Vibrational assignments of cyclic dimers and inter-monomers of adenine relating FT-IR, FT-Raman and UV spectra with SQMFF and DFT calculations

In this work, three different cyclic dimers and a tetramer of adenine taken from the experimental structure determined by X-ray diffraction have been studied by combination of experimental FT-IR, FT-Raman and UV-Visible spectra with hybrid B3LYP/6-311++G** and scaled quantum mechanical force field (SQMFF) calculations in order to perform the complete assignments of bands observed in the vibrational spectra. The characteristics of different N-H···N interactions of those three cyclic structures together with the group of IR bands observed between 2865 and 2599 cm-1 have been elucidated considering the tetrameric structure. The cyclic dimers and the tetramer of adenine confirm that the bands observed between 2865 and 2599 cm-1 are not due to N-H···N interactions but to bands of combination, as was previously suggested. The experimental available deuterated IR and terahertz spectra have allowed the complete assignments of regions of higher and lower wavenumbers. Good correlations were acquired comparing the theoretical IR, Raman and UV spectra of three species and the tetramer with the analogous experimental ones, suggesting the presence of all species in both phases. Vibronic bands are observed in the electronic spectra when adenine concentration is increased in aqueous solution evidencing the presence of monomer, tautomers and dimers, as reported by different studies. Similar characteristics of H bonds interactions are predicted for dimers 1 and 2 but different from the dimer 3, as revealed by using NBO and AIM calculations. Different scaled force constants values were found for the cyclic dimers 1 and 2, as compared to the corresponding to dimer 3.

Infrared Spectral Signatures of Nucleobases in Interstellar Ices I: Purines

The purine nucleobases adenine and guanine are complex organic molecules that are essential for life. Despite their ubiquitous presence on Earth, purines have yet to be detected in observations of astronomical environments. This work therefore proposes to study the infrared spectra of purines linked to terrestrial biochemical processes under conditions analogous to those found in the interstellar medium. The infrared spectra of adenine and guanine, both in neat form and embedded within an ice made of H2O:NH3:CH4:CO:CH3OH (10:1:1:1:1), were analysed with the aim of determining which bands attributable to adenine and/or guanine can be observed in the infrared spectrum of an astrophysical ice analogue rich in other volatile species known to be abundant in dense molecular clouds. The spectrum of adenine and guanine mixed together was also analysed. This study has identified three purine nucleobase infrared absorption bands that do not overlap with bands attributable to the volatiles that are ubiquitous in the dense interstellar medium. Therefore, these three bands, which are located at 1255, 940, and 878 cm-1, are proposed as an infrared spectral signature for adenine, guanine, or a mixture of these molecules in astrophysical ices. All three bands have integrated molar absorptivity values (ψ) greater than 4 km mol-1, meaning that they should be readily observable in astronomical targets. Therefore, if these three bands were to be observed together in the same target, then it is possible to propose the presence of a purine molecule (i.e., adenine or guanine) there.

Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions

The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream of highly contagious and antibody-resistant strains, which in turn led to classifying Omicron as a variant of concern. We systematically collected Raman spectra from six Omicron subvariants available in Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, and BA.2.75) and applied machine-learning algorithms to decrypt their structural characteristics at the molecular scale. Unique Raman fingerprints of sulfur-containing amino acid rotamers, RNA purines and pyrimidines, tyrosine phenol ring configurations, and secondary protein structures clearly differentiated the six Omicron subvariants. These spectral characteristics, which were linked to infectiousness, transmissibility, and propensity for immune evasion, revealed evolutionary motifs to be compared with the outputs of genomic studies. The availability of a Raman "metabolomic snapshot", which was then translated into a barcode to enable a prompt subvariant identification, opened the way to rationalize in real-time SARS-CoV-2 activity and variability. As a proof of concept, we applied the Raman barcode procedure to a nasal swab sample retrieved from a SARS-CoV-2 patient and identified its Omicron subvariant by coupling a commercially available magnetic bead technology with our newly developed Raman analyses.

