Changes in vibrational spectra are among the most important manifestations of the interaction between transition metal dichalcogenides and nucleic acid bases (NAB). Infrared and Raman spectra were calculated using the DFT/M06-2X method for the most stable stacked and covalently bonded complexes of pyrimidine bases with MoS2. Obtained spectra were analyzed to determine the spectral markers of the interactions between the pyrimidine bases and MoS2. We found that interaction with MoS2 leads to significant changes in both frequencies and intensities of NAB vibrations. The correlation between the changes and interaction energies of the NAB molecules with MoS2 was demonstrated. In general, changes in the vibrational frequencies in complexes with covalent bonds are significantly greater than ones in stacked ones. For the bonded complexes, the most significant changes are observed for those fragments of the NAB molecules that are directly involved in the formation of the covalent bonds. Calculations predict the decrease of the IR intensity and Raman activities of the NAB molecules in the spectra of stacked complexes and their increase in the spectra of covalently bonded complexes.

In recent years, the use of biomolecules as dispersants for the preparation of 2D nanomaterials by direct liquid-phase exfoliation (LPE) using ultrasonication has attracted increasing attention as a convenient and cost-effective approach to ensure simultaneously the biocompatibility of these nanostructures. In this work, we prepare MoS2 quantum dots (QDs) by the LPE method using deoxyadenosine monophosphate (dAMP) as an exfoliation agent that provides a good biocompatibility of the QDs too. As a result, a visible-range photoluminescence from MoS2 QDs surrounded by nucleotides is observed for the first time. Different structures of MoS2 QDs with dAMP are analyzed employing the DFT calculations. It is shown that dAMP can form coordination bonds with the Mo atoms located at the QD edges or at the defect sites where direct contacts with these atoms can occur. The covalent bonds facilitate strong adsorption of dAMP on a MoS2 QD. The structural flexibility of the nucleotide adsorbed on the MoS2 QD enables a combination of noncovalent stacking interaction of the nucleobase and a coordination bond of the phosphate group with the Mo atoms located at the edges to occur. This leads to the formation of a very energetically stable complex.

To analyze X-ray diffraction patterns obtained from polyimide films subjected to external influence (uniaxial tension and exposure at liquid helium temperature), radial distribution function (RDF) curves were constructed and the geometry of the 4,4′-oxydiphenylene-pyromellitimide monomer (PM) was calculated. From the RDF analysis, it follows that uniaxial tension of PM polymer films leads to a change in the geometry of the monomer, and exposure at low temperatures leads to mutual ordering of the polymer chains.

In this work we study stacked and covalently bonded complexes formed by MoS2 monolayer fragments and nucleic acid bases. The structures, interaction energies, and vibrational spectra of the complexes are determined using the DFT/M06-2X and MP2 quantum-chemical methods. The interaction energies of the covalently bonded complexes obtained in the calculations are much higher than the interaction energies of the stacked complexes. Accounting for the effects due to aqueous environment results in a significant decrease of the interaction energies of both types of complexes, but all complexes still remain stable in water. The covalent bonding in the complexes results in significant changes of the vibrational spectra of the bases, in particular, in a very significant increase in their Raman activities.

Carbon nanotubes are considered an effective nanoplatform for drug delivery, including therapeutic nucleic acids such as small interfering RNAs (siRNAs), which are used in cancer therapy. In this work, a noncovalent immobilization of a single-stranded oligonucleotide (with 17 nucleotides in length) on the single-walled carbon nanotube (SWNT) surface using a pyrene molecule as an anchor is simulated by molecular dynamics method. This oligonucleotide design supposes the following binding with siRNA ends to provide its keeping near the nanotube surface. In the model, the pyrene molecule is covalently conjugated to the oligonucleotide through an hexaethylene glycol oligomer (EG)6 and attached to the SWNT’s surface by means of π-π stacking interaction. Structures of the complex and the binding energy of pyrene in the complex with SWNT are determined. Two possible orientations of the oligonucleotide arrangement relative to SWNT were considered: mutually perpendicular orientation and arrangement of an oligonucleotide along the nanotube. In both cases, the pyrene-terminated flexible polyethylene glycol linker plays an important role in keeping the oligonucleotide near the nanotube surface and provides sufficiently rapid adsorption of the biopolymer on SWNT, which is important for the creation of new drug delivery systems into the cell and for biosensor design.

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.

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.

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.

Computer simulations of an argon fcc crystal fragment with embedded water clusters of different sizes are performed using the quantum mechanical DFT/M06-2X method. The effect of the argon matrix on the structural, energy, and spectral parameters of individual water clusters are investigated. The formation energies of (H2O)n@Arm complexes, as well as deformation energies of water clusters and of the argon crystal involved in the embedment, are computed for n = 1–7. Matrix shifts of the IR vibrational frequencies of water clusters isolated in argon matrices are predicted based on the results of the calculations. The predictions indicate a possibility of the formation of small stable water complexes in low-temperature argon matrices.

