• Bulletin of the Korean Chemical Society
• /
• 제31권12호
• /
• pp.3644-3652
• /
• 2010

The metallo-$\beta$-lactamases ($M{\beta}Ls$) are clinically significant enzymes which readily hydrolyze most $\beta$-lactam antibiotics. Discovering potential inhibitors for the $M{\beta}Ls$ is an expensive, time consuming endeavor. Virtual screening can sieve out inhibitor candidates with incompatible features prior to synthesis, decreasing these costs. Using Autodock 4.0, the binding locations and energies of four previously-studied potential inhibitors and four additional compounds obtained from the National Cancer Institute (NCI) database were computationally calculated. Based on the docking models of these eight compounds, we then designed several hypothetical inhibitor structures, compounds A through F, and performed their respective docking experiments. The docking results for compound F showed that it binds to the zinc containing active sites with a lowest predicted binding energy of -6.70 kcal/mol, suggesting F is the most likely potential $M{\beta}L$ inhibitor.

• Bulletin of the Korean Chemical Society
• /
• 제27권11호
• /
• pp.1851-1853
• /
• 2006

We herein report a new analytical application of XPS to the identification of organic molecules in room temperature ionic liquid for the first time. An organic compound, propargylamine (1), produced in 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][$PF_6$]), which is one of the room temperature ionic liquids (RTILs), via $A^3$ coupling reaction, is characterized by means of x-ray photoelectron spectroscopy (XPS) rather than using conventional organic compound analysis techniques. There are four non-equivalent carbons in RTILs and 1 each. The ratios of normalized integrated areas of the deconvoluted binding energy of core electron of carbon (C1s) peaks are well matched to the number of carbons in those compounds. The binding energies of C1s of the featured carbons in 1, C4 (sp carbons in acetylene group) and C5 ($sp^2$ carbons in benzene ring), are assigned 286.2 and 285.4 eV, respectively. These results will be able to provide an important tool and a new strategy for the analysis of organic molecules

• Bulletin of the Korean Chemical Society
• /
• 제15권7호
• /
• pp.581-584
• /
• 1994

A comparative investigation of the complexations of divalent metal ions (Cd, Cu, and Pb) by a well characterized soil humic acid (HA) from Okchun Metamorphic Belt was carried out in 0.05 M $KNO_3$ and pH of 4.5 using ion selective electrodes. A continuous distribution model based on the Scatchard Plot was used to determine the stability constants, because the constants obtained by this modeling technique takes the variations in binding energies into consideration without regards to the manner in which M(II) ion is bound on HA. The mean value of log $K_i$ were $4.05{\pm}0.60,\;4.92{\pm}0.36,\;and\;5.63{\pm}0.34\;{\ell}\;mol^{-1}$ for Cd(II)-, Pb(II), and Cu(II)-humate complexes respectively. The values of intrinsic constant (log $K_{int}$; binding at strongest site) were $7.12{\pm}0.30,\;6.59{\pm}0.32,\;and5.07{\pm}0.56\;{\ell}\; mol^{-1}$ in the order Cu(II) > Pb(II) > Cd(II) ion.

• Biomolecules & Therapeutics
• /
• 제32권3호
• /
• pp.390-398
• /
• 2024

FoxO1, a member of the Forkhead transcription factor family subgroup O (FoxO), is expressed in a range of cell types and is crucial for various pathophysiological processes, such as apoptosis and inflammation. While FoxO1's roles in multiple diseases have been recognized, the target has remained largely unexplored due to the absence of cost-effective and efficient inhibitors. Therefore, there is a need for natural FoxO1 inhibitors with minimal adverse effects. In this study, docking, MMGBSA, and ADMET analyses were performed to identify natural compounds that exhibit strong binding affinity to FoxO1. The top candidates were then subjected to molecular dynamics (MD) simulations. A natural product library was screened for interaction with FoxO1 (PDB ID-3CO6) using the Glide module of the Schrödinger suite. In silico ADMET profiling was conducted using SwissADME and pkCSM web servers. Binding free energies of the selected compounds were assessed with the Prime-MMGBSA module, while the dynamics of the top hits were analyzed using the Desmond module of the Schrödinger suite. Several natural products demonstrated high docking scores with FoxO1, indicating their potential as FoxO1 inhibitors. Specifically, the docking scores of neochlorogenic acid and fraxin were both below -6.0. These compounds also exhibit favorable drug-like properties, and a 25 ns MD study revealed a stable interaction between fraxin and FoxO1. Our findings highlight the potential of various natural products, particularly fraxin, as effective FoxO1 inhibitors with strong binding affinity, dynamic stability, and suitable ADMET profiles.

