Computational determination of the dominant triplet population mechanism in photoexcited benzophenone

2014

In benzophenone, intersystem crossing occurs efficiently between the S-1(n pi(star)) state and the T-1 state of dominant n pi(star) character, leading to excited triplet states after photoexcitation. The transition mechanism between S-1(n pi(star)) and T-1 is still a matter of debate, despite several experimental studies. Quantum mechanical calculations have been performed in order to assess the relative efficiencies of previously proposed mechanisms, in particular, the direct S-1 -> T-1 and indirect S-1 -> T-2(pi pi(star)) -> T-1 ones. Multiconfigurational wave function based methods are used to discuss the nature of the relevant states and also to determine minimum energy paths a…

Peptide Metal–Organic Frameworks for Enantioselective Separation of Chiral Drugs

2017

We report the ability of a chiral Cu(II) 3D MOF based on the tripeptide Gly-L-His-Gly (GHG) for the enantioselective separation of metamphetamine and ephedrine. Monte Carlo simulations suggest that chiral recognition is linked to preferential binding of one of the enantiomers as result of either stronger or additional H-bonds with the framework that lead to energetically more stable diastereomeric adducts. Solid phase extraction (SPE) of a racemic mixture by using Cu(GHG) as extractive phase permits isolating more than 50% of the (+)-ephedrine enantiomer as target compound in only four minutes. To the best of our knowledge, this represents the first example of a MOF capable of separating ch…

A theoretical analysis of the structure and properties of B26H30 isomers. Consequences to the laser and semiconductor doping capabilities of large bo…

2019

Decaborane(14), nido-B10H14, is the major commercially available molecular building block in boron cluster chemistry. The condensation of two such {nido-B10} blocks gives the known isomers of B18H22 – a molecule used in the fabrication of p-type semiconductors and capable of blue laser emission. Here, we computationally determine the structures and thermodynamic stabilities of 20 possible B26H30 regioisomers constructed from the fusion of three {nido-B10} blocks with the three subclusters conjoined by two-boron atom shared edges. In addition, density functional theory, time-dependent (TD)-DFT and multiconfigurational CASPT2 methods have been used to model and investigate the physical and ph…

Communication: Electronic UV-Vis transient spectra of the ·OH reaction products of uracil, thymine, cytosine, and 5,6-dihydrouracil by using the comp…

2013

Addition of ∙OH radicals to pyrimidine nucleobases is a common reaction in DNA/RNA damage by reactive oxygen species. Among several experimental techniques, transient absorption spectroscopy has been during the last decades used to characterize such compounds. Discrepancies have however appeared in the assignment of the adduct or adducts responsible for the reported transient absorption UV-Vis spectra. In order to get an accurate assignment of the transient spectra and a unified description of the absorption properties of the ∙OH reaction products of pyrimidines, a systematic complete active space self-consistent field second-order perturbation (CASPT2//CASSCF) theory study has been carried…

DNA nucleobase properties and photoreactivity: Modeling environmental effects

2009

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…

Photochemistry and Non-adiabatic Photodynamics of the HOSO Radical

2021

6 pags., 2 figs.

Hydroxyl Radical Addition to Thymine and Cytosine and Photochemistry of the Adducts at the C6 Position

2019

Theoretical study of the dark photochemistry of 1,3-butadiene via the chemiexcitation of Dewar dioxetane.

2015

Excited-state chemistry is usually ascribed to photo-induced processes, such as fluorescence, phosphorescence, and photochemistry, or to bio-and chemiluminescence, in which light emission originates from a chemical reaction. A third class of excited-state chemistry is, however, possible. It corresponds to the photochemical phenomena produced by chemienergizing certain chemical groups without light - chemiexcitation. By studying Dewar dioxetane, which can be viewed as the combination of 1,2-dioxetane and 1,3-butadiene, we show here how the photo-isomerization channel of 1,3-butadiene can be reached at a later stage after the thermal decomposition of the dioxetane moiety. Multi-reference mult…

Luminescence in Crystalline Organic Materials: From Molecules to Molecular Solids

2021

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

2006

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

Mechanism of activated chemiluminescence of cyclic peroxides: 1,2-dioxetanes and 1,2-dioxetanones

2017

Almost all chemiluminescent and bioluminescent reactions involve cyclic peroxides. The structure of the peroxide and reaction conditions determine the quantum efficiency of light emission. Oxidizable fluorophores, the so-called activators, react with 1,2-dioxetanones promoting the former to their first singlet excited state. This transformation is inefficient and does not occur with 1,2-dioxetanes; however, they have been used as models for the efficient firefly bioluminescence. In this work, we use the SA-CASSCF/CASPT2 method to investigate the activated chemiexcitation of the parent 1,2-dioxetane and 1,2-dioxetanone. Our findings suggest that ground state decomposition of the peroxide com…

Theoretical Study of the Hydroxyl Radical Addition to Uracil and Photochemistry of the Formed U6OH• Adduct

2014

Hydroxyl radical ((•)OH) is produced in biological systems by external or endogenous agents. It can damage DNA/RNA by attacking pyrimidine nucleobases through the addition to the C5═C6 double bond. The adduct resulting from the attachment at the C5 position prevails in the experimental measurements, although the reasons for this preference remain unclear. The first aim of this work is therefore to shed light on the comprehension of this important process. Thus, the thermal (•)OH addition to the C5═C6 double bond of uracil has been studied theoretically by using DFT, MP2, and the multiconfigurational CASPT2//CASSCF methodologies. The in-vacuo results obtained with the latter protocol plus th…

