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The eChem project features an e-book published as a web page (10.30746/978-91-988114-0-7), collecting a repository of Jupyter notebooks developed for the dual purpose of explaining and exploring the theory underlying computational chemistry in a highly interactive manner as well as providing a tutorial-based presentation of the complex workflows needed to simulate embedded molecular systems of real biochemical and/or technical interest. For students ranging from beginners to advanced users, the eChem book is well suited for self-directed learning, but workshops led by experienced instructors and targeting student bodies with specific needs and interests can readily be formed from its components. This has been done by using eChem as the base for a workshop directed toward graduate students learning the theory and practices of quantum chemistry, resulting in very positive assessment of the interactive nature of this framework. The members of the eChem team are engaged in both education and research, and as a mirroring activity, we develop the open-source software upon which this e-book is predominantly based. The overarching vision and goal of our work is to provide a science- and education-enabling software platform for quantum molecular modeling on contemporary and future high-performance computing systems, and to document the resulting development and workflows in the eChem book., QC 20230705

Finite-time stabilization of the driven dissipative nonlinear pendulum is investigated in this paper. First, asymptotic and nonasymptotic convergence towards stable and unstable orbits of the ordinary model of the driven dissipative nonlinear pendulum is considered. It is shown that the existence of nonasymptotic convergence does not contradict the fact that time-reversal invariance holds true for the ordinary model of the driven dissipative nonlinear pendulum. Then, finite-time stabilization of unstable orbits of the fractional model of the driven dissipative nonlinear pendulum is discussed. The proposed stabilization technique is based on a proper selection of initial conditions and does not require any feedback loops. Computational experiments are used to illustrate the efficacy of the proposed finite-time stabilization techniques., QC 20220420

For general exchange-correlation functionals with a dependence on the local spin densities and spin-density gradients, we provide computationally tractable expressions for the tensor-averaged quadratic response functions pertinent to the experimental observables in second-harmonic generation (SHG). We demonstrate how the tensor-averaged quantities can be implemented with reference to a derived minimal number of first- and second-order perturbed Fock matrices. Our consideration has the capability of treating a situation of resonance enhancement as it is based on damped response theory and allows for the evaluation of tensor-averaged resonant-convergent quadratic response functions using only similar to 25% (one-photon off-resonance regions) and similar to 50% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of SHG intensities in the one-photon off-resonance region are provided for a sample of makaluvamine derivatives recognized for their large nonlinear optical responses as well as a benchmark set of small- and medium-sized organic molecules., QC 20230222

Quantum chemistry is a powerful tool. It is now possible to model complex chemical processes even on a laptop getting insights into matter at its fundamental scale. But quantum chemistry is also very complex. Answering a chemical question requires selecting parameters among a wide variety of choices. Choosing a model system, an electronic structure method, a basis set, a set of properties, and a wide array of parameters which can affect the results in small but sometimes meaningful way… It can be a very daunting task, even for veterans of the field. Similarly, for those who wish to get a deeper understanding of a method, going through the pages of equation often riddled with inconsistent notations and formulations is very challenging. And at the end, the link between the equation and the computer implementation found in existing softwares can be vague at best. We believe that a core issue is that humans are not good at learning in abstract terms. We can get very far with a lecture or a textbook, but we will never build as much intuition about how a clock work as by simply breaking one apart and rebuilding it from scratch. This is exactly the aim of this page, allowing a hands-on approach to computational chemistry. Together we will dismantle the black box that a computational chemistry code often seems to be, go through all the cogs and gears, and build back together some of the main computational methods of modern computational chemistry. We will do this by presenting the underlying equations, all expressed with consistent notations, as well as by suggesting a simple python implementation, to really display in action how the theory is implemented into a practical tool. Additionally, we will put these methods in context by showing how they can be used to address concrete chemical questions, discussing the strengths and weaknesses of each method and how to best use them to solve practical problems., QC 20220819

