Guanine Complexes Research Articles

Spectroscopic characterization and quantum chemical calculations on Favipiravir-Guanine biomolecular complex

Favipiravir, a medication, has drawn a lot of interest recently as a possible therapeutic option for viral illnesses such as the COVID-19 pandemic. In the current work, Favipiravir + Guanine combination is being spectroscopically characterized using Fourier Transformed Infrared Spectroscopy, Raman, and Surface-Enhanced Raman Spectroscopy tools. Density functional theory along with the Becke 3-Parameter, Lee-Yang-Parr method and the basis set 6-311++ G(d,p) is used to explore the molecular interactions between the monomers of Guanine and Favipiravir. The stability of the complex resulting from the charge delocalization is thoroughly examined by natural bond orbital analysis that demonstrates the C=O∙∙∙H intermolecular hydrogen bond formation. The nature of the intermolecular hydrogen bond is described using atoms in molecules analysis. Molecular electrostatic potential mapping depicts various regions of electrostatic potential for the molecules, characterizing their reactive nature. The complex’s frontier molecular orbital gap of 2.39 eV indicates a higher possibility of electronic charge transfer, which in turn enhances the chemical reactivity of the complex. An analysis of the complex’s hyperpolarizability reveals a good non-linear optical response. The antiviral activity of the Favipiravir + Guanine complex is demonstrated by its molecular docking against the 6LU7 receptor (−5.61 kcal/mol).

Water Solvated Zn(II)-Guanine Complex: Structural Aspects and Luminescence Properties.

Understanding the role of metal ions in living organisms and their interactions with biological compounds is fundamental for our health and for developing technological devices for bioinorganic applications. In this work, structural aspects and photophysical mechanisms involved in the luminescence of the Zn(II)-guanine complex in water were studied by using computational quantum chemical methods, providing molecular-level explanations for reported experimental findings. Structural aspects were investigated with def2-SVP basis sets, Density Functional Theory, Resolution of Identity Algebraic Diagrammatic Construction in Second-Order (RI-ADC(2)), Polarizable Continuum Model (PCM), and Conductor-like Screening Model (COSMO) methods. Spectroscopic properties and photophysical deactivation mechanisms were explored with the atomic natural orbital basis sets including relativistic and semicore correlation (ANO-RCC-VDZP) basis sets, Multistate Complete-Active-Space Second-Order Perturbation Theory (MS-CASPT2), and Polarizable Continuum Model (PCM) methods. Our results indicate that Zn(II) ions bind preferentially to the N7 position, and three water molecules in its coordination sphere are sufficient for describing the photophysical properties. The complexation with Zn(II) ions and solvation effects favor fluorescence because the minimum energy region of the S1 (La) (1ππ*) ((La)min) potential energy hypersurface is stabilized, the (La/GS) crossing region is destabilized, and a high energetic barrier along the pathway from the (La)min and (La/GS) regions hampers fast nonradiative return of the electronic population to the ground state, as observed for isolated 9H-guanine.

Copper enhanced guanine electrochemical signal for nucleic acids detection in municipal tertiary wastewater

An electroanalytical method is developed for guanine detection based on its electrochemical oxidation on a clay-modified carbon paste electrode (clay-CPE). The electrochemical guanine signal is found to be significantly enhanced upon its complexation with Cu2+ ions. Cu2+-guanine complex formation is studied using UV–Vis spectroscopy and electrochemical pulse voltammetry at different ratios, with 1:2 Cu2+:guanine found to be the optimal stoichiometry. The clay modifier and the electrode are fully characterized using electron microscopy, Fourier-transform infrared, X-ray photoelectron and X-ray fluorescence spectroscopies, and X-ray diffractometry. The analytical method is fully optimized regarding the electrolyte, technique, and electrochemical parameters. A calibration curve is built obtaining a linear range of 0.1–45 µM, a limit of detection of 0.16 µM, a limit of quantification of 0.54 µM, and a sensitivity of 1.1 µA/µM, which are among the best reported so far and achieved with an environmentally friendly and low-cost method. Our system is very selective with minimal interference in the presence of interferents with concentrations as high as 100× that of guanine. The Cu2+-mediated clay-CPE-based analytical method is applied for the detection of nucleic acid in real-life wastewater, which is critical to achieving efficient wastewater treatment. This demonstrates the applicability of our method for environmental purposes and opens the door for other applications as well, such as diagnostics.

