Interaction of N-acetylneuraminic acid with surface silicon in aqueous solution with carbohydrates

The aim of the work is to study interaction of N-acetylneuraminic acid (NANA) with the surface of ultrafine silica (UFS) with the participation of glucose and sucrose in aqueous solution at the supramolecular level by density functional theory method (exchange-correlation functional B3LYP, basis set of 6-31G (d, p). The adsorption of N-acetylneuraminic acid, as well as individual carbohydrates (glucose and sucrose) on the hydrated surface of UFS in aqueous solution, was considered as a process of replacement of water molecules on the surface of silica by adsorbate molecules. This work considers two schemes of carbohydrate molecule influence on adsorption of N-acetylneuraminic acid. According to the first scheme the interaction of the NANA molecule occurs with the silica-monosaccharide complex, according to the second scheme, the silica cluster interacts with the NANA-monosaccharide complex, where silica binds to the complex through the carbohydrate molecule. The analysis of the calculated geometric and energy characteristics show that adsorption on the surface of silica, with hydration taken into account, is thermodynamically probable for the sucrose. The glucose molecule has a positive value (+9.8 and +2.7 kJ / mol) is an unfavorable process in terms of thermodynamics regardless of the hydrating water cluster size. The N-acetylneuraminic acid molecule has a value of -1.3 kJ / mol for the reaction with five water molecules and +0.9 kJ / mol with eight water molecules. It was found that the presence of sucrose on the silica surface in the aqueous solution weakens the hydration energy (i.e. it is easier to replace the cluster of water with the N-acetylneuraminic acid molecule from the surface of the modified adsorbent), which in turn promotes NANA adsorption on the silica surface. Therefore, scheme 1 is thermodynamically more likely than scheme 2. This indicates that there is a mutual influence of substances in a mixture of NANA with carbohydrates on the interaction with silica in comparison with the interaction of substances with silica alone.

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A quantum chemistry study on the interaction between silica surface and aqueous alkaline solutions

Фізика і хімія твердого тіла ◽

10.15330/pcss.19.1.74-78 ◽

2018 ◽

Vol 19 (1) ◽

pp. 74-78

Author(s):

A. A. Kravchenko ◽

E. M. Demianenko ◽

A. G. Grebenyuk ◽

V. V. Lobanov

Keyword(s):

Density Functional ◽

Silica Surface ◽

Density Functional Theory Method ◽

Equilibrium Structure ◽

Basis Set ◽

Alkaline Solutions ◽

Quantum Chemical Analysis ◽

Functional Theory ◽

Exchange Correlation ◽

Extended Basis

A quantum chemical analysis has been carried out of the equilibrium structure and energy parameters of hydrated Li+, Na+, and K+ cations interacting with ionized silica surface by means of density functional theory method with extended basis set 6-31++G(d,p) and exchange-correlation functional B3LYP. The calculated adsorption energy values related to those cations reproduce the experimental adsorption row of alkali metal cations at pH = 10.

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Supramolecular Complexes of Cucurbiturils with Second Group Metal Salts and Hydrates and Histamine

INEOS OPEN ◽

10.32931/io2109a ◽

2021 ◽

Vol 4 ◽

Author(s):

Yu. A. Borisov ◽

◽

S. S. Kiselev ◽

Keyword(s):

Aqueous Solution ◽

Density Functional Theory ◽

Density Functional ◽

Metal Salts ◽

Supramolecular Complexes ◽

Water Molecules ◽

Functional Theory ◽

Guest Molecules ◽

First Time ◽

Formation Energies

The interaction of cucurbiturils (Q6, Q7, and Q8) with Ca and Ba chlorides and iodides are studied for the first time by density functional theory. The thermodynamic parameters for the formation of host–guest complexes are calculated. The structures of complexes of Q6 and Q7 with one and two guest molecules are established. The energy parameters for the transfer of Be2+ and Ba2+ cations from an aqueous solution into the cavity of Q7 containing n water molecules are defined. The dependences of the formation energies for complexes Q7WnBe2+ and Q7WnBa2+ on the number of water molecules are shown to be parabolic, with the energy minima at n = 5 and n = 6, respectively. It is found that Q7 can form in an aqueous solution supramolecular complexes with protonated histamine (HA) and neutral histamine in the presence of Ca2+ ions.

