On the photorelease of nitric oxide by nitrobenzene derivatives: A CASPT2//CASSCF model
Nitroaromatic compounds can photorelease nitric oxide after UV absorption. The efficiency of the photoreaction depends on the molecular structure, and two features have been pointed out as particularly important for the yield of the process: the presence of methyl groups at the ortho position with respect to the nitro group and the degree of conjugation of the molecule. In this paper, we provide a theoretical characterization at the CASPT2//CASSCF (complete active space second-order perturbation theory//complete active space self-consistent field) level of theory of the photorelease of NO for four molecules derived from nitrobenzene through the addition of ortho methyl groups and/or the el…
Relaxation Mechanisms of 5-Azacytosine.
The photophysics and deactivation pathways of the noncanonical 5-azacytosine nucleobase were studied using the CASPT2//CASSCF protocol. One of the most significant differences with respect to the parent molecule cytosine is the presence of a dark (1)(nNπ*) excited state placed energetically below the bright excited state (1)(ππ*) at the Franck-Condon region. The main photoresponse of the system is a presumably efficient radiationless decay back to the original ground state, mediated by two accessible conical intersections involving a population transfer from the (1)(ππ*) and the (1)(nNπ*) states to the ground state. Therefore, a minor contribution of the triplet states in the photophysics o…
Induced Night-Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin
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
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…
Toward the Understanding of the Photophysics and Photochemistry of 1-Nitronaphthalene under Solar Radiation: The First Theoretical Evidence of a Photodegradation Intramolecular Rearrangement Mechanism Involving the Triplet States
1-Nitronaphthalene belongs to the class of nitrated polycyclic aromatic hydrocarbons, and constitutes an atmospheric pollutant commonly found in urban environments due to its production during incomplete combustions. On the basis of CASPT2//CASSCF quantum chemical calculations, the photophysics and photochemistry of the system under solar exposure have for the first time been studied. According to the characteristics of the incident radiation (either UVA or UVB, both present in the portion of the solar spectrum reaching the earth), a different excited state will be mainly populated. In both cases, the main decay path undertaken by the corresponding bright state leads to an efficient intersy…
OpenMolcas: From Source Code to Insight
In this article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multico…
Building a Functionalizable, Potent Chemiluminescent Agent: A Rational Design Study on 6,8-Substituted Luminol Derivatives.
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. …
On the Intrinsically Low Quantum Yields of Pyrimidine DNA Photodamages: Evaluating the Reactivity of the Corresponding Minimum Energy Crossing Points
The low quantum yield of photoformation of cyclobutane pyrimidine dimers and pyrimidine-pyrimidone (6-4) adducts in DNA bases is usually associated with the presence of more favorable nonreactive decay paths and with the unlikeliness of exciting the system in a favorable conformation. Here, we prove that the ability of the reactive conical intersection to bring the system either back to the absorbing conformation or to the photoproduct must be considered as a fundamental factor in the low quantum yields of the mentioned photodamage. In support of the proposed model, the one order of magnitude difference in the quantum yield of formation of the cyclobutane thymine dimer with respect to the t…
On the Importance of Ligand-Centered Excited States in the Emission of Cyclometalated Ir(III) Complexes
The photophysical behavior of the cyclometalating Ir(III) complexes [Ir(ppy)2(bpy)]+, where Hppy is 2-phenylpyridine and bpy is 2,2′-bipyridine (complex 1), and [Ir(diFppy)2(dtb-bpy)]+, where diFppy is 2-(2,4-difluorophenyl)pyridine and dtb-bpy is 4,4′-di-tert-butyl-2,2′-bipyridine (complex 2), has been theoretically investigated by performing density functional theory calculations. The two complexes share the same molecular skeleton, complex 2 being derived from complex 1 through the addition of fluoro and tert-butyl substituents, but present notable differences in their photophysical properties. The remarkable difference in their emission quantum yields (0.196 for complex 1 in dichloromet…
Combined Theoretical and Experimental Study of the Photophysics of Asulam
The photophysics of the neutral molecular form of the herbicide asulam has been described in a joint experimental and theoretical, at the CASPT2 level, study. The unique π → π* aromatic electronic transition (f, ca. 0.5) shows a weak red-shift as the polarity of the solvent is increased, whereas the fluorescence band undergoes larger red-shifts. Solvatochromic data point to higher dipole moment in the excited state than in the ground state (μ(g)μ(e)). The observed increase in pKa in the excited state (pKa* - pKa, ca. 3) is consistent with the results of the Kamlet-Abboud-Taft and Catalán et al. multiparametric approaches. Fluorescence quantum yield varies with the solvent, higher in water (…
ChemInform Abstract: Excitation of Nucleobases from a Computational Perspective I: Reaction Paths
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
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.
