Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations.

This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years. We first explain advantages and limitations of modern QM calculations of nucleobases and provide a brief history of this still rather new field. Then we provide an overview of key electronic properties of standard and selected modified nucleobases, such as their charge distributions, dipole moments, polarizabilities, proton affinities, tautomeric equilibria, and amino group hybridization. Then we continue with hydrogen bonding of nucleobases, by analyzing energetics of standard base pairs, mismatched base pairs, thio-base pairs, and others. After this, the nature of aromatic stacking interactions is explained. Also, nonclassical interactions in nucleic acids such as interstrand bifurcated hydrogen bonds, interstrand close amino group contacts, C—H … O interbase contacts, sugar–base stacking, intrinsically nonplanar base pairs, out-of-plane hydrogen bonds, and amino–acceptor interactions are commented on. Finally, we overview recent calculations on interactions between nucleic acid bases and metal cations. These studies deal with effects of cation binding on the strength of base pairs, analysis of specific differences among cations, such as the difference between zinc and magnesium, the influence of metalation on protonation and tautomeric equlibria of bases, and cation–π interactions involving nucleobases. In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed. © 2002 Wiley Periodicals, Inc. Biopoly (Nucleic Acid Sci) 61: 3–31, 2002; DOI 10.1002/bip.10048

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases.

Tautomeric equilibria in relation to pi-electron delocalization.

A comparison of the binding of DNA bases (adenine, cytosine, guanine, and thymine) and nucleosides (2‘deoxyadenosine, 2‘deoxycytidine, 2‘deoxyguanosine, and thymidine) to gold thin films is presented. Desorption of monolayer/submonolayer and multilayer films of the adsorbates on gold studied via temperature-programmed desorption (TPD) and reflection−absorption infrared (RAIR) spectroscopy reveals that there are major differences in the binding affinities of the different bases to gold, for example, thymine ΔHdes = 111 ± 2 kJ/mol compared to guanine ΔHdes = 146 ± 2 kJ/mol. The differences can be rationalized by molecular structures of the bases and their binding modes to gold surfaces deduced from IR data. Similar trends in desorption energies, shifted to lower desorption energy by more than 10 kJ/mol, are observed for deoxynucleoside layers on gold thin films.

Thermal Desorption Behavior and Binding Properties of DNA Bases and Nucleosides on Gold

The surface-enhanced Raman spectra (SERS) of adenine and three deuterated analogues adsorbed on colloids, electrochemically roughened electrodes, and vacuum deposited island films of silver have been investigated. All normal Raman and SERS bands were assigned to normal modes on the basis of density functional theory (DFT) calculations (B3LYP/6-31++G(d,p)) and isotope shifts. Surface selection rules derived from the electromagnetic enhancement model were employed to deduce adenine orientations on the different surfaces. On the colloids, adenine adopts an almost perpendicular orientation interacting with the metal surface via N7 and the exocyclic amino group. On the electrodes, adenine adsorbs in a more tilted orientation while on the island films the tilt is even more pronounced. Interaction with the electrodes takes place through N7 and the amino group, while interaction with the island film may be solely through N7.

Surface-Enhanced Raman Spectroscopic and Density Functional Theory Study of Adenine Adsorption to Silver Surfaces

The infrared spectra of matrix-isolated adenine and its 15N isotopomers with 15N at the N(9) or N(7) positions have been studied. The experimentally observed IR spectra were compared with the spectra predicted at the DFT(B3-LYP)/6-31G(d,p) level. This method was also used to calculate molecular parameters (rotational constants, dipole moments) of both N(9)H and N(7)H tautomers of adenine. The agreement between experimental and theoretical spectral positions, intensities, and isotopic shifts of the IR bands is good. That allows for reliable assignment of the IR spectra and for conclusion that the amino-N(9)H tautomer of adenine strongly dominates in low-temperature matrices.

Molecular Structure and Infrared Spectra of Adenine. Experimental Matrix Isolation and Density Functional Theory Study of Adenine 15N Isotopomers

Abstract The COVID-19 pandemic has attracted numerous research studies because of its impact on society and the economy. The pandemic has led to progress in the development of diagnostic methods, utilizing the polymerase chain reaction (PCR) as the gold standard for coronavirus SARS-CoV-2 detection. Numerous tests can be used at home within 15 min or so but of with lower accuracy than PCR. There is still a need for point-of-care tests available for mass daily screening of large crowds in airports, schools, and stadiums. The same problem exists with fast and continuous monitoring of patients during their medical treatment. The rapid methods can use exhaled breath analysis which is non-invasive and delivers the result quite fast. Electronic nose can detect a cocktail of volatile organic com-pounds (VOCs) induced by virus infection and disturbed metabolism in the human body. In our exploratory studies, we present the results of COVID-19 detection in a local hospital by applying the developed electronic setup utilising commercial VOC gas sensors. We consider the technical problems noticed during the reported studies and affecting the detection results. We believe that our studies help to advance the proposed technique to limit the spread of COVID-19 and similar viral infections. 

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Clinical studies of detecting COVID-19 from exhaled breath with electronic nose

The gas sensing properties of graphene back-gated field-effect transistor (GFET) sensors toward acetonitrile, tetrahydrofuran, and chloroform vapors were investigated with the focus on unfolding possible gas detection mechanisms. The FET configuration of the sensor device enabled gate voltage tuning for enhanced measurements of changes in DC electrical characteristics. Electrical measurements were combined with a fluctuation-enhanced sensing methodology and intermittent UV irradiation. Distinctly different features in 1/f noise spectra for the organic gases measured under UV irradiation and in the dark were observed. The most intense response observed for tetrahydrofuran prompted the decomposition of the DC characteristic, revealing the photoconductive and photogating effect occurring in the graphene channel with the dominance of the latter. Our observations shed light on understanding surface processes at the interface between graphene and volatile organic compounds for graphene-based sensors in ambient conditions that yield enhanced sensitivity and selectivity.

and Józef S. Kwiatkowski

Papers

Molecular Structure and Infrared Spectra of Adenine. Experimental Matrix Isolation and Density Functional Theory Study of Adenine 15N Isotopomers

Clinical studies of detecting COVID-19 from exhaled breath with electronic nose

Organic Vapor Sensing Mechanisms by Large-Area Graphene Back-Gated Field-Effect Transistors under UV Irradiation

The effects of gas exposure on the Graphene/AlGaN/GaN heterostructure under UV irradiation

Heterostructure of Graphene/Algan/Gan for Stable Gas Sensing