Crystal Structure, Hirhfeld surface Analysis and IR Analysis of 2-amino-1,9-dihydro-6H-purin-6-one-selenate-water

A new guanine complex was synthesized and the structure was elucidated by SXRD and IR spectroscopic methods. Single-crystal X-ray diffraction analysis (SXRD) was used to describe the crystal structure. Triclinic, in the space group P-1, with the following properties: a=9.5945(3), b=13.1171(3), c=14.1905(3), α =79.756(2), β =82.036(2), γ =84.902(2)°, V=1736.70(8) Å3, Z=2. N−H···O, O−H···O and C−H···O hydrogen bonds connect the molecules in the crystal, creating a three-dimensional supramolecular framework. The title structure is stabilized by the intra and intermolecular strong hydrogen bonds, according to a Hirshfeld surface analysis of the recorded intermolecular interactions. For the title complex, the two main interactions are H···O/ O··H (36.5%) and H···H (23.7 %).

Insight into structure, stability and hydrogen bond in complexes of guanine and thymine at the molecular level using computational chemical method

Nine stable structures of complexes formed by interaction of guanine with thymine were located on potential energy surface at B3LYP/6-311++G(2d,2p). The complexes are quite stable with interaction energy from -5,8 to -17,7 kcal.mol-1. Strength of complexes are contributed by hydrogen bonds, in which a pivotal role of N−H×××O/N overcoming C−H×××O/N hydrogen bond, up to to 3.5 times, determines stabilization of complexes investigated. It is found that polarity of N/C−H covalent bond over proton affinity of N/O site governs stability of hydrogen bond in the complexes. The obtained results show that the N/C−H×××O/N red-shifting hydrogen bonds occur in all complexes, and a larger magnitude of an elongation of N−H compared C-H bond length accompanied by a decrease of its stretching frequency is detected in the N/C−H×××O/N hydrogen bond upon complexation. The SAPT2+ analysis indicates the substantial contribution of attractive electrostatic energy versus the induction and dispersion terms in stabilizing the complexes.

Synthesis and Characterization of New Guanine Complexes of Pt(IV) and Pd(II) by X-ray Diffraction and Hirshfeld Surface Analysis

The aim of the work was to synthesize new perspective compounds of palladium and platinum with nitrogenous bases (guanine), promising for use in biomedicine and catalysis. The article describes the synthesis of new [PdCl2(HGua)2]Cl2·H2O and [PtCl5(HGua)]·2H2O compounds using wet chemistry methods. The structure of the obtained single crystals was established by the method of single crystal X-ray diffraction. The complexes have an M-N bond, and the organic ligand is included in the first coordination sphere. The analysis of Hirshfeld surfaces for the obtained complexes and their analogues for the analysis of intermolecular interactions was carried out. In the palladium complex we obtained, π-halogen and π-stacking interactions were found; in analogues, such interactions were not found. π-halogen and halogen interactions were found in structure of platinum complex and its analogues.

Electrochemical and surface enhanced Raman spectroscopy study of Guanine as corrosion inhibitor for copper

Guanine inhibition of copper corrosion in 0.1 M HCl was characterized by electrochemical and weight loss experiments under hydrodynamic conditions as well as by Surface-enhanced Raman spectroscopy (SERS). Cyclic voltammetry and polarization measurements revealed that Guanine adsorption modifies copper surface, thus inhibiting its corrosion. Weight loss and electrochemical impedance experiments showed that Guanine has an inhibition efficiency (ξ) of ∼87 % and that its protection is maintained up to 333 K. SERS measurements revealed that neutral Guanine adsorbs on copper at a wide potential range, forming a Cu(I)Guanine complex at greater immersion times.

