Influence of symmetry breaking on the absorption spectrum of crystal violet: from isolated cations at 5 K to room temperature solutions.

We report the resolution of a long-standing puzzle in molecular spectroscopy: the origin of the shoulder in the room temperature solution absorption spectrum of crystal violet (CV) - an archetypal cationic triphenylmethane dye. This was achieved by comparing experimental and theoretical results for CV in solution at room temperature and as an isolated cation in gas-phase at 5 K. The two lowest energy electronically excited states involved in the visible region absorption are degenerate and coupled a Jahn-Teller (JT) mechanism involving phenyl torsions, making CV particularly sensitive to environmental perturbations.

Hydride and halide abstraction reactions behind the enhanced basicity of Be and Mg clusters with nitrogen bases.

In this study, we investigate the protonation effects on the structure, relative stability and basicity of complexes formed by the interaction of monomers and dimers of BeX and MgX (X = H, F) with NH, CHNH, HCN, and NCH bases. Calculations were performed using the M06-2X/aug-cc-pVTZ formalism, along with QTAIM, ELF and NCI methods for electron density analysis and MBIE and LMO-EDA energy decomposition analyses for interaction enthalpies. The protonation of the MH- and MH-Base complexes occurs at the negatively charged hydrogen atoms of the MH and MH moieties through typical hydride abstraction reactions, while protonation at the N atom of the base is systematically less exothermic.

Characterization of 1,1- and 1,2-ethenedithiol, elusive compounds of potential astrochemical interest.

Context: 1,1- and 1,2-ethenedithiol are elusive systems that could potentially exist in interstellar space, similar to analogous diols. In this paper, we investigate the structure, stability, and bonding characteristics of these compounds as well as the ions produced by protonation, deprotonation, or simple ionization processes. 1,2-ethenedithiol has two isomers, Z and E, with the most stable conformer being syn-anti for the Z isomer and anti-anti for the E isomer.

Non-adiabatic direct quantum dynamics using force fields: Toward solvation.

Quantum dynamics simulations are becoming a powerful tool for understanding photo-excited molecules. Their poor scaling, however, means that it is hard to study molecules with more than a few atoms accurately, and a major challenge at the moment is the inclusion of the molecular environment. Here, we present a proof of principle for a way to break the two bottlenecks preventing large but accurate simulations.

Explicit Modelling of Spectral Bandshapes by a Mixed Quantum-Classical Approach: Solvent Order and Temperature Effects in the Optical Spectra of Distyrylbenzene.

The absorption and emission spectral shapes of a flexible organic probe, the distyrylbenzene (DSB) dye, are simulated accounting for the effect of different environments of increasing complexity, ranging from a homogeneous, low-molecular- weight solvent, to a long-chain alkane, and, eventually, a channel-forming organic matrix. Each embedding is treated explicitly, adopting a mixed quantum-classical approach, the Adiabatic Molecular Dynamics - generalized vertical Hessian (Ad-MD|gVH) model, which allows a direct simulation of the environment-induced constraining effects on the vibronic spectral shapes. In such a theoretical framework, the stiff modes of the dye are described at a quantum level within the harmonic approximation, including Duschinsky mixing effects, while flexible degrees of freedom of the solute (e.

Discovering trends in the Lewis acidity of beryllium and magnesium hydrides and fluorides with increasing clusters size.

We have reported in the last years the strong effect that Be- and Mg-containing Lewis acids have on the intrinsic properties of typical bases, which become acids upon complexation. In an effort to investigate these changes when the Be and Mg derivatives form clusters of increasing size, we have examined the behavior of the (MX) (M = Be, Mg; X = H, F; n = 1, 2, 3) clusters when they interact with ammonia, methanimine, hydrogen cyanide and pyridine, and with their corresponding deprotonated forms. The complexes obtained at the M06-2X/aug-cc-pVTZ level were analyzed using the MBIE energy decomposition formalism, in parallel with QTAIM, ELF, NCIPLOT and AdNDP analyses of their electron density.

Dynamic effects on the nonlinear optical properties of donor acceptor stenhouse adducts: insights from combined MD + QM simulations.

The second-order nonlinear optical (NLO) responses of a donor-acceptor stenhouse adduct (DASA) are investigated by using a computational approach combining molecular dynamics simulations and density functional theory (DFT) calculations. Specific force fields for the open and closed photoswitching forms are first parameterized and validated according to the Joyce protocol, in order to finely reproduce the geometrical features and potential energy surfaces of both isomers in chloroform solution. Then, DFT calculations are performed on structural snapshots extracted at regular time steps of the MD trajectories to address the influence of the thermalized conformational dynamics on the NLO responses related to hyper-Rayleigh scattering (HRS) experiments.

Effect of the DNA Polarity on the Relaxation of Its Electronic Excited States.

The DNA polarity, ., the order in which nucleobases are connected together via the phosphodiester backbone, is crucial for several biological processes. But, so far, there has not been experimental evidence regarding its effect on the relaxation of DNA electronic excited states.

Ionization, intrinsic basicity, and intrinsic acidity of unsaturated diols of astrochemical interest: 1,1- and 1,2-ethenediol: A theoretical survey.