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Computational Evidence Suggests That 1-chloroethanol May Be an Intermediate in the Thermal Decomposition of 2-chloroethanol into Acetaldehyde and HCl

10.26434/chemrxiv.7608857.v1 ◽

2019 ◽

Author(s):

Zoi Salta ◽

Agnie M. Kosmas ◽

Oscar Ventura ◽

Vincenzo Barone

Keyword(s):

Aqueous Solution ◽

Water Molecule ◽

Gas Phase ◽

Density Functional ◽

Water Molecules ◽

Functional Theory ◽

Direct Transformation ◽

The Density Functional Theory ◽

Successive Step ◽

The One

The dehalogenation of 2-chloroethanol (2ClEtOH) in gas phase with and without participation of catalytic water molecules has been investigated using methods rooted into the density functional theory. The well-known HCl elimination leading to vinyl alcohol (VA) was compared to the alternative elimination route towards oxirane and shown to be kinetically and thermodynamically more favorable. However, the isomerization of VA to acetaldehyde in the gas phase, in the absence of water, was shown to be kinetically and thermodynamically less favorable than the recombination of VA and HCl to form the isomeric 1-chloroethanol (1ClEtOH) species. This species is more stable than 2ClEtOH by about 6 kcal mol-1, and the reaction barrier is 22 kcal mol-1 vs 55 kcal mol-1 for the direct transformation of VA to acetaldehyde. In a successive step, 1ClEtOH can decompose directly to acetaldehyde and HCl with a lower barrier (29 kcal mol-1) than that of VA to the same products (55 kcal mol-1). The calculations were repeated using a single ancillary water molecule (W) in the complexes 2ClEtOH_W and 1ClEtOH_W. The latter adduct is now more stable than 2ClEtOH_W by about 8 kcal mol-1, implying that the water molecule increased the already higher stability of 1ClEtOH in the gas phase. However, this catalytic water molecule lowers dramatically the barrier for the interconversion of VA to acetaldehyde (from 55 to 6 kcal mol-1). This barrier is now smaller than the one for the conversion to 1ClEtOH (which also decreases, but not so much, from 22 to 12 kcal mol-1). Thus, it is concluded that while 1ClEtOH may be a plausible intermediate in the gas phase dehalogenation of 2ClEtOH, it is unlikely that it plays a major role in water complexes (or, by inference, aqueous solution). It is also shown that neither in the gas phase nor in the cluster with one water molecule, the oxirane path is competitive with the VA alcohol path.

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Density Functional Theory Based Modeling of the Corrosion on Iron Surfaces

Archives of Metallurgy and Materials ◽

10.2478/v10172-012-0190-5 ◽

2013 ◽

Vol 58 (2) ◽

pp. 321-323 ◽

Cited By ~ 3

Author(s):

N. Nunomura ◽

S. Sunada

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Atomic Orbital ◽

Atomic Layer ◽

Iron Surface ◽

Basis Set ◽

Water Molecules ◽

Aqueous Corrosion ◽

Functional Theory ◽

Adsorption Of Water

In order to understand the first steps of the aqueous corrosion of iron, we have performed density functional theory (DFT) based calculations for water molecules and pre-covered oxygen on iron surface. The surface structure is modeled by iron atomic layer and vacuum region, and then oxygen atom and water molecules are displaced on the surface. Self consistent DFT calculations were performed using a numerical atomic orbital basis set and a norm-conserve pseudopotential method. According to our calculations, with increasing surface oxygen coverage, the iron surface is found to be not activated, which leads to a feeble adsorption of water molecules on iron surface. Our results show that the surface covered oxygen exerts an influence on the adsorption of water molecules on iron surface.

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Vibrational spectroscopic and conformational studies of 1-(4-pyridyl)piperazine

Chemical Papers ◽

10.2478/s11696-010-0021-y ◽

2010 ◽

Vol 64 (4) ◽

Cited By ~ 1

Author(s):

Özgür Alver ◽

Mustafa Şenyel

Keyword(s):

Density Functional ◽

Structural Parameters ◽

Density Functional Theory Method ◽

Basis Set ◽

Stable Form ◽

Functional Theory ◽

B3lyp Method ◽

Ft Ir ◽

Hybrid Density Functional ◽

Ir And Raman

AbstractPossible stable conformers of the 1-(4-pyridyl)piperazine (1-4pypp) molecule were experimentally and theoretically studied by FT-IR and Raman spectroscopy. FT-IR and Raman spectra were recorded in the region of 4000–200 cm−1. Optimized geometric structures related to the minimum on the potential energy surface were investigated by the B3LYP hybrid density functional theory method using the 6-31G(d) basis set. Comparison of the experimental and theoretical results indicates that the density functional B3LYP method provides satisfactory results for the prediction of vibrational wavenumbers and structural parameters and equatorial-equatorial (e-e) isomer is supposed to be the most stable form of the 1–4pypp molecule.

