An analysis of structural, spectroscopic, quantum chemical and in silico studies of ethyl 3-[(pyridin-2-yl)amino]propanoate: A potential thrombin inhibitor

Nuthalapati, Poojith; Rani, N. Usha; Potla, Krishna Murthy; Rose, J. John; Suchetan, P.A.; Pillai, Renjith Raveendran; Vankayalapati, Suneetha

doi:10.1016/j.molstruc.2020.129378

Cited by 8 publications

(1 citation statement)

References 47 publications

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“…For the title compound, the optimized geometrical parameters (bond length (Å), bond angle (deg), dihedral angle (deg)) and their experimental counter values are listed in Table S1. For the title compound, the C–N bond lengths (DFT/X-ray diffraction (XRD)), namely, C11–N10 (1.37/1.349 Å) and C14–N2 (1.376/1.37 Å), are much shorter than the normal C–N bond length of 1.49 Å but significantly longer than a double bond (1.22 Å), suggesting that these bonds have some multiple bond character . At the N41 position, the C14–N41–C32 angle is decreased by 4.31°, while at the N2 position, the C15–N2–C14 angle is increased by 9.83°.…”

Section: Resultsmentioning

confidence: 99%

Multifaceted Study of a Y-Shaped Pyrimidine Compound: Assessing Structural Properties, Docking Interactions, and Third-Order Nonlinear Optics

Potla,

Nuthalapati,

Sasi Mohan

et al. 2024

ACS Omega

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In this study, we report the synthesis of a new compound, N4,N4-dimethyl-2-(methylsulfanyl)-N6-(4phenoxyphenyl)pyrimidine-4,6-diamine (DMS), and its comprehensive analysis through structural and spectroscopic characterizations, reactivity parameters, and nonlinear optical properties, utilizing a combination of experimental and computational techniques. The experimental aspect of the investigation encompassed structural characterization using X-ray diffraction and spectroscopic assessments employing Fourier-transform infrared, Raman, and nuclear magnetic resonance techniques, along with thermal analysis. Our computational approach involved density functional theory (DFT) calculations and molecular dynamics (MD) simulations to examine the local reactivity properties of DMS. We employed fundamental reactivity descriptors to evaluate DMS's local reactivity and utilized MD simulations to identify DMS atoms engaging in significant interactions with water molecules. We conducted periodic DFT calculations on DMS's crystal structure to investigate the contributions of specific atoms and groups to the compound's overall stability as well as to analyze noncovalent interactions between DMS molecules. We assessed the nonlinear optical properties through dynamic second hyperpolarizability and third-order nonlinear susceptibility calculations. Additionally, we conducted a comparative analysis of the static and dynamic second hyperpolarizability for the DMS molecule within the sum-over-states framework. The obtained value for the third-order nonlinear susceptibility, 3 = 65.41 10 20 × m /V 2 2 (λ = 1907 nm), exceeds those of other organic materials reported in previous studies, indicating that the DMS crystal holds promise as a nonlinear optical material for potential application in photonic device fabrication. Furthermore, molecular docking studies were performed with the 3E5A, 4EUT, and 4EUU proteins, yielding binding affinities of −8.1, −8.2, and −8.3 kcal/ mol, respectively, in association with the ligand.

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Section: Resultsmentioning

confidence: 99%