Javier Cerezo

Autonomous University of Madrid | UAM · Department of Chemistry

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 tr...

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 second-order nonlinear optical (NLO) responses of a Donor-Acceptor Stenhouse Adduct (DASA) are investigated by using a computational approach combining molec- ular dynamics simulations and density functional theory (DFT) calculations....

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...

Herein the manuscript, we report the interaction of an important drug, Imiquimod (IMQ), with Calf Thymus Deoxyribonucleic Acid (ct-DNA). Despite of being used IMQ in multiple medicinal applications such as immune response modifier, antitumor and antiviral drug its interaction with DNA is not studied yet. To understand their interaction and characte...

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...

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...

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 an...

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 concur to...

Following up on our previous work on vibrationally resolved electronic absorption spectra including the effect of vibrational pre-excitation [J. von Cosel et al., J. Chem. Phys. 147, 164116 (2017)], we present a combined theoretical and experimental study of two-photon induced vibronic transitions in polyatomic molecules that are probed in the Vibr...

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 im...

We present a viable protocol to compute vibrational resonance Raman (vRR) spectra for systems with several close-lying and potentially coupled electronic states. It is based on the parametrization of linear vibronic coupling (LVC) models from time-dependent density functional theory (TD-DFT) calculations and quantum dynamics propagations of vibroni...

Optical chemosensors caused a revolution in the field of sensing due to their high specificity, sen-sitivity, and fast detection features. Imidazole derivatives have offered promising features in the literature as they bear suitable donor/acceptor groups for the selective analytes in the skeleton. In this work, an isoindole−imidazole containing a S...

In this work, we calculate the partition functions and thermodynamic quantities of molecular hydrogen isotopologues using the rovibrational energy levels provided by the highly accurate ab initio adiabatic potential energy functions recently determined by Pachucki and Komasa (Pachucki, K.; Komasa, J. J. Chem. Phys.2014, 141, 224103). The partition...

We concisely review the main methodological approaches to model nonadiabatic dynamics in isotropic solutions and their applications. Three general classes of models are identified as the most used to include solvent effects in the simulations. The first model describes the solvent as a set of harmonic collective modes coupled to the solute degrees...

Protein folding evolves by exploring the conformational space with a subtle balance between enthalpy and entropy changes which eventually leads to a decrease of free energy upon reaching the folded structure. A complete understanding of this process requires, therefore, a deep insight into both contributions to free energy. In this work, we clarify...

The optical absorption spectrum of a perylene diimide (PDI) dye in acetonitrile solution is simulated using the recently developed (J. Chem. Theory Comput.2020, 16, 1215-1231) Ad-MD|gVH method. This mixed quantum-classical (MQC) approach is based on an adiabatic (Ad) separation of soft(classical)/stiff(quantum) nuclear degrees of freedom and expres...

Protein folding evolves by exploring the conformational space with a subtle balance between enthalpy and entropy changes which eventually leads to a decrease of the free energy upon reaching the folded structure. A complete understanding of this process requires, therefore, a deep insight into both contributions to the free energy. In this work, w...

For the rational design of new fluorophores, reliable predictions of fluorescence quantum yields from first principles would be of great help. However, efficient computational approaches for predicting transition rates usually assume that the vibrational structure is harmonic. While the harmonic approximation has been used successfully to predict v...

Absorption spectra of Cyanine⁺Br⁻ salts show a remarkable solvent dependence in non-/polar solvents, exhibiting a narrow, sharp band shapes in dichloromethane but broad features in toluene; this change was attributed to ion pair association, breaking the symmetry of the cyanine, similar to the situation in the crystals (P.-A. Bouit et al, J. Am. Ch...

We present a general mixed quantum classical method that couples classical Molecular Dynamics (MD) and vibronic models to compute the shape of electronic spectra of flexible molecules in condensed phase without, in principle, any phenomenological broadening. It is based on a partition of the nuclear motions of the solute+solvent system in "soft" an...

We investigate the interresidual and intraresidual correlations between dihedral displacements of adjacent residues within model polyalanine peptides by analyzing extensive molecular dynamics trajectories. Correlations are evaluated individually at different residue conformations covering the whole (ϕ i ,ψ i )-space. From these, we draw maps that u...

Conformational flexibility of polypeptide chains is mainly driven by changes in the (phi, psi) dihedrals of each residue. Such motions, however, are not completely independent, as certain (anti)correlated motions are favored. In this work, we investigate the correlations between the dihedral displacements of adjacent residues, (Δphi i, Δpsi i+1) an...

