Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations

2021 ◽  
Vol 17 (10) ◽  
pp. 6214-6224
Author(s):  
Haixin Wei ◽  
Zekai Zhao ◽  
Ray Luo
2013 ◽  
Vol 13 (1) ◽  
pp. 61-89 ◽  
Author(s):  
Sergio Decherchi ◽  
Jose Colmenares ◽  
Chiara Eva Catalano ◽  
Michela Spagnuolo ◽  
Emil Alexov ◽  
...  

AbstractThe definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric analysis seems to privilege the skin to the blobby surface, and points to an unexpected relationship between the non connectedness of the surface, caused by interstices in the solute volume, and the surface area dependence on atomic centers. In order to assess the ability to reproduce explicit solvent results, specific software tools have been developed to enable the use of the skin surface in Poisson-Boltzmann calculations with the DelPhi solver. The results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view.


2009 ◽  
Vol 46 (5) ◽  
pp. 272-278 ◽  
Author(s):  
E. A. M. Gad ◽  
E. M. S. Azzam ◽  
I. Aiad ◽  
W. I. M. El-azab

2003 ◽  
Vol 68 (12) ◽  
pp. 2344-2354 ◽  
Author(s):  
Edyta Małolepsza ◽  
Lucjan Piela

A molecular surface defined as an isosurface of the valence repulsion energy may be hard or soft with respect to probe penetration. As a probe, the helium atom has been chosen. In addition, the Pauli exclusion principle makes the electronic structure change when the probe pushes the molecule (at a fixed positions of its nuclei). This results in a HOMO-LUMO gap dependence on the probe site on the isosurface. A smaller gap at a given probe position reflects a larger reactivity of the site with respect to the ionic dissociation.


Molecules ◽  
2019 ◽  
Vol 24 (21) ◽  
pp. 3970 ◽  
Author(s):  
Bruna T. L. Pereira ◽  
Mateus A. Gonçalves ◽  
Daiana T. Mancini ◽  
Kamil Kuca ◽  
Teodorico C. Ramalho

Platinum complexes have been studied for cancer treatment for several decades. Furthermore, another important platinum characteristic is related to its chemical shifts, in which some studies have shown that the 195Pt chemical shifts are very sensitive to the environment, coordination sphere, and oxidation state. Based on this relevant feature, Pt complexes can be proposed as potential probes for NMR spectroscopy, as the chemical shifts values will be different in different tissues (healthy and damaged) Therefore, in this paper, the main goal was to investigate the behavior of Pt chemical shifts in the different environments. Calculations were carried out in vacuum, implicit solvent, and inside the active site of P13K enzyme, which is related with breast cancer, using the density functional theory (DFT) method. Moreover, the investigation of platinum complexes with a selective moiety can contribute to early cancer diagnosis. Accordingly, the Pt complexes selected for this study presented a selective moiety, the 2-(4′aminophenyl)benzothiazole derivative. More specifically, two Pt complexes were used herein: One containing chlorine ligands and one containing water in place of chlorine. Some studies have shown that platinum complexes coordinated to chlorine atoms may suffer hydrolyses inside the cell due to the low chloride ion concentration. Thus, the same calculations were performed for both complexes. The results showed that both complexes presented different chemical shift values in the different proposed environments. Therefore, this paper shows that platinum complexes can be a potential probe in biological systems, and they should be studied not only for cancer treatment, but also for diagnosis.


Nanomaterials ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1899
Author(s):  
Mattia Pizzone ◽  
Maria Grazia Grimaldi ◽  
Antonino La La Magna ◽  
Neda Rahmani ◽  
Silvia Scalese ◽  
...  

Molecular Doping (MD) involves the deposition of molecules, containing the dopant atoms and dissolved in liquid solutions, over the surface of a semiconductor before the drive-in step. The control on the characteristics of the final doped samples resides on the in-depth study of the molecule behaviour once deposited. It is already known that the molecules form a self-assembled monolayer over the surface of the sample, but little is known about the role and behaviour of possible multiple layers that could be deposited on it after extended deposition times. In this work, we investigate the molecular surface coverage over time of diethyl-propyl phosphonate on silicon, by employing high-resolution morphological and electrical characterization, and examine the effects of the post-deposition surface treatments on it. We present these data together with density functional theory simulations of the molecules–substrate system and electrical measurements of the doped samples. The results allow us to recognise a difference in the bonding types involved in the formation of the molecular layers and how these influence the final doping profile of the samples. This will improve the control on the electrical properties of MD-based devices, allowing for a finer tuning of their performance.


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