Vibrational Spectroscopic Characterization Research Articles

Van der Waals interactions regulating the hydration of 2-methacryloyloxyethyl phosphorylcholine, the constructing monomer of biocompatible polymers

Van der Waals (VDW) interactions provide fantastic properties for biological systems that function at room temperature. The VDW interaction, which primarily contributes to weak hydrogen bonding, is expected to play a key role in regulating hydrophobic hydration to express the biologically inert biocompatible function of polymerized MPCs (2-methacryloyloxyethyl phosphorylcholine). This report explores at the molecular level the biologically inert function of polymerized MPCs through an array of vibrational spectroscopic and computational characterization of MPC monomers, as temperature-dependent change of intramolecular weak hydrogen bonding. Synchrotron Fourier transform infrared microspectroscopy and terahertz time-domain spectroscopy were used to investigate temperature-dependent spectral changes in the low frequency vibrations of the MPC over the temperature range from cryogenic to room temperature, and the results were analysed by highly reliable well-established density functional theory (DFT) calculations. Complicated spectral features in the low frequency energy region and the uncertain conformations of the MPC in the amorphous powder state are clearly resolved under a polarizable continuum model and dispersion correction to pure DFT calculations.

Vibrational spectroscopic characterization and structural investigations of Cepharanthine, a natural alkaloid

Cepharanthine, a natural alkaloid obtained from the Stephania cepharantha Hayata plant, that has antitumor, anti-inflammatory, antioxidative, antiparasitic, and antiviral properties, has been widely used for many years to treat a wide variety of diseases in Japan. However, to elucidate its mechanism of action needs further study. This study aimed to enlighten the molecular structure, and the anticancer and antiviral action mechanisms of Cepharanthine. To evaluate the molecular structure of Cepharanthine, conformational analysis was performed using the DFT/B3LYP with 6-31G(d,p) basis set. The obtained most stable molecular geometry was then optimized at the DFT/B3LYP/6-311++G(d,p) level of theory. The observed IR and Raman bands were compared with harmonic vibrational frequencies of the optimized structure of cepharanthine, calculated using the same level of theory, and assigned on the base of potential energy distribution (PED). The experimental UV-Vis absorption spectrum was recorded and compared with the simulated Time Dependent (TD-DFT/B3LYP/6-311++G(d,p)) method. Moreover, 1H and 13C NMR spectra has been calculated and compared by the experimental spectra. To reveal pharmacological importance of Cepharanthine, a molecular docking study was performed with NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) receptor which controls transcription of DNA, cytokine production and cell survival. Molecular docking simulations revealed that Cepharanthine showed strong binding affinity to NF-κB receptor (ΔG = - 8.9 kcal/mol). In addition, to enlight the antiviral properties of cepharantine and to explore the possibility of its use in the treatment of COVID-19, the interactions of cepharanthine with ACE2, apo and holo forms of COVID-19 main protease enzyme (Mpro) and spike glycoprotein of SARSCoV-2 receptors were investigated.

Vibrational spectroscopic characterization, quantum chemical and molecular docking studies of Valyl-Methionine dipeptide

In this study, valyl-methionine dipeptide (Val-Met), a breakdown product of protein digestion or protein catabolism,has been investigated both theoretically and experimentally. Four different valyl-methionine conformations were formed, using the geometric parameters of two asymmetric units of L-Valine and L-Methionine, taken from the literature and their optimized geometric parameters were obtained by DFT/B3LYP level of theory, using different basis sets. The vibrational spectral analysis for the obtained two energetically most stable conformations were carried out theoretically by using 6-311++G(d,p) basis set. Experimental vibrational spectra of the title molecule were compared with the calculated spectra and the vibrational modes were assigned on the basis of potential energy distributions (PED) analysis, performed using the MOLVIB program. Furthermore, molecular electrostatic potential map analysis was carried out and dipole moment of the compound was calculated. Conformation analysis is an important step in molecular modeling. The selection of suitable conformers for many flexible drug molecules, which can be present in many conformations by turning around single bonds, to adopt different conformations, can easily be overlooked. In this work a series of dipeptide with A and B forms of valine and methionine amino acids have been chosen as examples to demonstrate the importance of conformational analysis. Energy differences between conformations underline the importance of a detailed conformational analysis and should be taken into account when defining their activities. Results show that the formation of hydrogen bonds between N1 and H17 and between H17 and O25 in Valyl(B)-Methionine(B) dipeptide, affects the stability of the molecule. The molecular electrostatic potential of the title molecule has also been calculated which is a very useful property in prediction of molecular reactive behavior. In addition, in silico molecular docking studies were performed for the title molecule with DNA. The results indicated the ability of the Val-Met dipeptide to bind DNA.