Theoretical Study on the Photo-Oxidation and Photoreduction of an Azetidine Derivative as a Model of DNA Repair

2021

Photocycloreversion plays a central role in the study of the repair of DNA lesions, reverting them into the original pyrimidine nucleobases. Particularly, among the proposed mechanisms for the repair of DNA (6-4) photoproducts by photolyases, it has been suggested that it takes place through an intermediate characterized by a four-membered heterocyclic oxetane or azetidine ring, whose opening requires the reduction of the fused nucleobases. The specific role of this electron transfer step and its impact on the ring opening energetics remain to be understood. These processes are studied herein by means of quantum-chemical calculations on the two azetidine stereoisomers obtained from photocyc…

Regioselectivity of the OH Radical Addition to Uracil in Nucleic Acids. A Theoretical Approach Based on QM/MM Simulations.

2017

Oxidation of nucleic acids is ubiquitous in living beings under metabolic impairments and/or exposed to external agents such as radiation, pollutants, or drugs, playing a central role in the development of many diseases mediated by DNA/RNA degeneration. Great efforts have been devoted to unveil the molecular mechanisms behind the OH radical additions to the double bonds of nucleobases; however, the specific role of the biological environment remains relatively unexplored. The present contribution tackles the study of the OH radical addition to uracil from the gas phase to a full RNA macromolecule by means of quantum-chemistry methods combined with molecular dynamics simulations. It is shown…

Photochemistry of oxidized Hg(I) and Hg(II) species suggests missing mercury oxidation in the troposphere.

2020

8 pags., 5 figs., 2 tabs.

Induced Night-Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin

2019

In humans, vision is limited to a small fraction of the whole electromagnetic spectrum. One possible strategy for enhancing vision in deep-red or poor-light conditions consists of recruiting chlorophyll derivatives in the rod photoreceptor cells of the eye, as suggested in the case of some deep-sea fish. Here, we employ all-atom molecular simulations and high-level quantum chemistry calculations to rationalize how chlorin e6 (Ce6), widely used in photodynamic therapy although accompanied by enhanced visual sensitivity, mediates vision in the dark, shining light on a fascinating but largely unknown molecular mechanism. First, we identify persistent interaction sites between Ce6 and the extra…

A theoretical analysis of the intrinsic light-harvesting properties of xanthopterin

2014

Belonging to the family of pterins, which are common chromophores in several bio-organisms, xanthopterin has been shown experimentally (Plotkin et al., 2010) to have the ability of acting as a light-harvesting molecule. In the present study, multiconfigurational second-order perturbation theory is used to determine the stability of distinct amino/imino and lactam/lactim tautomers and the absorption and emission spectroscopic characteristics, electron donor and acceptor properties and the electron and charge transfer efficiencies via π-stacking. The lactam–lactam form 3H5H (and in a lesser extent 1H5H) is predicted to have the most appropriate intrinsic characteristics for the light-harvesti…

Molecular Basis of DNA Photodimerization: Intrinsic Production of Cyclobutane Cytosine Dimers

2008

Based on CASPT2 results, the present contribution establishes for the first time that cytosine photodimer formation (CC) is mediated along the triplet and singlet manifold by a singlet-triplet crossing, (T1/S0)X, and by a conical intersection, (S1/S0)CI, respectively. The former can be accessed in a barrierless way from a great variety of photochemical avenues and exhibits a covalent single bond between the ethene C6-C6' carbon atoms of each monomer. The efficiency of the stepwise triplet mechanism, however, would be modulated by the effectiveness of the intersystem crossing mechanism. The results provide the grounds for the understanding of the potential photogenotoxicity of endogenous and…

Chemi- and Bioluminescence of Cyclic Peroxides

2018

Bioluminescence is a phenomenon that has fascinated mankind for centuries. Today the phenomenon and its sibling, chemiluminescence, have impacted society with a number of useful applications in fields like analytical chemistry and medicine, just to mention two. In this review, a molecular-orbital perspective is adopted to explain the chemistry behind chemiexcitation in both chemi- and bioluminescence. First, the uncatalyzed thermal dissociation of 1,2-dioxetane is presented and analyzed to explain, for example, the preference for triplet excited product states and increased yield with larger nonreactive substituents. The catalyzed fragmentation reaction and related details are then exemplif…

Building a Functionalizable, Potent Chemiluminescent Agent: A Rational Design Study on 6,8-Substituted Luminol Derivatives.

2021

Luminol is a prominent chemiluminescent (CL) agent, finding applications across numerous fields, including forensics, immunoassays, and imaging. Different substitution patterns on the aromatic ring can enhance or decrease its CL efficiency. We herein report a systematic study on the synthesis and photophysics of all possible 6,8-disubstituted luminol derivatives bearing H, Ph, and/or Me substituents. Their CL responses are monitored at three pH values (8, 10, and 12), thus revealing the architecture with the optimum CL efficiency. The most efficient pattern is used for the synthesis of a strongly CL luminol derivative, bearing a functional group for further, straightforward derivatization. …

Substitution of the laser borane anti-B18H22 with pyridine: a structural and photophysical study of some unusually structured macropolyhedral boron h…

