Bio-Inspired Crystalline Core-Shell Guanine Spherulites

Spherical particles with diameters within the wavelength of visible light, known as spherulites, manipulate light uniquely due to their spatial organization and their structural birefringence. Most of the known crystalline spherulites are branched, and composed of metals, alloys, and semi-crystalline polymers. Recently, a different spherulite architecture is discovered in the vision systems of decapod crustaceans - core-shell spherulites composed of highly birefringent (Δ n ≈ 30 % $\Delta n \approx \ 30\%$ ) organic single-crystal platelets, with exceptional optical properties. These metastructures, which efficiently scatter light even in dense aqueous environments, have no synthetic equivalence and serve as a natural proof-of-concept as well as synthetic inspiration for thin scattering media. Here, the synthesis of core-shell spherulites composed of guanine crystal platelets ((Δ n ≈ 25 % $\Delta n \approx 25\%$ ) is presented in a two-step emulsification process in which a water/oil/water emulsion and induced pH changes are used to promote interfacial crystallization. Carboxylic acids neutralize the dissolved guanine salts to form spherulites composed of single, radially stacked, β-guanine platelets, which are oriented tangentially to the spherulite surface. Using Mie theory calculations and forward scattering measurements from single spherulites, it is found that due to the single-crystal properties and orientation, the synthetic spherulites possess a high tangential refractive index, similarly to biogenic particles.

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.

Ultrahigh Nitrogen Content Carbon Nanosheets for High Stable Sodium Metal Anodes

Sodium metal, with a high theoretical specific capacity of 1165 mAh g-1 , is the ultimate anode for sodium batteries, yet how to deal with the inhomogeneous and dendritic sodium deposition and the infinite relative dimension change of sodium metal anodes during sodium depositing/stripping is still challenging. Here, a facile fabricated sodiuphilic 2D N-doped carbon nanosheets (N-CSs) are proposed as sodium host material for sodium metal batteries (SMBs) to prevent dendrite formation and eliminate volume change during cycling. Revealing from combined in situ characterization analyses and theoretical simulations, the high nitrogen content and porous nanoscale interlayer gaps of the 2D N-CSs can not only concede dendrite-free sodium stripping/depositing but also accommodate the infinite relative dimension change. Furthermore, N-CSs can be easily process into N-CSs/Cu electrode via traditional commercial battery electrode coating equipment that pave the way for large-scale industrial applications. On account of the abundant nucleation sites and sufficient deposition space, N-CSs/Cu electrodes demonstrate a superior cycle stability of more than 1500 h at a current density of 2 mA cm-2 with a high coulomb efficiency of more than 99.9% and ultralow nucleation overpotential, which enable reversible and dendrites-free SMBs and shed light on further development of SMBs with even higher performance.

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.

Modeling of Electron Hole Transport within a Small Ribosomal Subunit

Abstract—

Synchronized operation of various parts of the ribosome during protein synthesis implies the presence of a coordinating pathway, however, this is still unknown. We have recently suggested that such a pathway can be based on charge transport along the transfer and ribosomal RNA molecules and localization of the charges in functionally important areas of the ribosome. In the current study, using density functional theory calculations, we show that charge carriers (electron holes) can efficiently migrate within the central element of the small ribosomal subunit—the h44 helix. Monte-Carlo modeling revealed that electron holes tend to localize in the functionally important areas of the h44 helix, near the decoding center and intersubunit bridges. On the basis of the results obtained, we suggest that charge transport and localization within the h44 helix could coordinate intersubunit ratcheting with other processes occurring during protein synthesis.

Surface Chemical and Morphological Analysis of Chitosan/1,3-β-d-Glucan Polysaccharide Films Cross-Linked at 90 °C

The cross-linking temperature of polymers may affect the surface characteristics and molecular arrangement, which are responsible for their mechanical and physico-chemical properties. The aim of this research was to determine and explain in detail the mechanism of unit interlinkage of two-component chitosan/1,3-β-d-glucan matrices gelled at 90 °C. This required identifying functional groups interacting with each other and assessing surface topography providing material chemical composition. For this purpose, various spectroscopic and microscopic approaches, such as attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM), were applied. The results indicate the involvement mainly of the C-C and C-H groups and C=O⋯HN moieties in the process of biomaterial polymerization. Strong chemical interactions and ionocovalent bonds between the N-glucosamine moieties of chitosan and 1,3-β-d-glucan units were demonstrated, which was also reflected in the uniform surface of the sample without segregation. These unique properties, hybrid character and proper cell response may imply the potential application of studied biomaterial as biocompatible scaffolds used in regenerative medicine, especially in bone restoration and/or wound healing.

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.

