Иммобилизация глюкозооксидазы на сетку одностенных углеродных нанотрубок

When elaborating the biosensor based on single-walled carbon nanotubes (SWNTs), it is necessary to solve such an important problem as the immobilization of a target biomolecule on the nanotube surface. In this work, the enzyme (glucose oxidase (GOX)) was immobilized on the surface of a nanotube network, which was created by the deposition of nanotubes from their solution in 1,2-dichlorobenzene by the spray method. 1-Pyrenebutanoic acid succinimide ester (PSE) was used to form the molecular interface, the bifunctional molecule of which provides the covalent binding with the enzyme shell, and its other part (pyrene) is adsorbed onto the nanotube surface. First, the usage of such a molecular interface leaves out the direct adsorption of the enzyme (in this case, its activity decreases) onto the nanotube surface, and, second, it ensures the enzyme localization near the nanotube. The comparison of the resonance Raman (RR) spectrum of pristine nanotubes with their spectrum in the PSE environment evidences the creation of a nanohybrid formed by an SWNT with a PSE molecule which provides the further enzyme immobilization. As the RR spectrum of an SWNT:PSE:GOX film does not essentially differ from that of SWNT:PSE ones, this indicates that the molecular interface (PSE) isolates the enzyme from nanotubes strongly enough. The efficient immobilization of GOX along the carbon nanotubes due to PSE is confirmed with atomic force microscopy images. The method of molecular dynamics allowed us to establish the structures of SWNT:PSE:GOX created in the aqueous environment and to determine the interaction energy between hybrid components. In addition, the conductivity of the SWNT network with adsorbed PSE and GOX molecules is studied. The adsorption of PSE molecules onto the SWNT network causes a decrease of the conductivity, which can be explained by the appearance of scattering centers for charge carriers on the nanotube surface, which are created by PSE moleculesПри створеннi бiологiчних сенсорiв з використанням одностiнних вуглецевих нанотрубок (ОВНТ) треба вирiшити таку важливу проблему, як iммобiлiзацiя молекули, яка повинна розпiзнати мiшень, на поверхнi нанотрубок. В данiй роботi проведена iммобiлiзацiя ферменту глюкозооксидаза (ГОК) на поверхню сiтки нанотрубок, яка була одержана шляхом осадження нанотрубок з їх розчину у дiхлорбензолi за допомогою спрей-методу. У ролi молекулярного iнтерфейсу було застосовано сукцинiмiдний ефiр 1-пiренбутанової кислоти (ПСЕ), бiфункцiональна молекула якого забезпечує хiмiчний зв’язок з оболонкою ферменту, а друга її частина (пiренова) адсорбується на поверхню нанотрубки. Використання такого молекулярного iнтерфейсу виключає, з одного боку, пряму адсорбцію ферменту на поверхню нанотрубки, яка знижує його активнiсть, а з другого, забезпечує локалiзацiю ферменту поблизу нанотрубки. Порiвняння спектрiв резонансного комбiнацiйного розсiювання свiтла (РКРС) нанотрубок з їх спектром в оточеннi ПСЕ вказує на створення наногiбриду молекулою ПСЕ з нанотрубкою, що дає пiдставу для подальшої іммобілізації ферментiв. Оскiльки спектри РКРС плiвок ОВНТ:ПСЕ:ГОК суттєво не вiдрiзняються вiд спектрiв ОВНТ:ПСЕ, то можна стверджувати, що молекулярний iнтерфейс ПСЕ достатньо мiцно iзолює фермент вiд нанотрубки. Ефективна іммобілізація ферменту ГОК поблизу вуглецевої нанотрубки завдяки ПСЕ пiдтверджується за допомогою зображень, отриманих атомно-силовим мiкроскопом. Молекулярна динамiка дозволила встановити структури отриманих нанобiогiбридiв та енергiї мiжмолекулярної взаємодiї мiж компонентами потрiйного комплексу у водному оточеннi. Було також дослiджено провiднi властивостi сiтки ОВНТ з адсорбованими молекулами ПСЕ та ГОК. Адсорбцiя молекул ПСЕ на сiтку з ОВНТ супроводжується зменшенням провiдностi, яке, скорiш за все, пов’язано з появою розсiювальних центрiв для носiїв заряду у нанотрубкахПри создании биологических сенсоров с использованием одностiнних углеродных нанотрубок (ОВНТ) нужно решить такую ​​важную проблему, как iммобiлiзацiя молекулы, которая должна распознать мишень, на поверхности нанотрубок. В данной работе проведена iммобiлiзацiя фермента глюкозооксидаза (ГОК) на поверхность сетки нанотрубок, которая была получена путем осаждения нанотрубок с их раствора в дiхлорбензолi с помощью спрей - метода. В роли молекулярного интерфейса были применены сукцинiмiдний эфир 1 - пiренбутановои кислоты (ПСЭ), бiфункцiональна молекула которого обеспечивает химический связь с оболочкой фермента, а вторая ее часть (пiренова) адсорбируется на поверхность нанотрубки. Использование такого молекулярного интерфейса исключает, с одной стороны, прямую адсорбцию фермента на поверхность нанотрубки, которая снижает его активность, а с другой, обеспечивает локализацию фермента вблизи нанотрубки. Сравнение спектров резонансного комбiнацiйного рассеяния света (РКРС) нанотрубок с их спектром в окружении ПСЭ указывает на создание наногiбриду молекулой ПСЭ с нанотрубку, что дает основание для дальнейшей иммобилизации ферментов. Поскольку спектры РКРС пленок ОВНТ:ПСЭ:ГОК существенно не отличаются от спектров ОВНТ:ПСЭ, то можно утверждать, что молекулярный интерфейс ПСЭ достаточно крепко iзолюе фермент от нанотрубки. Эффективная иммобилизация фермента ГОК вблизи углеродной нанотрубки благодаря ПСЭ подтверждается с помощью изображений, полученных атомно - силовым микроскопом. Молекулярная динамика позволила установить структуры полученных нанобiогiбридiв и энергии мiжмолекулярнои взаимодействия между компонентами тройного комплекса в водном окружении. Было также исследовано ведущие свойства сетки ОВНТ с адсорбированными молекулами ПСЭ и ГОК. Адсорбции молекул ПСЭ на сетку с ОВНТ сопровождается уменьшением проводимости, которое, скорее всего, связано с появлением розсiювальних центров для носителей заряда в нанотрубка