2018

Reaction of anti-B18H221 with pyridine in neutral solvents gives sparingly soluble B16H18-3',8'-Py23a as the major product (ca. 53%) and B18H20-6',9'-Py22 (ca. 15%) as the minor product, with small quantities of B18H20-8'-Py 4 (ca. 1%) also being formed. The three new compounds 2, 3a and 4 are characterized by single-crystal X-ray diffraction analyses and by multinuclear multiple-resonance NMR spectroscopy. Compound 2 is of ten-vertex nido:ten-vertex arachno two-atoms-in-common architecture, long postulated for a species with borons-only cluster constitution, but previously elusive. Compound 3a is of unprecedented ten-vertex nido:eight-vertex arachno two-atoms-in-common architecture. The si…

Hydrogen abstraction by photoexcited benzophenone: consequences for DNA photosensitization

2016

International audience; We report a computational investigation of the hydrogen abstraction (H-abstraction) induced by triplet benzophenone (3BP) on thymine nucleobase and backbone sugar. The chemical process is studied using both high level multiconfigurational perturbation and density functional theory. Both methods show good agreement in predicting small kinetic barriers. Furthermore the behavior of benzophenone in DNA is simulated using molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. The accessibility of benzophenone to the labile hydrogens within B-DNA is demonstrated, as well as the driving force for this reaction. We evidence a strong dependence of the H-…

Thermochromic Fluorescence from B18H20(NC5H5)2: An Inorganic–Organic Composite Luminescent Compound with an Unusual Molecular Geometry

2017

BH(NCH) is a rare example of two conjoined boron hydride subclusters of nido and arachno geometrical character. At room temperature, solutions of BH(NCH) emit a 690 nm fluorescence. In the solid state, this emission is shifted to 620 nm and intensifies due to restriction of the rotation of the pyridine ligands. In addition, there is a thermochromicity to the fluorescence of BH(NCH). Cooling to 8 K engenders a further shift in the emission wavelength to 585 nm and a twofold increase in intensity. Immobilization in a polystyrene thin-film matrix results in an efficient absorption of pumping excitation energy at 414 nm and a 609 nm photostable fluorescence. Such fluorescence from polystyrene t…

On the Deactivation Mechanisms of Adenine–Thymine Base Pair

2012

In this contribution, the multiconfigurational second-order perturbation theory method based on a complete active space reference wave function (CASSCF/CASPT2) is applied to study all possible single and double proton/hydrogen transfers between the nucleobases in the adenine-thymine (AT) base pair, analyzing the role of excited states with different nature [localized (LE) and charge transfer (CT)], and considering concerted as well as step-wise mechanisms. According to the findings, once the lowest excited states, localized in adenine, are populated during UV irradiation of the Watson-Crick base pair, the proton transfer in the N-O bridge does not require high energy in order to populate a …

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

2006

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.

Mechanism of the OH Radical Addition to Adenine from Quantum-Chemistry Determinations of Reaction Paths and Spectroscopic Tracking of the Intermediat…

2016

The OH radical is a well-known mediator in the oxidation of biological structures like DNA. Over the past decades, the precise events taking place after reaction of DNA nucleobases with OH radical have been widely investigated by the scientific community. Thirty years after the proposal of the main routes for the reaction of •OH with adenine (Vieira, A.; Steenken, S. J. Am. Chem. Soc. 1990, 112, 6986−6994), the present work demonstrates that the OH radical addition to C4 position is a minor pathway. Instead, the dehydration process is mediated by the A5OH adduct. Conclusions are based on density functional theory calculations for the ground-state reactivity and highly accurate multiconfigur…

ChemInform Abstract: Excitation of Nucleobases from a Computational Perspective I: Reaction Paths

2016

The main intrinsic photochemical events in nucleobases can be described on theoretical grounds within the realm of non-adiabatic computational photochemistry. From a static standpoint, the photochemical reaction path approach (PRPA), through the computation of the respective minimum energy path (MEP), can be regarded as the most suitable strategy in order to explore the electronically excited isolated nucleobases. Unfortunately, the PRPA does not appear widely in the studies reported in the last decade. The main ultrafast decay observed experimentally for the gas-phase excited nucleobases is related to the computed barrierless MEPs from the bright excited state connecting the initial Franck…

Essential on the Photophysics and Photochemistry of the Indole Chromophore by Using a Totally Unconstrained Theoretical Approach

2015

Indole is a chromophore present in many different molecules of biological interest, such as the essential amino acid tryptophan and the neurotransmitter serotonin. On the basis of CASPT2//CASSCF quantum chemical calculations, the photophysical properties of the system after UV irradiation have been studied through the exploration of the potential energy hypersurfaces of the singlet and triplet low-lying valence excited states. In contrast to previous studies, the present work has been carried out without imposing any restriction to the geometry of the molecule (C1 symmetry) and by performing minimum energy path calculations, which is the only instrument able to provide the lowest-energy evo…

On the chemiluminescence emission of luminol: protic and aprotic solvents and encapsulation to improve the properties in aqueous solution.

