Photoswitchable Molecular Units with Tunable Nonlinear Optical Activity: A Theoretical Investigation.

The first-, second-, and third-order molecular nonlinear optical properties, including two-photon absorption of a series of derivatives, involving two dithienylethene (DTE) groups connected by several molecular linkers (bis(ethylene-1,2-dithiolato)Ni- (NiBDT), naphthalene, quasilinear oligothiophene chains), are investigated by employing density functional theory (DFT). These properties can be efficiently controlled by DTE switches, in connection with light of appropriate frequency. NiBDT, as a linker, is associated with a greater contrast, in comparison to naphthalene, between the first and second hyperpolarizabilities of the "open-open" and the "closed-closed" isomers.

Molecular simulations of fluoxetine in hydrated lipid bilayers, as well as in aqueous solutions containing β-cyclodextrin.

Fluoxetine, which is a well-known antidepressant drug, is studied in hydrated cholesterol-free and cholesterol-containing lipid bilayers through unbiased and biased atomistic molecular dynamics simulations. The latter are conducted for the calculation of the potential of mean force (PMF) of fluoxetine along an axis perpendicular to the two leaflets of the bilayer. The PMF indicates that the drug prefers to reside inside the lipid phase and allows us to calculate important thermodynamic properties, such as the Gibbs energy difference of partitioning from the water to the lipid phase and the Gibbs energy barrier for hopping events between the two leaflets of the bilayer.

In silico study of levodopa in hydrated lipid bilayers at the atomistic level.

This article presents atomistic molecular dynamics and umbrella sampling simulations of levodopa at various concentrations in hydrated cholesterol-free 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and cholesterol-containing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. Levodopa is the standard medication for Parkinson's disease and is marketed under various trade names; in the context of this article, the levodopa molecule is mostly studied in its zwitterionic form but some results concerning the neutral levodopa are presented as well for comparison purposes. The motivation is to study in detail how levodopa behaves in different hydrated lipid membranes, primarily from the thermodynamic point of view, and reveal aspects of mechanism of its permeation through them.

Computational investigation of fullerene-DNA interactions: Implications of fullerene's size and functionalization on DNA structure and binding energetics.

DNA is the building block of life, as it carries the biological information controlling development, function and reproduction of all organisms. However, its central role in storing and transferring genetic information can be severely hindered by molecules with structure altering abilities. Fullerenes are nanoparticles that find a broad spectrum of uses, but their toxicological effects on living organisms upon exposure remain unclear.

Compilation of Data and Modelling of Nanoparticle Interactions and Toxicity in the NanoPUZZLES Project.

The particular properties of nanomaterials have led to their rapidly increasing use in diverse fields of application. However, safety assessment is not keeping pace and there are still gaps in the understanding of their hazards. Computational models predicting nanotoxicity, such as (quantitative) structure-activity relationships ((Q)SARs), can contribute to safety evaluation, in line with general efforts to apply alternative methods in chemical risk assessment.

Tailoring Colors by O Annulation of Polycyclic Aromatic Hydrocarbons.

The synthesis of O-doped polyaromatic hydro- carbons in which two polycyclic aromatic hydrocarbon sub units are bridged through one or two O atoms has been achieved. This includes high-yield ring-closure key steps that, depending on the reaction conditions, result in the formation of furanyl or pyranopyranyl linkages through intramolecular C-O bond formation. Comprehensive photophysical measurements in solution showed that these compounds have exceptionally high emission yields and tunable absorption properties throughout the UV/Vis spectral region.

Advantages and limitations of classic and 3D QSAR approaches in nano-QSAR studies based on biological activity of fullerene derivatives.

In this contribution, the advantages and limitations of two computational techniques that can be used for the investigation of nanoparticles activity and toxicity: classic nano-QSAR (Quantitative Structure-Activity Relationships employed for nanomaterials) and 3D nano-QSAR (three-dimensional Quantitative Structure-Activity Relationships, such us Comparative Molecular Field Analysis, CoMFA/Comparative Molecular Similarity Indices Analysis, CoMSIA analysis employed for nanomaterials) have been briefly summarized. Both approaches were compared according to the selected criteria, including: efficiency, type of experimental data, class of nanomaterials, time required for calculations and computational cost, difficulties in the interpretation. Taking into account the advantages and limitations of each method, we provide the recommendations for nano-QSAR modellers and QSAR model users to be able to determine a proper and efficient methodology to investigate biological activity of nanoparticles in order to describe the underlying interactions in the most reliable and useful manner.

A Computational Study of the Interaction and Polarization Effects of Complexes Involving Molecular Graphene and C60 or a Nucleobases.

