scholarly journals BAl4Mg−/0/+: Global Minima with a Planar Tetracoordinate or Hypercoordinate Boron Atom

Atoms ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 89
Author(s):  
Maya Khatun ◽  
Saikat Roy ◽  
Sandip Giri ◽  
Sasanka Sankhar Reddy CH ◽  
Anakuthil Anoop ◽  
...  
Keyword(s):  
Electron Affinity ◽  
Global Minimum ◽  
Chemical Space ◽  
Search Algorithm ◽  
Decomposition Analysis ◽  
Ab Initio Molecular Dynamics ◽  
Stationary Points ◽  
Energy Decomposition Analysis ◽  
Dynamics Simulations ◽  
Bonding Patterns

We have explored the chemical space of BAl4Mg−/0/+ for the first time and theoretically characterized several isomers with interesting bonding patterns. We have used chemical intuition and a cluster building method based on the tabu-search algorithm implemented in the Python program for aggregation and reaction (PyAR) to obtain the maximum number of possible stationary points. The global minimum geometries for the anion (1a) and cation (1c) contain a planar tetracoordinate boron (ptB) atom, whereas the global minimum geometry for the neutral (1n) exhibits a planar pentacoordinate boron (ppB) atom. The low-lying isomers of the anion (2a) and cation (3c) also contain a ppB atom. The low-lying isomer of the neutral (2n) exhibits a ptB atom. Ab initio molecular dynamics simulations carried out at 298 K for 2000 fs suggest that all isomers are kinetically stable, except the cation 3c. Simulations carried out at low temperatures (100 and 200 K) for 2000 fs predict that even 3c is kinetically stable, which contains a ppB atom. Various bonding analyses (NBO, AdNDP, AIM, etc.) are carried out for these six different geometries of BAl4Mg−/0/+ to understand the bonding patterns. Based on these results, we conclude that ptB/ppB scenarios are prevalent in these systems. Compared to the carbon counter-part, CAl4Mg−, here the anion (BAl4Mg−) obeys the 18 valence electron rule, as B has one electron fewer than C. However, the neutral and cation species break the rule with 17 and 16 valence electrons, respectively. The electron affinity (EA) of BAl4Mg is slightly higher (2.15 eV) than the electron affinity of CAl4Mg (2.05 eV). Based on the EA value, it is believed that these molecules can be identified in the gas phase. All the ptB/ppB isomers exhibit π/σ double aromaticity. Energy decomposition analysis predicts that the interaction between BAl4−/0/+ and Mg is ionic in all these six systems.

scholarly journals Noncovalent Interactions of 1,4-Dithiafulvene and Nitroaromatics: A Combined DFT and Ab Initio Molecular Dynamics (AIMD) Study

2021 ◽  
Author(s):  
Yuming Zhao ◽  
Cody Marcus King-Poole
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Rational Design ◽  
Environmental Control ◽  
Noncovalent Interactions ◽  
Picric Acid ◽  
Decomposition Analysis ◽  
Ab Initio Molecular Dynamics ◽  
Energy Decomposition Analysis

The noncovalent interactions between a redox-active molecule, phenyl-substituted dithiafulvene (Ph-DTF), and ten commonly encountered nitroaromatic compounds (NACs) were systematically investigated by means of density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) simulations. Our modeling studies examined their 1:1 complexes in terms of equilibrium geometries, frontier molecular orbitals (FMOs), nature of noncovalent forces, intermolecular charge transfer (ICT), interaction energies and related energy decomposition analysis. The computational results indicate that Ph-DTF can form thermodynamically stable supramolecular complexes with trinitro-substituted benzenes (e.g., 2,4,6-trinisuchtrotoluene and picric acid), but its interactions with mono- and dinitrobenzenes do not exhibit such stability. The selective binding properties are further corroborated by AIMD simulations. Overall, this computational work establishes a comprehensive understanding of the nature of noncovalent interactions of Ph-DTF with various NACs, and the results can be used as theoretical guidance for the rational design of selective receptors and/or chemosensors for certain NACs that are of great concern in current industrial applications and environmental control.

scholarly journals In silico identification of A1 agonists and A2a inhibitors in pain based on molecular docking strategies and dynamics simulations

2021 ◽  
Author(s):  
Guangya Xu ◽  
Shutao Zhang ◽  
Lulu Zheng ◽  
Zhongjiao Hu ◽  
Lijia Cheng ◽  
...  
Keyword(s):  
Decomposition Analysis ◽  
Md Simulations ◽  
Energy Decomposition Analysis ◽  
Promising Candidate ◽  
Generalized Born ◽  
A2a Receptor ◽  
The Central Nervous System ◽  
A1 Receptor ◽  
In Silico Identification ◽  
Dynamics Simulations