Silicon nitride: a potent solid-state bioceramic inactivator of ssRNA viruses

Surface inactivation of human microbial pathogens has a long history. The Smith Papyrus (2600 ~ 2200 B.C.) described the use of copper surfaces to sterilize chest wounds and drinking water. Brass and bronze on doorknobs can discourage microbial spread in hospitals, and metal-base surface coatings are used in hygiene-sensitive environments, both as inactivators and modulators of cellular immunity. A limitation of these approaches is that the reactive oxygen radicals (ROS) generated at metal surfaces also damage human cells by oxidizing their proteins and lipids. Silicon nitride (Si₃N₄) is a non-oxide ceramic compound with known surface bacterial resistance. We show here that off-stoichiometric reactions at Si₃N₄ surfaces are also capable of inactivating different types of single-stranded RNA (ssRNA) viruses independent of whether their structure presents an envelop or not. The antiviral property of Si₃N₄ derives from a hydrolysis reaction at its surface and the subsequent formation of reactive nitrogen species (RNS) in doses that could be metabolized by mammalian cells but are lethal to pathogens. Real-time reverse transcription (RT)-polymerase chain reaction (PCR) tests of viral RNA and in situ Raman spectroscopy suggested that the products of Si₃N₄ hydrolysis directly react with viral proteins and RNA. Si₃N₄ may have a role in controlling human epidemics related to ssRNA mutant viruses.

Organic nanoelectronics inside us: charge transport and localization in RNA could orchestrate ribosome operation

Translation - protein synthesis at the ribonucleic acid (RNA) based molecular machine, the ribosome, - proceeds in a similar manner in all life forms. However, despite several decades of research, the physics underlying this process remains enigmatic. Specifically, during translation, a ribosome undergoes large-scale conformational changes of its distant parts, and these motions are coordinated by an unknown mechanism. In this study, we suggest that such a mechanism could be related to charge (electron hole) transport along and between the RNA molecules, localization of these charges at certain sites and successive relaxation of the molecular geometry. Thus, we suppose that RNA-based molecular machines, e.g., the ribosome, could be electronically controlled, having "wires", "actuators", "a battery", and other "circuitry". Taking transfer RNA as an example, we justify the reasonability of our suggestion using ab initio and atomistic simulations. Specifically, very large hole transfer integrals between the nucleotides (up to above 100 meV) are observed so that the hole can migrate over nearly the whole tRNA molecule. Hole localization at several guanines located at functionally important sites (G27, G10, G34 and G63) is predicted, which is shown to induce geometry changes in these sites, their neighborhoods and even rather distant moieties. If our hypothesis is right, we anticipate that our findings will qualitatively advance the understanding of the key biological processes and could inspire novel approaches in medicine.

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.

Metabolic machinery encrypted in the Raman spectrum of influenza A virus-inoculated mammalian cells

Raman spectroscopy was applied with a high spectral resolution to a structural study of Influenza (type A) virus before and after its inoculation into Madin-Darby canine kidney cells. This study exploits the fact that the major virus and cell constituents, namely DNA/RNA, lipid, and protein molecules, exhibit peculiar fingerprints in the Raman spectrum, which clearly differed between cells and viruses, as well as before and after virus inoculation into cells. These vibrational features, which allowed us to discuss viral assembly, membrane lipid evolution, and nucleoprotein interactions of the virus with the host cells, reflected the ability of the virus to alter host cells' pathways to enhance its replication efficiency. Upon comparing Raman signals from the host cells before and after virus inoculation, we were also able to discuss in detail cell metabolic reactions against the presence of the virus in terms of compositional variations of lipid species, the formation of fatty acids, dephosphorylation of high-energy adenosine triphosphate molecules, and enzymatic hydrolysis of the hemagglutinin glycoprotein.

Off-Stoichiometric Reactions at the Cell-Substrate Biomolecular Interface of Biomaterials: In Situ and Ex Situ Monitoring of Cell Proliferation, Differentiation, and Bone Tissue Formation

The availability of osteoinductive biomaterials has encouraged new therapies in bone regeneration and has potentially triggered paradigmatic shifts in the development of new implants in orthopedics and dentistry. Among several available synthetic biomaterials, bioceramics have gained attention for their ability to induce mesenchymal cell differentiation and successive bone formation when implanted in the human body. However, there is currently a lack of understanding regarding the fundamental biochemical mechanisms by which these materials can induce bone formation. Phenomenological studies of retrievals have clarified the final effect of bone formation, but have left the chemical interactions at the cell-material interface uncharted. Accordingly, the knowledge of the intrinsic material properties relevant for osteoblastogenesis and osteoinduction remains incomplete. Here, we systematically monitored in vitro the chemistry of mesenchymal cell metabolism and the ionic exchanges during osteoblastogenesis on selected substrates through conventional biological assays as well as via in situ and ex situ spectroscopic techniques. Accordingly, the chemical behavior of different bioceramic substrates during their interactions with mesenchymal cells could be unfolded and compared with that of biomedical titanium alloy. Our goal was to clarify the cascade of chemical equations behind the biological processes that govern osteoblastogenic effects on different biomaterial substrates.

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.

