scholarly journals Quantum Chemical Microsolvation by Automated Water Placement

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1793
Author(s):  
Miguel Steiner ◽  
Tanja Holzknecht ◽  
Michael Schauperl ◽  
Maren Podewitz

We developed a quantitative approach to quantum chemical microsolvation. Key in our methodology is the automatic placement of individual solvent molecules based on the free energy solvation thermodynamics derived from molecular dynamics (MD) simulations and grid inhomogeneous solvation theory (GIST). This protocol enabled us to rigorously define the number, position, and orientation of individual solvent molecules and to determine their interaction with the solute based on physical quantities. The generated solute–solvent clusters served as an input for subsequent quantum chemical investigations. We showcased the applicability, scope, and limitations of this computational approach for a number of small molecules, including urea, 2-aminobenzothiazole, (+)-syn-benzotriborneol, benzoic acid, and helicene. Our results show excellent agreement with the available ab initio molecular dynamics data and experimental results.

1998 ◽  
Vol 543 ◽  
Author(s):  
T. Çağin ◽  
Y. Zhou ◽  
E. S. Yamaguchi ◽  
R. Frazier ◽  
A. Ho ◽  
...  

AbstractTo understand antiwear phenomena in motor engines at the atomic level and provide evidence inselecting future ashless wear inhibitors, we studied the thermal stability of the self-assembled monolayer(SAM) model for dithiophosphate (DTP) and dithiocarbamate (DTC) molecules on the iron oxidesurface using molecular dynamics. The interactions for DTP, DTC and Fe2O3 are evaluated based on aforce field derived from fitting to ab initio quantum chemical calculations of dimethyl DTP (and DTC)and Fe(OH)2(H2O)2-DTP (DTC) clusters. MD simulations at constant-NPT are conducted to assesrelative thermal stabilities of the DTP and DTC with different pendant groups (n-propyl, i-propyl, npentyl.and i-pentyl). To investigate frictional process, we employ a steady state MD method, in whichone of the Fe2O3 slabs maintained at a constant linear velocity. We obtain the time averaged normaland frictional forces from the interatomic forces. Then, we calculated the friction coefficient at theinterface between SAMs of DTP and the confined lubricant, hexadecane, to assess the shear stability ofDTPs with different pendant groups.


2020 ◽  
Vol 22 (12) ◽  
pp. 6690-6697 ◽  
Author(s):  
Aman Jindal ◽  
Sukumaran Vasudevan

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.


2014 ◽  
Vol 1061-1062 ◽  
pp. 205-208
Author(s):  
Kun Li ◽  
Jing Jie Sha ◽  
Lei Liu ◽  
Gen Sheng Wu ◽  
Wei Si ◽  
...  

With the miniaturization of the NEMS/MEMS, the size effect becomes significant in the nanochannels/nanopores through which fluid flows as well as the interface effect. By all-atom molecular dynamics (MD) simulations, the ion transportation is investigated in nanopores as well as the physical properties at solid-liquid interface. To describe the anion and cation distributions of NaCl solution in vicinity of graphene nanopores, a new MD model was developed, taking thermal vibration of wall atoms, the structure of solvent molecules and ion sizes into consideration. The main peak locations of ion distributions stayed unchanged by changing the nanopore size, the solution concentration and the electric field strength. The ionic currents increased linearly with the diameter and the electric field strength, while it increased non-linearly with the solution concentration.


2017 ◽  
Vol 19 (31) ◽  
pp. 20551-20558 ◽  
Author(s):  
Raúl Guerrero-Avilés ◽  
Walter Orellana

The energetics and diffusion of water molecules and hydrated ions (Na+, Cl−) passing through nanopores in graphene are addressed by dispersion-corrected density functional theory calculations and ab initio molecular dynamics (MD) simulations.


Processes ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1749
Author(s):  
Yuqi Zhang ◽  
Li Chen ◽  
Xiaoyu Wang ◽  
Yanyan Zhu ◽  
Yongsheng Liu ◽  
...  