2020

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…

Ultrafast Twisting of the Indoline Donor Unit Utilized in Solar Cell Dyes: Experimental and Theoretical Studies

2015

Previous time-resolved measurements on D149, the most-studied dye of the indoline family, had shown a fast time-component of 20–40 ps that had tentatively been attributed to structural relaxation. Using femtosecond transient absorption, we have investigated the isolated indoline donor unit (i.e., without acceptor group) and found an ultrafast decay characterized by two lifetimes of 3.5 and 23 ps. Density functional theory calculations show π-bonding and π*-antibonding character of the central ethylene group for the highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO), respectively. The LUMO is localized on the flexible vinyl-diphenyl region of the donor unit and a twist…

Resolving the Benzophenone DNA-Photosensitization Mechanism at QM/MM Level

2015

International audience; Benzophenone, the parent of the diarylketone family, is a versatile compound commonly used as a UV blocker. It may also trigger triplet-based DNA photosensitization. Therefore, benzophenone is involved in DNA photodamage induction. In the absence of experimentally resolved structure, the mechanism of DNA damage production remains elusive. Employing a hybrid quantum mechanics/molecular mechanics approach, here we address the spin transfer mechanism between this drug and proximal thymine, that is, the DNA nucleobase most prone to suffer triplet damages.

Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism

2013

Proton/hydrogen-transfer processes have been broadly studied in the past 50 years to explain the photostability and the spontaneous tautomerism in the DNA base pairs. In the present study, the CASSCF/CASPT2 methodology is used to map the two-dimensional potential energy surfaces along the stretched NH reaction coordinates of the guanine–cytosine (GC) base pair. Concerted and stepwise pathways are explored initially in vacuo, and three mechanisms are studied: the stepwise double proton transfer, the stepwise double hydrogen transfer, and the concerted double proton transfer. The results are consistent with previous findings related to the photostability of the GC base pair, and a new contrib…

Quantum Chemistry of Excited States in Polyhedral Boranes

2015

In this Chapter we describe the electronic structure of ground states and excited states of the two isomers of octadecaborane (22), anti- and syn-B18H22, and the new derivative of anti-B18H22, the polyhedral substituted borane 4,4′-(HS)2-anti-B18H20. A theoretical interpretation is given on the fluorescence of the anti-B18H22 isomer, and the non-radiative decay of the syn-B18H22 isomer, an unsolved problem since 1962. For the new derivative of anti-B18H22, substitution of hydrogen atoms in positions 4 and 4′ by SH groups allows the tuning of the photophysical properties in 4,4′-(HS)2-anti-B18H20, facilitating intersystem crossing from the excited singlet state to the triplet state.

Ab initio quantum-chemical computations of the electronic states in HgBr2 and IBr: Molecules of interest on the Earth’s atmosphere

2016

The electronic states of atmospheric relevant molecules IBr and HgBr are reported, within the UV-Vis spectrum range (170nm≤λphoton≤600 nm) by means of the complete-active-space self-consistent field/multi-state complete-active-space second-order perturbation theory/spin-orbit restricted-active-space state-interaction (CASSCF/MS-CASPT2/SO-RASSI) quantum-chemical approach and atomic-natural-orbital relativistic-correlation-consistent (ANO-RCC) basis sets. Several analyses of the methodology were carried out in order to reach converged results and therefore to establish a highly accurate level of theory. Good agreement is found with the experimental data with errors not higher than around 0.1 …

Characterization of Locally Excited and Charge-Transfer States of the Anticancer Drug Lapatinib by Ultrafast Spectroscopy and Computational Studies

2020

[EN] Lapatinib (LAP) is an anticancer drug, which is metabolized to theN- and O-dealkylated products (N-LAP andO-LAP, respectively). In view of the photosensitizing potential of related drugs, a complete experimental and theoretical study has been performed on LAP,N-LAP andO-LAP, both in solution and upon complexation with human serum albumin (HSA). In organic solvents, coplanar locally excited (LE) emissive states are generated; they rapidly evolve towards twisted intramolecular charge-transfer (ICT) states. By contrast, within HSA only LE states are detected. Accordingly, femtosecond transient absorption reveals a very fast switching (ca. 2 ps) from LE (lambda(max)=550 nm) to ICT states (…

Light‐Induced On/Off Switching of the Surfactant Character of the o ‐Cobaltabis(dicarbollide) Anion with No Covalent Bond Alteration

2021

Cobaltabis(dicarbollide) anion ([o-COSAN]- ) is a well-known metallacarborane with multiple applications in a variety of fields. In aqueous solution, the cisoid rotamer is the most stable disposition in the ground state. The present work provides theoretical evidence on the possibility to photoinduce the rotation from the cisoid to the transoid rotamer, a conversion that can be reverted when the ground state is repopulated. The non-radiative decay mechanisms proposed in this work are coherent with the lack of fluorescence observed in 3D fluorescence mapping experiments performed on [o-COSAN]- and its derivatives. This phenomenon induced by light has the potential to destruct the vesicles an…

Ab initio quantum-chemical computations of the absorption cross sections of HgX2 and HgXY (X, y = Cl, Br, and I): Molecules of interest in the Earth'…

2018

13 pags., 4 figs., 2 tabs.

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

2016

The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess t…

Towards the understanding at the molecular level of the structured-water absorption and fluorescence spectra: a fingerprint of π-stacked water

2013

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…

Solid State Luminescence Enhancement in π-Conjugated Materials: Unraveling the Mechanism beyond the Framework of AIE/AIEE

2017

Solid state luminescence enhancement (SLE) of conjugated organic materials has had a great impact in materials science, but a deep understanding has been rather limited to date. Here, we investigate a prototype example of SLE materials, cyano-substituted distyrylbenzene (DCS), by varying systematically and subtly the substitution pattern (inter alia of the position of the cyano-substituent) to give largely different photoresponse in fluid and solid solution as well in the crystalline state. The combination of quantitative (ultra)fast optical spectroscopic techniques, appropriate quantum-chemical methods, and structural (X-ray) data allows us to elucidate and rationalize all details of the S…

Photochemistry of HOSO2 and SO3 and Implications for the Production of Sulfuric Acid

2021

9 pags., 5 figs.

