Robust Atomistic Modeling of Materials, Organometallic, and Biochemical Systems

Spicher, Sebastian; Grimme, Stefan

doi:10.1002/ange.202004239

Cited by 78 publications

(80 citation statements)

References 56 publications

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“…Interestingly, the substitution of the threshold had only minor effect of the optimized fitting parameters and their errors (Table 3). Moreover, the optimized fitting parameters, obtained from the both AnisoDipFit analyses, show in a good agreement with the corresponding parameters predicted by MD [73] (Table 3).…”

Section: High-spin Fe 3+ /Nitroxidesupporting

confidence: 76%

AnisoDipFit: Simulation and Fitting of Pulsed EPR Dipolar Spectroscopy Data for Anisotropic Spin Centers

Abdullin

2020

Appl Magn Reson

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Pulsed electron paramagnetic resonance dipolar spectroscopy (PDS) allows to measure the distances between electron spin centers and, in favorable cases, their relative orientation. This data is frequently used in structural biology for studying biomolecular structures, following their conformational changes and localizing paramagnetic centers within them. In order to extract the inter-spin distances and the relative orientation of spin centers from the primary, time-domain PDS signals, a specialized data analysis is required. So far, the software to do such analysis was available only for isotropic S = 1/2 spin centers, such as nitroxide and trityl radicals, as well as for high-spin Gd 3+ and Mn 2+ ions. Here, a new data analysis program, called AnisoDip-Fit, was introduced for spin systems consisting of one isotropic and one anisotropic S = 1/2 spin centers. The program was successfully tested on the PDS data corresponding to the spin systems Cu 2+ /organic radical, low-spin Fe 3+ /organic radical, and high-spin Fe 3+ /organic radical. For all tested spin systems, AnisoDipFit allowed determining the inter-spin distance distribution with a sub-angstrom precision. In addition, the spatial orientation of the inter-spin vector with respect to the g-frame of the metal center was determined for the last two spin systems. Thus, this study expands the arsenal of the PDS data analysis programs and facilitates the PDS-based distance and angle measurements on the highly relevant class of metolloproteins.

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Section: High-spin Fe 3+ /Nitroxidesupporting

confidence: 76%

AnisoDipFit: Simulation and Fitting of Pulsed EPR Dipolar Spectroscopy Data for Anisotropic Spin Centers

Abdullin

2020

Appl Magn Reson

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“…The simulation of the phospholipid interacting with the NFS and isolated silanol silica models have been carried out by means of the recently developed new generic force field named GFN-FF, which enables fast structure optimizations and molecular-dynamics simulations for basically any chemical structure consisting of elements up to radon (95). GFN-FF is inspired by the latest developments in the field of semiempirical quantum methods, especially the GNF0-xTB (96) method.…”

Section: Methodsmentioning

confidence: 99%

Nearly free surface silanols are the critical molecular moieties that initiate the toxicity of silica particles

Pavan

Santalucia

Leinardi

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

104

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Inhalation of silica particles can induce inflammatory lung reactions that lead to silicosis and/or lung cancer when the particles are biopersistent. This toxic activity of silica dusts is extremely variable depending on their source and preparation methods. The exact molecular moiety that explains and predicts this variable toxicity of silica remains elusive. Here, we have identified a unique subfamily of silanols as the major determinant of silica particle toxicity. This population of “nearly free silanols” (NFS) appears on the surface of quartz particles upon fracture and can be modulated by thermal treatments. Density functional theory calculations indicates that NFS locate at an intersilanol distance of 4.00 to 6.00 Å and form weak mutual interactions. Thus, NFS could act as an energetically favorable moiety at the surface of silica for establishing interactions with cell membrane components to initiate toxicity. With ad hoc prepared model quartz particles enriched or depleted in NFS, we demonstrate that NFS drive toxicity, including membranolysis, in vitro proinflammatory activity, and lung inflammation. The toxic activity of NFS is confirmed with pyrogenic and vitreous amorphous silica particles, and industrial quartz samples with noncontrolled surfaces. Our results identify the missing key molecular moieties of the silica surface that initiate interactions with cell membranes, leading to pathological outcomes. NFS may explain other important interfacial processes involving silica particles.

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“…Simulations with xTB code [ 52 , 53 ] (v. 6.4.0) were carried out at two different levels of theory: semiempirical with xTB-GFN2 [ 54 ] and force-field with xTB-GFNFF [ 55 ]. The acronym stands for Geometry, Frequency, Noncovalent, eXtendend Tight-Binding, highlighting the accuracy of this method in providing reasonable structures, vibrational properties and a good description of weak interactions, at a reduced computational cost, as it relies on Tight-Binding methodology.…”

Section: Methodsmentioning

confidence: 99%

On the Interactions of Melatonin/β-Cyclodextrin Inclusion Complex: A Novel Approach Combining Efficient Semiempirical Extended Tight-Binding (xTB) Results with Ab Initio Methods

et al. 2021

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Melatonin (MT) is a molecule of paramount importance in all living organisms, due to its presence in many biological activities, such as circadian (sleep–wake cycle) and seasonal rhythms (reproduction, fattening, molting, etc.). Unfortunately, it suffers from poor solubility and, to be used as a drug, an appropriate transport vehicle has to be developed, in order to optimize its release in the human tissues. As a possible drug-delivery system, β-cyclodextrin (βCD) represents a promising scaffold which can encapsulate the melatonin, releasing when needed. In this work, we present a computational study supported by experimental IR spectra on inclusion MT/βCD complexes. The aim is to provide a robust, accurate and, at the same time, low-cost methodology to investigate these inclusion complexes both with static and dynamic simulations, in order to study the main actors that drive the interactions of melatonin with β-cyclodextrin and, therefore, to understand its release mechanism.

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Robust Atomistic Modeling of Materials, Organometallic, and Biochemical Systems

Cited by 78 publications

References 56 publications

AnisoDipFit: Simulation and Fitting of Pulsed EPR Dipolar Spectroscopy Data for Anisotropic Spin Centers

AnisoDipFit: Simulation and Fitting of Pulsed EPR Dipolar Spectroscopy Data for Anisotropic Spin Centers

Nearly free surface silanols are the critical molecular moieties that initiate the toxicity of silica particles

On the Interactions of Melatonin/β-Cyclodextrin Inclusion Complex: A Novel Approach Combining Efficient Semiempirical Extended Tight-Binding (xTB) Results with Ab Initio Methods

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