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Analysis of the interaction between N-acetylneuraminic acid and disaccharides on silica surface

Himia Fizika ta Tehnologia Poverhni ◽

10.15407/hftp11.04.516 ◽

2020 ◽

Vol 11 (4) ◽

pp. 516-527 ◽

Cited By ~ 1

Author(s):

L. M. Ushakova ◽

◽

E. M. Demianenko ◽

M. I. Terets ◽

V. V. Lobanov ◽

...

Keyword(s):

Quantum Chemical ◽

Silica Surface ◽

Mutual Influence ◽

Molecular Form ◽

Intermolecular Complex ◽

Chemical Modeling ◽

Oh Groups ◽

Gas Phases ◽

Acetylneuraminic Acid ◽

Similar Complex

Nanocomposites based on biomolecules and highly dispersed silica are quite promising for use in many fields of biotechnology. There are many methods of obtaining such materials, in particular, adsorption from liquid or gas phases. Saccharides and their derivatives are present in the human body, they are involved in metabolic process, thus it is reasonable to use them while working with biomolecules. The work considers such disaccharides as sucrose, lactose and N-acetylneuraminic acid (NANA). Being a part of glycoproteins and glycolipids, NANA is also considered to be a carbohydrate. The main objective of the study was to study the ways of interaction of NANA on the disaccharide-modified silica surface. The methods of quantum chemistry have been used to find the probable structures of three-component adsorbtion complexes at molecular level and to clarify the mutual influence of these compounds in adsorbtion process. An analysis of the results of quantum chemical calculations shows that the adsorption of an anion of N-acetylneuraminic acid on silica surface is less likely than in its molecular form. Molecules of N-acetylneuraminic acid, disaccharides and silica form intermolecular complexes due to intermolecular hydrogen bonds between polar functional (mainly –OH) groups of the analytes. The sucrose dimer is 85.4 kJ/mol stronger than the lactose one. The sucrose molecule also forms a 38.1 kJ/mol stronger intermolecular complex with the N-acetylneuraminic acid molecule compared to a similar complex where lactose is used as a disaccharide. The highest energy (245.2 kJ/mol) is released when a silica cluster interacts with the intermolecular complex of N-acetylneuraminic acid and sucrose provided silica and the sucrose molecule are in a direct contact with each other. Therefore, as studies have shown, the adsorption of N-acetylneuraminic acid is possible if silica surface is pre-modified with disaccharides. The results of quantum chemical modeling confirm the obtained experimental data.

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Microwave synthesis of some N-phenylhydrazine-1-carbothioamide Schiff bases

European Journal of Chemistry ◽

10.5155/eurjchem.9.2.74-78.1673 ◽

2018 ◽

Vol 9 (2) ◽

pp. 74-78 ◽

Cited By ~ 2

Author(s):

Bushra Kamil Al-Salami

Keyword(s):

1H Nmr ◽

Density Functional ◽

Atomic Orbital ◽

Calculated Data ◽

Density Functional Theory Method ◽

13C Nmr Spectroscopy ◽

Basis Set ◽

Functional Theory ◽

B3lyp Method ◽

Ft Ir

We have synthesized and characterized a series of carbothioamide derivatived molecules, obtained by reaction of aromatic aldehyde (Anisaldehyde, 9-anthraldehyde, cinnamaldehyde, indole-3-carboxaldehyde, 1-naphthaldehyde and o-vanillin) with an equimolar amount of 4-phenylthiosemicarbazide with microwave irradiation. The synthesized compounds have been characterized by FT-IR, 1H NMR and 13C NMR spectroscopy. Quantum calculations of the physical properties, based on density functional theory method at B3LYP/6-31+G(d,p) level of theory, were performed, by means of the Gaussian 09W set of programs. The theoretical 1H NMR chemical shift results of the studied compounds have been calculated at B3LYP method and standard 6-31+G(d,p) basis set using the standard Gauge-Independent Atomic Orbital approach. The calculated values are also compared with the experimental data available for these molecules. A good linear relationship between the experimental and calculated data has been obtained.

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Proton transfer in the benzimidazolone and benzimidazolthione tautomerism process catalyzed by polar protic solvents

Progress in Reaction Kinetics and Mechanism ◽

10.1177/1468678319825740 ◽

2019 ◽

Vol 44 (2) ◽

pp. 143-156 ◽

Cited By ~ 1

Author(s):

Hasnia Abdeldjebar ◽

Yamina Belmiloud ◽

Wassila Djitli ◽

Sofien Achour ◽

Meziane Brahimi ◽

...