Synthesis of inulin hydrogels by electron beam irradiation: physical, vibrational spectroscopic and thermal characterization and arsenic removal as a possible application

Inulin is a natural polysaccharide from the fructan carbohydrate subgroup. It is a great candidate to be used as a precursor of new materials for environmental and medical applications. In this work, two novel inulin hydrogels were synthesized by electron-beam irradiation: inulin-acrylamide (Inu-AAm) and inulin-polyvinyl alcohol (Inu-PVA). The use of mixed factorial experimental designs, with the swelling percentage as the response variable, allowed to find the best conditions for the preparation of the hydrogels. The best hydrogels of each type were characterized by the determination of their gel fraction, thermogravimetry (TGA) and differential scanning calorimetry (DSC) measurements. The infrared and Raman spectra confirmed the formation of new materials (xerogels). The best conditions for the preparation of the Inu-Aam hydrogel were AAm concentration of 22% (w/w), Inu-AAm ratio of 20:80 (w/w) and radiation dose of 30 kGy. For the Inu-PVA hydrogel, the best conditions were PVA concentration of 7.5% (w/w), Inu-PVA ratio of 20.78:79.22 (w/w) and a radiation dose of 20 kGy. The best Inu-AAm and Inu-PVA hydrogels showed swelling percentages of 3013 and 2408%, respectively, and values of gel fraction higher than 70%. The Inu-AAm xerogel had higher thermal stability than its precursors, while the Inu-PVA xerogel had less thermal stability than polyvinyl alcohol but more than inulin. The Inu-AAm hydrogel was selected for the sorption tests of arsenic. The sorption of arsenic followed pseudo second-order kinetics and the equilibrium sorption of arsenic on the hydrogel had a good fit to the Freundlich model.

Pigments and plasters from the Roman temple of Deir El-Hagar, Dakhla Oasis, Egypt: vibrational spectroscopic characterization

Deir El-Hagar temple at the Dakhla Oasis of the Western desert is a rare example of the surviving complete Roman structures in Egypt. The temple was discovered in 1819, and since that date, several restoration attempts have been carried out for its preservation. In the present case study, pigment and plaster samples from Deir El-Hagar temple were analyzed, for the first time, using different analytical methods. Initially, the microscopic observations were applied to collect stratigraphic data on the pictorial layers and the appropriate areas for analysis. The vibrational characteristics of the contained mineral phases were determined using Raman microspectroscopy. The surface morphology and microfeatures of the samples were accomplished by an environmental scanning electron microscopy and the energy-dispersive X-ray micro-analyzer (SEM–EDAX). Additionally, the visible reflectance spectroscopy (vis-RS) was used as a complementary method to record the reflectance spectra of some pigment samples. As such, the analytical techniques used in this study allowed the identification of the vibrational spectroscopic characteristics and the mineralogical–chemical composition of the studied samples. The results showed that the temple walls were plastered with two layers, coarse plaster and thin whitewash render. The blue pigment sample was identified as Egyptian blue and the occurrence of arsenic-based compounds in the sample was also reported and discussed. It was confirmed that a heated goethite, rather than natural red ochre, was used to produce the red colour. Additionally, mixed pigments were used to produce different hues and tonalities. A charcoal black, most likely of a charred wood, was used as a black pigment. Moreover, several proportions of haematite and magnetite were detected along the scanned surface of the black pigment. The findings of the current research allowed delivering an analytical report on the painting materials used in an important example of the Roman monuments in the Western desert of Egypt.

Vibrational Spectroscopic Characterization of 2-(2,4-Dinitrobenzyl)-pyridine (α-DNBP) in Solution by Polarization-Resolved Spontaneous Raman Scattering and Broadband CARS.

