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Molecular dynamics and quantum simulations are performed to elucidate some aspects of the action mechanism of mercapto-benzamides, a proposed class of antivirals against HIV-1. These molecules act as prodrugs that, after modifications in the biological environment, are able to denature the HIV nucleocapsid protein 7, a metal binder protein, with two zinc finger motifs, vital for RNA maturation and viral replication. Despite their attractive features, these molecules and their biological target are not well understood. Simulations were performed to support a proposed action mechanism, based on the activation of mercapto-benzamides by acetylation, targeting a relatively rare protein hydrolyzed state, followed by

Circular dichroism (CD) spectroscopy is a useful technique for characterizing chiral molecules. It is more sensitive than total absorption to molecule conformation, and it is routinely used to identify enantiomers. We present here a first principles implementation of CD with application to three cyclo-dipeptides. Our CD approach for molecules has been integrated in the 5.0 release of the Yambo code [1], distributed under GPL., Comment: 9 pages, 5 figures

We predict the optical properties (in particular optical absorbance and reflectance anisotropy spectra (RAS)) of the silicon(001) surface organically functionalized by the adsorption of chosen tetr...

The ability to accurately measure or predict several physicochemical properties of molecules which play a role as active substances in drugs can be of strategic importance for pharmacological applications, in addition to its possible interest in fundamental research. Chirality is a relevant feature in the characterization of drug molecules: enantiomers can show different pharmacological activity and adverse effects. The ability to separate stereoisomers and to assign their absolute configuration can thus be crucial. Circular dichroism (CD) spectra are a useful tool to distinguish between enantiomers. In this work we apply an in-house developed code, based on an efficient DFT approach for circular dichroism, to fully characterize the molecular optical properties in the case of few selected fundamental molecules for current medical and pharmaceutical research, namely avibactam, as representative of non β-lactam inhibitors, two cephems (cefepime and cefoxitin), as examples of β-lactam antibiotics, and idelalisib, as a recent relevant anticancer active substance to treat major leukemias. For the above molecules, in addition to their optical absorption spectra, we calculate their CD spectra within state-of-the-art computational techniques. We then investigate both the conformational and chemical sensitivity of absorption and CD spectra for the chosen molecules. The outcomes of the present research could be of fundamental importance to gain additional information on molecules involved in therapeutic protocols for severe diseases or in drug design.

In this work, we study the optical absorption spectra of extensive stacking forms of four molecules known to be among eumelanin basic building blocks: 5,6-dihydroxyindole (DHI), 5,6-dihydroxyindole-2-carboxylic acid (DHICA), indolequinone (IQ) and quinone-methide (MQ). Stacked monomers can be considered as a minimal model of out-of-plane complexity in eumelanin, as complementary to in-plane oligomerization. The choice of a plane wave density functional theory (DFT) approach allows us to address extensive, i.e. several-layer, stacking of these DHI-like monomers at a relatively low computational cost, by treating stacked systems as periodic along the stacking direction. Absorption spectra of stacked monomers display interesting trends in terms of chemical and structural sensitivity, which can shed light on the role of extensive stacking in the transition from the optical properties of small molecules such as DHI to the typical broadband and monotonic absorption spectrum of the eumelanin pigment.

We report a systematic computational investigation on the electronic and optical properties of chromophores derived from hexeneuronic acids (HexA). In particular, we focus on five chemical structures, which account up to 90% of HexaA-derived chromophores. We performed all-electrons density functional theory (DFT) and time dependent DFT (TDDFT) calculations with a localized Gaussian basis set and the hybrid exchange correlation functional B3LYP. We quantified key molecular properties relevant as electron affinities, ionization energies, fundamental gaps, optical absorption spectra, and exciton binding energies. Furthermore, we modeled the HexA chromophores in the presence of peroxide (H2O2) solvent and evaluated the changes in the optical properties due to the solvent. Altogether, our results provide a complete description of molecular, electronic and optical properties of HexA derived chromophores, which can be useful to understand their role in bleaching mechanisms and also their potential application as organic conductors. Graphical abstract: [Figure not available: see fulltext.]. © 2018, Springer Nature B.V.

