A polarizable coarse-grained model for metal, metal oxide and composite metal/metal oxide nanoparticles and its applications.

We present a selected set of exemplifying applications of the novel polarizable coarse-grained model [see the first part] to various outstanding problems in the physics and chemistry of nanoparticles: electrostatic potential around silver and gold nanoparticles; spontaneous and external electric field-driven self-organization of gold and silver nanoparticle systems; and physisorption of carbon dioxide on titanium dioxide nanoparticles decorated with a gold catalyst. In the first application, the developed model has shown capabilities of predicting long-range potential with accuracy comparable to the tight-binding density functional theory methods. Furthermore, the electrostatic potential analysis in hot spot regions allowed us to identify twin defect lines in a silver nanostar as a promising candidate for an enhancer in surface-enhanced Raman spectroscopy. In the second application, the developed model has facilitated the elucidation of the microscopic mechanisms responsible for the self-organization of gold and silver nanoparticles. Analysis of Monte-Carlo simulations established that the self-organization process is driven by van der Waals interactions in the absence of an external electric field, and that it becomes gradually driven by electrostatic interactions in the presence of an external electric field with increasing strength of the external electric field. In the third application, the developed model combined with Monte-Carlo simulations has identified the dominant mechanism responsible for carbon dioxide transfer to the catalytic sites. Analysis of the obtained results indicates that surface diffusion is the dominant mechanism for the transport of carbon dioxide to the catalytic sites, and only in exceptional situations, direct physisorption becomes a competitive mechanism with the surface diffusion mechanism. These successful applications of the developed model indicate its wide range of applicability to various problems in the chemistry and physics of nanoparticles.

A polarizable coarse-grained model for metal, metal oxide and composite metal/metal oxide nanoparticles: development and implementation.

We present a polarizable coarse-grained model for metal, metal oxide, and composite metal/metal oxide nanoparticles with well-defined crystalline surfaces. The developed model uses a low-resolution polarizable "surface beads" representation of the nanoparticle's geometry and pairwise cross nanoparticle potential consisting of van der Waals and electrostatic interaction terms. The electrostatic interaction term of the cross nanoparticle potential incorporates a crucial physical aspect of electrostatic interaction into the metal and metal oxide systems, such as induced surface charges, making it possible to explore the nanoparticles' behavior in complex environments as well as investigate the interplay between electrostatic and van der Waals interactions in nanoparticle systems. The iterative stability, computational scaling, and performance of the presented model was tested on selected systems of gold, titanium dioxide, and composite gold/titanium dioxide nanoparticle systems. The model exhibits robust iterative stability and is able to converge the charge equilibration equation for fluctuating induced charges and dipoles within 10-60 "tug-tow" iterations in challenging situations, like crowded nanoparticle systems or nanoparticle systems in extreme external electric fields. The computation scaling of the presented model is semi-linear with respect to the number of nanoparticles in the system. It slightly varies depending on the size distribution of nanoparticles in a specific nanoparticle system. The computation cost of the model is significantly lower than that of conventional atomistic polarizable force field models and enables the treatment of large nanoparticle systems that are beyond the reach of currently existing atomistic force field models.

Electronic g-Tensor Calculations for Dangling Bonds in Nanodiamonds.

The electronic g-tensor calculations are performed for dangling bonds (DBs) introduced into nanodiamonds (NDs) with four different functional groups on their surfaces. For hydrogenated and fluorinated NDs, it is found that g-shifts of the latter vary in a much wider range, and the same is also true for the total energy differences between the highest and the lowest energy DBs. In addition, it is shown that the shape of NDs significantly impacts the energetics and g-shifts of DBs, whereas the influence of the size is much less pronounced, as is the influence of the presence of one DB in the vicinity of the other, resulting in no substantial change on their magnetic behavior. For hydroxylated and aminated NDs, it is demonstrated that the variation range of g-shifts is larger for the former, whereas the opposite is seen regarding the total energy differences. On the whole, some of the positions of DBs can be energetically very costly in these NDs; besides, the lowest energy DBs are irregular, that is, formed by OH- and NH2-bonded C atoms, contrasting with hydrogenated and fluorinated NDs, for which irregular DBs are the most energetically unfavorable.

