Testing and Optimizing the Drude Polarizable Force Field for Blocked Amino Acids Based on High-Level Quantum-Mechanical Energy Surfaces

The correct reproduction of conformational substates of amino acids was tested for the CHARMM Drude polarizable force field. This was achieved by evaluating the reorganization energies for all low lying energy minima occurring in all 15 neutral blocked amino acids on a quantum-mechanical (QM) energy surface at the MP2/cc-pVDZ level. The results indicate that the bonded parameters of the N-acetyl (ACE) and N-Methylamide (CT3) blocking groups lead to significant discrepancies. A reparametrization of five bond angles significantly improved the agreement with the QM energy surface. The corrected Drude force field exhibits almost the same average reorganization energies relative to the MP2 energy surface as the AM1 and PM3 semi-empirical methods.

A new global analytical ab initio potential energy surface for the dynamics of the C+(2P) + SH(X2Π) reaction

Relaxed triangular plot of the new PES in hyperspherical coordinates.

Global potential energy surface and product pair-correlated distributions for the F(2P) + SiH4 reaction. Comparison with experiments.

In this paper we study the gas-phase hydrogen abstraction reaction between fluorine atoms and silane in a three-step process: potential energy surface, kinetics and dynamics. Firstly, we developed for the...

Theoretically studying the optoelectronic properties of oligomers based on 2.7-divinyl-cabazole

This work consists of theoretically studying the electronic and optical properties of 9-(4-octyloxyphenyl)-2.7-divinyl-carbazole (PCrV) oligomers. This study has been undertaken using the density functional theory (DFT) method at the B3LYP/6-31G (d,p) level and BP86/6-31G (d,p) level of theory. To evaluate the PCrV-basis systems properties, the structural optimization without geometrical restrictions was performed on the total potential energy surface (TPES). In order to ensure good absorption of radiation, the interest was in increasing the efficiency of the organic photovoltaic cell. For this effect, the (HOMO-LUMO) gap energy of such compounds was reduced in terms of geometric and electronic structure. The BP86 functional gives good results at the energy gap level, while other parameters using the B3LYP functional give the best results.

Materials by Design at High Pressures

Pressure, a fundamental thermodynamic variable, can generate two essential effects on materials. First, pressure can create new high-pressure phases via modification of the potential energy surface. Second, pressure can produce...

GEOMETRY OPTIMIZATION OF COUPLING ALLIN -METFORMIN USING DFT/B3LYP MOLECULAR MODELLING TECHNIQUE

This researchpaper includes the incorporation of Alliin at various energy levels and angles With Metformin using Gaussian 09 and Gaussian view 06. Two computers were used in this work. Samples were generated to draw, integrate, simulate and measure the value of the potential energy surface by means of which the lowest energy value was (-1227.408au). The best correlation compound was achieved between Alliin and Metformin through the low energy values where the best place for metformin to bind was through (CH2-). This is considered to be very useful for the industrial application of drugs. This level of calculation was used for physical and quantum properties such as total energy, HOMO and LUMO orbitals energies, and power gap. Besides, the calculation of FT-IR spectra in the range 400-4000 cm-1 was calculated in addition to the essential vibrational frequencies and the intensity of the vibrational bands. Moreover, the chemical displacement of the 1H and 13C NMR of the compound in the ground state was studied.

Remdesivir: Mechanism of Metabolic Conversion from Prodrug to Drug

Background: Remdesivir (GS-5734) has emerged as a promising drug during the challenging times of COVID-19 pandemic. Being a prodrug, it undergoes several metabolic reactions before converting to its active triphosphate metabolite. It is important to establish the atomic level details and explore the energy profile of the prodrug to drug conversion process. Methods: In this work, Density Functional Theory (DFT) calculations were performed to explore the entire metabolic path. Further, the potential energy surface (PES) diagram for the conversion of prodrug remdesivir to its active metabolite was established. The role of catalytic triad of Hint1 phosphoramidase enzyme in P-N bond hydrolysis was also studied on a model system using combined molecular docking and quantum mechanics approach. Results: The overall energy of reaction is 11.47 kcal/mol exergonic and the reaction proceeds through many steps requiring high activation energies. In the absence of a catalyst, the P-N bond breaking step requires 41.78 kcal/mol, which is reduced to 14.26 kcal/mol in a catalytic environment. Conclusion: The metabolic pathways of model system of remdesivir (MSR) were completely explored completely and potential energy surface diagrams at two levels of theory, B3LYP/6-311++G(d, p) and B3LYP/6-31+G(d), were established and compared. The results highlight the importance of an additional water molecule in the metabolic reaction. The P-N bond cleavage step of the metabolic process requires the presence of an enzymatic environment.