We report a systematic investigation on the electronic and optical properties of the smallest stable clusters of alkaline-earth metal fluorides, namely, MgF2, CaF2, SrF2, and BaF2. For these clusters, we perform density functional theory (DFT) and time-dependent DFT (TDDFT) calculations with a localized Gaussian basis set. For each molecule ((MF2)n, n = 1–3, M = Mg, Ca, Sr, Ba), we determine a series of molecular properties, namely, ground-state energies, fragmentation energies, electron affinities, ionization energies, fundamental energy gaps, optical absorption spectra, and exciton binding energies. We compare electronic and optical properties between clusters of different sizes with the same metal atom and between clusters of the same size with different metal atoms. From this analysis, it turns out that MgF2 clusters have distinguished ground-state and excited-state properties with respect to the other fluoride molecules. Sizeable reductions of the optical onset energies and a consistent increase of excitonic effects are observed for all clusters under study with respect to the corresponding bulk systems. Possible consequences of the present results are discussed with respect to applied and fundamental research.

For many centuries, paper was considered the main support for recording cultural achievements all over the world. Archives represent the historical memory of our past, and the book conservation represents one main concern since many books and documents kept in libraries and archives are at risk because of their fragility. The use of portable, not destructive technique like NIR μ-Raman spectroscopy represents a valid instrument for monitoring the documentary heritage. In the present study, we investigated the degradation process, associated to the polymers breaking, in order to propose a successful kinetic model for determining the ageing time of cellulose. We compared the calculated results with respect to both experimental samples and literature data, covering a period of seven centuries, from XV to XXI centuries. Proposed model starts directly from Raman spectra, in particular by monitoring the band at 1100 cm− 1 ascribed to C-O-C inter-monomers bond, whose relative intensity is related to the cellulose chain length. We obtained a very good agreement with the experimental data with 8% of accuracy. Finally, with the help of Density Functional Theory (DFT) simulations, we confirmed our model by studying the structure and the grade of cellulose crystallinity in the paper. In particular, the reverse trend of the band at 900 cm− 1, related to the crystallinity grade of the cellulose, and the band at 1100 cm− 1, as a function of the dimer unit cell structure, supported the kinetic model, suggesting a shear stress like effect as the origin of the cellulose chain length decrease.

The organic/inorganic interface in thin nanosized porous structures has a key role in determining the final properties of the composite materials. By use of the porous silicon/eumelanin hybrids as a case study, the role of this interface was investigated by experimental and computational methods. Our results show that an increased polymer density close to the hybrid interface strongly modifies the diffusion of the chemical species within the polymer molecule, affecting then the oxidation level of the pores' inner Si surface. We observed a greater stability induced by increased pore diameter, a behavior that with computational and chemical arguments we attributed to a modified diffusion of the hydrogen peroxide toward the Si/eumelanin interface. Our results show that the overall behavior of a polymer when inserted in a tiny nanoscale structure must be taken into account for a correct understanding and control of the hybrids properties and that the formation of the interface alone may not be sufficient. © 2018 American Chemical Society.

Raman spectroscopy has been utilized to study ancient documents conserved at the University Library of Cagliari (Italy) with the aim to give an exhaustive scenario about the employment of inks, pigments and supporting materials (papers and parchments) related to specific historical periods (XIV–XV centuries). The samples studied are selected between the most prestigious texts present in the collection: two accounting books of sixteenth and fifteenth centuries, a mathematical text of the sixteenth century, a navigation text of the same period, a copy of the most important Sardinian medieval constitutional text “Carta De Logu”, a medieval copy of the famous Italian poem: “La Divina Commedia”. Finally we characterized a declared false of the nineteenth century reproducing a famous document of the XIII century. The present study gives fundamental knowledge on the history of different inks used in the manuscripts and also on the conservation as well degradation of supporting materials. In addition we focused our characterization on different techniques and materials applied in previous restorations. Finally, we certified with modern techniques the presence of deliberate falsification processes of some specimens.