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, QC 20230615

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., QC 20230613

The Gator program has been developed for computational spectroscopy and calculations of molecular properties using real and complex propagators at the correlated level of wave function theory. Currently, the focus lies on methods based on the algebraic diagrammatic construction (ADC) scheme up to the third order of perturbation theory. An auxiliary Fock matrix-driven implementation of the second-order ADC method for excitation energies has been realized with an underlying hybrid MPI/OpenMP parallelization scheme suitable for execution in high-performance computing cluster environments. With a modular and object-oriented program structure written in a Python/C++ layered fashion, Gator additionally enables time-efficient prototyping of novel scientific approaches, as well as interactive notebook-driven training of students in quantum chemistry. This article is categorized under: Computer and Information Science > Computer Algorithms and Programming Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry., QC 20220118

One of the promising methods for high-throughput fabrication of nanostructures is the spontaneous dewetting of an as-deposited thin film. The formation process of Au nanostructures (AuNS) on TiO2 thin films consisted of two steps: formation of Au thin films and post-deposition annealing at 500 degrees C temperature in Ar gas environment for 60 minutes. TiO2 thin films were deposited using reactive magnetron sputtering method on SiO2 and fused quartz substrates and soaked at 500 degrees C and 900 degrees C temperatures to understand the influence of crystalline structure and surface morphology of Au and TiO2 thin films on the formation of AuNS. Properties of the deposited thin films were investigated using XRD, SEM, AFM, and RAMAN. The mean diameter (D-mean), mean area of AuNS (A(mean)), and mean distance between centroids of nearest neighbor AuNS (NNDcentr) increased exponentially when thicker nanocrystalline Au films were annealed. Standard deviation from D-mean and coefficient of variation also increased indicating higher dispersion of AuNS diameter. It was found that the influence of surface roughness increased by annealing thicker nanocrystalline Au thin films. D-mean, A(mean), and NNDcentr increased and the density of AuNS (n) decreased (h(Au): 10 nm and 15 nm) with decreasing R-q of TiO2 thin films. The peaks of absorbance (500 nm-750 nm) were broad and not symmetrical indicating multiple localized surface plasmon resonance (LSPR) from various size AuNS. The position of peak shifted to the longer wavelengths when D-mean and NNDcentr was larger., QC 20210812

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., QC 20220504

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., QC 20200714

Hydrogenated and hydroxylated nanodiamonds (NDs) are modeled by putting emphasis on the most common paramagnetic impurities-dangling bonds as well as single substitutional nitrogen atoms-and their interaction with water. It is shown that, despite its overall hydrophobicity, hydrogenated ND can become locally hydrophilic due to the introduced defects; therefore, water molecules may be attracted to the particular sites at its surface. To assess the direct influence of water on the magnetic behavior of NDs, the solvent-induced shift of the g-tensor was employed, indicating that for the same types of impurities, the impact the water has strongly depends on their positions in ND. In addition, water molecules at the locally hydrophilic sites of hydrogenated ND may influence the magnetic behavior of defects to the same extent as it may be influenced in the case of hydroxylated ND. Moreover, the overall hydrophilic nature of the latter does not necessarily guarantee that water, although being strongly attracted to the vicinity of impurity, will form a hydrogen bond network with a substantial impact on the local environment of the unpaired electron. The obtained data imply that in the context of the Overhauser effect, for which the solvent-induced shift of the g-tensor is proposed as a tool to reveal whether some NDs are more favorable for it to occur compared to the others, hydrogenated NDs should perform no worse than hydroxylated ones, despite only the local hydrophilicity of the former., QC 20200525

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.

