Prediction of proton affinities of organic molecules using the any-particle molecular-orbital second-order proton propagator approach

2016 ◽  
Vol 18 (39) ◽  
pp. 27185-27189 ◽  
Author(s):  
Laura Pedraza-González ◽  
Jonathan Romero ◽  
Jorge Alí-Torres ◽  
Andrés Reyes
Keyword(s):  
Gas Phase ◽  
Molecular Orbital ◽  
Organic Molecules ◽  
Second Order ◽  
Proton Affinities ◽  
Wide Range

We assess the performance of the recently developed any-particle molecular-orbital second-order proton propagator. Our results show that this method provides quantitative predictions of gas phase proton affinities for a wide range of organic molecules.

Fast and accurate prediction of proton affinities: revisiting the extended Koopmans' theorem for protons

2017 ◽  
Vol 19 (37) ◽  
pp. 25324-25333 ◽  
Author(s):  
Laura Pedraza-González ◽  
Jorge Charry ◽  
William Quintero ◽  
Jorge Alí-Torres ◽  
Andrés Reyes
Keyword(s):  
Gas Phase ◽  
Molecular Orbital ◽  
Accurate Prediction ◽  
Quantitative Prediction ◽  
Proton Affinities ◽  
Koopmans Theorem

In this work we propose schemes based on the extended Koopmans' theorem for quantum nuclei (eKT), in the framework of the any particle molecular orbital approach (APMO/KT), for the quantitative prediction of gas phase proton affinities (PAs).

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens

2020 ◽  
Author(s):  
Christian Devereux ◽  
Justin Smith ◽  
Kate Davis ◽  
Kipton Barros ◽  
Roman Zubatyuk ◽  
...  
Keyword(s):  
Drug Development ◽  
Autonomous Vehicles ◽  
Potential Energy Surfaces ◽  
Organic Molecules ◽  
Chemical Elements ◽  
Molecular Potential ◽  
Wide Range ◽  
Energy Surfaces ◽  
New Applications ◽  
Physical Phenomena

<p>Machine learning (ML) methods have become powerful, predictive tools in a wide range of applications, such as facial recognition and autonomous vehicles. In the sciences, computational chemists and physicists have been using ML for the prediction of physical phenomena, such as atomistic potential energy surfaces and reaction pathways. Transferable ML potentials, such as ANI-1x, have been developed with the goal of accurately simulating organic molecules containing the chemical elements H, C, N, and O. Here we provide an extension of the ANI-1x model. The new model, dubbed ANI-2x, is trained to three additional chemical elements: S, F, and Cl. Additionally, ANI-2x underwent torsional refinement training to better predict molecular torsion profiles. These new features open a wide range of new applications within organic chemistry and drug development. These seven elements (H, C, N, O, F, Cl, S) make up ~90% of drug like molecules. To show that these additions do not sacrifice accuracy, we have tested this model across a range of organic molecules and applications, including the COMP6 benchmark, dihedral rotations, conformer scoring, and non-bonded interactions. ANI-2x is shown to accurately predict molecular energies compared to DFT with a ~10<sup>6</sup> factor speedup and a negligible slowdown compared to ANI-1x. The resulting model is a valuable tool for drug development that can potentially replace both quantum calculations and classical force fields for myriad applications.</p>

scholarly journals Spectral Broadening in a Continuously Pumped Singly Resonant Second-Harmonic Cavity

2021 ◽  
Vol 11 (15) ◽  
pp. 7122
Author(s):  
Simona Mosca ◽  
Tobias Hansson ◽  
Maria Parisi
Keyword(s):  
Continuous Wave ◽  
Frequency Comb ◽  
Second Harmonic ◽  
Input Power ◽  
Second Order ◽  
Optical Frequency ◽  
Frequency Combs ◽  
Research Areas ◽  
Mixed Regime ◽  
Wide Range

Optical frequency comb synthesizers with a wide spectral range are an essential tool for many research areas such as spectroscopy, precision metrology, optical communication, and sensing. Recent studies have demonstrated the direct generation of frequency combs, via second-order processes, that are centered on two different spectral regions separated by an octave. Here, we present the capability of optical quadratic frequency combs for broad-bandwidth spectral emission in unexplored regimes. We consider comb formation under phase-matched conditions in a continuous-wave pumped singly resonant second-harmonic cavity, with large intracavity power and control of the detuning over several cavity line widths. The spectral analysis reveals quite distinctive sidebands that arise far away from the pump, singularly or in a mixed regime together with narrowband frequency combs. Notably, by increasing the input power, the optical frequency lines evolve into widely spaced frequency clusters, and at maximum power, they appear in a wavelength range spanning up to 100 nm. The obtained results demonstrate the power of second-order nonlinearities for direct comb production within a wide range of pump wavelengths.