We present a systematic computational study of the effects of perfluorination on the charge-transport properties of three homologous classes of polyaromatic hydrocarbons of interest for molecular electronics: acenes, pyrenes, and circumacenes. By means of Density Functional Theory calculations we first obtained the key molecular properties for transport of both holes and electrons. We then used these parameters in the framework of Marcus theory to compare charge-transfer rates in the high temperatures regime for both unsubstituted and perfluorinated molecules. We additionally estimated the relative charge-mobility of each unsubstituted (perfluorinated) molecule with respect to unsubstituted (perfluorinated) pentacene. We found in all cases that perfluorination reduces the charge-transfer rate in absolute terms. This is largely due to the higher values of the molecular reorganization energies predicted for perfluorinated compounds. Interestingly, however, the charge-transfer rates for both holes and electrons of perfluorinated species are remarkably similar, especially for the larger species. In addition, in the case of the larger circumacenes the charge-mobility values relative to pentacene values are found to increase upon perfluorination.

We report a comparative and systematic computational analysis on the electronic and optical properties of the boron-nitride-made (BN) counterparts of the carbon-made circumacenes. Recently, these planar molecules have attracted interest for applications in the condensed matter physics domain. In particular, we focus on the five first members of this BN-family (from BN-coronene to BN-circumpentacene) presenting a comparison with their carbon analogues. For all the systems investigated, we calculate different electronic properties and the optical absorption spectra, performing all electron Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) calculations. In the context of ab initio calculations we select a localized Gaussian basis-set matched with a hybrid exchange-correlation functional. We discuss possible implications of the observed BN cluster properties, which could be an alternative material or complementar as compared to their carbon analogues. In particular, concerning the optical properties, we have found that the main difference between the two families is that the BN molecules absorb in the UV, rather than in the visible as happens for the C-made parents. Moreover, we demonstrate that the electronic and optical observables of the BN clusters are nearly independent of the cluster size in contrast to what happens for their carbonaceous counterparts.

Darkening of Red Vermilion (cinnabar) is a well-known phenomenon which needs, at the moment, a full comprehension of its nature. Some paintings reveal a disfiguring process of blackening degradation of Red Vermilion, albeit other relics preserve the original color during the time. The presence of halide elements like Cl− ions, in addition to the light exposure, represents the most alleged cause to explain the darkening phenomenon. However, the real effect of chlorine impurities is still not completely understood. In this study, starting from a multi-technique characterization, we propose a kinetic model of mutual composition of alpha/beta cinnabar derived by the experimental darkening of pure alpha synthetic cinnabar intentionally doped with Cl− ions and treated under prolonged UV light exposure. The model was further applied to ancient samples by analyzing the Raman spectra of antique cinnabar pigments belonging to manuscripts of XIII-XVII centuries.

Dialkali halides are materials of great interest from both fundamental and technological viewpoints, due to their wide transparency range. The accurate determination of their electronic, excitation and optical properties in bulk and low dimensional systems is therefore of crucial importance. Moreover, it is a challenge from the theoretical point of view to deal with quasiparticle band structure calculations for such large energy gap materials, requiring very expensive methods for achieving a desirable accuracy. Here we report electronic quasiparticle band structures for three representative bulk fluorides, BaF

We report a systematic computational investigation on the electronic and optical properties of the principal chromophores found in bacterial cellulose (BC). In particular, we focus on the three chromophoric leading structures that were isolated from aged BC (1) 2,5-dihydroxy-[1,4]benzoquinone (2) 5,8-dihydroxy-[1,4]naphthoquinone and (3) 2,5-dihydroxyacetophenone. For the isolated molecules we performed all-electrons density functional theory (DFT) and time dependent DFT calculations with a localized Gaussian basis set and the hybrid exchange correlation functional B3LYP. We quantified key molecular properties relevant as electron affinities, ionization energies, quasi-particle energy gaps, optical absorption spectra, and exciton binding energies. We address moreover the impact of the solvent on the optical properties of the above systems using starting configurations obtained after classical molecular dynamics simulations in water. Our results could be of importance to comprehend the mechanisms underlying the processes of degradation of BC, which are of fundamental relevance for cultural heritage applications. © 2018, Springer Science+Business Media B.V., part of Springer Nature.