Quantum mechanical studies of 2D nanobiohybrids

We considered the recent application of quantum mechanical methods for studying the structure, interaction energies, as well as vibrational and electronic spectra of complexes of 2D nanomaterials (graphene, graphene oxide) with biological molecules. We analyzed how to overcome the main problems arising in computational studies of 2D nanobiohybrids, namely, the large size of systems, the nonuniformity of 2D nanomaterials, the need to use methods that can correctly take into account dispersion interactions. An analysis of the results of quantum mechanical studies, published over the recent decade, showed that the development of theoretical calculation methods and a significant increase in the productivity of computing technology made it possible to calculate not only the structure and interaction energies of nanobiosystems, but also their vibrational and electronic spectra. © 2022 Author(s).12 month embargo; published online: 12 April 2022This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Tautomers of 6-thiopurine in low-temperature Ar matrices: FTIR spectroscopy analysis and quantum mechanical calculations

The structures and vibrational spectra of 6-thiopurine (6TP) molecules in an isolated state were studied by the spectroscopic and computational methods. FTIR spectra of 6TP molecules isolated in low-temperature Ar matrices (at 11 K) were obtained in the infrared range 3800-200 cm-1. The optimized structures of tautomers, model clusters and the population of tautomers were estimated by the DFT, MP2 and CCSD(T) methods. The vibrational spectra were calculated by the DFT/B3LYP method with different basis sets [6-311++G(df,pd), aug-cc-pVDZ, aug-cc-pVTZ] and the MP2/aug-cc-pVDZ/anharmonic method. In the spectral range of 1700-200 cm-1 of the experimental FTIR spectra, five combination modes enhanced by the Fermi resonance were observed. Fermi resonances with the participation of librational modes of domestic molecules were found in the 600-500 cm-1 region. It was revealed that the incorporation of 6TP between the closest packing planes of Ar lattice leads to a significant increase in the frequency of two out-of-plane "butterfly"modes. © 2022 Author(s).12 month embargo; published online: 12 April 2022This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Coronene-uracil complexes embedded in argon matrices: FTIR spectroscopy and quantum-mechanical calculations

