IR Spectra of Crystalline Nucleobases: Combination of Periodic Harmonic Calculations with Anharmonic Corrections Based on Finite Models

In-Vitro Study of the Binding of Atorvastatin with Adenine using Multi-Spectroscopic Approaches

Atorvastatin-an oral lipid regulating drug is a competitive inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA reductase), which is the rate determining enzyme for cholesterol synthesis. Adenine is a purine nucleobase that is found in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) to generate genetic information. The binding mechanism of atorvastatin and adenine was studied for the first time utilizing various techniques, including UV-visible spectrophotometry, spectrofluorimetry, synchronous fluorescence spectroscopy (SF), Fourier transform infrared (FTIR), fluorescence resonance energy transfer (FRET), and metal ion complexation. The fluorescence spectra of the complex indicated that atorvastatin is bound to adenine via hydrophobic interaction through a spontaneous binding process, and the fluorescence quenching mechanism was found to be static quenching with a binding constant of 1.4893 × 104 Lmol-1 at 298 K. Various temperature settings were used to investigate thermodynamic characteristics, such as binding forces, binding constants, and the number of binding sites. The interaction parameters, including the standard enthalpy change (ΔHο) and standard entropy change (ΔSο) were calculated using Van't Hoff's equation to be 42.82 kJmol-1 and 208.9 Jmol-1K-1, respectively. The findings demonstrated that the adenine- atorvastatin binding was endothermic. Furthermore, the results of the experiments revealed that some metal ions (K+, Ca+2, Co+2, Cu+2, and Al+3) facilitate the binding interaction between atorvastatin and adenine. Slight changes are observed in the FTIR spectra of adenine, indicating the binding interaction between adenine and atorvastatin.

Periodic and non-periodic DFT studies of an organic semiconductor material: Structural, electronic, optical, and vibrational properties of ninhydrin

The main purpose of the present study is to explore details of the structural, electronic, optical and vibrational properties of ninhydrin. To achieve this aim, the results of extensive DFT calculations have been employed. Because the accuracy of the results is essential in this study, some periodic DFT approximations have first been subjected to rigorous computational tests, and the RPBE-TS functional is finally selected. Then, the analysis of the RPBE-TS results has revealed that the studied crystal is a semiconductor with a direct band gap of 2.17 eV. The variation of some optical properties (dielectric constant, absorption coefficient, and refractive index) as a function of the polarization directions of the incident electromagnetic wave has also been presented. In addition, the complementarity of anharmonic isolated molecule and harmonic solid-state calculations is exploited in order to give precise assignments of the experimental IR spectrum in the region 400-3800 cm-1. The combination of these two theoretical approaches allows the precise identification of the four red-shifted OH-stretching bands based on the periodic DFT-calculations, and also to attribute, by using the isolated molecule model, some anharmonic bands in the CH/OH stretching regions 2700-3800 cm-1.

Characterization of tautomeric forms of anti-cancer drug gemcitabine and their interconversion upon mechano-chemical treatment, using ATR-FTIR spectroscopy and complementary methods

Gemcitabine is a widely used anti-cancer drug of pyrimidine structure, which can exist as a free base molecular form in crystals. Tautomers are structural isomers of molecules, which interconvert via proton transfer. Mechano-chemistry studies reactions of solids under mechanical impact. We investigated gemcitabine free base for the presence of specific molecular tautomers, using ATR-FTIR spectroscopic analysis, powder XRD, optical microscopy and HPLC. The amino-keto tautomer has the characteristic infrared (IR) peak of the amino group at 3390 cm-1. For the first time, the imino-keto tautomer of gemcitabine free base was detected. The imino-keto tautomer has the characteristic IR peak of the =N-H group, and its peak due to the CO group in pyrimidine ring is shifted vs. that of the amino-keto tautomer. This serves as the unique spectroscopic "fingerprints" of these tautomers. The ATR-FTIR spectroscopic analysis shows that gemcitabine free base can be enriched with the amino-keto or the imino-keto tautomer. Further, we studied the transformation of gemcitabine free base in crystals between its tautomers under conditions of liquid-assisted grinding (LAG). The imino-keto tautomer undergoes tautomerization to the amino-keto tautomer, while the amino-keto tautomer remains stable. No destruction of molecules of gemcitabine free base, when present as either tautomer, occurs during LAG as was verified by the HPLC-UV analysis. LAG is a new, straightforward, facile and fast method to interconvert tautomers in crystals, and ATR-FTIR spectroscopy is a method of choice to study tautomerization reactions of pharmaceuticals. The presented approach is promising for analysis of crystals of drugs containing one or more than one tautomer, and the knowledge-driven design of composite materials, which contain specific tautomeric molecular forms of pyrimidines, purines and other biologically active heterocyclic compounds.