Raman Multi-Omic Snapshot and Statistical Validation of Structural Differences between Herpes Simplex Type I and Epstein-Barr Viruses

Raman spectroscopy was applied to study the structural differences between herpes simplex virus Type I (HSV-1) and Epstein-Barr virus (EBV). Raman spectra were first collected with statistical validity on clusters of the respective virions and analyzed according to principal component analysis (PCA). Then, average spectra were computed and a machine-learning approach applied to deconvolute them into sub-band components in order to perform comparative analyses. The Raman results revealed marked structural differences between the two viral strains, which could mainly be traced back to the massive presence of carbohydrates in the glycoproteins of EBV virions. Clear differences could also be recorded for selected tyrosine and tryptophan Raman bands sensitive to pH at the virion/environment interface. According to the observed spectral differences, Raman signatures of known biomolecules were interpreted to link structural differences with the viral functions of the two strains. The present study confirms the unique ability of Raman spectroscopy for answering structural questions at the molecular level in virology and, despite the structural complexity of viral structures, its capacity to readily and reliably differentiate between different virus types and strains.

Instantaneous Inactivation of Herpes Simplex Virus by Silicon Nitride Bioceramics

Hydrolytic reactions taking place at the surface of a silicon nitride (Si3N4) bioceramic were found to induce instantaneous inactivation of Human herpesvirus 1 (HHV-1, also known as Herpes simplex virus 1 or HSV-1). Si3N4 is a non-oxide ceramic compound with strong antibacterial and antiviral properties that has been proven safe for human cells. HSV-1 is a double-stranded DNA virus that infects a variety of host tissues through a lytic and latent cycle. Real-time reverse transcription (RT)-polymerase chain reaction (PCR) tests of HSV-1 DNA after instantaneous contact with Si3N4 showed that ammonia and its nitrogen radical byproducts, produced upon Si3N4 hydrolysis, directly reacted with viral proteins and fragmented the virus DNA, irreversibly damaging its structure. A comparison carried out upon testing HSV-1 against ZrO2 particles under identical experimental conditions showed a significantly weaker (but not null) antiviral effect, which was attributed to oxygen radical influence. The results of this study extend the effectiveness of Si3N4's antiviral properties beyond their previously proven efficacy against a large variety of single-stranded enveloped and non-enveloped RNA viruses. Possible applications include the development of antiviral creams or gels and oral rinses to exploit an extremely efficient, localized, and instantaneous viral reduction by means of a safe and more effective alternative to conventional antiviral creams. Upon incorporating a minor fraction of micrometric Si3N4 particles into polymeric matrices, antiherpetic devices could be fabricated, which would effectively impede viral reactivation and enable high local effectiveness for extended periods of time.

Raman Fingerprints of the SARS-CoV-2 Delta Variant and Mechanisms of Its Instantaneous Inactivation by Silicon Nitride Bioceramics

Raman spectroscopy uncovered molecular scale markers of the viral structure of the SARS-CoV-2 Delta variant and related viral inactivation mechanisms at the biological interface with silicon nitride (Si3N4) bioceramics. A comparison of Raman spectra collected on the TY11-927 variant (lineage B.1.617.2; simply referred to as the Delta variant henceforth) with those of the JPN/TY/WK-521 variant (lineage B.1.617.1; referred to as the Kappa variant or simply as the Japanese isolate henceforth) revealed the occurrence of key mutations of the spike receptor together with profound structural differences in the molecular structure/symmetry of sulfur-containing amino acid and altered hydrophobic interactions of the tyrosine residue. Additionally, different vibrational fractions of RNA purines and pyrimidines and dissimilar protein secondary structures were also recorded. Despite mutations, hydrolytic reactions at the surface of silicon nitride (Si3N4) bioceramics induced instantaneous inactivation of the Delta variant at the same rate as that of the Kappa variant. Contact between virions and micrometric Si3N4 particles yielded post-translational deimination of arginine spike residues, methionine sulfoxidation, tyrosine nitration, and oxidation of RNA purines to form formamidopyrimidines. Si3N4 bioceramics proved to be a safe and effective inorganic compound for instantaneous environmental sanitation.

Raman Molecular Fingerprints of SARS-CoV-2 British Variant and the Concept of Raman Barcode

The multiple mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus have created variants with structural differences in both their spike and nucleocapsid proteins. While the functional relevance of these mutations is under continuous scrutiny, current findings have documented their detrimental impact in terms of affinity with host receptors, antibody resistance, and diagnostic sensitivity. Raman spectra collected on two British variant sub-types found in Japan (QK002 and QHN001) are compared with that of the original Japanese isolate (JPN/TY/WK-521), and found bold vibrational differences. These included: i) fractions of sulfur-containing amino acid rotamers, ii) hydrophobic interactions of tyrosine phenol ring, iii) apparent fractions of RNA purines and pyrimidines, and iv) protein secondary structures. Building upon molecular scale results and their statistical validations, the authors propose to represent virus variants with a barcode specially tailored on Raman spectrum. Raman spectroscopy enables fast identification of virus variants, while the Raman barcode facilitates electronic recordkeeping and translates molecular characteristics into information rapidly accessible by users.