Inverted energy gap law for the nonradiative decay in fluorescent floppy molecules: larger fluorescence quantum yields for smaller energy gaps

2019

A data survey on experimental fluorescence quantum yields of (multi)substituted dicyano-distyrylbenzenes in fluid solution evidences that non-radiative decay increases with the Franck-Condon energy (E-FC), being opposite to the conventional energy gap law. Quantum-chemistry indicates that this is controlled by access to the conical intersection (CI) following the Bell-Evans-Polanyi principle as a first-step approximation for this family of molecules; the variations in E-FC among the different compounds are found to be decisive, while those of E-CI are estimated to be weaker or even enhancing the effect. The current findings may have significant consequences for the design of molecules for o…

On the N1-H and N3-H Bond Dissociation in Uracil by Low Energy Electrons: A CASSCF/CASPT2 Study.

2015

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 …

Ab initio determination of the ionization potentials of water clusters (H2O)n (n = 2-6).

2012

High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic ionization potentials of several water clusters: dimer, trimer, tetramer, pentamer, hexamer book, hexamer ring, hexamer cage, and hexamer prism. The present results establish reference values at a level not reported before for these systems, calibrating different computational strategies and helping to discard less reliable theoretical and experimental data. The systematic study with the increasing size of the water cluster allows obtaining some clues on the structure and reductive properties of liquid water.

Photoinduced Formation Mechanism of the Thymine−Thymine (6−4) Adduct

2013

The photoinduced mechanism leading to the formation of the thymine-thymine (6-4) photolesion has been studied by using the CASPT2//CASSCF approach over a dinucleotide model in vacuo. Following light absorption, localization of the excitation on a single thymine leads to fast singlet-triplet crossing that populates the triplet (3)(nπ*) state of thymine. This state, displaying an elongated C(4)═O bond, triggers (6-4) dimer formation by reaction with the C(5)═C(6) double bond of the adjacent thymine, followed by a second intersystem crossing, which acts as a gate between the excited state of the reactant and the ground state of the photoproduct. The requirement of localized excitation on just …

Toward an understanding of the hydrogenation reaction of MO2 gas-phase clusters (M = Ti, Zr, and Hf).

2013

A theoretical investigation using density functional theory (DFT) has been carried out in order to understand the molecular mechanism of dihydrogen activation by means of transition metal dioxides MO2 (M = Ti, Zr, and Hf) according to the following reaction: MO2 + H2 → MO + H2O. B3LYP/6-311++G(2df,2pd)/SDD methodology was employed considering two possible reaction pathways. As the first step hydrogen activation by M═O bonds yields to metal-oxo hydride intermediates O═MH(OH). This process is spontaneous for all metal dioxides, and the stability of the O═MH(OH) species depends on the transition metal center. Subsequently, the reaction mechanism splits into two paths: the first one takes place…

On the hexagonal ice-like model of structured water: Theoretical analysis of the low-lying excited states

2014

Abstract The basic molecular unit ( BMU ) of the hexameric ice-like model has been identified as the negatively charged radical species [H 19 O 10 ] − . On the basis of high-level ab initio computations, by means of using the CASPT2 methodology, the low-lying excited states of BMU and its π-stacked dimer are analysed. It is concluded that the BMU constitutes certainly a versatile unit having two spectroscopic features in the near infrared region, two in the visible range and two in the near ultraviolet zone. The main absorption feature is found however for the π-stacked dimer formed by two BMUs , the H 38 O 20 system, which has a pronounced stabilization in the ground state with respect to …

A two-scale approach to electron correlation in multiconfigurational perturbation theory.

2014

We present a new approach for the calculation of dynamic electron correlation effects in large molecular systems using multiconfigurational second-order perturbation theory (CASPT2). The method is restricted to cases where partitioning of the molecular system into an active site and an environment is meaningful. Only dynamic correlation effects derived from orbitals extending over the active site are included at the CASPT2 level of theory, whereas the correlation effects of the environment are retrieved at lower computational costs. For sufficiently large systems, the small errors introduced by this approximation are contrasted by the substantial savings in both storage and computational de…

Excitation of Nucleobases from a Computational Perspective I: Reaction Paths

2013

The main intrinsic photochemical events in nucleobases can be described on theoretical grounds within the realm of non-adiabatic computational photochemistry. From a static standpoint, the photochemical reaction path approach (PRPA), through the computation of the respective minimum energy path (MEP), can be regarded as the most suitable strategy in order to explore the electronically excited isolated nucleobases. Unfortunately, the PRPA does not appear widely in the studies reported in the last decade. The main ultrafast decay observed experimentally for the gas-phase excited nucleobases is related to the computed barrierless MEPs from the bright excited state connecting the initial Franck…

Photochromic System among Boron Hydrides: The Hawthorne Rearrangement

2019

Photoswitchable molecules have attracted wide interest for many applications in chemistry, physics, and materials science. In this work, we revisit the reversible photochemical and thermal rearrangements of the two B20H182– isomers reported by Hawthorne and Pilling in 1966, whose mechanism had not been understood so far. We investigate the rearrangements by means of a joint experimental and computational study with the outcome that B20H182– represents the first boron-based photochromic system ever reported. Both photochemical and thermal isomerizations occur through the same intermediate and involve a diamond–square–diamond (DSD) mechanism. Given the absence within boron chemistry of named …

Photodissociation Mechanisms of Major Mercury(II) Species in the Atmospheric Chemical Cycle of Mercury

2020

7 pags., 4 figs.