Keyword(s):

Proton Transfer ◽

Density Functional ◽

Activation Barrier ◽

Solvent Molecule ◽

Density Functional Theory Method ◽

Polarizable Continuum Model ◽

Tautomeric Equilibrium ◽

Basis Set ◽

Stable Forms ◽

Intramolecular Transfer

The tautomeric equilibrium of benzimidazolone and benzimidazolthione have been studied by the density functional theory method using the CAM-B3LYP functional together with the 6-311G(d,p) basis set. Two separate mechanisms have been investigated: a direct intramolecular transfer using the polarizable continuum model and an indirect proton transfer assisted by a molecule of solvent (C6H12, H2O, CH3OH, and H2O2). In both cases, the results obtained indicate that ketone and thione are the most stable forms. However, the enhanced height of the activation barrier for the four-center mechanisms describing the tautomerism reaction as a direct intramolecular transfer implicates a relatively disadvantaged process. The participation of a polar protic solvent molecule allows the lowering of the activation energy barrier. Potential energy profiles of keto-enol and thio-enol tautomerism assisted by methanol and water are very different. The former one describes a concerted mechanism but the latter does not because it is associated with asynchronous processes that take place during the thio-enol tautomerism.

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Experimental FTIR and theoretical investigation of the molecular structure and vibrational spectra of acetanilide using DFT and dispersion correction to DFT

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633619500093 ◽

2019 ◽

Vol 18 (02) ◽

pp. 1950009 ◽

Cited By ~ 2

Author(s):

Yunusa Umar ◽

Nedal Abu-Thabit ◽

Paul Jerabek ◽

Ponnadurai Ramasami

Keyword(s):

Vibrational Spectra ◽

Density Functional ◽

Decomposition Analysis ◽

Density Functional Theory Method ◽

Molecular Structures ◽

Basis Set ◽

Potential Energy Distribution ◽

Energy Decomposition Analysis ◽

Dispersion Correction ◽

Vibrational Assignments

The FTIR spectrum of acetanilide (ACN) is recorded and analyzed. The optimized molecular structures, harmonic vibrational wavenumbers and corresponding vibrational assignments of the ACN are computationally examined by using the B3LYP density functional theory method together with the standard 6-311[Formula: see text]G([Formula: see text],[Formula: see text]) basis set. From the calculations, the ACN is predicted to exist predominantly in trans configuration with the relative energy, rotational barrier, and population of 2.8[Formula: see text]kcal/mol, 14.8[Formula: see text]kcal/mol, and 99.5%, respectively. The optimized structure shows that the amide group (CO–NH) of trans-ACN adopts a planar peptide-like conformation. The effect of the incorporation of dispersion correction to the B3LYP on the calculated equilibrium structure and vibrational spectra of ACN is investigated. The highest occupied and the lowest unoccupied molecular orbitals, IR intensities and molecular electrostatic potential results are reported. In addition, reliable vibrational assignments have been made on the basis of Potential Energy Distribution (PED) using VEDA4 program. Simulated IR spectrum are compared with the experimental FTIR and FT-Raman spectra. Energy decomposition analysis (EDA) revealed that Pauli repulsion is responsible for the increased stability of the trans over the cis isomer.

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Quantum chemical study on the atmospheric photooxidation of ethyl acetate

Canadian Journal of Chemistry ◽

10.1139/cjc-2014-0199 ◽

2014 ◽

Vol 92 (9) ◽

pp. 814-820 ◽

Cited By ~ 1

Author(s):

Yan Zhao ◽

Xiaomin Sun ◽

Wenxing Wang ◽

Laixiang Xu

Keyword(s):

Acetic Anhydride ◽

Ethyl Acetate ◽

Density Functional ◽

Single Point ◽

Quantum Chemical Study ◽

Density Functional Theory Method ◽

Basis Set ◽

Oh Radicals ◽

Point Energy ◽

Rearrangement Reaction

The mechanism for OH radical initiated atmospheric photoxidation reaction of ethyl acetate was carried out by using the density functional theory method. Geometries have been optimized at the B3LYP level with a standard 6-31G(d,p) basis set. The single-point energy calculations have been performed at the MP2/6-31G(d), MP2/6-311++G(d,p), and CCSD(T)/6-31G(d) levels, respectively. All of the possible degradation channels involved in the oxidation of ethyl acetate by OH radicals have been presented and discussed. Among the five possible hydrogen abstraction pathways of the reaction of ethyl acetate with OH radicals, the hydrogen abstractions from the C1–H3 and C2–H5 bonds are the dominant reaction pathways due to the low potential barriers and strong exothermicity. The β-ester rearrangement of IM6 is energetically favorable but is not expected to be important. The α-ester rearrangement reaction and O2 direct abstraction from IM17 are the more favorable pathways and are strongly competitive. In addition, the α-ester rearrangement reaction is confirmed to be a one-step process. Acetic acid, formic acetic anhydride, acetoxyacetaldehyde, and acetic anhydride are the main products for the reaction of ethyl acetate with OH radicals.

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