Mechanisms of instantaneous inactivation of SARS-CoV-2 by silicon nitride bioceramic

The hydrolytic processes occurring at the surface of silicon nitride (Si3N4) bioceramic have been indicated as a powerful pathway to instantaneous inactivation of SARS-CoV-2 virus. However, the virus inactivation mechanisms promoted by Si3N4 remain yet to be elucidated. In this study, we provide evidence of the instantaneous damage incurred on the SARS-CoV-2 virus upon contact with Si3N4. We also emphasize the safety characteristics of Si3N4 for mammalian cells. Contact between the virions and micrometric Si3N4 particles immediately targeted a variety of viral molecules by inducing post-translational oxidative modifications of S-containing amino acids, nitration of the tyrosine residue in the spike receptor binding domain, and oxidation of RNA purines to form formamidopyrimidine. This structural damage in turn led to a reshuffling of the protein secondary structure. These clear fingerprints of viral structure modifications were linked to inhibition of viral functionality and infectivity. This study validates the notion that Si3N4 bioceramic is a safe and effective antiviral compound; and a primary antiviral candidate to replace the toxic and allergenic compounds presently used in contact with the human body and in long-term environmental sanitation.

Variable temperature FTIR spectra of polycrystalline purine nucleobases and estimating strengths of individual hydrogen bonds

In the first part of this work, we report the FTIR spectra of pure NH and isotopically substituted ND (10-15% D and 80-90% D) polycrystalline hypoxanthine, xanthine, adenine and guanine recorded in the 400-4000 cm^-1 range, as a function of temperature (10-300 K). We provide assignments of the stretching and out-of-plane bending amine (NH₂) and imine (NH) bands to the distinct H-bonds present in the crystal, based on the temperature sensitivity and isotopic exchange behavior. Empirical correlations between spectral and thermodynamic or structural parameters enabled us to estimate the energies and lengths of H-bonds in the studied nucleobase crystals and to correlate them with literature data. The empirical H-bonding energies are compared with H-bonding and stacking energies computed for hypoxanthine. In the second part, strategies for using the empirical correlations together with information extracted from quantum mechanical data (in particular from the Bader's quantum theory of atoms in molecules, QTAIM) for the evaluation of hydrogen bonding properties are discussed, and their advantages and drawbacks pointed out. The justification for a cooperative use of quantum-mechanical calculations with empirical spectra-energy correlations is discussed.

Self-assembled nanostructures of phosphomolybdate, nucleobase and metal ions synthesis and their in vitro cytotoxicity studies on cancer cell lines

The ability of the multidentate nucleobases, adenine and thymine, to coordinate polyoxometalate and metal ions leading to the formation of self-assembled nanostructures and their strong cytotoxicity toward cancer cell lines have been demonstrated. A unique synthetic approach is developed to make a series of functional nanoscale hybrid materials consisting of nucleobases (adenine and thymine) and phosphomolybdic acid (PMA) through solid state chemical reaction and self-assembly process. Adenine was protonated through its ring nitrogen, while the ketone group in thymine was protonated during the addition of PMA to these nucleobases. The self-assembled nanostructures formed as a result of the electrostatic interaction between the protonated nucleobases and polyanionic PMA. To promote the base pairing between the nucleobases, chloroaurate ions and silver ions were added to each PMA/adenine and PMA/thymine nanostructures. The complexation between the nucleobases and the added metal ions was found to drive the formation of subsequent self-assembled nanostructures. All the materials were screened for their anticancer activity against breast (MDAMB-231) and prostate (PC-3) cancer cells, and non-cancerous keratinocyte cells HaCaT. PMA/adenine/[AuCl4]- and PMA/thymine/Ag+ nanostructures were found to have strong anti-cancer activity, while PMA/adenine/Ag+, PMA/thymine/[AuCl4]-, and PMA/pdenine, PMA/thymine nanostructures did not exhibit such activity. The unique redox properties of these materials and the self-assembly of the PMA and metal ions were the major factors responsible for the cytotoxicity. This unique approach of making functional nanomaterials incorporate the nucleobase, PMA and metal ions using solid state self-assembly and their anti-cancer applications are considered to be an effective approach for the development of inorganic nucleoside analogue bio-pharmaceutical agents.

