Point charge embedding for ONIOM excited states calculations.

Hybrid quantum mechanical methods can assist in the interpretation and prediction of the electronic spectra of large molecular structures. In this work, we study the performance of the ONIOM (Our own N-layered Integrated molecular Orbital molecular Mechanics) hybrid method for the calculation of transition energies and oscillator strengths by embedding the core region in a field of fixed point charges. These charges introduce polarization effects from the substituent groups to the core region. We test various charge definitions, with particular attention to the issue of overpolarization near the boundary between layers. To minimize this issue, we fit the charges on the electrostatic potential of the entire structure in the presence of the link atoms used to cap dangling bonds. We propose two constrained fitting strategies: one that produces an average set of charges common to both model system calculations, EE(L1), and one that produces two separate sets of embedding charges, EE(L2). The results from our tests show that indeed electronic embedding with constrained-fitted charges tends to improve the performance of ONIOM compared to non-embedded calculations. However, the EE(L2) charges work best for transition energies, and the EE(L1) charges work best for oscillator strengths. This may be an indication that fixed point charges do not have enough flexibility to adapt to each system, and other effects (e.g., polarization of the embedding field) may be necessary.

Accurate and inexpensive prediction of the color optical properties of anthocyanins in solution.

The simulation of the color optical properties of molecular dyes in liquid solution requires the calculation of time evolution of the solute absorption spectra fluctuating in the solvent at finite temperature. Time-averaged spectra can be directly evaluated by combining ab initio Car-Parrinello molecular dynamics and time-dependent density functional theory calculations. The inclusion of hybrid exchange-correlation functionals, necessary for the prediction of the correct transition frequencies, prevents one from using these techniques for the simulation of the optical properties of large realistic systems. Here we present an alternative approach for the prediction of the color of natural dyes in solution with a low computational cost. We applied this approach to representative anthocyanin dyes: the excellent agreement between the simulated and the experimental colors makes this method a straightforward and inexpensive tool for the high-throughput prediction of colors of molecules in liquid solvents.

Self-consistent continuum solvation for optical absorption of complex molecular systems in solution.

We introduce a new method to compute the optical absorption spectra of complex molecular systems in solution, based on the Liouville approach to time-dependent density-functional perturbation theory and the revised self-consistent continuum solvation model. The former allows one to obtain the absorption spectrum over a whole wide frequency range, using a recently proposed Lanczos-based technique, or selected excitation energies, using the Casida equation, without having to ever compute any unoccupied molecular orbitals. The latter is conceptually similar to the polarizable continuum model and offers the further advantages of allowing an easy computation of atomic forces via the Hellmann-Feynman theorem and a ready implementation in periodic-boundary conditions. The new method has been implemented using pseudopotentials and plane-wave basis sets, benchmarked against polarizable continuum model calculations on 4-aminophthalimide, alizarin, and cyanin and made available through the Quantum ESPRESSO distribution of open-source codes.

A theoretical and experimental investigation of the spectroscopic properties of a DNA-intercalator salphen-type Zn(II) complex.

The photophysical and DNA-binding properties of the cationic zinc(II) complex of 5-triethylammonium methyl salicylidene ortho-phenylenediiminato (ZnL(2+)) were investigated by a combination of experimental and theoretical methods. DFT calculations were performed on both the ground and the first excited states of ZnL(2+) and on its possible mono- and dioxidation products, both in vacuo and in selected solvents mimicked by the polarizable continuum model. Comparison of the calculated absorption and fluorescence transitions with the corresponding experimental data led to the conclusion that visible light induces a two-electron photooxidation process located on the phenylenediiminato ligand. Kinetic measurements, performed by monitoring absorbance changes over time in several solvents, are in agreement with a slow unimolecular photooxidation process, which is faster in water and slower in less polar solvents. Moreover, structural details of ZnL-DNA binding were obtained by DFT calculations on the intercalation complexes between ZnL and the d(ApT)2 and d(GpC)2 dinucleoside monophosphate duplexes. Two main complementary binding interactions are proposed: 1) intercalation of the central phenyl ring of the ligand between the stacked DNA base pairs; 2) external electrostatic attraction between the negatively charged phosphate groups and the two cationic triethylammonium groups of the Schiff-base ligand. Such suggestions are supported by fluorescence titrations performed on the ZnL/DNA system at different ionic strengths and temperatures. In particular, the values of the DNA-binding constants obtained at different temperatures provided the enthalpic and entropic contributions to the binding and confirmed that two competitive mechanisms, namely, intercalation and external interaction, are involved. The two mechanisms are coexistent at room temperature under physiological conditions.