Size-dependent polarizabilities and van der Waals dispersion coefficients of fullerenes from large-scale complex polarization propagator calculations.

While the anomalous non-additive size-dependencies of static dipole polarizabilities and van der Waals C6 dispersion coefficients of carbon fullerenes are well established, the widespread reported scalings for the latter (ranging from N2.2 to N2.8) call for a comprehensive first-principles investigation. With a highly efficient implementation of the linear complex polarization propagator, we have performed Hartree-Fock and Kohn-Sham density functional theory calculations of the frequency-dependent polarizabilities for fullerenes consisting of up to 540 carbon atoms. Our results for the static polarizabilities and C6 coefficients show scalings of N1.2 and N2.2, respectively, thereby deviating significantly from the previously reported values obtained with the use of semi-classical/empirical methods. Arguably, our reported values are the most accurate to date as they represent the first ab initio or first-principles treatment of fullerenes up to a convincing system size.

Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation.

Within the self-consistent field approximation, computationally tractable expressions for the isotropic second-order hyperpolarizability have been derived and implemented for the calculation of two-photon absorption cross sections. The novel tensor average formulation presented in this work allows for the evaluation of isotropic damped cubic response functions using only ∼3.3% (one-photon off-resonance regions) and ∼10% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of the two-photon absorption cross section in the one-photon off-resonance and resonance regions are provided for alanine-tryptophan and 2,5-dibromo-1,4-bis(2-(4-diphenylaminophenyl)vinyl)-benzene. Furthermore, a benchmark set of 22 additional small- and medium-sized organic molecules is considered. In all these calculations, a quantitative assessment is made of the reduced and approximate forms of the cubic response function in the one-photon off-resonance regions and results demonstrate a relative error of less than ∼5% when using the reduced expression as compared to the full form of the isotropic cubic response function.

Plasmonic nano-shells: atomistic discrete interaction versus classic electrodynamics models.

Using the extended discrete interaction model and Mie theory, we investigate the tunability of the optical polarizability of small metallic nano-shells. We show that the spectral positions of symmetric and antisymmetric dipolar plasmon resonances vary with the ratio of particle radius to hole radius in a manner similar to one predicted for uniform metallic nano-shells using a semiclassical approach of two coupled harmonic oscillators. We show that, according to the extended discrete interaction model, the dipolar plasmon resonances are also present for nano-shells in the 2-13 nm size region and show the same functional dependence seen for larger nano-shells. Using previously fitted data from experiment, we can predict the size-dependence of the plasma frequency for nano-shells in the 1-15 nm size region. We find that Mie theory, which utilizes the electron mean free path correction for the permittivity, is not able to reproduce the same functional form of the dipolar modes for the nano-shells of the same sizes.

Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems.

The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.

Optomagnetic Effect Induced by Magnetized Nanocavity Plasmon.

We propose a new type of optomagnetic effect induced by a highly confined plasmonic field in a nanocavity. It is shown that a very large dynamic magnetic field can be generated as the result of the inhomogeneity of nanocavity plasmons, which can directly activate spin-forbidden transitions in molecules. The dynamic optomagnetic effects on optical transitions between states of different spin multiplicities are illustrated by first-principles calculations for C60. Remarkably, the intensity of spin forbidden singlet-to-triplet transitions can even be stronger than that of singlet-to-singlet transitions when the spatial distribution of plasmon is comparable with the molecular size. This approach not only offers a powerful optomagnetic means to rationally fabricate molecular excited states with different multiplicities but also provides a groundbreaking concept of the light-matter interaction that could lead to the observation of new physical phenomena and the development of new techniques.

Mechanistic Studies on NaHCO3 Hydrogenation and HCOOH Dehydrogenation Reactions Catalysed by a FeII Linear Tetraphosphine Complex.