Activity and Mechanism of Action of the Bioceramic Silicon Nitride as an Environmentally Friendly Alternative for the Control of the Grapevine Downy Mildew Pathogen Plasmopara viticola

Downy mildew of grapevine, caused by Plasmopara viticola (Berk. and Curt.) Berl. and de Toni, is one of the most devastating diseases of grapevine, severely affecting grape and wine production and quality worldwide. Infections are usually controlled by the intensive application of synthetic fungicides or by copper-based products in organic farming, rising problems for soil contamination and adverse impacts on environment and human health. While strict regulations attempt to minimize their harmful consequences, the situation calls for the development of alternative fungicidal strategies. This study presents the unprecedented case of a bioceramic, silicon nitride, with antimicrobial properties against P. viticola, but without adverse effects on human cells and environment, opening the way to the possible extension of silicon nitride applications in agriculture. Raman spectroscopic assessments of treated sporangia in conjunction with microscopic observations mechanistically showed that the nitrogen-chemistry of the bioceramic surface affects pathogen's biochemical components and cell viability, thus presenting a high potential for host protection from P. viticola infections.

Silicon Nitride: A Bioceramic with a Gift

In the closing decades of the 20th century, silicon nitride (Si₃N₄) was extensively developed for high-temperature gas turbine applications. Technologists attempted to take advantage of its superior thermal and mechanical properties to improve engine reliability and fuel economy. Yet, this promise was never realized in spite of the worldwide research, which was conducted at that time. Notwithstanding this disappointment, its use in medical applications in the early 21st century has been an unexpected gift. While retaining all of its engineered mechanical properties, it is now recognized for its peculiar surface chemistry. When immersed in an aqueous environment, the slow elution of silicon and nitrogen from its surface enhances healing of soft and osseous tissue, inhibits bacterial proliferation, and eradicates viruses. These benefits permit it to be used in a wide array of different disciplines inside and outside of the human body including orthopedics, dentistry, virology, agronomy, and environmental remediation. Given the global public health threat posed by mutating viruses and bacteria, silicon nitride offers a valid and straightforward alternative approach to fighting these pathogens. However, there is a conundrum behind these recent discoveries: How can this unique bioceramic be both friendly to mammalian cells while concurrently lysing invasive pathogens? This unparalleled characteristic can be explained by the pH-dependent kinetics of two ammonia species-NH₄⁺ and NH₃-both of which are leached from the wet Si₃N₄ surface.

Estimating Strengths of Individual Hydrogen Bonds in RNA Base Pairs: Toward a Consensus between Different Computational Approaches

Noncoding RNA molecules are composed of a large variety of noncanonical base pairs that shape up their functionally competent folded structures. Each base pair is composed of at least two interbase hydrogen bonds (H-bonds). It is expected that the characteristic geometry and stability of different noncanonical base pairs are determined collectively by the properties of these interbase H-bonds. We have studied the ground-state electronic properties [using density functional theory (DFT) and DFT-D3-based methods] of all the 118 normal base pairs and 36 modified base pairs, belonging to 12 different geometric families (cis and trans of WW, WH, HH, WS, HS, and SS) that occur in a nonredundant set of high-resolution RNA crystal structures. Having addressed some of the limitations of the earlier approaches, we provide here a comprehensive compilation of the average energies of different types of interbase H-bonds (E _HB). We have also characterized each interbase H-bond using 13 different parameters that describe its geometry, charge distribution at its bond critical point (BCP), and n → σ*-type charge transfer from filled π orbitals of the H-bond acceptor to the empty antibonding orbital of the H-bond donor. On the basis of the extent of their linear correlation with the H-bonding energy, we have shortlisted five parameters to model linear equations for predicting E _HB values. They are (i) electron density at the BCP: ρ, (ii) its Laplacian: ∇²ρ, (iii) stabilization energy due to n → σ*-type charge transfer: E(2), (iv) donor-hydrogen distance, and (v) hydrogen-acceptor distance. We have performed single variable and multivariable linear regression analysis over the normal base pairs and have modeled sets of linear relationships between these five parameters and E _HB. Performance testing of our model over the set of modified base pairs shows promising results, at least for the moderately strong H-bonds.