Plasmon-controlled light-harvesting: design rules for biohybrid devices via multiscale modeling.

Photosynthesis is triggered by the absorption of light by light-harvesting (LH) pigment-protein complexes followed by excitation energy transfer to the reaction center(s). A promising strategy to achieve control on and to improve light harvesting is to complement the LH complexes with plasmonic particles. Here a recently developed QM/MM/continuum approach is used to investigate the LH process of the peridinin-chlorophyll-protein (PCP) complex on a silver island film. The simulations not only reproduce and interpret the experiments but they also suggest general rules to design novel biohybrid devices; hot-spot configurations in which the LH complex is sandwiched between couples of metal aggregates are found to produce the largest amplifications. Indications about the best distances and orientations are also reported together with illumination and emission geometries of the PCP-NP system necessary to achieve the maximum enhancement.

An investigation of the photophysical properties of minor groove bound and intercalated DAPI through quantum-mechanical and spectroscopic tools.

The fluorescent probe 4',6-diamidino-2-phenylindole (DAPI) is a dye known to interact with polynucleotides in a non-univocal manner, both intercalation and minor groove binding modes being possible, and to specifically change its photophysical properties according to the different environments. To investigate this behavior, quantum-mechanical calculations using time-dependent density functional theory (TDDFT), coupled with polarizable continuum and/or atomistic models, were performed in combination with spectroscopic measurements of the probe in the different environments, ranging from a homogeneous solution to the minor groove or intercalation pockets of double stranded nucleic acids. According to our simulation, the electronic transition involves a displacement of the electron charge towards the external amidine groups and this feature makes the absorption energies very environment-sensitive while a much smaller sensitivity is seen in the fluorescence energies. Moreover, the calculations show that the DAPI molecule, when minor groove bound to the nucleic acid, presents both a reduced geometrical flexibility because of the rigid DNA pocket and a reduced polarization due to the very "apolar" microenvironment. All these effects can be used to better understand the observed enhancement of the fluorescence, which makes it an excellent marker for DNA.

Thiazole orange (TO) as a light-switch probe: a combined quantum-mechanical and spectroscopic study.

A Density Functional Theory (DFT) study of the absorbance and fluorescence emission characteristics of the cyanine thiazole orange (TO) in solution and when intercalated in DNA was carried out in combination with spectrophotometric and spectrofluorometric experiments under different conditions (temperature, concentration, solvent viscosity). T-jump relaxation kinetics of the TO monomer-dimer conversion enabled the thermodynamic parameters of this process to be evaluated. The overall data collected provided information on the features of the "light-switch" by the fluorescent TO and the comparison between experimental and calculated photo-physical properties allowed us to explain and rationalize both shifts and quenching/enhancing effects on fluorescence due to solvation, dimerisation and intercalation in the DNA.

A Benchmark Study of Electronic Couplings in Donor-Bridge-Acceptor Systems with the FMR-B Method.

We present a benchmarking study for the evaluation of electronic couplings in donor-bridge-acceptor systems with the Fock matrix reconstruction-bridge (FMR-B) method. We compile a data set for the benchmark that contains 29 molecules for which reliable experimental coupling values are available: DBA29. This data set is general and includes different types of donor, acceptor, and bridge units as well as different bridge lengths, and it spans a range of couplings from 0.1 to 0.8 eV. We use DBA29 to test FMR-B with 11 density functionals belonging to different classes (pure, global hybrid, and range-separated) and the Hartree-Fock (HF) method. We also test a subset of these methods with nine basis sets from the Pople and Dunning families, which include a varying number of polarization and diffuse functions. We find that the best accuracy and lowest computational cost is obtained with range-separated functionals and compact basis sets. Global hybrids with a large amount of HF exchange also work well because of error cancellation between the approximate exchange-correlation kernel and the HF part. Pure functionals, although less accurate, still provide reasonable results with a consistent underestimation of the experimental values, and they can be used for larger and more computationally demanding systems.