We employ low-temperature matrix-isolation FTIR spectroscopy and quantum chemical calculations to study the interaction between nucleobase uracil and coronene which models the graphene surface. To observe the dimer FTIR spectrum, we use a quartz microbalance that allows us to produce matrix samples with precisely determined concentrations of coronene and uracil (with the concentration ratio of 2.5:1:1000 for coronene:uracil:argon). The interaction between coronene and uracil results in spectral shifts of uracil spectral bands. These shifts do not exceed 10 cm−1. The maximum shifts are observed for the C=O stretching and NH out-of-plane vibrations of uracil. The structures and interaction energies of stacked and H-bonded coronene-uracil complexes are calculated at the DFT/B3LYP(GD3BJ)/aug-cc-pVDZ and MP2/aug-cc-pVDZ levels of theory. In total, 19 stable stacked and two H-bonded coronene-uracil dimer structures are found in the calculations. The interaction energy obtained for the most stable stacked dimer is −12.1 and −14.3 kcal/mol at the DFT and MP2 levels, respectively. The interaction energies of the H-bonded dimers do not exceed − 3 kcal/mol. The IR spectra of the studied monomeric molecules and of all the dimers are calculated at the DFT/B3LYP(GD3BJ)/aug-cc-pVDZ level of theory. The spectral shifts of the most stable stacked coronene-uracil dimer obtained in the calculations are in good agreement with the experimental results. © 2021 Author(s).12 month embargo; published online: 27 April 2021This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Missing conformers. Comparative study of conformational cooling in cyanoacetic acid and methyl cyanoacetate isolated in low temperature inert gas matrixes

A comparative conformational study of two related systems, methyl cyanoacetate (MCA) and cyanoacetic acid (CAA), is presented. Ab initio calculations predicted that both systems have two nearly isoenergetic conformers separated by similar low energy barriers (about 3 kJ mol-1). In xenon matrixes deposited at temperatures above 40 K for MCA and above 20 K for CAA only one conformer was observed for each of the two systems. However, below those temperatures two MCA and two CAA conformers were trapped into the matrixes. Conformational cooling was found responsible for this behavior. Factors contributing to this effect are discussed.http://www.sciencedirect.com/science/article/B6TFN-48TKJKM-10/1/c820c83eb483dc2d94efa8527f1cbd9

Adsorption of Polyadenylic acid on graphene oxide: experiments and computer modeling

In this work, we study the adsorption of poly(rA) on graphene oxide (GO) using AFM and UV absorption spectroscopies. A transformation of the homopolynucleotide structure on the GO surface is observed. It is found that an energetically favorable conformation of poly(rA) on GO is achieved after a considerable amount of time (days). It is revealed that GO can induce formation of self-structures of single-stranded poly(rA) including a duplex at pH 7. The phenomenon is analyzed by polymer melting measurements and observed by AFM. Details of the noncovalent interaction of poly(rA) with graphene are also investigated using molecular dynamics simulations. The adsorption of (rA)10 oligonucleotide on graphene is compared with the graphene adsorption of (rC)10. DFT calculations are used to determine equilibrium structures and the corresponding interaction energies of the adenine-GO complexes with different numbers of the oxygen-containing groups. The IR intensities and vibrational frequencies of free and adsorbed adenines on the GO surface are calculated. The obtained spectral transformations are caused by the interaction of adenine with GO

Binding of Polycitydylic Acid to Graphene Oxide: Spectroscopic Study and Computer Modeling

Hybridization of nucleic acids with graphene nanomaterials is of great interest due to its potential application in genosensing and nanomedicine. In this work we study the interaction between polyribocytidylic acid (poly(rC)) and graphene oxide (GO). The study involves comparing the UV absorption spectra of the free polymer and the polymer bonded to graphene oxide and analyzing the vibrational structure of the systems and their components using FTIR spectroscopy. Spectral shifts of the electronic and vibrational bands of the poly(rC) and changes of their thermostability due to the adsorption on GO are observed. Molecular dynamics simulation of the adsorption process of the r(C)10 and r(C)30 oligomers on graphene demonstrates their disordering due to the π-π stacking of cytosine on graphene and shows that the longer oligomer adsorbs slower. The binding energies of a single cytosine stacked with graphene in water and in vacuum were determined. The calculated IR lines of the stacked cytosine with graphene are red shifted by up to 20 cm-1 compared to free cytosine. A strong decrease of the intensities of the cytosine vibrations in the 1800-1400 cm-1 range resulting from the interaction with graphene is revealed in the spectra. When cytosine is adsorbed to graphene oxide, their complex is additionally stabilized by H-bonding. It leads to an increase of the red shifting of the cytosine lines