Evidence of Excited-State Vibrational Mode Governing the Photorelaxation of a Charge-Transfer Complex.

Modern, nonlinear, time-resolved spectroscopic techniques have opened new doors for investigating the intriguing but complex world of photoinduced ultrafast out-of-equilibrium phenomena and charge dynamics. The interaction between light and matter introduces an additional dimension, where the complex interplay between electronic and vibrational dynamics needs the most advanced theoretical-computational protocols to be fully understood on the molecular scale. In this study, we showcase the capabilities of ab initio molecular dynamics simulation integrated with a multiresolution wavelet protocol to carefully investigate the excited-state relaxation dynamics in a noncovalent complex involving tetramethylbenzene (TMB) and tetracyanoquinodimethane (TCNQ) undergoing charge transfer (CT) upon photoexcitation.

Validation of a guideline to reduce variability in diagnosing cervical dystonia.

Background: Cervical dystonia is characterized by a variable pattern of neck muscle involvement. Due to the lack of a diagnostic test, cervical dystonia diagnosis is based on clinical examination and is therefore subjective. The present work was designed to provide practical guidance for clinicians in confirming or refuting suspected cervical dystonia.

Writing tremor in Parkinson's disease: frequency and associated clinical features.

Action tremor in Parkinson's disease may present in up to 46% of patients, either as postural or kinetic tremor. How action tremor may affect handwriting has been the object of some investigations; however, clinical features of writing tremor in Parkinson's disease are still not well-characterised. One hundred consecutive patients with idiopathic Parkinson's disease were included in the study.

Electronic and Vibrational Manifold of Tetracyanoethylene-Chloronaphthalene Charge Transfer Complex in Solution: Insights from TD-DFT and Ab Initio Molecular Dynamics.

The interplay between light absorption and the molecular environment has a central role in the observed photophysics of a wide range of photoinduced chemical and biological phenomena. The understanding of the interplay between vibrational and electronic transitions is the focus of this work, since it can provide a rationale to tune the optical properties of charge transfer (CT) materials used for technological applications. A clear description of these processes poses a nontrivial challenge from both the theoretical and experimental points of view, where the main issue is how to accurately describe and probe drastic changes in the electronic structure and the ultrafast molecular relaxation and dynamics.

Exploring the Franck-Condon region of a photoexcited charge transfer complex in solution to interpret femtosecond stimulated Raman spectroscopy: excited state electronic structure methods to unveil non-radiative pathways.

We present electronic structure methods to unveil the non-radiative pathways of photoinduced charge transfer (CT) reactions that play a main role in photophysics and light harvesting technologies. A prototypical π-stacked molecular complex consisting of an electron donor (1-chloronaphthalene, 1ClN) and an electron acceptor (tetracyanoethylene, TCNE) was investigated in dichloromethane solution for this purpose. The characterization of TCNE:π:1ClN in both its equilibrium ground and photoinduced low-lying CT electronic states was performed by using a reliable and accurate theoretical-computational methodology exploiting molecular dynamics simulations.

Deep grey matter involvement and altered sensory gating in multiple sclerosis.

Background: Somatosensory temporal discrimination threshold (STDT) is altered in multiple sclerosis (MS). In healthy subjects (HS), voluntary movement modulates the STDT through mechanisms of subcortical sensory gating.

Objective: With neurophysiological and magnetic resonance imaging (MRI) techniques, we investigated sensory gating and sensorimotor integration in MS.

From ascorbic acid to furan derivatives: the gas phase acid catalyzed degradation of vitamin C.

Furan derivatives, potentially carcinogenic to humans, can be formed, in addition to carbohydrates and other sources, from the degradation of ascorbic acid (AA). At present, the mechanisms involved in the ascorbic acid degradation are not yet fully understood. In this study, we reported a gas-phase investigation, performed using Triple Quadrupole (TQ/MS) and Ion Trap Mass Spectrometry (QIT/MS) together with quantum mechanical calculations at the B3LYP/6-31+G(d,p) level of theory, on the non-oxidative degradation mechanism of l-ascorbic acid (AA) to furan derivatives.

Insight into the Mechanism of Action of Marine Cytotoxic Thiazinoquinones.

The electrochemical response of four natural cytotoxic thiazinoquinones isolated from the species was studied using conventional solution-phase and solid-state techniques, based on the voltammetry of immobilized particles methodology. The interaction with O₂ and electrochemically generated reactive oxygen species (ROS) was electrochemically monitored. At the same time, a molecular modeling study including density functional theory (DFT) calculations was performed in order to analyze the conformational and electronic properties of the natural thiazinoquinones, as well as those of their reduced intermediates.

Vitamin C: an experimental and theoretical study on the gas-phase structure and ion energetics of protonated ascorbic acid.