Towards understanding the interaction of (S)-thalidomide with nucleobases

Interaction of (S)-thalidomide molecule with four nucleobases: adenine, guanine, cytosine and thymine, is investigated in details employing density functional theory methods. Different mutual positions of the molecules are considered, with the starting geometries enabling hydrogen bond interactions between the monomers. Optimization of geometrical parameters is carried out within the B3LYP/6-311G** approximation and followed by evaluation of vibrational frequencies. Binding and interaction energies are calculated employing exchange-correlation functionals including long-range corrections and properly diffuse basis sets. The strongest interaction exists within the (S)-thalidomide–guanine complex. Interestingly, in one of the investigated (S)-thalidomide–guanine complexes two bifurcated hydrogen bonds are observed. The two hydrogens involved in one of them are bonded to a carbon atom in the α position relative to carbonyl group. The present study can be useful in the design of new anticancer and antiviral drugs interacting selectively with DNA or RNA.

Application of Cu (II)-Guanine Complexes Anchored on SBA-15 and MCM-41 as Efficient Nanocatalysts for One-Pot, Four-Component Domino Synthesis of Phenazine Derivatives and Investigation of Their Antimicrobial Behavior

A one-pot, two-step, four-component synthesis of benzo[c]pyrano[3,2-a]phenazine and bis-benzo[c]pyrano[3,2-a]phenazine derivatives was carried out by the reaction of 2-hydroxy-1,4-naphthoquinone, benzene-1,2-diamine, carbonyl compounds and alkylmalonates using new copper (II) ions complexes of guanine (2-amino-1H-purin-6(9H)-one) supported into MCM-41 (Cu-guanine-MCM-41) and SBA-15 (Cu-guanine-SBA-15) channels as efficient and heterogeneous catalysts in PEG. The desired products were obtained in good to excellent yields. The prepared catalysts have been extensively characterized by different methods and can be reused for several times without any significant loss of their catalytic activities. The phenazine derivatives were also tested for their antimicrobial activities.

DFT study of [Pt(Cl)2L] complex (L = rubeanic acid) and its derived compounds with DNA purine bases

In this study, we present a systematic computational investigation on the electronic properties of cisplatin (cis-[Pt(Cl)2(NH3)2] (CP) and complex [Pt(Cl)2L] (1) (L = rubeanic acid) employing all-electron density functional theory. In detail, we analyzed essential molecular properties such as geometrical parameters, ionization energies, electron affinity, highest occupied molecular orbital, and lowest unoccupied molecular orbital energies. Concerning CP, molecule 1 exhibited improved lipophilicity and a pronounced electrophilic property. Furthermore, to investigate and compare the DNA binding capability between CP and molecule 1, we extended the investigation to the guanine and adenine derived complexes, respectively. Complexes of molecule 1 with the adenine and guanine bases followed a similar trend of stability found for CP systems, with the highest affinity found for guanine complexes. Altogether, molecule 1 displayed promising physicochemical and druglikeness features to serve as a starting point for developing a drug-like enough that could be therapeutically useful.

Electron detachment dynamics of the iodide-guanine cluster: does ionization occur from the iodide or from guanine?

Laser photodissociation spectroscopy of the I‐·guanine complex has been conducted for the first time across the regions above the electron detachment threshold to explore the excited states and whether vertical ionisation occurs from the iodide or the nucleobase. The photofragment spectra reveal a prominent dipole-bound excited state (I) close to the calculated vertical electron detachment energy (∼4.0 eV) and a second excited (II) centred around 4.8 eV, which we assign to π-π* nucleobase-localised transitions. The ionic photofragments are identified as I‐ and I‐·[G-H], with the later fragment being produced significantly more strongly than the former. Both photofragments are observed across the two excited states, with production of the iodide being attributed to internal conversion to the ground state followed by evaporation. We trace the formation of the I‐·[G-H] photofragment to initial vertical ionisation of guanine, followed by ejection of a proton. This two-step process is important as it follows known steps in radiation-induced damage to DNA, namely initial formation of a guanine radical cation which then forms a free radical [G-H] moiety through deprotonation. Production of the I‐·[G-H] photofragment is pronounced through II indicating that its formation is enhanced by coupling of the π-π* transitions to the electron detachment continuum.