The structure, stability, and bonding characteristics of 1,1- and 1,2-ethenediol, their radical cations, and their protonated and deprotonated species were investigated using high-level ab initio G4 calculations. The electron density of all the neutral and charged systems investigated was analyzed using the QTAIM, ELF, and NBO approaches. The vertical ionization potential (IP) of the five stable tautomers of 1,2-ethenediol and the two stable tautomers of 1,1-ethenediol go from 11.

Quantum-Classical Protocol for Efficient Characterization of Absorption Lineshape and Fluorescence Quenching upon Aggregation: The Case of Zinc Phthalocyanine Dyes.

A quantum-classical protocol that incorporates Jahn-Teller vibronic coupling effects and cluster analysis of molecular dynamics simulations is reported, providing a tool for simulations of absorption spectra and ultrafast nonadiabatic dynamics in large molecular photosystems undergoing aggregation in solution. Employing zinc phthalocyanine dyes as target systems, we demonstrated that the proposed protocol provided fundamental information on vibronic, electronic couplings and thermal dynamical effects that mostly contribute to the absorption spectra lineshape and the fluorescence quenching processes upon dye aggregation. Decomposing the various effects arising upon dimer formation, the structure-property relations associated with their optical responses have been deciphered at atomistic resolution.

The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study.

We here study the effect that a lowering of the pH has on the excited state processes of cytidine and a cytidine/cytidine pair in solution, by integrating time-dependent density functional theory and CASSCF/CASPT2 calculations, and including solvent by a mixed discrete/continuum model. Our calculations reproduce the effect of protonation at N3 on the steady-state infrared and absorption spectra of a protonated cytidine (CH ), and predict that an easily accessible non-radiative deactivation route exists for the spectroscopic state, explaining its sub-ps lifetime. Indeed, an extremely small energy barrier separates the minimum of the lowest energy bright state from a crossing region with the ground electronic state, reached by out-of-plane motion of the hydrogen substituents of the CC double bond, the so-called ethylenic conical intersection typical of cytidine and other pyrimidine bases.

Non-Phenomenological Description of the Time-Resolved Emission in Solution with Quantum-Classical Vibronic Approaches-Application to Coumarin C153 in Methanol.

We report a joint experimental and theoretical work on the steady-state spectroscopy and time-resolved emission of the coumarin C153 dye in methanol. The lowest energy excited state of this molecule is characterized by an intramolecular charge transfer thus leading to remarkable shifts of the time-resolved emission spectra, dictated by the methanol reorganization dynamics. We selected this system as a prototypical test case for the first application of a novel computational protocol aimed at the prediction of transient emission spectral shapes, including both vibronic and solvent effects, without applying any phenomenological broadening.

Sensitized Singlet Fission in Rigidly Linked Axial and Peripheral Pentacene-Subphthalocyanine Conjugates.

The goal of harnessing the theoretical potential of singlet fission (SF), a process in which one singlet excited state is split into two triplet excited states, has become a central challenge in solar energy research. Covalently linked dimers provide crucial models for understanding the role of chromophore arrangement and coupling in SF. Sensitizers can be integrated into these systems to expand the absorption bandwidth through which SF can be accessed.

Light-Responsive Elastin-Like Peptide-Based Targeted Nanoparticles for Enhanced Spheroid Penetration.

We describe here a near infrared light-responsive elastin-like peptide (ELP)-based targeted nanoparticle (NP) that can rapidly switch its size from 120 to 25 nm upon photo-irradiation. Interestingly, the targeting function, which is crucial for effective cargo delivery, is preserved after transformation. The NPs are assembled from (targeted) diblock ELP micelles encapsulating photosensitizer TT1-monoblock ELP conjugates.

The Resonance Raman Spectrum of Cytosine in Water: Analysis of the Effect of Specific Solute-Solvent Interactions and Non-Adiabatic Couplings.

In this contribution, we report a computational study of the vibrational Resonance Raman (vRR) spectra of cytosine in water, on the grounds of potential energy surfaces (PES) computed by time-dependent density functional theory (TD-DFT) and CAM-B3LYP and PBE0 functionals. Cytosine is interesting because it is characterized by several close-lying and coupled electronic states, challenging the approach commonly used to compute the vRR for systems where the excitation frequency is in quasi-resonance with a single state. We adopt two recently developed time-dependent approaches, based either on quantum dynamical numerical propagations of vibronic wavepackets on coupled PES or on analytical correlation functions for cases in which inter-state couplings were neglected.

Vibrationally resolved two-photon electronic spectra including vibrational pre-excitation: Theory and application to VIPER spectroscopy with two-photon excitation.

Following up on our previous work on vibrationally resolved electronic absorption spectra including the effect of vibrational pre-excitation [von Cosel et al., J. Chem.

Unraveling the contributions to the spectral shape of flexible dyes in solution: insights on the absorption spectrum of an oxyluciferin analogue.