In this work, we predict and analyze the optical spectra of pyrimidinic uracil-like nucleobases thymine (THY), uracil (URA), and 5-fluorouracil (5-FU) and their reflection anisotropy spectra (RAS) upon adsorption on the silicon (001) surface. First-principles results based on plane-wave density functional theory show chemically sensitive features in gas phase optical absorption spectra that redshift/blueshift according to the orbitals involved in the corresponding transition. In the RAS, a characteristic lineshape is found, typical of the energetically favored "dimer bridge" configuration, and remarkably similar for all the investigated Si(001):X systems (X = THY, URA, 5-FU). We show that molecular tilting and breaking of the glide plane symmetry have a negligible effect on the optical spectra, despite their influence on the surface bandstructure. Contrarily to gas phase spectra, chemically sensitive RAS features only appear above 4.5 eV, and can be recognized as molecular contributions consistent with gas phase optical absorption results whereas substrate effects dominate at lower energies. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

International audience; Using many-body perturbation theory, the optical properties of modified compact and angular dibenzochrysenes are investigated. First, for a series of already existing molecules in that family, the computed absorption spectra are benchmarked against experimental data in order to evaluate the strengths and the limitations of the method. Then, the computed absorption spectra are presented for newly designed dibenzochrysenes. One of the main results is that the addition of thiophenyl groups at specific positions produces an enhancement of the absorption in the visible region. The information provided in this study can be used as a guide to synthesize optimized materials for solar cells.

We present a computational study on the electronic and optical properties of a representative C-made and Boron-Nitride-made (BN) planar molecule of interest for potential applications in the solid state domain. In particular, we analyzed the case of Coronene (C24H12) in its BN and perfluorinated analogues. We performed all electrons Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) calculations using a localized Gaussian basis-set in combination with a hybrid exchange-correlation functional. For all the systems we have calculated different electronic properties and the optical absorption spectra. A discussion on the possible implications of the general trends, observed for the BN-made clusters properties as compared to their C-based parents, will be given.

We report a computational comparative study of the ground and excited states properties of graphene nanoribbons, analyzing the case of coronene (C24H12) and ovalene (C32H14) and their silicon-atoms substituted counterparts with single, double and triple atomic insertions. We used density functional theory (DFT) and time-dependent DFT to quantify the effects on the electronic and optical properties as a result of the chemical modifications. In particular, we compared ground-state total energies, electron affinities, ionization energies, fundamental gaps and optical absorption spectra, between the original systems and each substituted one. For both the molecules, we observed a general reduction of the fundamental gap after chemical modification. Concerning the optical properties, therefore, we observed a redshift of the optical onset in all the cases; in particular, we have found that, in one ovalene and coronene trimer-substituted configuration, the absorption edge takes place in the IR.

International audience; Using density functional theory (DFT) and its time-dependent (TD) extension, the electronic and optical properties of the hexathiapentacene (HTP) molecule, a derivative of pentacene (PNT) obtained by symmetric substitution of the six central H atoms with S atoms, are investigated for its gas and solid phases. For the molecular structure, all-electron calculations are performed using a Gaussian localized orbital basis set in conjunction with the Becke three-parameter Lee-Yang-Parr (B3LYP) hybrid exchange-correlation functional. Electron affinities, ionization energies, quasiparticle energy gaps, optical absorption spectra, and exciton binding energies are calculated and compared with the corresponding results for PNT, as well as with the available experimental data. The DFT and TDDFT results are also validated by performing many-body perturbation theory calculations within the GW and Bethe-Salpeter equation formalisms. The functionalization with S atoms induces an increase of both ionization energies and electron affinities, a sizable reduction of the fundamental electronic gap, and a redshift of the optical absorption onset. Notably, the intensity of the first absorption peak of HTP falling in the visible region is found to be nearly tripled with respect to the pure PNT molecule. For the crystal structures, pseudopotential calculations are adopted using a plane-wave basis set together with the Perdew-Burke-Ernzerhof exchange-correlation functional empirically corrected in order to take dispersive interactions into account. The electronic excitations are also obtained within a perturbative B3LYP scheme. A comparative analysis is carried out between the ground-state and excited-state properties of crystalline HTP and PNT linking to the findings obtained for the isolated molecules.