Folic acid and sodium folate salts: Thermal behavior and spectroscopic (IR, Raman, and solid-state 13C NMR) characterization

Folic acid (FA; vitamin B9) and its associated sodium salts, strongly relevant for many scientific and technological applications - from nutrition to pharmacology and nanomedicine, suffer from a lack of characterization combining experimental and theoretical. In this work, a spectroscopic investigation of FA and its synthesized sodium salts in the form of dianion (Na₂HFol) or trianion (Na₃Fol) was scrutinized in their solid state. The spectroscopic (infrared, Raman, and solid state ¹³C-nuclear magnetic resonance) data interpretation was supported by theoretical calculations using the Density Functional Theory (DFT). Additionally, the compounds were characterized by UV-VIS diffuse-reflectance spectroscopy, combined thermal analysis (TG/DTG-DSC) coupled to mass spectrometry, and X-ray diffractometry. The main signatures of each species were identified, as well as the influence of the protonation level on their physicochemical properties. These distinct properties for the three compounds are mainly based on signals assigned to glutamic acid (glutamate) and pterin (neutral or anionic) moieties. This work should help developing new products based on FA or its anionic forms, such as theragnostic/drug delivery systems, supramolecular structures, nanocarbons, or metal complexes.

Molecular Self-Assembly of an Unusual Dinuclear Ruthenium(III) Complex Based on the Nucleobase Guanine

The study of crystal structures based on complexes containing purine nucleobases is a significant research subject, mainly regarding the diagnosis and treatment of some diseases and the investigation of genetic mutations and biochemical structures in life sciences. We have obtained and characterized a new dinuclear ruthenium(III) complex based on guanine with the formula [{Ru(µ-Cl)(µ-gua)}2Cl4]·2H2O (1) (gua = guanine). 1 was characterized by means of Fourier transform infrared spectroscopy (FT–IR), scanning electron microscopy and energy dispersive X-ray analysis (SEM–EDX), single-crystal X-ray diffraction (XRD), Hirshfeld surface analysis and cyclic voltammetry (CV). The study of its electrochemical properties allowed us to investigate the presence of guanine molecules when linked to the ruthenium(III) ion in 1. The well-resolved voltammetric response together with the reliability and stability achieved through 1 could provide a step forward to developing new ruthenium-based platforms, devices and modified electrodes adequate to study this purine nucleobase.

Anharmonicity and Spectra-Structure Correlations in MIR and NIR Spectra of Crystalline Menadione (Vitamin K3)

Mid-infrared (MIR) and near-infrared (NIR) spectra of crystalline menadione (vitamin K3) were measured and analyzed with aid of quantum chemical calculations. The calculations were carried out using the harmonic approach for the periodic model of crystal lattice and the anharmonic DVPT2 calculations applied for the single molecule model. The theoretical spectra accurately reconstructed the experimental ones permitting for reliable assignment of the MIR and NIR bands. For the first time, a detailed analysis of the NIR spectrum of a molecular system based on a naphthoquinone moiety was performed to elucidate the relationship between the chemical structure of menadione and the origin of the overtones and combination bands. In addition, the importance of these bands during interpretation of the MIR spectrum was demonstrated. The overtones and combination bands contribute to 46.4% of the total intensity of menadione in the range of 3600-2600 cm-1. Evidently, these bands play a key role in shaping of the C-H stretching region of MIR spectrum. We have shown also that the spectral regions without fundamentals may provide valuable structural information. For example, the theoretical calculations reliably reconstructed numerous overtones and combination bands in the 4000-3600 and 2800-1800 cm-1 ranges. These results, provide a comprehensive origin of the fundamentals, overtones and combination bands in the NIR and MIR spectra of menadione, and the relationship of these spectral features with the molecular structure.

Advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase

The purpose of this review is to demonstrate advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Molecular spectroscopy, particularly vibrational spectroscopy and electronic spectroscopy, has been used extensively for a wide range of areas of chemical sciences and materials science as well as nano- and biosciences because it provides valuable information about structure, functions, and reactions of molecules. In the meantime, quantum chemical approaches play crucial roles in the spectral analysis. They also yield important knowledge about molecular and electronic structures as well as electronic transitions. The combination of spectroscopic approaches and quantum chemical calculations is a powerful tool for science, in general. Thus, our article, which treats various spectroscopy and quantum chemical approaches, should have strong implications in the wider scientific community. This review covers a wide area of molecular spectroscopy from far-ultraviolet (FUV, 120-200 nm) to far-infrared (FIR, 400-10 cm-1)/terahertz and Raman spectroscopy. As quantum chemical approaches, we introduce several anharmonic approaches such as vibrational self-consistent field (VSCF) and the combination of periodic harmonic calculations with anharmonic corrections based on finite models, grid-based techniques like the Numerov approach, the Cartesian coordinate tensor transfer (CCT) method, Symmetry-Adapted Cluster Configuration-Interaction (SAC-CI), and the ZINDO (Semi-empirical calculations at Zerner's Intermediate Neglect of Differential Overlap). One can use anharmonic approaches and grid-based approaches for both infrared (IR) and near-infrared (NIR) spectroscopy, while CCT methods are employed for Raman, Raman optical activity (ROA), FIR/terahertz and low-frequency Raman spectroscopy. Therefore, this review overviews cross relations between molecular spectroscopy and quantum chemical approaches, and provides various kinds of close-reality advanced spectral simulation for condensed phases.