We present a computational investigation of the absorption spectrum in water of 5,5-spirocyclopropyl-oxyluciferin (5,5-CprOxyLH), an analogue of the emitter compound responsible for the bioluminescence in fireflies. Several factors participate in determining the 5,5-CprOxyLH's spectral shape: (i) the contribution of the four close-energy excited states, which show significant non-adiabatic couplings, (ii) the flexible molecular structure and (iii) the specific interactions established with the surrounding environment, which strongly couple the protic solvent dynamics with the dye's spectral response. To tackle the challenge to capture and dissect the role of all these effects we preliminarily investigate the role of non-adiabatic couplings with quantum dynamics simulations and a linear vibronic coupling model in the gas phase.

FCclasses3: Vibrationally-resolved spectra simulated at the edge of the harmonic approximation.

We introduce FCclasses3, a code to carry out vibronic simulations of electronic spectra and nonradiative rates, based on the harmonic approximation. Key new features are: implementation of the full family of vertical and adiabatic harmonic models, vibrational analysis in curvilinear coordinates, extension to several electronic spectroscopies and implementation of time-dependent approaches. The use of curvilinear valence internal coordinates allows the adoption of quadratic model potential energy surfaces (PES) of the initial and final states expanded at arbitrary configurations.

Disrupting bonding in azoles through beryllium bonds: Unexpected coordination patterns and acidity enhancement.

Although triazoles and tetrazole are amphoteric and may behave as weak acids, the latter property can be hugely enhanced by beryllium bonds. To explain this phenomenon, the structure and bonding characteristics of the complexes between triazoles and tetrazoles with one and two molecules of BeF have been investigated through the use of high-level G4 ab initio calculations. The formation of the complexes between the N basic sites of the azoles and the Be center of the BeF molecule and the (BeF) dimer leads to a significant bonding perturbation of both interacting subunits.

Z-α-antitrypsin polymers impose molecular filtration in the endoplasmic reticulum after undergoing phase transition to a solid state.

Misfolding of secretory proteins in the endoplasmic reticulum (ER) features in many human diseases. In α-antitrypsin deficiency, the pathogenic Z variant aberrantly assembles into polymers in the hepatocyte ER, leading to cirrhosis. We show that α-antitrypsin polymers undergo a liquid:solid phase transition, forming a protein matrix that retards mobility of ER proteins by size-dependent molecular filtration.

Dismantlement of ammonia upon interaction with Be (n ≤ 10) clusters.

The interaction of ammonia with Be (n < 1-10) clusters has been investigated by density functional theory and ab initio calculations. The main conclusion is that, regardless of the size of the Be cluster, neither the structure of ammonia nor that of the Be clusters are preserved due to a systematic dissociation of its NH bonds and a spontaneous H-shift toward the available Be atoms. This H migration not only leads to rather stable BeH bonds, but dramatically enhances the strength of the BeN bonds as well.

A self-assembled subphthalocyanine-based nanophotosensitiser for photodynamic therapy.

A subphthalocyanine substituted with nine tetra(ethylene glycol) chains on the periphery has been synthesised. This novel amphiphilic and cone-shaped compound can self-assemble in water into spherical nanoparticles with a hydrodynamic diameter of 154 nm. These nanoparticles can be taken up readily by cancer cells and localised predominately in lysosomes where they disassemble gradually, leading to activation in fluorescence emission and, photocytotoxicity, showing IC values of as low as 1.

Regioselective Monoborylation of Spirocyclobutenes.

We present a strategy for the synthesis of spirocyclic cyclobutanes with modulable exit vectors based on the regioselective monoborylation of spirocyclobutenes. Using an inexpensive copper salt and a commercially available bidentate phosphine, a broad variety of borylated spirocycles have been prepared with complete regiocontrol. The boryl moiety provides a synthetic handled for further functionalization, allowing access to a wide array of spirocyclic building blocks from a common intermediate.

Molecular fragmentation as a way to reveal early electron dynamics induced by attosecond pulses.

We present a theoretical study of the electron and nuclear dynamics that would arise in an attosecond two-color XUV-pump/XUV-probe experiment in glycine. In this scheme, the broadband pump pulse suddenly ionizes the molecule and creates an electronic wave packet that subsequently evolves under the influence of the nuclear motion until it is finally probed by the second XUV pulse. To describe the different steps of such an experiment, we have combined a multi-reference static-exchange scattering method with a trajectory surface hopping approach.

Accounting for Vibronic Features through a Mixed Quantum-Classical Scheme: Structure, Dynamics, and Absorption Spectra of a Perylene Diimide Dye in Solution.

The optical absorption spectrum of a perylene diimide (PDI) dye in acetonitrile solution is simulated using the recently developed ( , , 1215-1231) Ad-MD|VH method. This mixed quantum-classical (MQC) approach is based on an adiabatic (Ad) separation of soft(classical)/stiff(quantum) nuclear degrees of freedom and expresses the spectrum as a conformational average (over the soft coordinates) of vibronic spectra (for the stiff coordinates) obtained through the generalized vertical Hessian (VH) vibronic approach. The average is performed over snapshots extracted from classical molecular dynamics (MD) runs, performed with a specifically parameterized quantum-mechanically derived force field (QMD-FF).