Initial Excited-State Structural Dynamics of dT and dA Oligonucleotide Homopentamers Using Resonance Raman Spectroscopy

Photochemical damage of DNA is initiated by absorption of ultraviolet light, and the photoproducts are formed as a result of excited-state structural and electronic dynamics. We have used UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of homopentamers of adenosine monophosphate (3'-dApdApdApdApdAp-5') and thymidine monophosphate (3'-dTpdTpdTpdTpdTp-5') and compare them to those of the monomeric nucleobases. The resonance Raman spectra of the homopentamers are similar to those of the corresponding monomers. Initial excited-state slopes, homogeneous and inhomogeneous broadening, and other excited-state parameters were extracted by self-consistent simulation of the resonance Raman excitation profiles and absorption spectra with a time-dependent formalism and are also similar to the initial excited-state slopes and broadening in the nucleotide monomers. The lack of differences between the initial excited-state structural dynamics of the nucleotides within the pentamer and the isolated nucleobases is consistent with a model in which the formation of photochemical products in oligonucleotides and DNA is dependent on the formation of the transition-state structure within these polymers, dictated by their large-scale dynamics. These results are discussed in light of the known photochemistry of DNA and the nucleobases.

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.

The bioconjugation mechanism of purine cross-linkers affects microstructure and cell response to ultra rapidly gelling purine–chitosan sponges

As a cell carrier, cross-linking is one of the most common approaches used to provide chitosan with greater structural integrity.

Guanine-oligothiophene conjugates: liquid-crystalline properties, photoconductivities and ion-responsive emission of their nanoscale assemblies

Liquid-crystalline conjugated guanine–oligothiophene derivatives show electron or ambipolar carrier transport properties and ion-induced phase transition accompanied by a luminescence colour change.

We here report the supramolecular self-assembly of hydrogen-bonded motifs for the development of nanostructured materials that exhibit dynamic functions such as stimuli-responsive properties and molecular recognition behaviour. We have designed and synthesised new thermotropic bicontinuous and columnar liquid-crystalline (LC) guanine–oligothiophene conjugates tethered with lipophilic chains, which exhibit ionic, electronic and photoluminescence properties. Their potassium salt complexes self-assemble into thermotropic columnar LC phases. Time-of-flight photoconductivity measurements have revealed that the guanine–oligothiophene conjugates in the LC states possess charge transport abilities with either electron or ambipolar mobility values of 10^–4 to 10^–3 cm² V^–1 s^–1. Furthermore, we have found that the complexation of potassium ions with the guanine motif could lead not only to structural change and thermal stabilization of the LC phases but also to a photoluminescence colour change in the solid states. The strategy presented in this work could lead to the design of new functional LC materials that could potentially be applicable as sensors and electronic devices.

First-Principles Vibrational Electron Energy Loss Spectroscopy of β-Guanine

A general approach to model vibrational electron energy loss spectra obtained using an electron beam positioned away from the specimen is presented. The energy-loss probability of the fast electron is evaluated using first-principles quantum mechanical calculations (density functional theory) of the dielectric response of the specimen. The validity of the method is assessed using recently measured anhydrous β-guanine, an important molecular solid used by animals to produce structural colors. The good agreement between theory and experiments lays the basis for a quantitative interpretation of this spectroscopy in complex systems.

Solution structure of ligands involved in purine salvage pathway

Analogues of intermediates involved in the purine salvage pathway can be exploited as potential drug molecules against enzymes of protozoan parasites. To develop such analogues we need knowledge of the solution structures, predominant tautomer at physiological pH and protonation-state of the corresponding natural ligand. In this regard, we have employed ultraviolet resonance Raman spectroscopy (UVRR) in combination with density functional theory (DFT) to study the solution structures of two relatively unexplored intermediates, 6-phosphoryl IMP (6-pIMP) and succinyl adenosine-5'-monophosphate (sAMP), of purine salvage pathway. These molecules are intermediates in a two step enzymatic process that converts inosine-5'-monpophosphate (IMP) to adenosine-5'-monophosphate (AMP). Experimental data on the molecular structure of these ligands is lacking. We report UVRR spectra of these two ligands, obtained at an excitation wavelength of 260 nm. Using isotope induced shifts and DFT calculations we assigned observed spectra to computed normal modes. We find that sAMP exists as neutral species at physiological pH and the predominant tautomer in solution bears proton at N10 position of purine ring. Though transient in solution, 6-pIMP is captured in the enzyme-bound form. This work provides the structural information of these ligands in solution state at physiological pH. We further compare these structures with the structures of AMP and IMP. Despite the presence of similar purine rings in AMP and sAMP, their UVRR spectra are found to be very different. Similarly, though the purine ring in 6-pIMP resembles that of IMP, UVRR spectra of the two molecules are distinct. These differences in the vibrational spectra provide direct information on the effects of exocyclic groups on the skeletal structures of these molecules. Our results identify key bands in the vibrational spectra of these ligands which may serve as markers of hydrogen bonding interactions upon binding to the active-sites of enzymes.

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.

Experimental and first-principles investigation of the adsorption and entrapping of guanine with SiO2 clusters of sol–gel silicate material for understanding DNA photodamage

A sol–gel silicate matrix containing entrapped guanine was prepared. The SiO₂ matrix provides UVA protection by reducing the light penetration to the entrapped guanine molecules.

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.

Experimental and first-principles study of guanine adsorption on ZnO clusters

Electronic structure for interaction of guanine with Zn₂O₂ cluster and the most preferred N1-site to form a stable G–Zn₂O₂ model.