We present a theoretical extension of the previously published bicarbonate hydrogenation to formate and formic acid dehydrogenation catalysed by FeII complexes bearing the linear tetraphosphine ligand tetraphos-1. The hydrogenation reaction was found to proceed at the singlet surface with two competing pathways: A) H2 association to the Fe-H species followed by deprotonation to give a Fe(H)2 intermediate, which then reacts with CO2 to give formate. B) CO2 insertion into the Fe-H bond, followed by H2 association and subsequent deprotonation. B was found to be slightly preferred with an activation energy of 22.8 kcal mol-1 , compared to 25.3 for A. Further we have reassigned the Fe-H complex, as a Fe(H)(H2 ), which undergoes extremely rapid hydrogen exchange.

Origin of the Absorption Band of Bromophenol Blue in Acidic and Basic pH: Insight from a Combined Molecular Dynamics and TD-DFT/MM Study.

We study the linear and nonlinear optical properties of a well-known acid-base indicator, bromophenol blue (BPB), in aqueous solution by employing static and integrated approaches. In the static approach, optical properties have been calculated using time-dependent density functional theory (TD-DFT) on the fully relaxed geometries of the neutral and different unprotonated forms of BPB. Moreover, both closed and open forms of BPB were considered. In the integrated approach, the optical properties have been computed over many snapshots extracted from molecular dynamics simulation using a hybrid time-dependent density functional theory/molecular mechanics approach. The static approach suggests closed neutral ⇒ anionic interconversion as the dominant mechanism for the red shift in the absorption spectra of BPB due to a change from acidic to basic pH. It is found by employing an integrated approach that the two interconversions, namely open neutral ⇒ anionic and open neutral ⇒ dianionic, can contribute to the pH-dependent shift in the absorption spectra of BPB. Even though both static and integrated approaches reproduce the pH-dependent red shift in the absorption spectra of BPB, the latter one is suitable to determine both the spectra and spectral broadening. Finally, the computed static first hyperpolarizability for various protonated and deprotonated forms of BPB reveals that this molecule can be used as a nonlinear optical probe for pH sensing in addition to its highly exploited use as an optical probe.

Toward fully nonempirical simulations of optical band shapes of molecules in solution: a case study of heterocyclic ketoimine difluoroborates.

This study demonstrates that a hybrid density functional theory/molecular mechanics approach can be successfully combined with time-dependent wavepacket approach to predict the shape of optical bands for molecules in solutions, including vibrational fine structure. A key step in this treatment is the estimation of the inhomogeneous broadening based on the hybrid approach, where the polarization between solute and atomically decomposed solvent is taken into account in a self-consistent manner. The potential of this approach is shown by predicting optical absorption bands for three heterocyclic ketoimine difluoroborates in solution.

Non-linear optical properties of molecules in heterogeneous environments: a quadratic density functional/molecular mechanics response theory.

We generalize a density functional theory/molecular mechanics approach for heterogeneous environments with an implementation of quadratic response theory. The updated methodology allows us to address a variety of non-linear optical, magnetic and mixed properties of molecular species in complex environments, such as combined metallic, solvent and confined organic environments. Illustrating calculations of para-nitroaniline on gold surfaces and in solution reveals a number of aspects that come into play when analyzing second harmonic generation of such systems--such as surface charge flow, coupled surface-solvent dynamics and induced geometric and electronic structure effects of the adsorbate. Some ramifications of the methodology for applied studies are discussed.

A time-dependent density-functional theory and complete active space self-consistent field method study of vibronic absorption and emission spectra of coumarin.