In order to investigate the gas-phase mechanisms of the acid catalyzed degradation of ascorbic acid (AA) to furan, we undertook a mass spectrometric (ESI/TQ/MS) and theoretical investigation at the B3LYP/6-31 + G(d,p) level of theory. The gaseous reactant species, the protonated AA, [C H O ]H , were generated by electrospray ionization of a 10  M H O/CH OH (1 : 1) AA solution. In order to structurally characterize the gaseous [C H O ]H ionic reactants, we estimated the proton affinity and the gas-phase basicity of AA by the extended Cooks's kinetic method and by computational methods at the B3LYP/6-31 + G(d,p) level of theory.

On the Driving Force of the Excited-State Proton Shuttle in the Green Fluorescent Protein: A Time-Dependent Density Functional Theory (TD-DFT) Study of the Intrinsic Reaction Path.

We simulated the intrinsic reaction path of the Green Fluorescent Protein (GFP) proton shuttle in both the ground state (S) and first singlet excited state (S), accounting for the main energetic and steric effects of the protein in a convenient model including the chromophore, the crystallographic water, and the residues directly involved in the proton transfer event. We adopted density functional theory (DFT) and time-dependent density functional theory (TD-DFT) levels to define the potential energy surfaces of the two electronic states, and we compared results obtained by the Damped Velocity Verlet and the Hessian-based Predictor-Corrector integrators of the intrinsic reaction coordinate, which gave a comparable and consistent picture of the mechanism. We show that, at S, the GFP proton transfer becomes favored, with respect to S, as suggested by the experimental evidence.

Use of Integrated Computational Approaches in the Search for New Therapeutic Agents.

Computer-aided drug discovery plays a strategic role in the development of new potential therapeutic agents. Nevertheless, the modeling of biological systems still represents a challenge for computational chemists and at present a single computational method able to face such challenge is not available. This prompted us, as computational medicinal chemists, to develop in-house methodologies by mixing various bioinformatics and computational tools.

Accurate Infrared (IR) Spectra for Molecules Containing the C≡N Moiety by Anharmonic Computations with the Double Hybrid B2PLYP Density Functional.

Herein, we report a comprehensive benchmark of C≡N stretching vibrations computed at harmonic and anharmonic levels with the aim of proposing and validating a reliable computational strategy to get accurate results for this puzzling vibrational mode without any ad hoc scaling factor. Anharmonic calculations employing second-order vibrational perturbation theory provide very good results when performed using the B2PLYP double-hybrid functional, in conjunction with an extended basis set and supplemented by semiempirical dispersion contributions. For larger systems, B2PLYP harmonic frequencies, together with B3LYP anharmonic corrections, offer a very good compromise between accuracy and computational cost without the need of any empirical scaling factor.

CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study.

The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.

Extension of the AMBER force-field for the study of large nitroxides in condensed phases: an ab initio parameterization.

The popular AMBER force-field has been extended to provide an accurate description of large and flexible nitroxide free-radicals in condensed phases. New atom types have been included, and relevant parameters have been fitted based on geometries, vibrational frequencies and potential energy surfaces computed at the DFT level for several different classes of nitroxides, both in vacuo and in different solvents. The resulting computational tool is capable of providing reliable structures, vibrational frequencies, relative energies and spectroscopic observables for large and flexible nitroxide systems, including those typically used as spin labels.

An integrated computational protocol for the accurate prediction of EPR and PNMR parameters of aminoxyl radicals in solution.

Magnetic spectroscopic techniques such as electron paramagnetic resonance (EPR) and paramagnetic NMR (PNMR) are valuable tools for understanding the structure and dynamics of complex systems such as, for example, biomolecules or nanomaterials labeled with suitable free radicals. Unfortunately, such spectra do not give direct access to the radical structure because of the subtle interplay between several different effects not easily separable and evaluable by experimentalists alone. In this respect, computational spectroscopy is becoming an essential and versatile tool for the assignment and interpretation of experimental spectra.

Double C-H activation of ethane by metal-free SO2*+ radical cations.

The room-temperature C-H activation of ethane by metal-free SO(2)(*+) radical cations has been investigated under different pressure regimes by mass spectrometric techniques. The major reaction channel is the conversion of ethane to ethylene accompanied by the formation of H(2)SO(2)(*+), the radical cation of sulfoxylic acid. The mechanism of the double C-H activation, in the absence of the single activation product HSO(2)(+), is elucidated by kinetic studies and quantum chemical calculations.

Interplay of stereo-electronic, environmental, and dynamical effects in determining the EPR parameters of aromatic spin-probes: INDCO as a test case.