The photochromic molecule 2-(2,4-dinitro-benzyl)-pyridine (α-DNBP) is characterized in solution by a combination of density functional theory employing a polarizable continuum model and polarization-resolved spontaneous and nonlinear Raman spectroscopies. By the comparison of theoretically predicted wavenumber positions and depolarization ratios with the experimental spectra acquired under electronically nonresonant conditions, polarized and depolarized Raman bands are assigned. Specifically, the symmetric stretching vibrations of the two nitro groups in ortho and para positions to the pyridine ring can be experimentally differentiated, mainly because of their different Raman depolarization ratios, which supports our prediction from theory. Compared to the polarization-resolved spontaneous Raman experiments, the vibrational spectroscopic differentiation of the two nitro groups is more pronounced in time-delayed polarization-resolved coherent anti-Stokes Raman scattering experiments. Overall, this linear and nonlinear vibrational spectroscopic characterization of the CH form paves the way for the interpretation of future time-resolved pump/nonlinear Raman probe studies on the ultrafast photoinduced intramolecular proton transfer in α-DNBP involving a nitro group as an intramolecular proton acceptor.

Synthesis, single crystal X-ray structure and vibrational spectroscopic characterization study of a new hybrid material crystal: Bis(2,4,6-trihydroxy-1,3,5-triazin-1-ium) bischloride monohydrate

A new hybrid material bis(2,4,6-trihydroxy-1,3,5-triazin-1-ium) bischloride monohydrate (2C3H4N3O3+.2Cl-.H2O) as a crystal has been synthesized and its structure was identified by single-crystal X-ray diffraction and studied by UV–Vis, FT-IR, FT-Raman and 1H NMR. The crystal of 2C3H4N3O3+.2Cl-.H2O belongs to monoclinic with C2/m space group system with Z = 4, a = 12.3845 (9) Å, b = 17.6236 (14) Å, c = 7.0260 (5) Å and β = 115.341 (2)°. The UV–Vis spectrum shows that the compound is transparent in visible and UV near visible domains. The FT-IR, FT-RAMAN and 1H NMR spectra of the crystal were discussed on the basis of crystallographic structure and the results were coherent and provides spectroscopic evidence for the crystal formation. In addition, the thermal decomposition of 2C3H4N3O3+.2Cl-.H2O has been also studied by TGA/DTG and DSC techniques and reveals that the material has a good thermal stability with the melting point about 310 °C.

Crystal structure, vibrational spectroscopic characterization, thermal behavior and antifungal activity of a novel coordination polymer of indole‑3‑carboxylic acid with cobalt(II) and a comparison with the isostructural Zn(II) complex

A new cobalt(II) coordination polymer of indole‑3‑carboxylic acid (I3CAH2), [Co(I3CAH)2(H2O)]n has been synthesized and characterized using single-crystal X-ray diffraction, infrared spectroscopy and thermal (TGA/DTG analysis). The crystal structure is monoclinic, space group Cc, with a = 33.406(7), b = 5.9287(12), c = 8.2790(17) Å, β = 91.52(3)°, V = 1639.1(6) Å3 and Z = 4. Each cobalt cation is five-coordinated by the bidentate chelating indole‑3‑carboxylato ligand, one bridging oxygen atom from the other ligand in the same independent unit, one water molecule, and one bridging oxygen atom of the indole‑3‑carboxylato group from an adjacent [Co(I3CAH)2(H2O)] unit. Infrared spectra and TGA/DTG analysis of [Co(I3CAH)2(H2O)]n in the solid state support the results from X-ray analysis. Comparison of the X-ray data and the vibrational spectra of the title compound with those of the previously reported zinc(II) coordination polymer [Zn(I3CAH)2(H2O)]n has shown that these compounds are isostructural. The antifungal activity of [Co(I3CAH)2(H2O)]n against Aspergillus niger and Candida albicans has been investigated. The new Co(II) compound is remarkably effective against Candida albicans.