Time-dependent density-functional theory (TD-DFT) and complete active space multiconfiguration self-consistent field (CASSCF) calculations have been used to determine equilibrium structures and vibrational frequencies of the ground state and several singlet low-lying excited states of coumarin. Vertical and adiabatic transition energies of S1, S2, and S3 have been estimated by TD-B3LYP and CASSCF/PT2. Calculations predict that the dipole-allowed S1 and S3 states have a character of (1)(ππ*), while the dipole-forbidden (1)(nπ*) state is responsible for S2. The vibronic absorption and emission spectra of coumarin have been simulated by TD-B3LYP and CASSCF calculations within the Franck-Condon approximation, respectively. The simulated vibronic spectra show good agreement with the experimental observations available, which allow us to reasonably interpret vibronic features in the S0→S1 and S0→S3 absorption and the S0←S1 emission spectra. Based on the calculated results, activity, intensity, and density of the vibronic transitions and their contribution to the experimental spectrum profile have been discussed.

Toward Accurate Two-Photon Absorption Spectrum Simulations: Exploring the Landscape beyond the Generalized Gradient Approximation.

In this Letter, we present a pioneering analysis of the density functional approximations (DFAs) beyond the generalized gradient approximation (GGA) for predicting two-photon absorption (2PA) strengths of a set of push-pull π-conjugated molecules. In more detail, we have employed a variety of meta-generalized gradient approximation (meta-GGA) functionals, including SCAN, MN15, and M06-2X, to assess their accuracy in describing the 2PA properties of a chosen set of 48 organic molecules. Analytic quadratic response theory is employed for these functionals, and their performance is compared against the previously studied DFAs and reference data obtained at the coupled-cluster CC2 level combined with the resolution-of-identity approximation (RI-CC2). A detailed analysis of the meta-GGA functional performance is provided, demonstrating that they improve upon their predecessors in capturing the key electronic features of the π-conjugated two-photon absorbers. In particular, the Minnesota functional MN15 shows very promising results as it delivers pleasingly accurate chemical rankings for two-photon transition strengths and excited-state dipole moments.

Association dynamics and linear and nonlinear optical properties of an N-acetylaladanamide probe in a POPC membrane.

Along with the growing evidence that relates membrane abnormalities to various diseases, biological membranes have been acknowledged as targets for therapy. Any such abnormality in the membrane structure alters the membrane potential which in principle can be captured by measuring properties of specific optical probes. There exists by now many molecular probes with absorption and fluorescence properties that are sensitive to local membrane structure and to the membrane potential. To suggest new high-performance optical probes for membrane-potential imaging it is important to understand in detail the membrane-induced structural changes in the probe, the membrane association dynamics of the probe, and its membrane-specific optical properties. To contribute to this effort, we here study an optical probe, N-acetylaladanamide (NAAA), in the presence of a POPC lipid bilayer using a multiscale integrated approach to assess the probe structure, dynamics, and optical properties in its membrane-bound status and in water solvent. We find that the probe eventually assimilates into the membrane with a specific orientation where the hydrophobic part of the probe is buried inside the lipid bilayer, while the hydrophilic part is exposed to the water solvent. The computed absorption maximum is red-shifted when compared to the gas phase. The computations of the two-photon absorption and second harmonic generation cross sections of the NAAA probe in its membrane-bound state which is of its first kind in the literature suggest that this probe can be used for imaging the membrane potential using nonlinear optical microscopy.

π-Stacking effects on the EPR parameters of a prototypical DNA spin label.

The character and value of spin labels for probing environments like double-stranded DNA depend on the degree of change in the spin Hamiltonian parameters of the spin label induced by the environment. Herein we provide a systematic theoretical investigation of this issue, based on a density functional theory method applied to a spin labeled DNA model system, focusing on the dependence of the EPR properties of the spin label on the π stacking and hydrogen bonding that occur upon incorporating the spin label into the selected base pair inside DNA. It is found that the EPR spin Hamiltonian parameters of the spin label are only negligibly affected by its incorporation into DNA, when compared to its free form. This result gives a theoretical ground for the common empirical assumption regarding the behaviour of spin Hamiltonian parameters made in EPR based measurements of the distance between spin labels incorporated into DNA.

EPR spin Hamiltonian parameters of encapsulated spin-labels: impact of the hydrogen bonding topology.

