scholarly journals Effects of Hydroxyl Group on the Interaction of Carboxylated Flavonoid Derivatives with S. Cerevisiae α-Glucosidase

2020 ◽  
Vol 16 (1) ◽  
pp. 31-44
Author(s):  
Huining Lu ◽  
Yanjiao Qi ◽  
Yaming Zhao ◽  
Nengzhi Jin
Keyword(s):  
Hydrogen Atom ◽  
Charge Density ◽  
Density Functional ◽  
Noncovalent Interactions ◽  
Hydroxyl Group ◽  
Hydroxyl Groups ◽  
Binding Affinities ◽  
Functional Theory ◽  
Density Analysis ◽  
Hydroxyl Hydrogen

Introduction: Carboxyalkyl flavonoids derivatives are considered as effective inhibitors in reducing post-prandial hyperglycaemia. Methods: Combined with Density Functional Theory (DFT) and the theory of Atoms in Molecules (AIM), molecular docking and charge density analysis are carried out to understand the molecular flexibility, charge density distribution and the electrostatic properties of these carboxyalkyl derivatives. Results: Results show that the electron density of the chemical bond C14-O17 on B ring of molecule II increases while O17-H18 decreases at the active site, suggesting the existence of weak noncovalent interactions, most prominent of which are H-bonding and electrostatic interaction. When hydroxyl groups are introduced, the highest positive electrostatic potentials are distributed near the B ring hydroxyl hydrogen atom and the carboxyl hydrogen atom on the A ring. It was reported that quercetin has a considerably inhibitory activity to S. cerevisiae α-glucosidase, from the binding affinities, it is suggested that the position and number of hydroxyl groups on the B and C rings are also pivotal to the hypoglycemic activity when the long carboxyalkyl group is introduced into the A ring. Conclusion: It is concluded that the presence of three well-defined zones in the structure, both hydrophobicity alkyl, hydrophilicity carboxyl and hydroxyl groups are necessary.

Activation of the Hydrogen-Terminated Diamond [100] by Hydrogen Atoms and Hydroxyl Groups

2020 ◽  
Vol 996 ◽  
pp. 151-156
Author(s):  
Xiao Gang Jian ◽  
Ji Bo Hu ◽  
Xin Huang ◽  
Pei Kang Yang ◽  
Jun Peng Wang
Keyword(s):  
Hydrogen Atom ◽  
Low Temperature ◽  
Density Functional ◽  
Diamond Surface ◽  
Hydroxyl Group ◽  
Hydroxyl Groups ◽  
Hydrogen Atoms ◽  
Activation Rate ◽  
Limiting Stage ◽  
Rate Limiting

The process of producing active vacancies on a hydrogen-terminated diamond surface is the most important rate-limiting stage in CH4/H2 and CH4/H2/CO2 atmospheres. Hydrogen atom and the hydroxyl group can bone to the hydrogen atom on the diamond surface and create an active vacancy. Density functional theory (DFT) was used to study the extraction reaction by two reactants both hydrogen atom and the hydroxyl group. The result indicated that the hydroxyl group could reduce the energy required for diamond surface activation. What is more, the activation rate of the surface by the hydroxyl group was livelier at low temperature, while the activation rate of the hydrogen atom predicts on the contrary. The scanning electron microscope (SEM) and Raman spectra demonstrated that the introduction of CO2 in the CH4/H2 atmosphere could reduce the deposition temperature and raise the deposition rate at low temperature.

scholarly journals SIMULASI PERUBAHAN DENSITAS MUATAN ADSORPSI ATOM HIDROGEN-GRAFENA DENGAN TEORI FUNGSI KERAPATAN

2018 ◽  
Vol 3 (2) ◽  
pp. 179-184
Author(s):  
Albert Zicko Johannes
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Atom ◽  
Charge Density ◽  
Density Functional ◽  
Structural Changes ◽  
Density Functional Theory Method ◽  
Hexagonal Structure ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Center Position