AbstractMost recently, the adenosine is considered as one of the most promising targets for treating pain, with few side effects. It exists in the central nervous system, and plays a key role in nociceptive afferent pathway. It is reported that the A1 receptor (A1R) could inhibit Ca2+ channels to reduce the pain like analgesic mechanism of morphine. And, A2a receptor (A2aR) was reported to enhance the accumulation of AMP (cAMP) and released peptides from sensory neurons, resulting in constitutive activation of pain. Much evidence showed that A1R and A2aR could be served as the interesting targets for the treatment of pain. Herein, virtual screening was utilized to identify the small molecule compounds towards A1R and A2aR, and top six molecules were considered as candidates via amber scores. The molecular dynamic (MD) simulations and molecular mechanics/generalized born surface area (MM/GBSA) were employed to further analyze the affinity and binding stability of the six molecules towards A1R and A2aR. Moreover, energy decomposition analysis showed significant residues in A1R and A2aR, including His1383, Phe1276, and Glu1277. It provided basics for discovery of novel agonists and antagonists. Finally, the agonists of A1R (ZINC19943625, ZINC13555217, and ZINC04698406) and inhibitors of A2aR (ZINC19370372, ZINC20176051, and ZINC57263068) were successfully recognized. Taken together, our discovered small molecules may serve as the promising candidate agents for future pain research.

scholarly journals Identification of 13 Guanidinobenzoyl- or Aminidinobenzoyl-Containing Drugs to Potentially Inhibit TMPRSS2 for COVID-19 Treatment

2021 ◽  
Vol 22 (13) ◽  
pp. 7060
Author(s):  
Xiaoqiang Huang ◽  
Robin Pearce ◽  
Gilbert S. Omenn ◽  
Yang Zhang
Keyword(s):  
Viral Entry ◽  
Catalytic Domain ◽  
Binding Free Energy ◽  
Decomposition Analysis ◽  
Salt Bridge ◽  
Domain Model ◽  
Energy Decomposition Analysis ◽  
Energy Assessment ◽  
Dynamics Simulations ◽  
Positively Charged

Positively charged groups that mimic arginine or lysine in a natural substrate of trypsin are necessary for drugs to inhibit the trypsin-like serine protease TMPRSS2 that is involved in the viral entry and spread of coronaviruses, including SARS-CoV-2. Based on this assumption, we identified a set of 13 approved or clinically investigational drugs with positively charged guanidinobenzoyl and/or aminidinobenzoyl groups, including the experimentally verified TMPRSS2 inhibitors Camostat and Nafamostat. Molecular docking using the C-I-TASSER-predicted TMPRSS2 catalytic domain model suggested that the guanidinobenzoyl or aminidinobenzoyl group in all the drugs could form putative salt bridge interactions with the side-chain carboxyl group of Asp435 located in the S1 pocket of TMPRSS2. Molecular dynamics simulations further revealed the high stability of the putative salt bridge interactions over long-time (100 ns) simulations. The molecular mechanics/generalized Born surface area-binding free energy assessment and per-residue energy decomposition analysis also supported the strong binding interactions between TMPRSS2 and the proposed drugs. These results suggest that the proposed compounds, in addition to Camostat and Nafamostat, could be effective TMPRSS2 inhibitors for COVID-19 treatment by occupying the S1 pocket with the hallmark positively charged groups.

scholarly journals Tumbling with a limp: local asymmetry in water's hydrogen bond network and its consequences

2020 ◽  
Vol 22 (19) ◽  
pp. 10397-10411 ◽  
Author(s):  
Hossam Elgabarty ◽  
Thomas D. Kühne
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Liquid Water ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Energy Decomposition ◽  
Bond Network ◽  
Dynamics Simulations

Ab initio molecular dynamics simulations of ambient liquid water and energy decomposition analysis have recently shown that water molecules exhibit significant asymmetry between the strengths of the two donor and/or the two acceptor interactions.

scholarly journals CAl4Mg0/−: Global Minima with a Planar Tetracoordinate Carbon Atom

Atoms ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 24
Author(s):  
Nisha Job ◽  
Maya Khatun ◽  
Krishnan Thirumoorthy ◽  
Sasanka Sankhar Reddy CH ◽  
Vijayanand Chandrasekaran ◽  
...  
Keyword(s):  
Carbon Atom ◽  
Valence Electron ◽  
Global Minimum ◽  
Experimental Studies ◽  
Ab Initio Molecular Dynamics ◽  
Global Minima ◽  
Ionic Radii ◽  
Valence Electrons ◽  
Dynamics Simulations ◽  
First Time

