Structural, vibrational, NMR, quantum chemical, DNA binding and protein docking studies of two flexible imine oximes

Abstract

Two flexible imine oxime molecules, namely, 3-(pyridin-2-ylmethylimino)-butan-2-one oxime (HL 1) and 3-(pyridin-2-ylmethylimino)-pentan-2-one oxime (HL 2) have been synthesized and characterized by elemental analysis, IR and NMR techniques. The conformational behavior was investigated using the density functional theory (DFT) with the B3LYP method combined with the 6-311++G(d,p) basis set. As a result of the conformational studies, three stable molecules and the most stable conformer were determined for the both imine oximes. The spectroscopic properties such as vibrational and NMR were calculated for the most stable conformer of the HL 1 and HL 2. The calculation results were applied to simulate infrared spectra of the title compounds, which show good agreement with observed spectra. In addition, the stable three molecules of the both imine oximes have been used to carry out DNA binding and protein docking studies with DNA and protein structures (downloaded from Protein Data Bank) using Discovery Studio 3.5 to find the most preferred binding mode of the ligands inside the DNA and protein cavity.

The synthesis and spectroscopic characterization of (+)-demethoxyaspidospermine: Density functional theory calculations of the structural, electronic, and non-linear optic and spectroscopic properties

“…In the past, the aromatic C-C stretching modes for the imine oxime derivative were recorded at 1582 and 1579 cm −1 and simulated by the B3LYP/6-311++G(d, p) level at 1594 and 1577 cm −1 . 37 Also, Kanaani et al 38 recorded the aromatic C-H stretching signals for the phenyl rings of a heterocyclic imidazole compound in the range 3182-2929 cm −1 by FTIR spectroscopy and simulated them in the range 3048-3086 cm −1 by the B3LYP/6-311++G(d, p) level of the theory. Moreover, they 38 observed in-theplane (IPB) and out-of-the-plane (OPB) HCC bending modes in the range of 1334-1012 cm −1 and 926-560 cm −1 , respectively.…”

“…Moreover, they 38 observed in-theplane (IPB) and out-of-the-plane (OPB) HCC bending modes in the range of 1334-1012 cm −1 and 926-560 cm −1 , respectively. Also, these bending modes for the imine oximes were calculated 37 in the range 1470-1040 cm −1 and 963-511 cm −1 by the B3LYP/6-311++G(d, p) level, respectively. Moreover, the symmetric CH 3 (νCH 3 ) and asymmetric CH 3 (ν as CH 3 ) stretching modes for the heterocyclic imidazole derivatives were calculated by DFT at 3031-3015 cm −1 and 2944 cm −1 and were recorded at 2895 and 2845 cm −1 in the IR spectrum, respectively.…”

A DFT Investigation on the Structure, Spectroscopy (FT‐IR and NMR), Donor‐Acceptor Interactions and Non‐Linear Optic Properties of (±)‐1,2‐Dehydroaspidospermidine

“…As it is well known, the N−C (single or double bonded) vibrational modes occur in the middle region of FT‐IR spectra and is very difficult to predict them because of the contributions by the other vibrational signals. Recently, the νN 13 C stretching band for the oxime compounds in the imine family was observed to be in the range of 1628–1599 cm −1 , and it was assigned by the same theory level as this work in the range of 1647–1540 cm −1 . According to the results of the PED analysis, the N13=C and N26‐C stretching (νN 13 C and νN 26 C) modes were calculated in the range of 1630 (63% together νCC)‐ 863 cm −1 (16%) and 1232 (15%)‐ 428 cm −1 (17%) respectively, and they were observed in 1002 cm −1 .…”

“…Recently, the νN 13 C stretching band for the oxime compounds in the imine family was observed to be in the range of 1628-1599 cm À 1 , and it was assigned by the same theory level as this work in the range of 1647-1540 cm À 1 . [42] According to the results of the PED analysis, the N13 = C and N26-C stretching (νN 13 C and νN 26 C) modes were calculated in the range of 1630 (63% together νCC)-863 cm À 1 (16%) and 1232 (15%)-428 cm À 1 (17%) respectively, and they were observed in 1002 cm À 1 . Table S3 shows that νN 13 C mode (unscaled) was simulated in the range of 1696-890 cm À 1 by M06-2X and in the range of 1584-661 cm À 1 by G96LYP, while the νN 26 C frequency was assigned in the range of 1253-442 cm À 1 by M06-2X and 1104-661 cm À 1 by G96LYP respectively.…”