Cover Feature: Molecular Basis of the Chemiluminescence Mechanism of Luminol (Chem. Eur. J. 20/2019)

2019

Excited-state non-radiative decay in stilbenoid compounds: An: Ab initio quantum-chemistry study on size and substituent effects

2019

In the framework of optoelectronic luminescent materials, non-radiative decay mechanisms are relevant to interpret efficiency losses. These radiationless processes are herein studied theoretically for a series of stilbenoid derivatives, including distyrylbenzene (DSB) and cyano-substituted distyrylbenzene (DCS) molecules in vacuo. Given the difficulties of excited-state reaction path determinations, a simplified computational strategy is defined based on the exploration of the potential energy surfaces (PES) along the elongation, twisting, and pyramidalization of the vinyl bonds. For such exploration, density functional theory (DFT), time-dependent (TD)DFT, and complete-active-space self-co…

A Series of Ultra-Efficient Blue Borane Fluorophores

2020

13 pags., 14 figs., 5 tabs.

Ketorolac beats ketoprofen: lower photodecarboxylation, photohemolysis and phototoxicity

2013

Ketorolac shows reduced photohemolytic activity and low phototoxicity against human skin fibroblasts when compared to ketoprofen. The low decarboxylation quantum yield together with the efficient non-radiative deactivation of the triplet and singlet excited states of ketorolac are believed to be responsible for this behaviour.

Experimental and Theoretical Study on the Cycloreversion of a Nucleobase-Derived Azetidine by Photoinduced Electron Transfer.

2018

[EN] Azetidines are interesting compounds in medicine and chemistry as bioactive scaffolds and synthetic intermediates. However, photochemical processes involved in the generation and fate of azetidine-derived radical ions have scarcely been reported. In this context, the photoreduction of this four-membered heterocycle might be relevant in connection with the DNA (6-4) photoproduct obtained from photolyase. Herein, a stable azabipyrimidinic azetidine (AZT(m)), obtained from cycloaddition between thymine and 6-azauracil units, is considered to be an interesting model of the proposed azetidine-like intermediate. Hence, its photoreduction and photo-oxidation are thoroughly investigated throug…

Multiconfigurational Quantum Chemistry Determinations of Absorption Cross Sections (σ) in the Gas Phase and Molar Extinction Coefficients (ε) in Aque…

2021

Theoretical determinations of absorption cross sections (σ) in the gas phase and molar extinction coefficients (e) in condensed phases (water solution, interfaces or surfaces, protein or nucleic acids embeddings, etc.) are of interest when rates of photochemical processes, J = ∫ ϕ(λ) σ(λ) I(λ) dλ, are needed, where ϕ(λ) and I(λ) are the quantum yield of the process and the irradiance of the light source, respectively, as functions of the wavelength λ. Efficient computational strategies based on single-reference quantum-chemistry methods have been developed enabling determinations of line shapes or, in some cases, achieving rovibrational resolution. Developments are however lacking for stron…

Mechanism of excited state deactivation of indan-1-ylidene and fluoren-9-ylidene malononitriles.

2016

Herein, we report complementary computational and experimental evidence supporting the existence, for indan-1-ylidene malononitrile and fluoren-9-ylidene malononitrile, of a non-radiative decay channel involving double bond isomerisation motion. The results of UV-Vis transient absorption spectroscopy highlight that the decay takes place within hundreds of picoseconds. In order to understand the related molecular mechanism, photochemical reaction paths were computed by employing multiconfigurational quantum chemistry. The results indicate that the excited state deactivation occurs via concerted double bond twisting of the dicyanovinyl (DCV) unit coupled with a pyramidalisation of its substit…

Revisiting the Nonadiabatic Process in 1,2-Dioxetane.

2015

Determining the ground and excited-state decomposition mechanisms of 1,2-dioxetane is essential to understand the chemiluminescence and bioluminescence phenomena. Several experimental and theoretical studies has been performed in the past without reaching a converged description. The reason is in part associated with the complex nonadiabatic process taking place along the reaction. The present study is an extension of a previous work (De Vico, L.; Liu, Y.-J.; Krogh, J. W.; Lindh, R. J. Phys. Chem. A 2007, 111, 8013-8019) in which a two-step mechanism was established for the chemiluminescence involving asynchronous O-O' and C-C' bond dissociations. New high-level multistate multi configurati…

Molecular Basis of the Chemiluminescence Mechanism of Luminol

2019

Light emission from luminol is probably one of the most popular chemiluminescence reactions due to its use in forensic science, and has recently displayed promising applications for the treatment of cancer in deep tissues. The mechanism is, however, very complex and distinct possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism has been studied in three steps: 1)luminol oxygenation to generate the chemiluminophore, 2)a chemiexcitation step, and 3)generation of the light emitter. The findings demonstrate that the luminol double-deprotonated dianion activates molecular oxygen, diazaquinone is not formed, and the chemiluminopho…