Resonance Raman and UV–vis characterization of charge transfer complexes of TCNQ and aromatic amines

Although the molecular charge transfer complexes formed by 7,7,8,8-tetracyanoquinodimethane (TCNQ) and several different donors have been widely investigated in the past, in this paper it is shown for the first time the vibrational spectroscopic characterization of the complexes formed by TCNQ and the simplest series of substituted anilines in solution. The UV–vis spectra indicate the formation of TCNQ complexes stabilized by two aromatic amines in a sandwich π type complex. It was observed that the charge transfer transition energies of the complexes follow a linear correlation with the ionization potential of the amines. The resonance Raman spectra revealed, by the analysis of the ν(CC) and ν(CN) stretching modes of TCNQ, that the complexes keep their neutral character in the ground electronic state, and not as a TCNQ2− dianion species as reported before. The observed enhancement of the TCNQ bands as the amine donor capacity increases, confirmed the charge transfer nature of the electronic transitions. The DFT and TDDFT results were obtained and the theoretical Raman and electronic spectra data supported the experimental findings. The results of the model systems presented herein can contribute to a deep understanding of the photoinduced charge transfer process in complexes of TCNQ, which is a key step in the designing of organic molecular devices.

Hydrogel-Embedded Model Photocatalytic System Investigated by Raman and IR Spectroscopy Assisted by Density Functional Theory Calculations and Two-Dimensional Correlation Analysis.

The presented study reports the synthesis and the vibrational spectroscopic characterization of different matrix-embedded model photocatalysts. The goal of the study is to investigate the interaction of a polymer matrix with photosensitizing dyes and metal complexes for potential future photocatalytic applications. The synthesis focuses on a new rhodamine B derivate and a Pt(II) terpyridine complex, which both contain a polymerizable methacrylate moiety and an acid labile acylhydrazone group. The methacrylate moieties are afterward utilized to synthesize functional model hydrogels mainly consisting of poly(ethylene glycol) methacrylate units. The pH-dependent and temperature-dependent behavior of the hydrogels is investigated by means of Raman and IR spectroscopy assisted by density functional theory calculations and two-dimensional correlation spectroscopy. The spectroscopic results reveal that the Pt(II) terpyridine complex can be released from the polymer matrix by cleaving the C═N bond in an acid environment. The same behavior could not be observed in the case of the rhodamine B dye although it features a comparable C═N bond. The temperature-dependent study shows that the water evaporation has a significant influence neither on the molecular structure of the hydrogel nor on the model photocatalytic moieties.

Mixed salt of sarcosine containing dimeric undecafluoridodialuminate anion and fluoride ion

We report on synthesis, structural and vibrational spectroscopic characterization of the (SarH)6[F5Al-F-AlF5]F (I) salt. The compound (I) is the first salt of amino acids with a dimeric undecafluoridodialuminate [F5Al-F-AlF5]5− anion and the first mixed salt of sarcosine with different anions. It crystallizes in orthorhombic system, space group Pbca. The simulated FT-IR spectrum for a cluster which comprises 13 cations, [F5Al-F-AlF5]5− anion and a fluoride anions built from the crystal structure is compared with the experimental spectrum and agree reasonably well.

Revisiting empirical rules for the determination of the absolute configuration of cascarosides and other (ox‐)anthrones

The introduction of the C10 -stereocenter of (ox-)anthrones by plant organisms is not stereospecific. Consequently, often, both (10S)- and (10R)-diastereomers can be found in the same plant. Motivated by the importance of a correct assignment of the configuration at C10 , this study revisits the nuclear magnetic resonance and electronic circular dichroism-based empirical rules for the determination of the absolute configuration by molecular dynamic simulations and electronic circular dichroism spectrum calculations. Furthermore, a vibrational circular dichroism spectroscopic characterization of these large and conformationally very flexible molecules reveals spectral signatures, which can be used to specifically distinguish the C10 stereochemistry. A detailed analysis of the underlying vibrational modes suggests that the observed spectral pattern of the investigated cascarosides may be generally characteristic for the C10 -stereocenter of (ox-)anthrones and that they can be used for empirical spectra-structure correlations.

Experimental and theoretical studies on the structural, spectroscopic and hydrogen bonding on 4-nitro-n-(2,4-dinitrophenyl) benzenamine

Synthesized 4-nitro-N-(2,4-dinitrophenyl) benzenamine (NDPBA) molecule was confirmed applying the tool of NMR. Theoretical prediction addressed the NMR chemical shifts and correlated well with the experimental data. The molecule subjected to theoretical DFT at 6–311++G** level unraveled the spectroscopic and structural properties of the NDPBA molecule. Moreover the structural features proved the occurrence of intramolecular NH· · O hydrogen bonding in the molecule which was further confirmed with the help of Frontier molecular orbital analysis. Vibrational spectroscopic characterization through FT-IR and Raman experimentally and theoretically gave an account for the vibrational properties. An illustration of the topology of the molecule theoretically helped also in finding the hydrogen bonding energy.