scholarly journals Not Just Transporters: Alternative Functions of ABC Transporters in Bacillus subtilis and Listeria monocytogenes

2021 ◽  
Vol 9 (1) ◽  
pp. 163
Author(s):  
Jeanine Rismondo ◽  
Lisa Maria Schulz
Keyword(s):  
Bacillus Subtilis ◽  
Listeria Monocytogenes ◽  
Abc Transporters ◽  
Organic Molecules ◽  
Atp Hydrolysis ◽  
The Past ◽  
Wide Range ◽  
Regulatory Functions ◽  
Complex Organic ◽  
Detoxification Mechanisms

ATP-binding cassette (ABC) transporters are usually involved in the translocation of their cognate substrates, which is driven by ATP hydrolysis. Typically, these transporters are required for the import or export of a wide range of substrates such as sugars, ions and complex organic molecules. ABC exporters can also be involved in the export of toxic compounds such as antibiotics. However, recent studies revealed alternative detoxification mechanisms of ABC transporters. For instance, the ABC transporter BceAB of Bacillus subtilis seems to confer resistance to bacitracin via target protection. In addition, several transporters with functions other than substrate export or import have been identified in the past. Here, we provide an overview of recent findings on ABC transporters of the Gram-positive organisms B. subtilis and Listeria monocytogenes with transport or regulatory functions affecting antibiotic resistance, cell wall biosynthesis, cell division and sporulation.

The chemistry of stabilized clusters

1982 ◽  
Vol 308 (1501) ◽  
pp. 27-34 ◽  
Keyword(s):  
Electron Donor ◽  
Organic Molecules ◽  
Metal Cluster ◽  
Organic Substrates ◽  
Insertion Reactions ◽  
Donor Ligand ◽  
Small Organic Molecules ◽  
Wide Range ◽  
Metal Metal ◽  
High Yields

Studies of the chemistry of metal cluster complexes and, in particular, their reactions with small organic molecules, have been confined to relatively few systems. Among the reasons for this are: (i) not many clusters are easily synthesized in high yields; (ii) their reactions often give a multitude of products that are difficult to separate and characterize; (iii) the conditions required to bring about reactions often lead to fragmentation of the cluster into lower nuclearity (often mononuclear) species. One cluster whose chemistry has been extensively studied is [Os 3 H 2 (CO) 10 ]. This can be synthesized in high yields from [Os 3 (CO) 12 ] + H 2 (Knox et al. 1975) and reacts readily under mild conditions with a wide range of electron-donor molecules by virtue of its coordinative unsaturation (Shapley et al. 1975; Deeming & Hasso 1976; Adams & Golembeski 1979). Formally, one may consider that a metal—metal double bond is present, which is reduced to a single bond on coordination of an additional two-electron donor ligand such as an organophosphine. The presence of metal—hydrogen bonds in this cluster and the cluster’s ability to coordinate organic substrates enable it to undergo a wide variety of insertion reactions, leading to products that may be regarded as intermediates in the reduction of organic molecules by clusters (Deeming & Hasso 1975; Keister & Shapley 1975).

NOHSO4/HF – A Novel Etching System for Crystalline Silicon

2007 ◽  
Vol 62 (11) ◽  
pp. 1411-1421 ◽  
Author(s):  
Sebastian Patzig ◽  
Gerhard Roewer ◽  
Edwin Kroke ◽  
Ingo över
Keyword(s):  
Gas Phase ◽  
Chemical Etching ◽  
Silicon Surface ◽  
Crystalline Silicon ◽  
Etching Solution ◽  
Wide Range ◽  
Ft Ir ◽  
Wet Chemical ◽  
Wet Chemical Etching ◽  
Etching System

Solutions consisting of HF - NOHSO4 - H2SO4 exhibit a strong reactivity towards crystalline silicon which is controlled by the concentrations of the reactive species HF and NO+. Selective isotropic and anisotropic wet chemical etching with these solutions allows to generate a wide range of silicon surface morphology patterns. Traces of Ag+ ions stimulate the reactivity and lead to the formation of planarized (polished) silicon surfaces. Analyses of the silicon surface, the etching solution and the gas phase were performed with scanning electron microscopy (SEM), DR/FT-IR (diffusive reflection Fourier transform infra-red), FT-IR, Raman and NMR spectroscopy, respectively. It was found that the resulting silicon surface is hydrogen-terminated. The gas phase contains predominantly SiF4, NO and N2O. Furthermore, NH4+ is produced in solution. The study has confirmed the crucial role of nitrosyl ions for isotropic wet chemical etching processes. The novel etching system is proposed as an effective new way for selective surface texturing of multi- and monocrystalline silicon. A high etching bath service lifetime, besides a low contamination of the etching solution with reaction products, provides ecological and economical advantages for the semiconductor and solar industry.

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