A Combined Experimental and Theoretical Approach to the Photogeneration of 5,6-Dihydropyrimidin-5-yl Radicals in Nonaqueous Media

2016

The chemical fate of radical intermediates is relevant to understand the biological effects of radiation and to explain formation of DNA lesions. A direct approach to selectively generate the putative reactive intermediates is based on the irradiation of photolabile precursors. But, to date, radical formation and reactivity have only been studied in aqueous media, which do not completely mimic the micro environment provided by the DNA structure and its complexes with proteins. Thus, it is also important to evaluate the photogeneration of nucleoside-based radicals in nonaqueous media. The attention here is focused on the independent generation of 5,6-dihydropyrimidin-5-yl radicals in organic…

On the photophysics and photochemistry of the water dimer

2012

The photochemistry of the water dimer irradiated by UV light is studied by means of the complete active space perturbation theory//complete active space self-consistent field (CASPT2//CASSCF) method and accurate computational approaches like as minimum energy paths. Both electronic structure computations and ab initio molecular dynamics simulations are carried out. The results obtained show small shifts relative to a single water molecule on the vertical excitation energies of the dimer due to the hydrogen bond placed between the water donor (W(D)) and the water acceptor (W(A)). A red-shift and a blue-shift are predicted for the W(D) and W(A), respectively, supporting previous theoretical a…

Effect of Iodination on the Photophysics of the Laser Borane anti-B18H22: Generation of Efficient Photosensitizers of Oxygen

2019

Treatment of the laser borane anti-B18H22 (compound 1) with iodine in ethanol gives the monoiodinated derivative 7-I-anti-B18H21 (compound 2) in 67% yield, or, by reaction with iodine or ICl in the presence of AlCl3 in dichloromethane, the diiodinated derivative 4,4'-I2-anti-B18H20 (compound 3) in 85% yield. On excitation with 360 nm light, both compounds 2 and 3 give strong green phosphorescent emissions (λmax = 525 nm, ΦL = 0.41 and λmax = 545 nm, ΦL = 0.71 respectively) that are quenched by dioxygen to produce O2(1Δg) singlet oxygen with quantum yields of ΦΔ = 0.52 and 0.36 respectively. Similarly strong emissions can be stimulated via the nonlinear process of two-photon absorption when …

Photoreduction of gaseous oxidized mercury changes global atmospheric mercury speciation, transport and deposition

2018

9 pags, 8 figs. -- Correction autor: https://doi.org/10.1038/s41467-022-28455-w http://hdl.handle.net/10261/268181

Complete-active-space second-order perturbation theory (CASPT2//CASSCF) study of the dissociative electron attachment in canonical DNA nucleobases ca…

2015

Low-energy (0-3 eV) ballistic electrons originated during the irradiation of biological material can interact with DNA/RNA nucleobases yielding transient-anion species which undergo decompositions. Since the discovery that these reactions can eventually lead to strand breaking of the DNA chains, great efforts have been dedicated to their study. The main fragmentation at the 0-3 eV energy range is the ejection of a hydrogen atom from the specific nitrogen positions. In the present study, the methodological approach introduced in a previous work on uracil [I. González-Ramírez et al., J. Chem. Theory Comput. 8, 2769-2776 (2012)] is employed to study the DNA canonical nucleobases fragmentations…

Regiochemical memory in the adiabatic photolysis of thymine-derived oxetanes. A combined ultrafast spectroscopic and CASSCF/CASPT2 computational stud…

2020

[EN] The photoinduced cycloreversion of oxetanes has been thoroughly investigated in connection with the photorepair of the well-known DNA (6-4) photoproducts. In the present work, the direct photolysis of the two regioisomers arising from the irradiation of benzophenone (BP) and 1,3-dimethylthymine (DMT), namely the head-to-head (HH-1) and head-to-tail (HT-1) oxetane adducts, has been investigated by combining ultrafast spectroscopy and theoretical multiconfigurational quantum chemistry analysis. Both the experimental and computational results agree with the involvement of an excited triplet exciplex(3)[BPMIDLINE HORIZONTAL ELLIPSISDMT]* for the photoinduced oxetane cleavage to generate(3)…

A surface hopping algorithm for nonadiabatic minimum energy path calculations

2015

The article introduces a robust algorithm for the computation of minimum energy paths transiting along regions of near-to or degeneracy of adiabatic states. The method facilitates studies of excited state reactivity involving weakly avoided crossings and conical intersections. Based on the analysis of the change in the multiconfigurational wave function the algorithm takes the decision whether the optimization should continue following the same electronic state or switch to a different state. This algorithm helps to overcome convergence difficulties near degeneracies. The implementation in the MOLCAS quantum chemistry package is discussed. To demonstrate the utility of the proposed procedur…

Unveiling the role of upper excited electronic states in the photochemistry and laser performance of: anti -B18H22

2020

13 pags., 7 figs., -- This article is part of the themed collection: Journal of Materials Chemistry C HOT Papers

Toward Understanding the Photochemistry of Photoactive Yellow Protein: A CASPT2/CASSCF and Quantum Theory of Atoms in Molecules Combined Study of a M…

2009

Photochemical processes that take place in biological molecules have become an increasingly important research topic for both experimentalists and theoreticians. In this work, we report the reaction mechanism of a model of the photoactive yellow protein (PYP) chromophore in vacuo. The results obtained here, using a strategy based on the simultaneous use of the minimum energy path concept and the quantum theory of atoms in molecules applied to this excited state process, suggest a possible way in which the protein could increase the efficiency of the reaction. The role played by other electronic states of the same and different spin multiplicities in the reaction process is also analyzed, wi…