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a type of Ribonucleic Acid (RNA) coronavirus and it has infected and killed many people around the world. It is reported that the receptor binding domain of the spike protein (S_RBD) of the SARS-CoV-2 virus is responsible for attachment to human angiotensin converting enzyme II (ACE2). Many researchers are attempting to search potential inhibitors for fighting SARS-CoV-2 infection using theoretical or experimental methods. In terms of experimental and theoretical research, Cefuroxime, Erythromycin, Lincomycin and Ofloxacin are the potential inhibitors of SARS-CoV-2. However, the interactive mechanism of the protein SARS-CoV-2 and the inhibitors are still elusive. Here, we investigated the interactions between S_RBD and the inhibitors using molecular dynamics (MD) simulations. Interestingly, we found that there are two binding sites of S_RBD for the four small molecules. In addition, our analysis also illustrated that hydrophobic and π-π stacking interactions play crucial roles in the interactions between S_RBD and the small molecules. In our work, we also found that small molecules with glycosyl group have more effect on the conformation of S_RBD than other inhibitors, and they are also potential inhibitors for the genetic variants of SARS-CoV-2. This study provides in silico-derived mechanistic insights into the interactions of S_RBD and inhibitors, which may provide new clues for fighting SARS-CoV-2 infection.


2021 ◽  
Author(s):  
Omer Tayfuroglu ◽  
Abdul Kadir Kocak ◽  
Yunus Zorlu

Metal‑organic frameworks (MOFs) with their exceptional porous and organized structures have been subject of numerous applications. Predicting macroscopic properties from atomistic simulations require the most accurate force fields, which is still a major problem due to MOFs’ hybrid structures governed by covalent, ionic and dispersion forces. Application of ab‑initio molecular dynamics to such large periodic systems are thus beyond the current computational power. Therefore, alternative strategies must be developed to reduce computational cost without losing reliability. In this work, we describe the construction of a neural network potential (NNP) for IRMOF‑n series (n=1,4,7,10) trained by PBE-D4/def2-TZVP reference data of MOF fragments. We validated the resulting NNP on both fragments and bulk MOF structures by prediction of properties such as equilibrium lattice constants, phonon density of states and linker orientation. The energy and force RMSE values for the fragments are only 0.0017 eV/atom and 0.15 eV/Å, respectively. The NNP predicted equilibrium lattice constants of bulk structures, which are not included in training, are off by only 0.2-2.4% from experimental results. Moreover, our fragment trained NNP greatly predicts phenylene ring torsional energy barrier, equilibrium bond distances and vibrational density of states of bulk MOFs. Furthermore, NNP allows us to investigate unusual behaviors of selected MOFs such as the thermal expansion properties and the effect of mechanical strain on the adsorption of hydrogen and methane molecules. The NNP based molecular dynamics (MD) simulations suggest the IRMOF‑4 and IRMOF‑7 to have positive‑to‑negative thermal expansion coefficients while the rest to have only negative thermal expansion under the studied temperatures of 200 K to 400 K. The deformation of bulk structure by reduction of unit cell volume has shown to increase volumetric methane uptake in IRMOF‑1 but decrease in IRMOF‑7 due to the steric hindrance.


2009 ◽  
Vol 01 (03) ◽  
pp. 469-482 ◽  
Author(s):  
S. JUN ◽  
S. PENDURTI ◽  
I.-H. LEE ◽  
S. Y. KIM ◽  
H. S. PARK ◽  
...  

Action-derived molecular dynamics (ADMD) is a numerical method to search for minimum-energy dynamic pathways on the potential-energy surface of an atomic system. The method is based on Hamilton's least-action principle and has been developed for problems of activated processes, rare events, and long-time simulations. In this paper, ADMD is further extended to incorporate ab initio total-energy calculations, which enables the detailed electronic analysis of transition states as well as the exploration of energy landscapes. Three numerical examples are solved to demonstrate the capability of this action-derived ab initio molecular dynamics (MD). The proposed approach is expected to circumvent the severe time-scale limitation of conventional ab intio MD simulations.


2020 ◽  
Vol 38 (4) ◽  
pp. 277-284
Author(s):  
Ying Zhang ◽  
Xing Wang ◽  
Zhongfeng Xu

AbstractThe ab initio molecular dynamics (MD) simulations using an atom-centered density matrix propagation method are carried out in the first time to investigate the dissociative electron attachment (DEA) processes of adenine and its tautomer in the gas phase. Since the incoming electron are captured on the lowest π∗ anti-bond orbital, which is led to the different N–H bond, the C–H bond and the C–N bond are broken. The dominant anion observed in DEA dissociation process is the closed-shell dehydrogenated anion (Ade − H)−. The additional anions (Ade − NH2)− and (Ade − 2H)− are also obtained in ADMP simulation. The results are well consistent with the previous DEA experimental results. Thus, the ADMP method is used to gain a more intuitive and better understanding of the necessary dissociation process in the DEA experiment.


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