The application of various action spectroscopy and absorption spectroscopy methods for studying the structure of biological molecules and their constituent fragments in an isolated state is considered. The main attention is paid to the results achieved in the study of the nucleosides which are the structural units of DNA and RNA. It has been demonstrated that modern low-temperature spectroscopy methods allow registration the vibrational spectra of isolated nucleosides in neutral or ionized form. It was shown that most of the nucleosides can be converted into the gas phase by prolonged evaporation from the Knudsen cell without thermal decomposition. Cooling molecules to cryogenic temperatures plays an important role in these studies. The conformational equilibrium of the gas phase between syn and anti subsets of nucleosides is maintained due to fast cooling when frozen in inert matrices. Within these subsets, interconversion processes between conformers can occur during cooling if the conformers are separated by low energy barriers. In inert gas matrices at 6 K, subsets of the syn-conformers of deoxyribonucleosides are mainly frozen with the C2′-endo structure of the deoxyribose ring. The structures of molecular ions of nucleosides are very different from their neutral forms. In particular protonation leads to the domination of the enol forms of thymidine, as well as syn-conformations of adenosine, stabilized by the intramolecular hydrogen bond N3H+•••O5.

In this study the electrospray ionization mass spectrometry (ESI MS) and quantum chemical modeling methods are employed to examine the interactions of molecules of artemisinin-type drugs and of ascorbic acid (ASC). These biologically significant interactions are relevant to antimalarial therapy, in particular, when artemisinin agents are co-administrated with supporting vitamin/antioxidant preparations or could be affiliated with the patient's food. The formation of stable noncovalent complexes of the artemisinin-type drugs (artemisinin, dihydroartemisinin, alpha-artemether, and beta-arteether) with ascorbic acid molecules in a polar solvent, such as methanol, is revealed by the ESI MS probing of binary systems containing an antimalarial drug and ASC in the 1:1 molar ratio. Also, a peak corresponding to noncovalent [ASC center dot DPPC center dot Na]+ cationized complexes is identified in the spectrum of the mixture of ASC and dipalmitoylphosphatidylcholine (DPPC, membrane phospholipid) with the 1:5 molar ratio. Next, the ternary system containing dihydroartemisinin (DHAn; the assumed active metabolite of the artemisinintype drugs in the human organism), ASC, and DPPC in the 1:1:5 molar ratio is examined. The study reveals a competition between the antimalarial agent and ASC for binding with the DPPC molecules. The existence of the competition is supported by the observation of peaks with similar intensities corresponding to the noncovalent DHAn center dot DPPC and ASC center dot DPPC complexes in the mass spectra. An evidence for the complexation between the antimalarial drug and ASC is also found in the spectra of triple model systems studied. To elucidate the structural and energetic characteristics of the noncovalent complexes observed in the ESI MS experiments, model ab initio calculations of DHAn and ASC complexes and clusters of the drug molecules with the polar phosphatidylcholine head of DPPC are performed using the DFT/B3LYP/aug-cc-pVDZ approach. The results of the model study show the possibility of the noncovalent complexation and of the modulation of the biological activity of artemisin-type agents and of the ascorbic acid when they are co-administered in the therapy. (C) 2021 Elsevier B.V. All rights reserved.

Hybrids of graphene nanomaterials with porphyrins possess distinct photo and electronic properties that enable a wide spectrum of applications involving interaction with light. In this work we analyze structural and spectral transformations of cationic meso-5,10,15,20-tetra-(N-methyl-4-pyridyl) porphyrin (T\MPyP4) at adsorption on graphene. It is shown that the binding of TMPyP4 with graphene is stronger as compared to the neutral porphyrin (TPP) with a similar structure (-111.0 vs-22.6 kcal/mol). This is due to a large contribution from the cation-pi-electrons interaction. The interaction of TMPyP4 with graphene is accompanied with a distortion of the flat structure of the porphyrin core and twisting of the side rings. As a result, the porphyrin molecule flattens. The cationic porphyrin adsorbed to graphene induces a stronger molecule flattening in comparison with the neutral porphyrin. A comparison of the experimental and calculated (DFT) UV spectra allows estimating the contribution of the pi-pi stacking and the twisting of the side rings to the observed red-shifting. The TMPyP4 molecule creates an area of negative potential in graphene close to the porphyrin adsorption site. The adsorption of TMPyP4 on graphene is also investigated with DFT calculations and with molecular dynamics simulations in water environment and in vacuum. (C) 2021 Published by Elsevier B.V.

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.