Modeling hole transfer in DNA: Low-lying excited states of oxidized cytosine homodimer and cytosine–adenine heterodimer

2008

Abstract Charge transport in DNA strands has been studied by characterizing on theoretical grounds the lowest doublet states of the oxidized cytosine homodimer (CC + ) and adenine–cytosine heterodimer (CA + ) along the intermolecular separation of the monomers. The high-level quantum-chemical ab initio CASPT2 method and accurate one-electron basis sets have been employed. Both cationic species are found to be bound with comparable binding energies as those of neutral CC and reduced CC − . The results suggest that charge transport in DNA and the distinct photophysical attributes related to the polymer can be described within the framework of a unified theory. A cooperative micro-hopping mech…

Ab initio determination of the electron affinities of DNA and RNA nucleobases

2008

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…

Gas-Phase Photolysis of Hg(I) Radical Species: A New Atmospheric Mercury Reduction Process

2019

The efficient gas-phase photoreduction of Hg(II) has recently been shown to change mercury cycling significantly in the atmosphere and its deposition to the Earth's surface. However, the photolysis of key Hg(I) species within that cycle is currently not considered. Here we present ultraviolet-visible absorption spectra and cross-sections of HgCl, HgBr, HgI, and HgOH radicals, computed by high-level quantum-chemical methods, and show for the first time that gas-phase Hg(I) photoreduction can occur at time scales that eventually would influence the mercury chemistry in the atmosphere. These results provide new fundamental understanding of the photobehavior of Hg(I) radicals and show that the …

Determination of the electron-detachment energies of 2'-deoxyguanosine 5'-monophosphate anion: influence of the conformation.

2009

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…

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

2006

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 π-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. Gloria.Olaso@uv.es Daniel.Roca@uv.es Luis.Serrano@uv.es Manuela.Merchan@uv.es

Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA

2018

Multiscale molecular dynamics simulations reveal out-of-plane distortions that favour DNA photostability. A novel photostability mechanism involving four proton transfers and triggered by a nearby Na+ ion is also unveiled.

CCDC 1444537: Experimental Crystal Structure Determination

2016

Related Article: Isabel Aparici-Espert, Antonio Francés-Monerris, Gemma M. Rodríguez-Muñiz, Daniel Roca-Sanjuán, Virginie Lhiaubet-Vallet, Miguel A. Miranda|2016|J.Org.Chem.|81|4031|doi:10.1021/acs.joc.6b00314

CCDC 1441506: Experimental Crystal Structure Determination

2018

Related Article: Michael G. S. Londesborough, Jiří Dolanský, Tomáš Jelínek, John D. Kennedy, Ivana Císařová, Robert D. Kennedy, Daniel Roca-Sanjuán, Antonio Francés-Monerris, Kamil Lang, William Clegg|2018|Dalton Trans.|47|1709|doi:10.1039/C7DT03823B

CCDC 1514165: Experimental Crystal Structure Determination

2020

Related Article: Michael G. S. Londesborough, Jiří Dolanský, Luis Cerdán, Kamil Lang, Tomáš Jelínek, Josep M. Oliva, Drahomír Hnyk, Daniel Roca-Sanjuán, Antonio Francés-Monerris, Jiří Martinčík, Martin Nikl, John D. Kennedy|2017|Adv. Opt. Mater.|5|1600694|doi:10.1002/adom.201600694

CCDC 1859436: Experimental Crystal Structure Determination

2019

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CCDC 1441507: Experimental Crystal Structure Determination

2018

Related Article: Michael G. S. Londesborough, Jiří Dolanský, Tomáš Jelínek, John D. Kennedy, Ivana Císařová, Robert D. Kennedy, Daniel Roca-Sanjuán, Antonio Francés-Monerris, Kamil Lang, William Clegg|2018|Dalton Trans.|47|1709|doi:10.1039/C7DT03823B

CCDC 1441504: Experimental Crystal Structure Determination

2018

Related Article: Michael G. S. Londesborough, Jiří Dolanský, Tomáš Jelínek, John D. Kennedy, Ivana Císařová, Robert D. Kennedy, Daniel Roca-Sanjuán, Antonio Francés-Monerris, Kamil Lang, William Clegg|2018|Dalton Trans.|47|1709|doi:10.1039/C7DT03823B

CCDC 1859437: Experimental Crystal Structure Determination

2019

Related Article: Michael G. S. Londesborough, Jiří Dolanský, Jonathan Bould, Jakub Braborec, Kaplan Kirakci, Kamil Lang, Ivana Císařová, Pavel Kubát, Daniel Roca-Sanjuán, Antonio Francés-Monerris, Lenka Slušná, Eva Noskovičová, Dušan Lorenc|2019|Inorg.Chem.|58|10248|doi:10.1021/acs.inorgchem.9b01358

CCDC 1441505: Experimental Crystal Structure Determination

2018

Related Article: Michael G. S. Londesborough, Jiří Dolanský, Tomáš Jelínek, John D. Kennedy, Ivana Císařová, Robert D. Kennedy, Daniel Roca-Sanjuán, Antonio Francés-Monerris, Kamil Lang, William Clegg|2018|Dalton Trans.|47|1709|doi:10.1039/C7DT03823B