Abstrak Peristiwa adsorpsi atom Hidrogen pada Grafena menyebabkan terjadinya perubahan struktur Grafena. Perubahan ini mempengaruhi keadaan densitas muatan Grafena. Pada simulasi ini posisi atom Hidrogen pada permukaan lembaran Grafena divariasikan, yaitu pada posisi tepat di atas atom Karbon (Top), posisi di tengah antara dua atom Karbon (Bridge), dan posisi pusat struktur heksagonal (Hollow). Simulasi dilakukan dengan metode Teori Fungsi Kerapatan dengan model Grafena ukuran 2x2. Hasil yang diperoleh menunjukkan adsorpsi atom Hidrogen memilih posisi Top sebagai yang paling stabil dibandingkan dengan posisi Bridge dan Hollow. Hasil dari posisi Top menunjukkan elektron dari atom Hidrogen digunakan mengikat Grafena dengan energi ikat sebesar -1.7 eV. Perubahan densitas muatan menunjukkan terjadinya perpindahan elektron menuju Grafena disertai transformasi isosurface yang unik untuk setiap posisi atom Hidrogen dengan perubahan terbesar terjadi pada posisi Top.  Kata kunci: Densitas muatan, Grafena, Adsorpsi, Teori Fungsi Kerapatan  Abstract [Title: The Simulation of Charge Density Diffrential for Hydrogen Atom - Graphene Adsorption with Density Functional Theory] Hydrogen atom adsorption on Graphene cause structural changes. This change affect Graphene charge density. In this simulation the position of Hydrogen atom on the surface of Graphene sheet are varied out, which is on the position directly above the Carbon atom (Top), the position on the middle between two Carbon atoms (Bridge), and the center position of the hexagonal structure (Hollow). The simulation is done by the Density Functional Theory method with a 2x2 size Graphene model. The results obtained showed that Hydrogen atom adsorption chose the Top position as the most balanced compared with the position of Bridge and Hollow. The results from the Top position indicate that electrons from Hydrogen atom are used to bind the Graphene with binding energy of -1.7 eV. The charge density differential indicate the occurrence of electron transfer towards Graphene accompanied by a transformation of the isosurface that are unique for each Hydrogen atom positions with the biggest change is shown in the Top position.  Keywords: Charge Density, Graphene, Adsorption, Density Functional Theory

scholarly journals Molecular Modeling of Ammonia Gas Adsorption onto the Kaolinite Surface with DFT Study

Minerals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 46 ◽  
Author(s):  
Qi Cheng ◽  
Yongbing Li ◽  
Xiaojuan Qiao ◽  
Yang Guo ◽  
Yang Zhao ◽  
...  
Keyword(s):  
Hydrogen Atom ◽  
Density Functional ◽  
Gas Adsorption ◽  
Hydroxyl Group ◽  
Partial Density ◽  
Hydroxyl Groups ◽  
High Porosity ◽  
Ammonia Gas ◽  
Nh3 Adsorption ◽  
Kaolinite Surface

With high porosity and being one of the most abundant clay minerals, dried kaolinite may be an excellent adsorbent to remove ammonia gas (NH3). Here, the plane wave pseudopotential method based on density functional theory (DFT) was used to explore the mechanism of ammonia gas adsorption on the dried kaolinite, the Mulliken electric charge, and the partial density of states of atoms of the NH3/kaolinite (001) system. NH3 adsorption on kaolinite can happen in three different type adsorption positions: “top”, “bridge” and “hollow”. The “hollow” position is enclosed by two "upright" hydroxyl groups perpendicular to the (001) surface of kaolinite and a "lying" hydroxyl group parallel to the surface. At this position, the adsorption is the most stable and has the highest adsorption energy. The nitrogen atom of the NH3 molecule bonds with the hydrogen atom in the "upright" hydroxyl group on the (001) surface and its hydrogen atom forms HN…O hydrogen bond with oxygen atom in the "lying" hydroxyl group, which leads to the NH3 stably adsorbed on kaolinite (001) surface. A small part of electrons transfer between NH3 molecules and kaolinite creates weakly electrostatic adsorption between them.