Electronic Coupling for Donor-Bridge-Acceptor Systems with a Bridge-Overlap Approach.

Understanding the modulation of the electronic coupling in donor-acceptor systems connected through an aliphatic bridge is crucial from a fundamental point of view as well as for the development of organic electronics. In this work, we present a first-principles approach for the calculation of the electronic coupling (or transfer integrals) in such systems via a block-diagonalization of the Fock/Kohn-Sham matrix of the supersystem, followed by a projection on the basis of the fragment orbitals of the donor and acceptor groups. The strength of the approach is that the bridge is shared by the donor and acceptor blocks in the diagonalization step, so that through-space and through-bond couplings are obtained simultaneously. The method is applied to two test sets: a series of fused-ring bridged systems and G(T)nG DNA oligomers. The results for the first set are compared to experiment and show an average error lower than 10%. For the DNA set, we show that the coupling may be significantly larger (and the decay with length slower) when the entire backbone is included.

How the Number of Layers and Relative Position Modulate the Interlayer Electron Transfer in π-Stacked 2D Materials.

Understanding the interfacial electron transfer (IET) between 2D layers is central to technological applications. We present a first-principles study of the IET between a zinc phthalocyanine film and few-layer graphene by using our recent method for the calculation of electronic coupling in periodic systems. The ultimate goal is the development of a predictive in silico approach for designing new 2D materials. We find IET to be critically dependent on the number of layers and their stacking orientation. In agreement with experiment, IET to single-layer graphene is shown to be faster than that to double-layer graphene due to interference effects between layers. We predict that additional graphene layers increase the number of IET pathways, eventually leading to a faster rate. These results shed new light on the subtle interplay between structure and IET, which may lead to more effective "bottom up" design strategies for these materials.

Polarity-sensitive fluorescent probes in lipid bilayers: bridging spectroscopic behavior and microenvironment properties.

We have studied the emission features of the fluorescent polarity-sensitive probes known as Prodan and Laurdan in a liquid-crystalline DPPC bilayer. To this purpose, we have combined high-level quantum mechanical electronic structure calculations with a molecular field theory for the positional-orientational-conformational distribution of the probes, in their ground and excited states, inside of the lipid bilayer, taking into account at both levels the nonuniformity and anisotropy of the environment. Thus, we can interpret the features of the fluorescence spectra of Prodan and Laurdan in relation to the position and orientation of their chromophore in the bilayer. We have found that the environment polarity is not sufficient to explain the large red shifts experimentally observed and that specific effects due to hydrogen bonding must be considered. We show that the orientation of the probe is important in determining the accessibility to water of the H-bond-acceptor group; in the case of Laurdan interesting conformational effects are highlighted.

What is solvatochromism?

Solvatochromism is commonly used in many fields of chemical and biological research to study bulk and local polarity in macrosystems (membranes, etc.), or even the conformation and binding of proteins. Despite its wide use, solvatochromism still remains a largely unknown phenomenon due to the extremely complex coupling of many different interactions and dynamical processes which characterize it. In this study we analyze the influence of different solvents on the photophysical properties of selected charge-transfer probes (4-AP, PRODAN, and FR0). The purpose is to achieve a microscopic understanding of the intermolecular effects which govern the absorption and fluorescence properties of solvated molecular probes, such as solvent-induced structural modifications, polarization effects, solubility, solute-solvent hydrogen-bonding interactions, and solute aggregation. To this aim we have exploited a time dependent density functional theory (TDDFT) approach coupled to complementary solvation approaches (continuum, discrete and mixed discrete and continuum). Such an integration has allowed us to clearly disentangle the complex interplay between specific and nonspecific interactions of the solvent with the probes and show that strong H-bonding effects not only can lead to large solvatochromic shifts but also can affect the nature of the emitting species with resulting reduction of the quantum yield.