An integrated computational strategy for the evaluation of reliable structures and magnetic properties of spin probes and spin labels has been extended to aromatic species. From an electronic point of view, delocalization of the unpaired electron density over aromatic moieties reduces significantly the computed nitrogen isotropic hyperfine coupling constant (A(N)) with respect to values characteristic of aliphatic nitroxides. Solvent effects in not too high polarity media are quite small, but not negligible.

Insight into the mechanism of action of plakortins, simple 1,2-dioxane antimalarials.

A multidisciplinary approach, based on molecular dynamics/mechanics, ab initio calculations, dynamic docking studies, and chemical reactions, has been employed to gain insight into the mechanism of the antimalarial action of plakortin and dihydroplakortin, simple 1,2-dioxanes isolated from the sponge Plakortis simplex. Our results show that these molecules, after interaction of the endoperoxide bond with Fe(ii), likely coming from the heme molecule, give rise to the formation of an oxygen radical, followed by rearrangement to give a carbon radical centered on the "western" alkyl side-chain. The carbon radicals generated on the side-chain, amenable for intermolecular reactions, should represent the toxic intermediates responsible for subsequent reactions leading to plasmodium death.

Magnetic interactions in phenyl-bridged nitroxide diradicals: conformational effects by multireference and broken symmetry DFT approaches.

In the present paper we report the key results of a comprehensive computational study aimed at investigating the dependence of the singlet-triplet energy gap in phenyl-bridged bis-nitroxide diradicals, on the basis set and on soft structural parameters like torsion and pyramidalization. We have compared the BS-DFT technique with the post-Hartree-Fock DDCI2 multireference approach. With this latter method we have also studied the different role that sigma and pi core and virtual orbitals have in the resulting singlet-triplet energy gap.

Magneto-structural relationships for radical cation and neutral pyridinophane structures with intrabridgehead nitrogen atoms. An integrated experimental and quantum mechanical study.

An integrated experimental and computational approach was used to compare the properties of representative molecules containing intrabridgehead nitrogen atoms with those of the corresponding radical cations issuing from one-electron oxidation with the aim of unraveling the characteristics of the three-electron sigma-bonds formed in the open-shell species. From a quantitative point of view, last-generation density functional methods coupled with proper basis sets and, when needed, continuum models for describing bulk solvent effects confirm their reliability for the computation of structures and magnetic properties of organic free radicals. From an interpretative point of view, different hybridizations of nitrogen atoms tuned by their chemical environment lead to markedly different magnetic properties that represent reliable and sensitive probes of structural and electronic characteristics.

Validation of the B3LYP/N07D and PBE0/N07D Computational Models for the Calculation of Electronic g-Tensors.

Calculations on a large set of free radicals containing atoms of the second and third row show that the computational model defined by the new N07D basis set and hybrid density functionals (B3LYP and PBE0) provides remarkably accurate g-tensor values at reasonable computational costs. Since in previous works it has been shown that the same computational model delivers reliable results also for structural parameters and hyperfine couplings, the route seems paved toward full a priori computation of EPR spectra of large free radicals both in vacuo and in condensed phases.

Formation of cross-linked adducts between guanine and thymine mediated by hydroxyl radical and one-electron oxidation: a theoretical study.

The role of local geometric and stereo-electronic effects in tuning the preference for different cross-linked adducts between thymine and purinic bases has been analyzed by a computational approach rooted in density functional theory. Our study points out that G--T and T--G tandem lesions are produced according to the same mechanism as A--T and T--A intrastrand adducts, and in both cases purine--T adducts are preferred rather than the opposite sequences. Moreover, use of conceptual DFT tools allows the rationalization of the preferential occurrence of G--T and T--G tandem lesions in place of their A--T and T--A counterparts.

Development and Validation of the B3LYP/N07D Computational Model for Structural Parameter and Magnetic Tensors of Large Free Radicals.

Extensive calculations on a large set of free radicals containing atoms of the second and third row show that the B3LYP/N07D computational model provides remarkably accurate structural parameters and magnetic tensors at reasonable computational costs. The key of this success is the optimization of core-valence s functions for hyperfine coupling constants, while retaining (and even improving) the good performances of the parent 6-31+G(d,p) basis set for valence properties through reoptimization of polarization and diffuse p functions.

On the interpretation of continuous wave electron spin resonance spectra of tempo-palmitate in 5-cyanobiphenyl.

Electron spin resonance (ESR) measurements are highly informative on the dynamic behavior of molecules, which is of fundamental importance to understand their stability, biological functions and activities, and catalytic action. The wealth of dynamic information which can be extracted from a continuous wave electron spin resonance (cw-ESR) spectrum can be inferred by a basic theoretical approach defined within the stochastic Liouville equation formalism, i.e.