• Bulletin of the Korean Chemical Society
• /
• 제33권5호
• /
• pp.1719-1721
• /
• 2012

We have investigated the $H_2$ adsorption structures and binding energies of the metal (M)-doped (M = Li, Na, K, Mg, and Al) silicon complexes, $M-Si_{19}H_{11}$ and $M-Si_{24}H_{12}$, using density functional calculations. Alkali metals are preferred as doping elements because the Mg-Si and Al-$H_2$ interactions are weak. The maximum numbers of $H_2$ molecules that can be adsorbed are four and five for M=Li and K, respectively. We propose that the K-decorated silicon material might be an effective hydrogen storage material with high hydrogen capacity and high reversibility.

• Bulletin of the Korean Chemical Society
• /
• 제35권9호
• /
• pp.2738-2742
• /
• 2014

Geometry relaxation effects on the formation of benzene excimer were investigated by means of ab initio calculation at SOS-CIS($D_0$)/aug-cc-pVDZ level. In the case of T-shaped dimer configuration, intermolecular interactions in the excited states are found to be nearly the same as those in the ground state and structural deformations are limited within a single molecule; the geometry relaxation effects are then negligible and singlet-triplet energy gap remains constant. As for face-to-face eclipsed dimer, on the other hand, both molecules undergo structural change. As a result, intermolecular interactions in the excited states are significantly different than those in the ground state. Although the intermolecular distances obtained from potential energy curve calculation with frozen molecular structures are in qualitative agreement, the excited-state binding energies are notably overestimated with respect to those at optimized structures. In particular, the effects are calculated to be larger in $T_1$ state and hence singlet-triplet energy gap, which reduces markedly in this configuration, is underestimated without relaxation.

• 한국전기화학회:학술대회논문집
• /
• 한국전기화학회 2002년도 연료전지심포지움 2002논문집
• /
• pp.179-182
• /
• 2002

The electrooxidation of methanol was studied using Pt, PtRu(1:1), PtNi(1:1), PtRh(1:1) and PtOs(1:1) alloy nanoparticles for application as electrocatalysts. The effects of the second metals in the electrocatalytic activity was investigated using cyclic voltammetry (CV), chronoamperometry (CA), X-ray photoelectron spectroscopy (XPS). There are the metallic and oxygen states in the PtRu and PtOs electrocatalysts . In the XPS of PtRu and PtOs alloy nanoparticles, the oxygen sources were dominant as the second metal's effects. Negative shifts of the binding energies of Pt for the PtNi, PtRh alloy nanoparticles were determined by XPS measurements, which can be explained by electronic effects.

• 대한화학회지
• /
• 제44권3호
• /
• pp.190-193
• /
• 2000

M-Rg 및 M-Rg2 (M=Li,Na,Rg=He,Ar) 반데르발스 복합체들에 대한양자화학적계산을 시행하였다. AIl-electron MP2(6-311++G(3df,3pd))에 의하여 계산된 LiHe, LiAr 및 NaAr의 균형 핵간 거리와 결합 에너지는 실험값과 잘 일치하였다. $LiHe_2,\;LiAr_2$ 및 $NaAr_2$에 대하여 계산된 분광학적 성질들도 또한 계산하였다.

• Journal of Korean Vacuum Science & Technology
• /
• 제6권4호
• /
• pp.153-157
• /
• 2002

The electronic structures of Gd$_{5}$Si$_2$Ge$_2$ compound, which has a giant magnetocaloric effect, in the monoclinic and orthorhombic phases were calculated using the tight-binding linear-muffin-tin-orbital method within the atomic-sphere approximation. The calculated total energies of the monoclinic and orthorhombic structures in the paramagnetic phase confirm that the orthorhombic structure is more stable than monoclinic structure. The density of states (DOS) at the Fermi level of the orthorhombic phase is higher than that of the monoclinic phase in the paramagnetic phase, fulfilling the Stoner criterion. The calculated charge density verified the breaking of Ge(Si)-Ge(Si) bonding in the basal plane upon the orthorhombic-monoclinic phase transition. The DOS curve fairly well reproduces the photoemission spectrum.m.

• 대한화학회지
• /
• 제15권6호
• /
• pp.352-358
• /
• 1971

열가지 유기물질, 즉 니트로벤젠, m-디니트로벤젠, o-디니트로벤젠 1,3,5-트리니트로벤젠, m-크실렌, 메시틸렌, 비벤질, 비페닐, o-페난트린, 및 나프탈린등과 dimethylsulfoxide사이의 상호작용을 검토했다. 이 유기분자들은 모두 라울의 법칙에서 음의 편차를 나타내며, 전하전이착물을 형성한다고 생각된다. 그 착물의 안정도상수를 분광광도법으로 측정하고, 몇가지 열력학함수를 계산했으며 결합에너지가 대개 -1∼-4 kcal/몰임을 알았다. 한편 용매의 영향을 검토하여 착물의 안정도가 용매의 극성은 물론 염기도에 크게 의존함을 알았다.