A novel energetic route driving the folding of a polyalanine peptide from an extended conformation to its α-helix native conformation is described, supported by a new method to compute mean potential energy surfaces accurately in terms of the dihedral angles of the peptide chain from extensive Molecular Dynamics simulations. The Energetic Self-Fold...

We have investigated the performance of a core-valence separated scheme within the coupled cluster (CC) hierarchy of methods CC singles (CCS), CC singles and approximate doubles (CC2), and CC singles and doubles (CCSD) in reproducing the K-edge x-ray absorption spectra of the low-Z elements carbon, oxygen, and fluorine in formaldehyde (CH2O), carbo...

The excited states of three radical derivatives of guanine, i. e. guanine cation (G⁺) and its two main deprotonated derivatives (G−H1 and G−H2), have been characterized in the Franck‐Condon region by TD‐DFT, using different functionals, CASPT2, and EOM‐EE‐CCSD calculations. In the gas phase, all the methods provide a similar description of the main...

We face the challenging description of the excited states responsible for one photon (OPA) and two photon (TPA) absorption in squaraine dyes, adopting both time‐dependent density functional theory and a large variety of post Hartree Fock methods, including coupled cluster and adiabatic diagrammatic construction methods (ADC, to the second and third...

A novel energetic route driving the folding of a polyalanine peptide from an extended conformation to its α-helix native conformation is described, supported by a new method to compute mean potential energy surfaces accurately in terms of the dihedral angles of the peptide chain from extensive Molecular Dynamics simulations. The Energetic Self-Fold...

Evidences of subtle effects in the dynamic reorganization of a protic solvent in its firstand farther-neighbor shells, in response to the sudden change in the solute’s electronic distribution upon excitation, are unveiled by a multi-level computational approach. By combining non-equilibrium molecular dynamics and quantum mechanical calculations, th...

Animal colouration is characterized by the concentration of pigments in integumentary structures and by the nanoscale arrangement of constitutive elements. However, the influence of molecular vibration on colour expression has been overlooked in biology. Molecular vibration occurs in the infrared spectral region, but vibrational and electronic prop...

Quantum dynamics simulations, with the Multiconfigurational Time Dependent Hartree method, are used to assign the very broad absorption spectrum of Cytosine in gas phase and study the relation between spectral features and the ultrafast internal conversions among its excited states. For each of the four populated tautomers of Cytosine we built a Li...

We simulate the vibronic profile of the electronic circular dichorism (ECD) spectra of oligothiophenes in cisoid and transoid chiral arrangements. We consider oligomers of different lenghts, from two to fifteen units, and investigate extensively how the ECD spectral shapes depend on the inter-ring torsions. In general, the molecular structures we c...

The Watson-Crick hydrogen bonded pair formed by deoxyguanosine and deoxycytidine (GC) in chloroform has been analysed by classical Molecular Dynamics simulations, which shows the existence of several fairly stable solute/solvent hydrogen bonds. Time-Dependent Density Functional Theory (TD-DFT) calculations with M052X functional, including solvation...

The accuracy of molecular mechanics force fields (FF) reveals critical for applications where precise molecular structures along a conformational sampling are required, as in the simulation of electronic spectroscopies. This implies abandoning generalized FFs in favor of specific FFs, with non-transferable parameters able to accurately describe the...

We extend a recently proposed mixed quantum/classical method for computing the vibronic electronic circular dichroism (ECD) spectrum of molecules with different conformers, to cases where more than one hindered rotation is present. The method generalizes the standard procedure, based on the simple Boltzmann average of the vibronic spectra of the st...

We consider the nonadiabatic dynamics of internal conversions (ICs) in systems rigid enough to allow a description of the coupled potential energy surfaces (PES) within the harmonic approximation. Through a hierarchical representation of the Hamiltonian, we define a set of sequentially coupled effective modes and obtain reduced-dimensionality model...

We present a novel mixed quantum classical dynamical method to include solvent effects on internal conversion (IC) processes. All the solute degrees of freedom are represented by a wavepacket moving according to nonadiabatic quantum dynamics, while the motion of an explicit solvent model is described by an ensemble of classical trajectories. The mu...

Comparison between chiroptical spectra and theoretical predictions is the method of choice for assignment of absolute configuration of chiral compounds in solution. Here we report the case of an apparently simple biarylcarbinol, whose electronic circular dichroism (ECD) in the 1Lb region exhibits a peculiar alternation of negative and positive band...