scholarly journals SIMULASI PERUBAHAN DENSITAS MUATAN ADSORPSI ATOM HIDROGEN-GRAFENA DENGAN TEORI FUNGSI KERAPATAN

2018 ◽  
Vol 3 (3) ◽  
pp. 179-184
Author(s):  
Albert Zicko Johannes
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Atom ◽  
Charge Density ◽  
Density Functional ◽  
Structural Changes ◽  
Density Functional Theory Method ◽  
Hexagonal Structure ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Center Position

Abstrak Peristiwa adsorpsi atom Hidrogen pada Grafena menyebabkan terjadinya perubahan struktur Grafena. Perubahan ini mempengaruhi keadaan densitas muatan Grafena. Pada simulasi ini posisi atom Hidrogen pada permukaan lembaran Grafena divariasikan, yaitu pada posisi tepat di atas atom Karbon (Top), posisi di tengah antara dua atom Karbon (Bridge), dan posisi pusat struktur heksagonal (Hollow). Simulasi dilakukan dengan metode Teori Fungsi Kerapatan dengan model Grafena ukuran 2x2. Hasil yang diperoleh menunjukkan adsorpsi atom Hidrogen memilih posisi Top sebagai yang paling stabil dibandingkan dengan posisi Bridge dan Hollow. Hasil dari posisi Top menunjukkan elektron dari atom Hidrogen digunakan mengikat Grafena dengan energi ikat sebesar -1.7 eV. Perubahan densitas muatan menunjukkan terjadinya perpindahan elektron menuju Grafena disertai transformasi isosurface yang unik untuk setiap posisi atom Hidrogen dengan perubahan terbesar terjadi pada posisi Top.  Kata kunci: Densitas muatan, Grafena, Adsorpsi, Teori Fungsi Kerapatan  Abstract [Title: The Simulation of Charge Density Diffrential for Hydrogen Atom - Graphene Adsorption with Density Functional Theory] Hydrogen atom adsorption on Graphene cause structural changes. This change affect Graphene charge density. In this simulation the position of Hydrogen atom on the surface of Graphene sheet are varied out, which is on the position directly above the Carbon atom (Top), the position on the middle between two Carbon atoms (Bridge), and the center position of the hexagonal structure (Hollow). The simulation is done by the Density Functional Theory method with a 2x2 size Graphene model. The results obtained showed that Hydrogen atom adsorption chose the Top position as the most balanced compared with the position of Bridge and Hollow. The results from the Top position indicate that electrons from Hydrogen atom are used to bind the Graphene with binding energy of -1.7 eV. The charge density differential indicate the occurrence of electron transfer towards Graphene accompanied by a transformation of the isosurface that are unique for each Hydrogen atom positions with the biggest change is shown in the Top position.  Keywords: Charge Density, Graphene, Adsorption, Density Functional Theory

scholarly journals Isolation of a Bimetallic Cobalt(III) Nitride and Examination of its Hydrogen Atom Abstraction Chemistry and Reactivity Towards H2

2020 ◽  
Author(s):  
Debabrata Sengupta ◽  
Christian Sandoval-Pauker ◽  
Emily Schueller ◽  
Angela M. Encerrado-Manriquez ◽  
Alejandro J. Metta-Magaña ◽  
...  
Keyword(s):  
Hydrogen Atom ◽  
Density Functional ◽  
Room Temperature ◽  
Hydrogen Atom Abstraction ◽  
Functional Theory ◽  
Kinetic Rate ◽  
Rate Analysis ◽  
Stable Product ◽  
Activation Pathways ◽  
Computational Analyses