The electronic g-tensor dependence on the size, shape, and surface functionalization of nanodiamonds (NDs) is theoretically investigated by selecting dangling bonds and single substitutional nitrogen atoms as a main source of the unpaired electrons. The performed g-tensor calculations reveal that aforementioned paramagnetic impurities introduced into octahedrally shaped ND of C84H64 size behave in a very similar manner as those embedded into a smaller octahedral model of C35H36 size. Since cubic and tetrahedral NDs-C54H48 and C51H52-demonstrate a wider range of g-shift values than octahedral systems, the g-tensor dependence on different shapes can be considered as more pronounced. However, a different surface functionalization scheme, namely, fluorination, results in a much larger variation of the g-shifts, pointing to a significant impact the F atoms have on the local environment of the unpaired electrons in C35F36. A partial surface functionalization of C35H36 with benzoic acid and aniline groups indicates that, in some special cases, these linkers might induce a noticeable spin density redistribution which in turn substantially modifies the g-shift values of the system. Additional infrared (IR) spectra calculations show that some of paramagnetic defects in C35H36 and C35F36 possess clearly expressed signatures which could be useful while analyzing the experimental IR spectra of NDs. Published under license by AIP Publishing., QC 20200107

Bacterial infections are a major concern responsible for several million deaths every year. Our work and paper describe computational methods to develop multi-scale models and coarse grain molecular dynamic simulations of cell envelopes of gram-negative bacteria and its interactions with nano particles by studying its binding free energies and optical properties using QM/MM methods., QC 20200609

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QC 20190904

An open-source program named VeloxChem has been developed for the calculation of electronic real and complex linear response functions at the levels of Hartree–Fock and Kohn–Sham density functional theories. With an object-oriented program structure written in a Python/C++ layered fashion, VeloxChem enables time-efficient prototyping of novel scientific approaches without sacrificing computational efficiency, so that molecular systems involving up to and beyond 500 second-row atoms (or some 10,000 contracted and in part diffuse Gaussian basis functions) can be routinely addressed. In addition, VeloxChem is equipped with a polarizable embedding scheme for the treatment of the classical electrostatic interactions with an environment that in turn is modeled by atomic site charges and polarizabilities. The underlying hybrid message passing interface (MPI)/open multiprocessing (OpenMP) parallelization scheme makes VeloxChem suitable for execution in high-performance computing cluster environments, showing even slightly beyond linear scaling for the Fock matrix construction with use of up to 16,384 central processing unit (CPU) cores. An efficient—with respect to convergence rate and overall computational cost—multifrequency/gradient complex linear response equation solver enables calculations not only of conventional spectra, such as visible/ultraviolet/X-ray electronic absorption and circular dichroism spectra, but also time-resolved linear response signals as due to ultra-short weak laser pulses. VeloxChem distributed under the GNU Lesser General Public License version 2.1 (LGPLv2.1) license and made available for download from the homepage https://veloxchem.org. This article is categorized under: Software > Quantum Chemistry Electronic Structure Theory > Density Functional Theory Theoretical and Physical Chemistry > Spectroscopy., QC 20200429

We present a new atomistic model for plasmonic excitations and optical properties of metallic nanoparticles, which collectively describes their complete response in terms of fluctuating dipoles and charges that depend on the local environment and on the morphology of the composite nanoparticles. Being atomically dependent, the total optical properties, the complex polarizability, and the plasmonic excitation of a cluster refer to the detailed composition and geometric characteristics of the cluster, making it possible to explore the role of the material, alloy mixing, size, form shape, aspect ratios, and other geometric factors down to the atomic level and making it useful for the design of plasmonic particles with particular strength and field distribution. The model is parameterized from experimental data and, at present, practically implementable for particles up to more than 10 nm (for nanorods even more), thus covering a significant part of the gap between the scales where pure quantum calculations are possible and where pure classical models based on the bulk dielectric constant apply. We utilized the method to both spherical and cubical clusters along with nanorods where we demonstrate both the size, shape, and ratio dependence of plasmonic excitations and connect this to the geometry of the nanoparticles using the plasmon length., QC 20191129

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 C-60. 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., QC 20191002