Vibrationally resolved electronic absorption spectra including the effect of vibrational pre-excitation are computed in order to interpret and predict vibronic transitions that are probed in the Vibrationally Promoted Electronic Resonance (VIPER) experiment [L. J. G. W. van Wilderen et al., Angew. Chem. Int. Ed. 53, 2667 (2014)]. To this end, we em...

Vibrationally resolved electronic absorption spectra including the effect of vibrational pre-excitation are computed in order to interpret and predict vibronic transitions that are probed in the Vibrationally Promoted Electronic Resonance (VIPER) experiment [L. J. G. W. van Wilderen et al., Angew. Chem. Int. Ed. 53, 2667 (2014)]. To this end, we em...

Benzazolate complexes of Ni(II), [Ni(pbz)(tren)]ClO4 (pbz = 2-(2'-hydroxyphenyl)-benzimidazole (pbm), 1, 2-(2'-hydroxyphenyl)-benzoxazole (pbx), 2, 2-(2'-hydroxyphenyl)-benzothiazole (pbt), 3; tren = tris(2-aminoethyl)amine), are prepared by self-assembly reaction and structurally characterized. Theoretical DFT simulations are carried out to reprod...

We present a novel mixed method suitable for computing the low-to-middle resolution spectra of systems characterized by a large-amplitude motion s (defined by either a reaction or an internal path) coupled to a bath of harmonic oscillators r which change with s. The method is based on an adiabatic approximation whereby s is considered much slower t...

In this study, we analyze the photophysics of the N-methyl-6-oxyquinolinium betaine (MQ) solvatochromic dye in aqueous solution, focussing on the important structural rearrangement of its first solvation shell following the electronic excitation, which is characterized by a strong charge transfer. To this aim, we compare the results provided by gro...

Vertical models for the simulation of spectroscopic lineshapes expand the potential energy surface (PES) of the final state around the equilibrium geometry of the initial state. These models provide, in principle, a better approximation of the region of the band maximum. At variance, adiabatic models expand each PES around its own minimum. In the h...

We compute the rate of the charge recombination (CR) process from the minimum of the charge transfer (CT) Guanine–Cytosine stacked dimer in water solution to the ground electronic state (GS). We adopt the quantum non-adiabatic theory of electron transfer reactions, where key ingredients to determine the CR rate are the electronic coupling and the s...

The one-photon absorption spectrum of a carbazole derivative has been studied by employing density functional response theory combined with a mixed quantum/classical (QC) approach to simulate the spectral shape. In a first step of our analysis we employed the vertical gradient (VG) vibronic model to investigate the role of Franck-Condon (FC) profil...

The simulation of optical properties in complex and heterogeneous systems, as those involved in photovoltaic devices, requires efficient protocols able to account for the complexity of the environment. An usual procedure is based on molecular dynamics (MD) sampling and subsequent computation of the transition properties, at quantum mechanics/molecu...

We present the simulation of the absorption (ABS), electronic circular dichroism (ECD), emission (EMI) and circularly polarized luminescence (CPL) spectra for the weak electronic transition between the ground (S0) and the lowest excited state (S1) of hexahelicene, 2-methyl-hexahelicene, 2-bromo-hexahelicene and 5-aza-hexahelicene. Vibronic contribu...

We present a protocol to estimate the solvent-induced broadening of electronic spectra based on a model that explicitly takes into account the environment embedding the solute. Starting from a classical approximation of the solvent contribution to the spectrum, the broadening arises from the spread of the excitation energies due to the fluctuation...

Titanium propoxide, titanium isopropoxide, and titanium (triethanolaminato) isopropoxide are proposed as high-performance additives to overcome the oxygen inhibition effects in the free radical photopolymerization of a low-viscosity monomer thin film, under air and upon a low-intensity UV light activation. Indeed, when added to a Type I photoinitia...

Inflammation is considered to be a key factor of major diseases like cancer, Alzheimer’s disease, Parkinson’s disease etc. For the past few decades pharmaceutical companies are trying to explore new effective medications against inflammation. As a part of their detailed studies, lot of drug targets and drugs were introduced against inflammation. In...

We simulate from first-principles the absorption spectra of five structure-related coumarin derivatives utilized in dye sensitized solar cells (DSSC), investigating the vibronic and solvent contributions to the position and width of the spectra in ethanol. Ground and excited state potential energy surfaces (PES) are modeled by Density Functional Th...