The standard approach involving the sensibilization of naphthalene phosphorescence is employed to study the mono-substituted ortho-bromobenzophenone (2-BrBP). A new feature of the approach is the use of octane as the passive neutral matrix. This matrix is chosen due to the absence of the triplet-excitation mobility in pure 2-BrBP crystal. The problem of common phosphorescence kinetics of 2-BrBP and naphthalene is solved in analytic form. Unlike in the classical problem involving unsubstituted benzophenone, the relevant phosphorescence measurements have been performed at low temperatures (as low as 1.6 K). A new approach is suggested to account for the large difference between the typical experimental pulse-delay time and the slow naphthalene phosphorescence. Relevant computations allow us to explain the nature of the two sets of phosphorescence lines of 2-BrBP.

Ab-initio quantum-mechanical calculations are performed to determine structures and energetic of anions formed by the trimer of an acetonitrile molecule and two water molecules. In total, eight anion configurations corresponding to separate local minima of the anion potential energy surface are identified. All eight anions have positive vertical electron detachment energies. The identified anions belong to the following three categories: dipole-bound anions, anions where the excess electron is suspended between two fragments of the trimer, and solvated covalent anions.

We present a study of noncovalent coupling of single-walled carbon nanotubes (SWNTs) with graphene/graphene oxide (GO) employing optical spectroscopy (UV–visible optical absorption, Raman spectroscopy), scanning microscopy, and theoretical calculations (molecular dynamics simulations, DFT calculations). The optical absorption of SWNT-GO aqueous solution reveals a transformation of bands corresponding to both SWNTs and GO that can be explained by the formation of nanohybrids of two systems. The spectra showed suppression of the intensities of the bands related to the electronic transitions between the first pair of Van Hove singularities in the electronic density of states of semiconducting SWNTs that was explained by the charge transfer from SWNTs to GO. The nanohybrids are not destroyed after deposition of SWNT-GO aqueous solution on a film. The analysis of Raman spectra of the SWNT-GO film reveals the charge transfer between the components. The strong coupling induces stress and causes structural deformations in the carbon nanostructures. The appearance of this effect is in good agreement with the performed calculations. This work provides new experimental and theoretical results on the energetics and structural characteristics of SWNT-GO nanohybrids which may be scientifically and practically significant as they can be used to elaborate solar cells, batteries, sensors, etc.

We analyze the influence of the charge and the degree of oxidation of the surface of graphene (Gr) on its interaction with cytosine and oligonucleotide r(C)(10). This is a computational study involving DFT calculations and molecular dynamics simulations. It is shown that cytosine interacts stronger with graphene oxide (GO) than with Gr, while the energy of the interaction of cytosine with GO only weakly depends on the degree of the Gr oxidation. A correlation between the shifts of vibrational frequencies of cytosine due to complexation with GO and the degree of the Gr oxidation is found. The adsorption of anionic oligonucleotide r(C)(10)onto neutral and positively charged surfaces has a certain conformational similarity to conformations formed with similar van der Waals interactions. Also, for charged surfaces, the Coulombic attraction gives a noticeable contribution to the total interaction energy. For a negatively charged graphene surface the electrostatic repulsion between Gr surface and negatively charged phosphate backbone of oligonucleotide weakens the total binding energy. Competition between the Coulombic repulsion and the van der Waals attraction results in formation of a unique oligonucleotide conformation where all 10 cytosines are stacked onto Gr.

Using the DFT/M06-2X method, we simulated the structure and vibrational spectra of inert gas (Ne, Ar, Kr, Xe) clusters with an isolated formic acid molecule. The impact of the matrix environment on the vibrational spectra of formic acid is established. The values of the matrix shifts of the vibrational frequencies predicted by calculations matched those obtained experimentally. We found that the best agreement between the calculated and experimental shifts occurred for clusters with the smallest deformation energy of the inert gas crystal. At the same time, the ratio of the volume of the molecule embedded in the matrix, and the volume of substituted matrix gas atoms, allowed one to determine only the minimum possible size of the matrix site. The calculated and experimental values of the matrix shifts are in good agreement, indicating the computation method matches the actual experimental conditions.

The conformational equilibrium of thymidine and deuterothymidine molecules in low-temperature Ar matrices has been studied using low-temperature matrix-isolation Fourier IR spectroscopy and quantum-chemical calculations by the DFT/B3LYP and MP2 methods. It has been found that two anti-conformers ta2_0 and ta3_0 with different structures of the sugar ring, C2′-endo and C3′-endo, predominate in low-temperature matrices. In isolated state, each of these conformers has a few low-barrier satellites that can fully pass into more stable structures when a molecule enters the matrix. The main syn conformer ts2_0 is stabilized by an intramolecular hydrogen bond between the O5′H group of the sugar and the C2O group of the base (O5′H⋅⋅⋅O2), while C2′-endo is the predominant conformation of the deoxyribose ring. The considerably lower population of ts2_0 compared to the anti-conformers ta2_0, ta3_0 can be explained by the smaller population of satellite conformations. It has been shown that the absorption band of νN3D stretching vibration is split by the Fermi resonance.