We report a systematic computational investigation on the electronic and optical properties of some representive polyaromatic hydrocarbons of interest for solid-state applications. We focus in particular on the five first members of the circumacenes family (i.e., coronene, ovalene, circumanthracene, circumtetracene, and circumpentacene). For the isolated gas-phase molecules we performed all-electrons Density Functional Theory (DFT) and Time Dependent DFT (TDDFT) calculations with a localized Gaussian basis-set and the hybrid exchange-correlation functional B3LYP. We quantified the effect of the complete substitution of peripheral hydrogen atoms with fluorine atoms for a series of key molecular properties relevant for molecular electronics and photonics: electron affinities, ionization energies, quasi-particle energy-gaps, optical absorption spectra, and exciton binding energies. We discuss the possible implications of the general trends observed with respect to both fundamental research and opto-electronic applications.

We study the electronic properties of the Si(001):Uracil, Si(001):Thymine, and Si(001):5-Fluorouracil systems, focusing on the Si dimer-bridging configuration with adsorption governed by carbonyl groups. While the overall structural and electronic properties are similar, with small differences due to chemical substitutions, much larger effects on the surface band dispersion and bandgap show up as a function of the molecular orientation with respect to the surface. An off-normal orientation of the molecular planes is favored, showing larger bandgap and lower total energy than the upright position. We also analyze the localization of gap-edge occupied and unoccupied surface states.

Homologous classes of Polycyclic Aromatic Hydrocarbons (PAHs) in their crystalline state are among the most promising materials for organic opto-electronics. Following previous works on oligoacenes we present a systematic comparative study of the electronic, optical, and transport properties of oligoacenes, phenacenes, circumacenes, and oligorylenes. Using density functional theory (DFT) and time-dependent DFT we computed: (i) electron affinities and first ionization energies; (ii) quasiparticle correction to the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap; (iii) molecular reorganization energies; (iv) electronic absorption spectra of neutral and $\pm1$ charged systems. The excitonic effects are estimated by comparing the optical gap and the quasiparticle corrected HOMO-LUMO energy gap. For each molecular property computed, general trends as a function of molecular size and charge state are discussed. Overall, we find that circumacenes have the best transport properties, displaying a steeper decrease of the molecular reorganization energy at increasing sizes, while oligorylenes are much more efficient in absorbing low-energy photons in comparison to the other classes., Comment: 26 pages, 9 figures, 4 tables, accepted for pubblication in Chemical Physics (14/04/2011)

Oligoacenes in their crystalline state are increasingly used in the field of electronics and photonics. Following a recent systematic theoretical study of the five smallest oligoacene molecules (naphthalene, anthracene, tetracene, pentacene, and hexacene), we evaluate their one- and two-particle properties (electron affinities, ionisation energies, quasiparticle correction to the highest occupied molecular orbital—lowest unoccupied molecular orbital gap, exciton binding energy, electronic absorption), using different exchange-correlation functionals in the framework of Density Functional Theory (DFT) and Time Dependent DFT. The hybrid functional B3LYP is found to yield the best agreement with the available experimental data.

We present theoretical electron affinities, calculated as total energy differences, for a large sample of polycyclic aromatic hydrocarbons (PAHs), ranging in size from azulene (C10H8) to dicoronylene (C48H20). For 20 out of 22 molecules under study we obtained electron affinity values in the range 0.4-2.0 eV, showing them to be able to accept an additional electron in their LUMO π � orbital. For the mono-anions we computed the absolute photo-absorption cross-sections up to the vacuum ultraviolet (VUV) using an implementation in real time and real space of the Time-Dependent Density Functional Theory (TD-DFT), an approach which has already been proven to yield accurate results for neutral and cationic PAHs. Comparison with available experimental data hints that this is the case for mono-anions as well. We find that PAH anions, like their parent molecules and the corresponding cations, display strong π ∗ ← π electronic transitions in the UV. The present results provide a quantitative foundation to estimate the fraction of specific PAHs which can be singly negatively charged in various interstellar environments, to simulate their photophysics in detail and to evaluate their contribution to the interstellar extinction curve.