We study the absorption and emission electronic spectra in aqueous solution of N-methyl-6-oxyquinolinium betaine (MQ), an interesting dye characterized by a large change of polarity and H-bond ability between the ground (S0) and the excited (S1) state. To that end we compare alternative approaches based either on explicit solvent models and density...

DNA is constantly exposed to exogenous agents that randomly damage the genetic code. However, external perturbations might also be used to induce malignant cell death if the mutation processes are controlled. The present communication reports a set of parameters allowing DNA mutation through the use of intense external electric fields. This is a st...

Rovibrational energy levels, partition functions and relative abundances of the stable isotopologues of CO2 in gas phase at equilibrium are calculated using an empirical Morse-cosine potential energy surface (PES) refined by fitting to the updated pure (l2=0l2=0) vibrational frequencies observed for the main 12C16O2 isotopologue. The rovibrational...

This contribution is an investigation of both the structures and optical properties of a set of 14 diverse, recently synthesized diarylethenes using Time-Dependent Density Functional Theory (TD-DFT) at the omega B97X-D/6-31G(d) level of theory. The linear response (LR) and state-specific (SS) versions of the Polarizable Continuum Model (PCM) have b...

The clinical use of platinum(II)-based drugs has serious side effects due to the non-specific reactions with both malignant and normal cells. To circumvent such major drawback, novel metallodrugs might be combined with suitable carrier molecules, as antibodies, to ensure selective attacks on tumours while sparing healthy tissues. In this contributi...

We compute the line shape of absorption and emission electronic spectra of two different dyes, Coumarin C153 and N-methyl-6-Quinolinium betaine accounting for the vibronic structure, temperature effects and polar solvent inhomogeneous broadening, without using any phenomenological parameter. We exploit a number of recent developments including a ti...

The syntheses, crystal structures, and spectroscopic absorption properties of pentacoordinate Ni(II) complexes of aromatic N,O-chelate ligands are described, along with density functional theory (DFT) calculations conducted to support them. In addition, the luminescence properties of the complexes in solution and the solid state, and the fluorescen...

The prediction of antioxidant properties is not straightforward due to the complexity of the in vivo systems. Here, we use theoretical descriptors, including the potential of ionization, the electrodonating power and the spin density distribution, to characterize the antioxidant capacity of edaravone (EDV) derivatives. Our computations reveal the r...

The characterization and the photochemical investigation of a RuII complex (Ru(PPh3)3Cl2) having phosphine ligands are reported. DFT calculations and ESR spin trapping experiments revealed for the first time that the photodecomposition of the complex is governed by a homolytic cleavage of the P–(C6H5) bond generating phenyl radicals Ph• which are a...

When large structural displacements take place between the ground state (GS) and excited state (ES) minima of polyatomic molecules, the choice of a proper set of coordinates can be crucial for a reliable simulation of the vibrationally resolved absorption spectrum. In this work, we study two carotenoids that undergo structural displacements from GS...

In this work, we investigate systems formed by β-carotene and zeaxanthin embedded separately in a model lipid bilayer of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) through molecular dynamics (MD) simulations. The study is conducted using an all-atoms model and by analyzing the structural changes that occur at both the carotenoid molecule an...

In this work we carefully investigate the relationship between computed data and experimental electronic spectra. To that end, we compare both vertical transition energies, EV, and characteristic frequencies of the spectrum like the maximum, νmax, and the center of gravity, M1, taking advantage of an analytical expression of M1 in terms of the para...

The oxygen inhibition of acrylate photopolymerization using visible light was depth characterized by confocal Raman microscopy. The sample thickness was found to influence the depth conversion profile. With increasing sample thickness, the conversion at the surface was increased and the oxygen-affected layer (OAL) decreased, up to a limit where the...

In this work we investigate the effect of cis isomerizations and conformational changes on the antioxidant activity of β-carotene, one of the most important pigments in nature. The electrodonating (ω(-)) and electroaccepting (ω(+)) powers of the most relevant isomers of β-carotene are first evaluated in polar and nonpolar solvents using density fun...

Fatty oleic acid (OA) and, recently, its derivative 2-hydroxyoleic acid (2OHOA) have been reported to display an important therapeutic activity. To understand better these therapeutic effects at the molecular and cellular levels, in this work we have carried out molecular dynamics simulations to elucidate the structural and dynamical changes taking...