Isomers of CAl4Mg and CAl4Mg− have been theoretically characterized for the first time. The most stable isomer for both the neutral and anion contain a planar tetracoordinate carbon (ptC) atom. Unlike the isovalent CAl4Be case, which contains a planar pentacoordinate carbon atom as the global minimum geometry, replacing beryllium with magnesium makes the ptC isomer the global minimum due to increased ionic radii of magnesium. However, it is relatively easier to conduct experimental studies for CAl4Mg0/− as beryllium is toxic. While the neutral molecule containing the ptC atom follows the 18 valence electron rule, the anion breaks the rule with 19 valence electrons. The electron affinity of CAl4Mg is in the range of 1.96–2.05 eV. Both the global minima exhibit π/σ double aromaticity. Ab initio molecular dynamics simulations were carried out for both the global minima at 298 K for 10 ps to confirm their kinetic stability.

scholarly journals Alkyne-Functionalized Cyclooctyne on Si(001): Reactivity Studies and Surface Bonding from an Energy Decomposition Analysis Perspective

Molecules ◽  
2021 ◽  
Vol 26 (21) ◽  
pp. 6653
Author(s):  
Fabian Pieck ◽  
Ralf Tonner-Zech
Keyword(s):  
Density Functional ◽  
Selective Adsorption ◽  
Decomposition Analysis ◽  
High Reactivity ◽  
Structural Deformation ◽  
Ab Initio Molecular Dynamics ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Elastic Band ◽  
Reaction Barriers

The reactivity and bonding of an ethinyl-functionalized cyclooctyne on Si(001) is studied by means of density functional theory. This system is promising for the organic functionalization of semiconductors. Singly bonded adsorption structures are obtained by [2+2] cycloaddition reactions of the cyclooctyne or ethinyl group with the Si(001) surface. A thermodynamic preference for adsorption with the cyclooctyne group in the on-top position is found and traced back to minimal structural deformation of the adsorbate and surface with the help of energy decomposition analysis for extended systems (pEDA). Starting from singly bonded structures, a plethora of reaction paths describing conformer changes and consecutive reactions with the surface are discussed. Strongly exothermic and exergonic reactions to doubly bonded structures are presented, while small reaction barriers highlight the high reactivity of the studied organic molecule on the Si(001) surface. Dynamic aspects of the competitive bonding of the functional groups are addressed by ab initio molecular dynamics calculations. Several trajectories for the doubly bonded structures are obtained in agreement with calculations using the nudged elastic band approach. However, our findings disagree with the experimental observations of selective adsorption by the cyclooctyne moiety, which is critically discussed.

Vapour Pressure Isotope Effect on Evaporation from Pure Organic Phases - a PIMD Approach

2020 ◽  
Author(s):  
Luis Vasquez ◽  
Agnieszka Dybala-Defratyka
Keyword(s):  
Path Integral ◽  
Vapour Pressure ◽  
Density Functional ◽  
Isotope Effects ◽  
Tight Binding ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Special Importance ◽  
Non Covalent Interactions ◽  
Covalent Interactions

<p></p><p>Very often in order to understand physical and chemical processes taking place among several phases fractionation of naturally abundant isotopes is monitored. Its measurement can be accompanied by theoretical determination to provide a more insightful interpretation of observed phenomena. Predictions are challenging due to the complexity of the effects involved in fractionation such as solvent effects and non-covalent interactions governing the behavior of the system which results in the necessity of using large models of those systems. This is sometimes a bottleneck and limits the theoretical description to only a few methods.<br> In this work vapour pressure isotope effects on evaporation from various organic solvents (ethanol, bromobenzene, dibromomethane, and trichloromethane) in the pure phase are estimated by combining force field or self-consistent charge density-functional tight-binding (SCC-DFTB) atomistic simulations with path integral principle. Furthermore, the recently developed Suzuki-Chin path integral is tested. In general, isotope effects are predicted qualitatively for most of the cases, however, the distinction between position-specific isotope effects observed for ethanol was only reproduced by SCC-DFTB, which indicates the importance of using non-harmonic bond approximations.<br> Energy decomposition analysis performed using the symmetry-adapted perturbation theory (SAPT) revealed sometimes quite substantial differences in interaction energy depending on whether the studied system was treated classically or quantum mechanically. Those observed differences might be the source of different magnitudes of isotope effects predicted using these two different levels of theory which is of special importance for the systems governed by non-covalent interactions.</p><br><p></p>

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