DFT modeling of the prevention of Fe(II)-mediated redox damage by imidazole-based thiones and selones

Peroxide reduction involving Fe(II) (i.e., Fenton chemistry) forms hydroxyl radicals which cause oxidative damage to DNA in vivo. Sulfur and selenium compounds have been investigated for their antioxidant properties in preventing this metal-mediated oxidative damage. The effect of the coordination of sulfur/selenium derivatives of imidazolidinone (thiones/selones) on the electronic structure and reduction potential of Fe(II) ions solvated or coordinated to guanine are examined using density functional theory (DFT). The zwitterionic character of the thione/selone ligands increases with substitution of electron donating methyl groups and results in more stable complexes with Fe(II). The highest occupied molecular orbital (HOMO) for the Fe(II)-aqua complex is metal centered, but the HOMO of the Fe(II)-guanine complex is localized on the nucleobase. Complexation of the thione/selone shifts the HOMO to the sulfur/selenium center suggesting a mechanism for protection of DNA by sacrificial oxidation of the sulfur/selenium ligand in preference to Fe(II) or DNA.

Treatment of traumatic prosthetic stomatitis in elderly and senium people with 'dry mouth' syndrome

There was clinical observation of the treatment of traumatic prosthetic stomatitis in 44 people (9 men and 35 women) aged 61 and 82 years suffering from 'dry mouth' syndrome due to radiation and (or) drug sialoadenopathies developed after combined treatment of malignant neoplasms of the organs of the oropharyngeal zone. Using semi-quantitative method, a comparative evaluation of the effectiveness of a new drug based on chelate organic germanium guanine complex, sodium alginate and xylitol (main study group) and previously used drug (control group) for local therapy of traumatic lesions of the oral mucosa was made. It was found that on day 9 in the main study group the effectiveness of treatment was significantly higher (95.0%) than in the control group (80.8%).

The solvent (water) and metal effects on HOMO-LUMO gaps of guanine base pair: A computational study

The most stable structures of guanine dimer and metal-mediated guanine base pair complexes were determined both in vacuum and solvent (water). Density functional theory (DFT) method is generally used in the calculations. The calculations of systems containing C, H, N, O is described by 6-311++G(d,p) basis set and LANL2DZ basis set is used for transition metals. Some geometrical parameters, the LUMO, HOMO energy levels and energy gaps of compounds are calculated. Hydrogen bond stabilization energies in dimer and charge transfer in metal complexes are also determined using NBO analysis. The solvent and metal effects on energy gaps of molecules are found. Cu-mediated guanine complex can be preferred for nanotechnological applications due to its good electronic properties.

Synthesis, Antibacterial Activity, Interaction with Nucleobase and Molecular Docking Studies of 4-Formylbenzoic Acid Based Thiazoles.

Synthesis, characterization and investigation of antibacterial activity of ten novel Schiff base derivatives of 4-formylbenzoic acid is presented. Their structures were determined using 1H and 13CNMR, EI(+)-MS and elemental analyses. Additionally, DFT calculations of interaction energies in complexes of the novel drugs and DNA bases are carried out. Design and synthesis of thiazole derivatives with benzoic acid scaffold to obtain compounds with an improved antibacterial activity. The examined compounds were screened in vitro for antibacterial activity using the broth microdilution method. Geometrical parameters of the investigated complexes were optimized within the Density Functional Theory (DFT) approximation using the B3LYP functional and the 6-311G** basis set. The docking simulations were performed using the FlexX docking module. Among the derivatives, compound 4b showed very strong bacterial activity against staphylococci, MIC 1.95-3.91 µg/ml, micrococci, MIC 0.98 µg/ml, and Bacillus spp., MIC 7.81-15.62 µg/ml. The compounds 4c, 4d, 4e and 4j also showed high bioactivity against staphylococci, MIC 3.91-31.25 µg/ml, and micrococci, MIC 0.98-15.62 µg/ml. Interaction energy values for investigated guanine complexes are about 2 kcal/mol lower than for the corresponding cytosine complexes. Molecular docking studies of all compounds on the active sites of bacterial enzymes indicated gyrase B as possible target. To conclude, an efficient and economic method for the synthesis of thiazoles containing benzoic acid moiety has been developed. The results of antibacterial screenings reveal that some obtained compounds show high to very strong antibacterial activity. The DFT calculations showed that interaction of the obtained drugs with guanine is stronger than with cytosine. Molecular docking studies of all compounds on the active sites of bacterial enzymes indicated gyrase B as possible target.