Room temperature photolysis of the bis(azide)cobaltate(II) complex [Na(THF)<sub>x</sub>][(<sup>ket</sup>guan)Co(N3)2] (<sup>ket</sup>guan = [(tBu2CN)C(NDipp)2]–, Dipp = 2,6-diisopropylphenyl) (3a) in THF cleanly forms the binuclear cobalt nitride [Na(THF)4{[(<sup>ket</sup>guan)Co(N3)]2(μ-N)}]<sub>n</sub> (1). Compound 1 represents the first example of an isolable, bimetallic cobalt nitride complex, and it has been fully characterized by spectroscopic, magnetic, and computational analyses. Density functional theory supports a CoIII=N=CoIII canonical form with significant π-bonding between the cobalt centers and the nitride atom. Unlike other Group 9 bridging nitride complexes, no radical character is detected at the bridging N-atom of 1. Indeed, 1 is unreactive towards weak C-H donors and even co-crystallizes with a molecule of cyclohexadiene (CHD) in its crystallographic unit cell to give 1·CHD as a room temperature stable product. Notably, addition of pyridine to 1 or photolyzed solutions of [(<sup>ket</sup>guan)Co(N3)(py)]<sub>2</sub> (4a) leads to destabilization via activation of the nitride unit, resulting in the mixed-valent Co(II)/(III) bridged imido species [(<sup>ket</sup>guan)Co]2(μ-NH)(μ-N3) (5) formed from intermolecular hydrogen atom abstraction (HAA) of strong C-H bonds (BDE ~ 100 kcal/mol). Kinetic rate analysis of the formation of 5 in the presence of C6H12 or C6D12 gives a KIE = 2.5±0.1, supportive of a HAA formation path-way. The reactivity of our system was further probed by photolyzing C6D6/py-d5 solutions of 4a under an H2 atmosphere (150 psi), which leads to the exclusive formation of the bis(imido)[(<sup>ket</sup>guan)Co(μ-NH)]2 (6) as a result of dihydrogen activa-tion. These results provide unique insights into the chemistry and electronic structure of late 3d-metal nitrides while providing entryway into C-H activation pathways.

DENSITY FUNCTIONAL THEORY STUDY OF H2O ADSORPTION AND DISSOCIATION ON Al (111) SURFACE

2013 ◽  
Vol 12 (05) ◽  
pp. 1350035 ◽  
Author(s):  
LIXIA YANG ◽  
XIAOLI LEI ◽  
JUN FENG ◽  
YUXIN ZHANG ◽  
MINGXING LIU
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Catalytic Effect ◽  
Geometry Optimization ◽  
Vacancy Defect ◽  
Hydroxyl Group ◽  
Dissociation Pathway ◽  
Functional Theory ◽  
Lower Activation ◽  
Adsorption And Dissociation

Comparative study about the adsorption and dissociation behaviors of H2O molecule on clean and vacancy defective Al (111) surface was conducted by extensive density functional theory (DFT) calculations, the interaction mechanisms between H2O molecule and Al (111) surface were also figured out. Geometry optimization results indicated that H2O molecule was apt to be adsorbed at top site on these two kinds of surfaces, whereas, the adsorption configurations, the adsorption type and inclination of H2O molecule planes away from the normal were different. The calculated adsorption energies demonstrated that the adsorption of H2O molecule occurred more readily on vacancy defective Al (111) surface. The electron density distribution indicated that the vacancy defect enhanced the interactions between H2O molecule and surface Al atoms. Further analysis of the density of states (DOS) showed that the vacancy defect increased the number of bonding electrons between H2O molecule and surface Al atoms. The detailed exploration of dissociation pathways demonstrated that the dissociation of H2O molecule on these two kinds of surfaces was a two-step process: (1) H2O → H + OH , (2) OH → H + O . However, for each step the dissociation pathway variations on vacancy defective Al (111) surface were different with those on clean Al (111) surface. Compared with the first step, the dissociation of hydroxyl group into O atom and H atom was kinetically difficult. The calculated lower activation energy barriers on vacancy defective Al (111) surface showed that the vacancy defect had catalytic effect for the dissociation of H2O molecule to some extent, especially for the first step.

scholarly journals A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions

2017 ◽  
Vol 19 (48) ◽  
pp. 32184-32215 ◽  
Author(s):  
Lars Goerigk ◽  
Andreas Hansen ◽  
Christoph Bauer ◽  
Stephan Ehrlich ◽  
Asim Najibi ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
Density Functional ◽  
Noncovalent Interactions ◽  
Main Group ◽  
Density Functionals ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Benchmark Database ◽  
Electronic Structure Methods

We present the updated and extended GMTKN55 benchmark database for more accurate and extensive energetic evaluation of density functionals and other electronic structure methods with detailed guidelines for method users.