A systematic analysis of the molecular structure, energetics, electronic (hyper)polarizabilities and their interaction-induced counterparts of C60 with a series of molecular graphene (MG) models, CmHn, where m = 24, 84, 114, 222, 366, 546 and n = 12, 24, 30, 42, 54, 66, was performed. All the reported data were computed by employing density functional theory and a series of basis sets. The main goal of the study is to investigate how alteration of the size of the MG model affects the strength of the interaction, charge rearrangement, and polarization and interaction-induced polarization of the complex, C60-MG.

A Comprehensive Computational Study of the Interaction between Human Serum Albumin and Fullerenes.

Human serum albumin (HSA) is the most abundant blood plasma protein, which transports fatty acids, hormones, and drugs. We consider nanoparticle-HSA interactions by investigating the binding of HSA with three fullerene analogs. Long MD simulations, quantum mechanical (fragment molecular orbital, energy decomposition analysis, atoms-in-molecules), and free energy methods elucidated the binding mechanism in these complexes.

Elucidation of the binding mechanism of renin using a wide array of computational techniques and biological assays.

We investigate the binding mechanism in renin complexes, involving three drugs (remikiren, zankiren and enalkiren) and one lead compound, which was selected after screening the ZINC database. For this purpose, we used ab initio methods (the effective fragment potential, the variational perturbation theory, the energy decomposition analysis, the atoms-in-molecules), docking, molecular dynamics, and the MM-PBSA method. A biological assay for the lead compound has been performed to validate the theoretical findings.

Stability and binding effects of silver(I) complexes at lipoxygenase-1.

An anti-inflammatory complex of Ag(I), namely [Ag(tpp)3(asp)](dmf) [tpp = triphenylphosphine, aspH = aspirin, dmf = N,N-dimethylformamide], was synthesized in an attempt to develop novel metallotherapeutic molecules. STD (1)H NMR experiments were used to examine if this complex binds to LOX-1. The (1)H NMR spectra in buffer Tris/D2O betrayed the existence of two complexes: the complex of aspirin and the complex of salicylic acid produced after deacetylation of aspirin.

Elucidation of conformational states, dynamics, and mechanism of binding in human κ-opioid receptor complexes.

Opioid G protein-coupled receptors (GPCRs) have been implicated in modulating pain, addiction, psychotomimesis, mood and memory, among other functions. We have employed the recently reported crystal structure of the human κ-opioid receptor (κ-OR) and performed molecular dynamics (MD), free energy, and ab initio calculations to elucidate the binding mechanism in complexes with antagonist JDTic and agonist SalA. The two systems were modeled in water and in DPPC lipid bilayers, in order to investigate the effect of the membrane upon conformational dynamics.

Systematic molecular dynamics, MM-PBSA, and ab initio approaches to the saquinavir resistance mechanism in HIV-1 PR due to 11 double and multiple mutations.

Mutations in the human immunodeficiency virus (HIV) enable virus replication even when appropriate antiretroviral therapy is followed, thus leading to the emergence of drug resistance. In a previous work, we systematically examined seven single mutations that are associated with saquinavir (SQV) resistance in HIV-1 protease (Tzoupis, H.; Leonis, G.

Theoretical modelling of photoswitching of hyperpolarisabilities in ruthenium complexes.

Static excited-state polarisabilities and hyperpolarisabilities of three Ru(II) ammine complexes are computed at the density functional theory (DFT) and several correlated ab initio levels. Most accurate modelling of the low energy electronic absorption spectrum is obtained with the hybrid functionals B3LYP, B3P86 or M06 for the complex [Ru(II)(NH3)5(MeQ(+))](3+) (MeQ(+)=N-methyl-4,4'-bipyridinium, 3) in acetonitrile. The match with experimental data is less good for [Ru(II)(NH3)5L](3+) (L=N-methylpyrazinium, 2; N-methyl-4-{E,E-4-(4-pyridyl)buta-1,3-dienyl}pyridinium, 4).

Performance of density functional theory in computing nonresonant vibrational (hyper)polarizabilities.

A set of exchange-correlation functionals, including BLYP, PBE0, B3LYP, BHandHLYP, CAM-B3LYP, LC-BLYP, and HSE, has been used to determine static and dynamic nonresonant (nuclear relaxation) vibrational (hyper)polarizabilities for a series of all-trans polymethineimine (PMI) oligomers containing up to eight monomer units. These functionals are assessed against reference values obtained using the Møller-Plesset second-order perturbation theory (MP2) and CCSD methods. For the smallest oligomer, CCSD(T) calculations confirm the choice of MP2 and CCSD as appropriate for assessing the density functionals.

On the vibrational linear and nonlinear optical properties of compounds involving noble gas atoms: HXeOXeH, HXeOXeF, and FXeOXeF.

The vibrational (hyper)polarizabilities of some selected Xe derivatives are studied in the context of Bishop-Kirtman perturbation theory (BKPT) and numerical finite field methodology. It was found that for this set of rare gas compounds, the static vibrational properties are quite large, in comparison to the corresponding electronic ones, especially those of the second hyperpolarizability. This also holds for the dc-Pockels β(-ω;ω,0), Kerr γ(-ω;ω,0,0) and electric field second harmonic generation γ (-2ω;ω,ω,0) effects, although the computed nuclear relaxation (nr) vibrational contributions are smaller in magnitude than the static ones.