Study on the structure and electronic property of adsorbed guanine on aluminum doped graphene: First principles calculations

The adsorption of guanine on aluminum doped graphene was theoretically studied using density functional theory to explore its potential application as an adsorbent for guanine. We found that the structural and electronic properties of the graphene–guanine complex strongly depend on the Al atom. Guanine molecule is adsorbed imperceptibly on pristine graphene, while strong chemisorption is observed on Al-doped graphene. The adsorption configurations are discussed using the charge transfers, dipole moment, Frontier molecular orbital, and density of states (DOSs). This work proves that the adsorbent capability of graphene for guanine can be considerably improved by incorporation of Al dopant.

A Study of π-π Stacking Interactions and Aromaticity in Polycyclic Aromatic Hydrocarbon/Nucleobase Complexes.

We analysed the interactions and aromaticity electron-density delocalisation observed in π-π complexes between the phenalenyl radical and acenaphthylene, and the DNA and RNA nucleobases (adenine, guanine, cytosine, thymine and uracil). Interaction energies are obtained at the M06-2X/6-311++G(2df,p) computational level for gas phase and PCM-water conditions. For both the phenalenyl radical and acenaphthylene, the complexes formed with guanine are the most stable ones. Atoms in molecules and natural bond orbital results reveal weak π-π interactions between both interacting moieties, characterized by bond critical points between C⋅⋅⋅C and C⋅⋅⋅N atoms. Nucleus independent chemical shifts (NICS) indicate the retention of the aromatic character of the monomers in the outer region of the complex. The fluctuation indexes reveal a loss of electron delocalisation upon complexation for all cases except guanine complexes. Nevertheless, the interface region shows large negative NICS values, which is not associated with an increase of the aromaticity or electron-density delocalisation, but with magnetic couplings of both molecules, leading to an unrealistic description of the aromatic behaviour in that region.

Solvent effects on binding energy, stability order and hydrogen bonding of guanine–cytosine base pair

In this study, the effect of various solvents on the stability order, binding energy and hydrogen bond (HB) strength of cytosine–guanine (C–G) complex are investigated by using the density functional theory. The results show that the stability of cytosine–guanine complex in polar solvent is higher than non-polar solutions while it is lower than solution in vacuum. The binding energy of cytosine–guanine complex in polar solvent is lower than non-polar solutions. Its HB strength in polar solvent with respect to water as natural solvent is close to each other. The natural bond orbital and frontier molecular orbital analysis have been carried out from the optimized structure. The Quantum Theory of “Atoms in Molecules” (QTAIM) of Bader is also applied here to get more details about the nature of intermolecular interactions. Finally, the chemical properties have been presented to investigate the chemical stability of cytosine–guanine complex.

The Complexation of the Anticancer Drug ThioTEPA with Methylated DNA Base Guanine: Combined Ab Initio and QTAIM Investigation.

Non-covalent complexes of methylated nitrogenous DNA base guanine (m(9) Gua) with 1 to 6 molecules of anticancer drug ThioTEPA (1,1',1''-phosphorothioyltriaziridine) have been investigated by molecular modeling techniques (molecular docking and DFT geometry optimization), ab initio wavefunction calculations and the quantum theory of atoms in molecules (QTAIM). The accuracy of complex structures predicted by standard molecular docking techniques have been assessed by comparing them with ab initio calculations, and the most important differences have been discussed. Obtained stabilization enthalpies (kcal/mol) for the m(9) Gua⋅⋅⋅(ThioTEPA)n complexes with n=1…6 have been found to be -15.6, -26.5, -38.4, -49.6, -60.5 and -69.3 respectively. The non-covalent interactions revealed by the QTAIM method have been shown to be a dominating factor responsible for the complex stability, with hydrogen bonds of NH⋅⋅⋅N type being the most important interactions in small (n=1 to 4) and CH⋅⋅⋅N bonds - in large (n=5, 6) complexes. The obtained results may help to understand ThioTEPA-DNA interactions and clarify the mechanism of the drug action.

Guanine–copper coordination polymers: crystal analysis and application as thin film precursors

Three copper-N9-modified guanine complexes are reported with structures ranging from a discrete trinuclear motif to a mixed-valence coordination polymer. These complexes were used as precursors for the deposition and growth of copper oxide thin films on Si(100), at two different annealing temperatures, by using a CVD technique. Subsequent resistivity measurements suggest the formation of conductive thin films, raising the possibility of using nucleobase-metal complexes as versatile thin film precursors.