Energetics and Vibrational Signatures of Nucleobase Argyrophilic Interactions

This study investigates the interactions of both purine (adenine and guanine) and pyrimidine (cytosine, thymine, and uracil) nucleobases with a pair of silver atoms (Ag2). Full geometry optimizations were performed on several structures of each nucleobase/Ag2 complex and the corresponding isolated monomers using the M06-2X density functional with a correlation consistent triple-ζ basis set augmented with diffuse functions on all atoms and a relativistic pseudopotential on Ag (aug-cc-pVTZ for H, C, N, and O and aug-cc-pVTZ-PP for Ag; denoted aVTZ). Harmonic vibrational frequency computations indicate that each optimized structure corresponds to a minimum on the M06-2X/aVTZ potential energy surface. Relative electronic energies for interactions between Ag2 and each nucleobase were compared to elucidate energetic differences between isomers. Further analysis of the changes in vibrational frequencies, infrared intensities, and Raman scattering activities reveals how different Ag2 binding sites might be differentiated spectroscopically. These results provide molecular-level insight into the interactions between nucleobases and silver, which may lead to better understanding and interpretation of surface-enhanced Raman spectroscopy experiments on nucleobases and related systems.

Influence of amine and thiol modifications at the 3' ends of single stranded DNA molecules on their adsorption on gold surface and the efficiency of their hybridization

Adsorption of molecules of DNA (deoxyribonucleic acid) or modified DNA on gold surfaces is often the first step in construction of many various biosensors, including biosensors for detection of DNA with a particular sequence. In this work we study the influence of amine and thiol modifications at the 3' ends of single stranded DNA (ssDNA) molecules on their adsorption on the surface of gold substrates and on the efficiency of hybridization of immobilized DNA with the complementary single stranded DNA. The characterization of formed layers has been carried out using infrared spectroscopy and atomic force microscopy. As model single stranded DNA we used DNA containing 20 adenine bases, whereas the complementary DNA contained 20 thymine bases. We found that the bands in polarization modulation-infrared reflection-adsorption spectroscopy (PM-IRRAS) spectra of layers formed from thiol-modified DNA are significantly narrower and sharper, indicating their higher regularity in the orientation of DNA on gold surface when using thiol linker. Also, hybridization of the layer of thiol-modified DNA containing 20 adenine bases with the respective DNA containing thymine bases leads to formation of much more organized structures than in the case of unmodified DNA or DNA with the amine linker. We conclude that the thiol-modified ssDNA is more promising for the preparation of biosensors, in comparison with the amine-modified or unmodified ssDNA. We have also found that the above-mentioned modifications at the 3' end of ssDNA significantly influence the IR spectrum (and hence the structure) of polycrystalline films formed from such compounds, even though adsorbed fragments contain less than 5% of the DNA chain. This effect should be taken into account when comparing IR spectra of various polycrystalline films formed from modified and unmodified DNA.

Novel platinum-based anticancer drug: a complete vibrational study

The introduction of cisplatin to oncology, in the 1970s, marked the onset of the search for novel and improved metal-based anticancer drugs. Polynuclear PtII and PdII complexes with linear alkylamines as bridging ligands are a class of potential antineoplastic agents that have shown promising cytotoxicity against low-prognosis human cancers, such as metastatic breast adenocarcinoma and osteosarcoma. The present study reports an analysis of [μ-N,N′-bis(3-aminopropyl)butane-1,4-diamine-κ4 N,N′:N′′,N′′′]bis[dichloridoplatinum(II)], [Pt2Cl4(C10H26N4)], denoted Pt2Spm (Spm is spermine), by vibrational spectroscopy coupled to theoretical calculations. Within the latter, the Density Functional Theory (DFT – mPW1PW/6-31G*) and Effective Core Potential (ECP – LANL2DZ) approaches were used, in order to ensure the most accurate representation of the molecule and achieve a maximum agreement with the experimental data. The solid-state geometry of Pt2Spm corresponds to Ci symmetry, displaying 132 vibrational modes. A complete assignment of the experimental vibrational profile of the system was attained through the combined application of complementary Raman, FT–IR and Inelastic Neutron Scattering (INS) techniques. INS allowed an unequivocal identification of the CH2 and NH2 rocking modes, not clearly detected by the optical techniques, while Raman measurements led to a clear discrimination of the Pt—N stretching frequencies from the two distinct Pt—N moieties within the chelate. The metal-to-metal distances calculated for the molecule under study were found to allow the establishment of effective inter- and intrastrand crosslinks with DNA. These results will hopefully help to clarify the mode of action of the compound, at the molecular level, contributing to the development of improved cisplatin-like chemotherapeutic drugs having a higher efficacy and specificity coupled to lower acquired resistance and deleterious side effects.