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…
How important is roaming in the photodegradation of nitrobenzene?
At low excitation energies nitrobenzene photoreleases NO with low translational and rotational energy, while at higher excitation energies NO is photoreleased with both low and high translational and rotational energy. The fast products are formed through a singlet-triplet crossing (STC) region featuring an oxaziridine ring, while a ground state roaming mechanism was suggested to produce the slow molecules. Computing translational and rotational energies performing CASSCF classical dynamics, we here prove how the same oxaziridine STC can account for both fast and slow photoproducts, depending on the region of the seam through which the ground state is populated. A roaming-type STC/CI has al…
Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate
The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D-UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine 1La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine 1Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter-base hydrogen transfer and decay to the ground state through a conical …
Photoinduced Formation Mechanism of the Thymine−Thymine (6−4) Adduct
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 …
Excitation of Nucleobases from a Computational Perspective I: Reaction Paths
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…
Cover Feature: Molecular Basis of the Chemiluminescence Mechanism of Luminol (Chem. Eur. J. 20/2019)
Pyrene, a Test Case for Deep-Ultraviolet Molecular Photophysics
We determined the complete relaxation dynamics of pyrene in ethanol from the second bright state, employing experimental and theoretical broadband heterodyne detected transient grating and two-dimensional photon echo (2DPE) spectroscopy, using pulses with duration of 6 fs and covering a spectral range spanning from 250 to 300 nm. Multiple lifetimes are assigned to conical intersections through a cascade of electronic states, eventually leading to a rapid population of the lowest long-living excited state and subsequent slow vibrational cooling. The lineshapes in the 2DPE spectra indicate that the efficiency of the population transfer depends on the kinetic energy deposited into modes requir…
Molecular Basis of the Chemiluminescence Mechanism of Luminol
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…
Similar chemical structures, dissimilar triplet quantum yields: a CASPT2 model rationalizing the trend of triplet quantum yields in nitroaromatic systems
The photophysics of nitroaromatics compounds stand out for being characterized by an ultrafast decay into the triplet manifold and by a significant value of the triplet quantum yield. The latter quantity can change dramatically from one system to another, as proven for the molecules 2- nitronaphthalene, 1-nitronaphthalene, and 2methyl-1nitronaphthale, whose triplet quantum yield have been previously measured to be 0.93 ± 0.15, 0.64 ± 0.12, and 0.33 ± 0.05, respectively (J. Phys. Chem. A 2013, 117, 14100). In the present contribution we rationalize the reported trend for the triplet quantum yield on the basis of the different ability that the excited S 1 state has in the three molecules to r…
On the photophysics and photochemistry of biological chromophores: An ab initio quantum chemical study
La presente tesis se enmarca dentro de las líneas de investigación del grupo QCEXVAL, y en particular en el estudio de la fotofísica y fotoquímica de cromóforos de interés biológico. A continuación, se van a resumir los resultados obtenidos en los cinco trabajos publicados y presentados en esta tesis: la fotofísica de la molécula 1-aminonaftaleno, la fotofísica del cromóforo indol, el mecanismo fotoinducido de formación del fotodímero (6-4) timina-timina, el estudio y descripción crítica de la principal vía de decaimiento noradiativo en la citosina, y la respuesta del herbicida asulam frente a la radiación UVA y UVB. 1-aminonaftaleno La optimización del estado fundamental converge a una est…
Regiochemical memory in the adiabatic photolysis of thymine-derived oxetanes. A combined ultrafast spectroscopic and CASSCF/CASPT2 computational study.
[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)…
Azole-containing cationic bis-cyclometallated iridium(iii) isocyanide complexes: a theoretical insight into the emission energy and emission efficiency
Using a density functional theory approach, we explore the emission properties of a family of bis-cyclometallated cationic iridium(iii) complexes of general formula [Ir(C^N)2(CN-tert-Bu)2]+ that have tert-butyl isocyanides as neutral auxiliary ligands. Taking the [Ir(ppy)2(CN-tert-Bu)2]+ complex (Hppy = 2-phenylpyridine) as a reference, the effect of replacing the pyridine ring in the cyclometallating ppy ligand by a five-membered azole ring has been examined. To this end, two series of complexes differing by the nature of the atom (either nitrogen or carbon) linking the azole to the phenyl ring of the cyclometallating ligand have been designed. Each series is composed of three molecules ha…
Calculations Yb [Dataset]
Orca outputs of TDDFT and DFT calculations on a Yb complex Archivos OUT. Abrir con Windows Notepad, WordPad, TextEdit o Text editor. Archivos OUT. Abrir con Windows Notepad, WordPad, TextEdit o Text editor.