scholarly journals Analysis and visualization of energy densities. II. Insights from linear-response time-dependent density functional theory calculations

2020 ◽  
Vol 22 (46) ◽  
pp. 26852-26864 ◽  
Author(s):  
Zheng Pei ◽  
Junjie Yang ◽  
Jingheng Deng ◽  
Yuezhi Mao ◽  
Qin Wu ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Response Time ◽  
Linear Response ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Time Dependent ◽  
Functional Theory ◽  
Tddft Calculations ◽  
Density Analysis ◽  
Dependent Density

Inspired by the analysis of Kohn–Sham energy densities by Nakai and coworkers, we extended the energy density analysis to linear-response time-dependent density functional theory (LR-TDDFT) calculations.

scholarly journals Understanding the Lack of Reactivity of 2,4-Dihydroxybenzaldehyde Towards the Biginelli Adduct Using Density Functional Theory Molecular Modeling

Processes ◽  
2019 ◽  
Vol 7 (8) ◽  
pp. 521
Author(s):  
Virginia Flores-Morales ◽  
Eduardo D. Ayala-Medrano ◽  
José García-Elías ◽  
Margarita L. Martínez-Fierro ◽  
Edgar Marquez ◽  
...  
Keyword(s):  
Density Functional ◽  
Natural Bond Orbital ◽  
Activation Enthalpy ◽  
Computational Study ◽  
Theoretical Calculations ◽  
Condensation Reaction ◽  
Biginelli Reaction ◽  
Hydroxyl Group ◽  
Functional Theory ◽  
Multiple Substitution

The Biginelli reaction is a multicomponent reaction for obtaining dihydropyrimidinthiones quickly, with multiple substitution patterns. The reaction mechanism remains unclear. Three possible pathways proposed for the reaction are the iminium route, an enamine intermediate, and the Knoevenagel pathway. However, when thiourea was used, no theoretical calculations were reported. Thus, based on the literature, the iminium pathway was used to obtain evidence explaining the lack of reactivity of 2,4-dihydroxybenzaldehyde towards the Biginelli adduct, compared with 4-hydroxybenzaldehyde. This computational study, carried out using the B3LYP/6-31++G(d,p) level of theory, showed an increment of 150 kJ/mol in the activation energy of the slowest pathway, due to the presence of a hydroxyl group in position 2 (ortho) of the aromatic aldehyde, decreasing its reactivity. Natural bond orbital (NBO) calculations suggest that the determinant steps are simultaneous, i.e., the polarization of the carbonyl group and its corresponding protonation by the hydrogen of the SH fragment of the thiourea tautomer. The activation enthalpy values suggest that the nucleophile attack takes place later on the compound 2,4-dihydroxybenzaldehyde compared to 4-hydroxybenzaldehyde-TS, confirming that the OH group in position 2 hinders the condensation reaction.

The Theory Investigation for the Antioxidant Activity of Phloretin: A Comparation with Naringenin

2014 ◽  
Vol 513-517 ◽  
pp. 359-362
Author(s):  
Ming Xun Yan ◽  
Jin Dong Gong ◽  
Ping Shen ◽  
Chang Ying Yang
Keyword(s):  
Density Functional Theory ◽  
Antioxidant Activity ◽  
Density Functional ◽  
Radical Scavenging ◽  
Basis Set ◽  
Hydroxyl Groups ◽  
Bond Dissociation Energies ◽  
Functional Theory ◽  
Dissociation Energies ◽  
Radical Scavenging Properties

Density functional theory (DFT) calculations, based on B3LYP/6-311G (d, p) basis set, were performed to evaluate the OH bond dissociation energies (BDEs) for phloretin, compared with naringenin, in order to assess the contribution of hydroxyl groups at different position to the radical-scavenging properties. It is indicated clearly that A6 OH is determined as the weakest O-H bond, give rise to the smallest BDE, 73.98 kcal/mol. BDE of B4 OH decreases 2.5 kcal/mol in benzene, very close to that of A6OH, indicated that B4 OH group is also mainly contributed to the reaction with free radicals, especially in non-polar environments.

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