Encapsulation of spin-labels into "host" compounds, like cucurbit[n]urils or cyclodextrins, in solutions has profound effects on the EPR spin Hamiltonian parameters of the spin-labels. In this work we study the microscopic origin of the EPR spin Hamiltonian parameters of spin-labels enclosed in hydrophobic cavities. We focus on the dependence of the EPR properties of encapsulated spin-labels on the hydrogen bonding topologies that occur upon encapsulation, and quantize various contributions to these parameters according to specific hydrogen bonding patterns. The obtained results provide refined insight into the role of the hydrogen bonding induced encapsulation shifts of EPR spin Hamiltonian parameters in solvated "spin-label@host compound" complexes.

Hybrid density functional-molecular mechanics calculations for core-electron binding energies of glycine in water solution.

We report hybrid density functional theory-molecular mechanics (DFT/MM) calculations performed for glycine in water solution at different pH values. In this paper, we discuss several aspects of the quantum mechanics-molecular mechanics (QM/MM) simulations where the dynamics and spectral binding energy shifts are computed sequentially, and where the latter are evaluated over a set of configurations generated by molecular or Car-Parrinello dynamics simulations. In the used model, core ionization takes place in glycine as a quantum mechanical (QM) system modeled with DFT, and the solution is described with expedient force fields in a large molecular mechanical (MM) volume of water molecules. The contribution to the core electronic binding energy from all interactions within and between the two (DFT and MM) parts is accounted for, except charge transfer and dispersion. While the obtained results were found to be in qualitative agreement with experiment, their precision must be qualified with respect to the problem of counter ions, charge transfer and optimal division of QM and MM parts of the system. Results are compared to those of a recent study [Ottoson et al., J. Am. Chem. Soc., 2011, 133, 3120].

Breakdown of the first hyperpolarizability/bond-length alternation parameter relationship.

We have investigated the dependence of the static first hyperpolarizability on the bond-length alternation (BLA) parameter. Our analysis indicates that the validity of the first hyperpolarizability/BLA parameter relationship is restricted to the no-field, vacuum, limit, while it successively breaks down along with increasing polarity of a surrounding medium, becoming invalid, for instance, in an aqueous solution. This contention is based on a series of TD-DFT, TD-DFT/PCM and hybrid TD-DFT/MM calculations of the first hyperpolarizability for a set of molecular configurations generated from Car-Parrinello hybrid QM/MM simulations of the stilbazolium merocyanine chromophore in chloroform and water solvents, and on a rationalization by means of the two-state model for the first hyperpolarizability. The BLA dependence of the three parameters entering the two-state model is shown to be qualitatively different in vacuum and in solvents. Particularly, in the vacuum case, the difference between ground and excited state dipole moments goes to zero for a vanishing BLA, which is not true in the presence of an aqueous medium. In the aqueous medium, an opposing behavior of the parameters involved in the two-state model results in an almost constant first hyperpolarizability with varying BLA parameter.

Radiation-Driven Polymerisation of Methacrylic Acid in Aqueous Solution: A Chemical Events Monte Carlo Study.

This study employed a coarse-grained Monte Carlo (MC) simulation to investigate the radiation-induced polymerisation of methacrylic acid (MAA) in an aqueous solution. This method provides an alternative to traditional kinetic models, enabling a detailed examination of the micro-structure and growth patterns of MAA polymers, which are often not captured in other approaches. In this work, we generated multiple clones of a simulation box, each containing a specific chemical composition. In these simulations, every coarse-grained (CG) bead represents an entire monomer. The growth function, defined by the chemical behaviour of interacting substances, was determined through repeated random sampling. This approach allowed us to simulate the complex process of radiation-induced polymerisation, enhancing our understanding of the formation of poly(methacrylic acid) hydrogels at a microscopic level; while Monte Carlo simulations have been applied in various contexts of polymerisation, this study's specific approach to modelling the radiation-induced polymerisation of MAA in an aqueous environment, utilising the data obtained by quantum chemistry modelling, with an emphasis on micro-structural growth, has not been extensively explored in existing studies. This understanding is important for advancing the synthesis of these hydrogels, which have potential applications in diverse fields such as materials science and medicine.