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.

Sodium valproate (VPA) interactions with DNA and histones

Valproic acid/sodium valproate (VPA) constitutes a widely prescribed drug for the treatment of seizure disorders and is a well-known epigenetic agent, inducing the acetylation of histones and affecting the methylation status of DNA and histones, with consequences on gene expression. Because this drug has been recently reported to exert affinity for histone H1, and to a minor degree for DNA, in this work, we investigated a possible interaction of sodium valproate with DNA and histones H1 and H3 using high-performance polarization microscopy and Fourier-transform infrared (FTIR) microspectroscopy. The preparations under examination consisted of hemispheres resulting from drop-casting samples containing VPA-DNA and VPA-histone mixtures. The results indicated that VPA may interact with DNA and histones, inducing changes in the textural superstructure and molecular order of the DNA possibly through van der Waals forces, and in histone H1 and H3 conformations, probably as a result of electrostatic binding between the drug and protein amino acid residues. These results contribute to a better understanding of the pharmacological potential of VPA. The precise sites and mechanisms involved in these interactions would certainly benefit from investigations provided by complementary methodologies.

Near-Infrared Spectroscopy in Bio-Applications

Near-infrared (NIR) spectroscopy occupies a specific spot across the field of bioscience and related disciplines. Its characteristics and application potential differs from infrared (IR) or Raman spectroscopy. This vibrational spectroscopy technique elucidates molecular information from the examined sample by measuring absorption bands resulting from overtones and combination excitations. Recent decades brought significant progress in the instrumentation (e.g., miniaturized spectrometers) and spectral analysis methods (e.g., spectral image processing and analysis, quantum chemical calculation of NIR spectra), which made notable impact on its applicability. This review aims to present NIR spectroscopy as a matured technique, yet with great potential for further advances in several directions throughout broadly understood bio-applications. Its practical value is critically assessed and compared with competing techniques. Attention is given to link the bio-application potential of NIR spectroscopy with its fundamental characteristics and principal features of NIR spectra.

Vibrational Dynamics of Crystalline 4-Phenylbenzaldehyde from INS Spectra and Periodic DFT Calculations

The present work emphasizes the value of periodic density functional theory (DFT) calculations in the assessment of the vibrational spectra of molecular crystals. Periodic calculations provide a nearly one-to-one match between the calculated and observed bands in the inelastic neutron scattering (INS) spectrum of crystalline 4-phenylbenzaldehyde, thus validating their assignment and correcting previous reports based on single molecule calculations. The calculations allow the unambiguous assignment of the phenyl torsional mode at ca. 118-128 cm-1, from which a phenyl torsional barrier of ca. 4000 cm-1 is derived, and the identification of the collective mode involving the antitranslational motion of CH···O bonded pairs, a hallmark vibrational mode of systems where C-H···O contacts are an important feature.

Vibrations of the guanine-cytosine pair in chloroform: an anharmonic computational study

We compute at the anharmonic level the vibrational spectra of the Watson-Crick dimer formed by guanosine (G) and cytidine (C) in chloroform, together with those of G, C and the most populated GG dimer. The spectra for deuterated and partially deuterated GC are also computed. We use DFT calculations, with B3LYP and CAM-B3LYP as reference functionals. Solvent effects from chloroform are included via the Polarizable Continuum Model (PCM), and by performing tests on models including up two chloroform molecules. Both B3LYP and CAM-B3LYP calculations reproduce the shape of the experimental spectra well in the fingerprint region (1500-1700 cm-1) and in the N-H stretching region (2800-3600 cm-1), with B3LYP providing better quantitative agreement with experiments. According to our calculations, the N-H amido streching mode of G falls at ∼2900 cm-1, while the N-H amino of G and C falls at ∼3100 cm-1 when hydrogen-bonded, or ∼3500 cm-1 when free. Overtone and combination bands strongly contribute to the absorption band at ∼3300 cm-1. Inclusion of bulk solvent effects significantly increases the accuracy of the computed spectra, while solute-solvent interactions have a smaller, though still noticeable, effect. Some key aspects of the anharmonic treatment of strongly vibrationally coupled supermolecular systems and the related methodological issues are also discussed.

Molecular Spectroscopic Markers of DNA Damage

Every cell in a living organism is constantly exposed to physical and chemical factors which damage the molecular structure of proteins, lipids, and nucleic acids. Cellular DNA lesions are the most dangerous because the genetic information, critical for the identity and function of each eukaryotic cell, is stored in the DNA. In this review, we describe spectroscopic markers of DNA damage, which can be detected by infrared, Raman, surface-enhanced Raman, and tip-enhanced Raman spectroscopies, using data acquired from DNA solutions and mammalian cells. Various physical and chemical DNA damaging factors are taken into consideration, including ionizing and non-ionizing radiation, chemicals, and chemotherapeutic compounds. All major spectral markers of DNA damage are presented in several tables, to give the reader a possibility of fast identification of the spectral signature related to a particular type of DNA damage.