Structural and static electric response properties of highly symmetric lithiated silicon cages: theoretical predictions.

It is shown by density functional theory calculations that high symmetry silicon cages can be designed by coating with Li atoms. The resulting highly symmetric lithiated silicon cages (up to D(5d) symmetry) are low-lying true minima of the energy hypersurface with binding energies of the order of 4.6 eV per Si atom and moderate highest occupied molecular orbital-lowest unoccupied molecular orbital gaps.

On the stability, electronic structure, and nonlinear optical properties of HXeOXeF and FXeOXeF.

The electronic ground state, stability, and linear and nonlinear optical properties of HXeOXeF and FXeOXeF have been studied theoretically by employing complete active space valence bond (CASVB), multistate complete active space perturbation theory (MS-CASPT2), and coupled cluster methods. It is shown that the oxygen inserted between the two Xe atoms significantly modifies the ground-state electronic configuration of the formed derivative by increasing the closed-shell contribution (σ(2)) and removing the diradicaloid character observed in HXe(2)F. The electronic charge distribution has been analyzed by employing the atoms-in-molecules (AIM) method.

Electronic and vibrational contributions to first hyperpolarizability of donor-acceptor-substituted azobenzene.

In this study we report on the electronic and vibrational (hyper)polarizabilities of donor-acceptor-substituted azobenzene. It is observed that both electronic and vibrational contributions to the electric dipole first hyperpolarizability of investigated photoactive molecule substantially depend on the conformation. The contributions to the nuclear relaxation first hyperpolarizability are found to be quite important in the case of two considered isomers (cis and trans).

Theoretical investigations of the IR spectroscopy of Ni(C(2)S(2)H(2))(2). A case study of the P_VMWCI(2) algorithm including anharmonic effects.

The near infrared (NIR) spectra of bis(ethylene-1,2-dithiolato)nickel, Ni(C(2)S(2)H(2))(2) are fully interpreted here by applying a method developed for efficient automatic computation of both the infrared wave numbers and the intensities. The employed procedure uses parallel variational multiple window configuration interaction wave functions, the so-named P_VMWCI(2) algorithm, which incorporates both the mechanical and the electric anharmonic effects. It is shown that inclusion of anharmonicities is crucial for correctly assigning the fundamental, combination, and overtone vibrational frequencies in the infrared spectrum of the target system, for which conflicting assignments are found in literature.

Linear and nonlinear optical properties of triphenylamine-functionalized C60: insights from theory and experiment.

In the present study we report on the linear and nonlinear optical properties of C(60)-triphenylamine (TPhA) hybrids. The synthesized materials were prepared following the 1,3-dipolar cycloaddition of azomethine ylides onto the skeleton of C(60) forming the TPhA-based monoadduct, equatorial bis-adduct and dumbell C(60). Complementary spectroscopic techniques, such as NMR, MALDI-TOF-MS, and ATR-IR are applied for the structural characterization of the hybrid materials, while intermolecular electronic interactions are investigated by UV-Vis measurements.

Linear and nonlinear optical properties of a series of Ni-dithiolene derivatives.

Some linear and nonlinear optical (NLO) properties of Ni(SCH)(4) and several of its derivatives have been computed by employing a series of basis sets and a hierarchy of methods (e.g., HF, DFT, coupled cluster, and multiconfigurational techniques).

On the origin of the large electron correlation contribution to the hyperpolarizabilities of some diacetylene rare gas compounds.

A comprehensive study of the linear and nonlinear molecular optical properties of HRgC(4)H, where Rg = Ar,Kr,Xe, has been performed. Dynamical electron correlation effects were computed by employing the coupled cluster methodology. A large electron correlation contribution to the nonlinear properties of HArC(4)H has been revealed.

Linear and nonlinear optical properties of some organoxenon derivatives.

We employ a series of state-of-the-art computational techniques to study the effect of inserting one or more Xe atoms in HC2H and HC4H, on the linear and nonlinear optical (L&NLO) properties of the resulting compounds. It has been found that the inserted Xe has a great effect on the L&NLO properties of the organoxenon derivatives. We analyze the bonding in HXeC2H, and the change of the electronic structure, which is induced by inserting Xe, in order to rationalize the observed extraordinary L&NLO properties.

The dipole moment, polarizabilities, and first hyperpolarizabilities of HArF. A computational and comparative study.

The electronic and vibrational contributions to the dipole moment, polarizabilities, and first hyperpolarizabilities of HArF are reported. These have been computed by using a series of systematically built basis sets and a hierarchy of computational methods. HArF has a very large first hyperpolarizability along the z axis.