Dependence of Adenine Raman Spectrum on Excitation Laser Wavelength: Comparison between Experiment and Theoretical Simulations

We acquired the Raman spectra of adenine in powder and aqueous phase using excitation lasers with 532, 633, and 785 nm wavelengths for the region between 300 and 1500 cm^-1. In comparison to the most distinct peak at 722 cm^-1, the peaks between 1200 and 1500 cm^-1 exhibited a characteristic increase in cross-section with decreasing excitation wavelength in both phases. This trend can be reproduced by different density functional theory (DFT) calculations for the adenine molecule in the gas phase as well as in the aqueous phase. Furthermore, from the calculation on the π-stacked dimer, hydrogen-bonded dimer, and trimer, we find that this trend toward excitation laser wavelength is not sensitive to the packing. When comparing the Raman spectra given by different excitation wavelength, one should take care in analyzing the cross-section, and present day DFT calculations are able to capture general trends in the excitation laser wavelength dependence of the Raman activity.

Vibrational Spectroscopy and Phonon-Related Properties of the L-Aspartic Acid Anhydrous Monoclinic Crystal

The infrared absorption and Raman scattering spectra of the monoclinic P21 l-aspartic acid anhydrous crystal were recorded and interpreted with the help of density functional theory (DFT) calculations. The effect of dispersive forces was taken into account, and the optimized unit cells allowed us to obtain the vibrational normal modes. The computed data exhibits good agreement with the measurements for low wavenumbers, allowing for a very good assignment of the infrared and Raman spectral features. The vibrational spectra of the two lowest energy conformers of the l-aspartic molecule were also evaluated using the hybrid B3LYP functional for the sake of comparison, showing that the molecular calculations give a limited description of the measured IR and Raman spectra of the l-aspartic acid crystal for wavenumbers below 1000 cm(-1). The results obtained reinforce the need to use solid-state calculations to describe the vibrational properties of molecular crystals instead of calculations for a single isolated molecule picture even for wavenumbers beyond the range usually associated with lattice modes (200 cm(-1) < ω < 1000 cm(-1)).

On the correction of calculated vibrational frequencies for the effects of the counterions - α,ω-diamine dihydrochlorides

The present work provides sets of correction factors to adjust the calculated vibrational frequencies of a series of α,ω-diamines hydrochloride salts to account for the intermolecular interactions with the counterion. The study was performed using different theory levels for predicting the vibrational data of isolated dicationic α,ω-diamines and their hydrochloride forms, with and without the explicit account of the interactions with the chloride counterions. Different sets of correction factors were determined for each theory level considering the four smallest elements for the α,ω-diamines series, while their transferability and reliability was evaluated considering the larger elements of the series. The theory level simplification was also evaluated and was found to neither compromise the vibrational frequencies estimates nor the magnitude and accuracy of the pre-defined scaling factors. This suggests that transferability of the correction factors is possible not only for different diamines but also between different levels of theory with the averaged group correction factor, ζ g (a) , being the best choice to account for the effects of the N-H · · · Cl interactions. The possibility of simplifying the theory level without compromising efficiency and accuracy is additionally of utmost importance. This computational approach can constitute a valuable tool in the future for studying the hydrochloride forms of larger and more complex diamine systems. Graphical Abstract A computational approach that may constitute a valuable tool for studying the hydrochloride forms of large and complex diamine systems. Correction factors to adjust the vibrational frequencies calculated for isolated dicationic primary diamines for the effects of the interactions with chloride counterions, without their explicit account in the calculations, are presented and evaluated for eficiency.

A molecular view of cisplatin's mode of action: interplay with DNA bases and acquired resistance

A definite molecular picture of cisplatin's MOA is presented, including a detailed interpretation of the glutathione-mediated drug scavenging process.

Conformational insights and vibrational study of a promising anticancer agent: the role of the ligand in Pd(ii)–amine complexes

This study reports the first complete vibrational analysis of a dinuclear polyamine-based compound displaying antitumour properties.

Quantum chemical and spectroscopic investigations of 3-methyladenine

FTIR, FT-Raman and UV-Vis spectra of 3-methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory.