry and hybrid approaches, and developing herein a computational approach for accurately determining "molar negative extinction (or gain) coefficients of emission", we firstl…
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'-quictterthiophene (tetrdthiophene) are discussed on the basis of high-level ab initio. computations. The spectrascopic features determined experimentally for short α-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 S 1 state of terthiophene, the S' 1 and T 2 states become degenerate, which leads. to a…
Electronic Transitions in Tetrathiafulvalene and Its Radical Cation: A Theoretical Contribution
The low-lying electronic states of tetrathiafulvalene (TTF) and its radical cation (TTF+) have been studied using the multistate extension of a multiconfigurational second-order perturbation method (MS−CASPT2). The minimum-energy equilibrium geometries optimized at the CASSCF level have a boatlike conformation for the neutral molecule, with no significant barrier toward planarity. A more aromatic planar structure is, however, found for the ionic system. For TTF, the calculations of the vertical excitation energies comprise valence singlet and triplet states as well as the lowest members of the Rydberg series converging to the first ionization limit. Valence doublet states have been consider…
Are most of the stationary points in a molecular association minima? Application of Fraga's potential to benzene-benzene
The importance of characterizing the stationary points of the intermolecular potential by means of Hessian eigenvalues is illustrated for the calculation of the benzene–benzene interaction using an atom-to-atom pair potential proposed by Fraga (FAAP). Two models, the standard one-center-per atom and another using three-centers-per atom due to Hunter and Sanders, are used to evaluate the electrostatic contributions and the results are compared. It is found in both cases that although using low-gradient thresholds allows optimization procedures to avoid many stationary points that are not true minima computing time considerations makes the usual procedure of using high-gradient thresholds [sa…
A theoretical study of the electronic spectrum of bithiophene
The electronic spectrum of bithiophene in the energy range up to 6.0 eV has been studied using multiconfigurational second order perturbation theory (CASPT2) and a basis set of ANO type, with split valence quality and including polarization functions on all heavy atoms. Calculations were performed at a planar (trans) and twisted geometry. The calculated ordering of the excited singlet states is 1Bu, 1Bu, 1Ag, 1Ag, and 1Bu with 0–0 transition energies: 3.88, 4.15, 4.40, 4.71, and 5.53 eV, respectively. The first Rydberg transition (3s) has been found at 5.27 eV. The results have been used in aiding the interpretation of the experimental spectra, and in cases where a direct comparison is poss…
Theoretical study of the electronic spectrum of magnesium-porphyrin
Multiconfigurational self-consistent field (SCF) and second order perturbation methods have been used to study the electronic spectrum of magnesium-porphyrin (MgP). An extended ANO-type basis set including polarization functions on all heavy atoms has been used. Four allowed singlet states of E1u symmetry have been computed and in addition a number of forbidden transitions and a few triplet states. The results lead to a consistent interpretation of the electronic spectrum, where the Q band contains one transition, the B band two, and the N band one. The computed transition energies are consistently between 0.1 and 0.5 too low compared to the measured band maxima. The source of the discrepan…
Electronic Spectra of 2,2‘-Bithiophene and 2,2‘:5‘,2‘ ‘-Terthiophene Radical Cations: A Theoretical Analysis
Analysis of the electronic spectra of 2,2‘-bithiophene and 2,2‘:5‘,2‘ ‘-terthiophene radical cations has been performed by using multiconfigurational second-order perturbation theory (CASPT2). Atomic natural orbital (ANO) type basis sets of split valence quality, including polarization functions on all heavy atoms, have been used. In agreement with experimental data, in the energy range below the lowest optically allowed transition of the respective neutral system, theoretical results predict two main absorption bands for both cations. The 22Au and 32Au states computed at 1.94 and 2.80 eV, respectively, are related to the corresponding band maxima recorded for bithiophene cation. The 12B1 s…
The internal rotational barrier of biphenyl studied with multiconfigurational second-order perturbation theory (CASPT2)
A detailedab initio study of the molecular structure and rotational barriers of biphenyl has been performed. First, non-dynamical correlation effects involving the π system are taken into account at the CASSCF level. These wave functions are subsequently employed as reference functions in a multiconfigurational second-order perturbation treatment (CASPT2). The performance single-reference approaches is in addition analysed. The molecular geometries of biphenyl in twisted, coplanar, and perpendicular conformations have been optimized at the CASSCF level. A rotational angle of 44.3° is predicted for the minimum energy conformer in agreement with gas-phase electron diffraction data (44.4±1.2°)…
Towards the understanding at the molecular level of the structured-water absorption and fluorescence spectra: a fingerprint of π-stacked water
An intriguing absorption peak around ∼270 nm (4.59 eV) has been recurrently recorded in aqueous solutions of salts, sugars, amino acids, in the free-solute zone (exclusion zone) adjacent to various hydrophilic surfaces, as well as a transient in the conversion process of ice to water. The corresponding associated fluorescence has been observed in the interval 480–490 nm (2.58–2.53 eV). The spectroscopic features have been related to the presence of structured water but its nature remains incompletely understood. On the basis of high-level ab initio computations, the main absorption feature of structured water is assigned to the presence of two π-stacked ground-state water molecules, prefera…
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 B u and 2'B u , 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 A g and 2 3 B u ,…
On the N1-H and N3-H Bond Dissociation in Uracil by Low Energy Electrons: A CASSCF/CASPT2 Study.
The dissociative electron-attachment (DEA) phenomena at the N1-H and N3-H bonds observed experimentally at low energies (<3 eV) in uracil are studied with the CASSCF/CASPT2 methodology. Two valence-bound π(-) and two dissociative σ(-) states of the uracil anionic species, together with the ground state of the neutral molecule, are proven to contribute to the shapes appearing in the experimental DEA cross sections. Conical intersections (CI) between the π(-) and σ(-) are established as the structures which activate the DEA processes. The N1-H and N3-H DEA mechanisms in uracil are described, and experimental observations are interpreted on the basis of two factors: (1) the relative energy of …
Theoretical studies of isomers of C 3 H 2 using a multiconfigurational approach
The C3H2 isomers are important molecules in interstellar space. An understanding of their electronic structure can contribute significantly to the interpretation of interstellar spectra. In a theoretical study of the C3H2 isomers a multiconfigurational treatment is of interest because many of the isomers are carbenes or diradicals. We present such an investigation of all possible C3H2 isomers. The most important features of their electronic and vibrational spectra are calculated. Earlier theoretical studies are reviewed and it is shown that the present study yields the same order of stability for the singlet and triplet states as most previous studies.
Interpretation of the electronic absorption spectrum of free base porphin by using multiconfigurational second-order perturbation theory
Abstract Multiconfigurational second-order perturbation (CASPT2) calculations have been performed on the low-lying optically allowed valence excited states of the free base porphin molecule in order to assign the four lowest bands of the spectrum. The low-lying triplet states have also been characterized. A basis set of the atomic natural orbital type of split-valence plus polarization quality for first-row atoms has been employed. Polarization functions are important for an accurate description of the transitions. These CASPT2 results provide a consistent picture of the experimental spectrum. Each band of the spectrum up to 4.5 eV is composed of a pair of states, which become degenerate in…
A theoretical study of the electronic spectrum of biphenyl
Abstract The electronic spectrum of biphenyl in the energy range up to 6.0 eV has been studied using multiconfigurational second-order perturbation theory (CASPT2) and a basis set of ANO type, including polarization functions on all carbon atoms. The calculated spectrum gives conclusive assignments to all valence excited singlet states and the low-lying triplet states. The change of the torsional angle between the two benzene rings in the different excited states is shown to be of considerable importance and explains the different excitation energies observed in the gas phase as compared to solution or crystalline biphenyl at low temperatures. The intense transition to the 1 1B1u state is m…
An Accurate Quartic Force Field and Fundamental Frequencies for the Ozonide Anion: A Rare Positive Anharmonicity for the Antisymmetric Stretch
The CCSD(T) method has been used to compute a highly accurate quartic force field and fundamental frequencies for all 16O and 18O isotopomers of the ozonide anion. The CCSD and CASPT2 methods have also been used to verify the reliability of the CCSD(T) fundamental frequencies. The computed fundamental frequencies are in agreement with gas-phase experiments, but disagree with matrix isolation experiments for the antisymmetric stretch, ν3. CASPT2 calculations show that the antisymmetric part of the O3- potential surface is sensitive to the external environment. It is concluded that the antisymmetric stretch exhibits a significant matrix shift in the matrix isolation experiments and that the m…
Theoretical spectroscopy of organic systems
Abstract The complete active space (CAS) SCF method in conjunction with the multiconfigurational second-order perturbation theory (CASPT2) has been applied to study the electronically excited states of basic organic compounds. As shown in the lecture with a number of examples, the CASPT2 method is capable of yielding accurate results for relative energies and other properties of excited states, provided that flexible one-electron basis sets are employed. The applications comprise an ample range of systems and problems, including polyenes, conjugated and unconjugated dienes, alternant and nonalternant hydrocarbons, polyenals, etc. As a whole these studies enable both qualitative and quantita…
Excited states of the water molecule: Analysis of the valence and Rydberg character
The excited states of the water molecule have been analyzed by using the extended quantum-chemical multistate CASPT2 method, namely, MS-CASPT2, in conjunction with large one-electron basis sets of atomic natural orbital type. The study includes 13 singlet and triplet excited states, both valence and 3s-, 3p-, and 3d-members of the Rydberg series converging to the lowest ionization potential and the 3s- and 3p-Rydberg members converging to the second low-lying state of the cation, 1 math. The research has been focused on the analysis of the valence or Rydberg character of the low-lying states. The computation of the 1 math state of water at different geometries indicates that it has a predom…
Ab initio determination of the electron affinities of DNA and RNA nucleobases
High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic electron affinities of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. The present results aim for the accurate determination of the intrinsic electron acceptor properties of the isolated nucleic acid bases as described by their electron affinities, establishing an overall set of theoretical reference values at a level not reported before and helping to rule out less reliable theoretical and experimental data and to calibrate theoretical strategies. Daniel.Roca@uv.es Manuela.Merchan@uv.es Luis.Se…
AMYR 2: A new version of a computer program for pair potential calculation of molecular associations
AMYR is a computer program for the calculation of molecular associations using Fraga's pairwise atom-atom potential. The interaction energy is evaluated through a 1R expansion. The electrostatic energy is calculated through either the one-centre-per atom or the three-centres-per atom model by Hunter and Sanders. A pairwise dispersion energy term is included in the potential and corrected by a damping function. The program carries out energy minimizations through variable metric methods. The new version allows for the stationary point analysis of the intermolecular potential by means of the Hessian eigenvalues. Although using low-gradient thresholds optimization procedures to avoid many stat…
A study of coronene?coronene association using atom?atom pair potentials
A study of the coronene—coronene association using different interaction potentials based on an atom-atom pair potential proposed by Fraga has been performed. The interaction potentials employed differ in the way the electrostatic and/or dispersion contributions are computed. The influence of both contributions on the geometries predicted for the coronene dimer is discussed in order to analyze the effectiveness of the different interaction potentials. The stationary points found in each interaction energy hypersurface are characterized by calculating the Hessian eigenvalues. Results are discussed in the light of those previously reported for the benzene dimer. Stacked-displaced structures a…
Determination of the electron-detachment energies of 2'-deoxyguanosine 5'-monophosphate anion: influence of the conformation.
The vertical electron-detachment energies (VDEs) of the singly charged 2'-deoxyguanosine 5'-monophosphate anion (dGMP - ) are determined by using the multiconfigurational second-order perturbation CASPT2 method at the MP2 ground-state equilibrium geometry of relevant conformers. The origin of the unique low-energy band in the gas phase photoelectron spectrum of dGMP - , with maximum at around 5.05 eV, is unambiguously assigned to electron detachment from the highest occupied molecular orbital of π-character belonging to guanine fragment of a syn conformation. The presence of a short H-bond linking the 2-amino and phosphate groups, the guanine moiety acting as proton donor, is precisely resp…