Vibrational spectroscopic characterization of cyclic and acyclic molecular rotors with 1,4-diethynylphenylene-d4 rotators

The synthesis and characterization of acyclic and cyclic molecular rotors with 1,4-diethynylphenylene-d4 rotators are described. The ATR-FTIR and Raman spectra of acyclic rotor 3 and cyclic rotor 5E were measured and interpreted. A feature of ATR-FTIR spectrum of rotor 5E is a strong two-component band around 1730cm−1 attributed to symmetric and asymmetric stretching vibration of the carbonyl group, while this is not observed in rotor 3. Raman investigation in the wide temperature range of 350 - 10K was carried out. The splitting of Raman bands in the region of stretching vibration of CC double and triple bonds at 170 and 260K for rotor 5E is observed. The splitting of bands is due to changes in molecular structure.

Methanesulfonamide in Superacids: Investigations of the CH3 SO2 NH3 + Cation

The preparation of protonated methanesulfonamide was carried out using the superacidic systems HF/AsF5 and HF/SbF5. The vibrational spectroscopic characterization was supported by quantum chemical calculations performed with the PBE1PBE method using the 6-311G++(3df, 3pd) basis set. A remarkable long nitrogen-sulfur bond length of 1.804(6) angstrom was observed in a single-crystal X-ray structure analysis of [CH3SO2NH3](+)[Sb2F11](-). It crystallizes in the orthorhombic space group P2(1)/c with four formula units in the unit cell. Furthermore the crystal structure of CH3SO2NH2 was revisited.

Undervalued N3 Coordination Revealed in the Cisplatin Complex with 2'-Deoxyadenosine-5'-monophosphate by a Combined IRMPD and Theoretical Study.

The complex obtained by the reaction of cisplatin and 2'-deoxyadenosine-5'-monophosphate (5'-dAMP) in water has been isolated and detected by electrospray ionization mass spectrometry. The so-formed cis-[PtCl(NH3)2(5'-dAMP)]+ complex has been studied in detail by infrared multiple photon dissociation (IRMPD) spectroscopy in two spectral ranges, namely, 700-1900 and 2800-3800 cm-1, backed by quantum-chemical calculations at the B3LYP/LACV3P/6-311G** level of theory. In agreement with the computational results, the vibrational spectroscopic characterization of cis-[PtCl(NH3)2(5'-dAMP)]+ shows that the sampled ionic population comprises two major isomers, differentiated in the X-H stretching region by their distinct fragmentation patterns. One of these species presents coordination of the platinum moiety at the N3 position of adenine, whereas in the second one, platinum is bound at the N1 position of adenine. IRMPD kinetics have allowed an estimation of their relative proportions. Surprisingly, the most abundant component of cis-[PtCl(NH3)2(5'-dAMP)]+ is the N3 isomer, although it is slightly less stable than the other potential isomers in the gas phase. In contrast, the lowest-energy species, namely, the one showing cisplatin binding to the N7 position of adenine, seems to be the one less represented in the sampled ionic population. These findings suggest that the reaction of cisplatin with 5'-dAMP is governed by the kinetics of the process occurring in solution rather than by the thermodynamic factors.

Crystallographic aspects of hydrated salts of 4,6-diaminopyrimidine with the first five dicarboxylic acids

Abstract The preparation, X-ray single-crystal structure determination and vibrational spectroscopic characterisation of five novel salts, i.e. bis(4,6-diaminopyrimidinium(1+)) oxalate tetrahydrate; 4,6-diaminopyrimidinium(1+) hydrogen malonate monohydrate; bis(4,6-diaminopyrimidinium(1+)) succinate octahydrate; bis(4,6-diaminopyrimidinium(1+)) glutarate dihydrate and bis(4,6-diaminopyrimidinium (1+)) adipate octahydrate, are presented. It is the first crystallographic study with the title cation. All the structures are centrosymmetric. The oxalate, succinate and adipate anions are situated about inversion centres in their respective structures. The dependence on the parity of the number of carbon atoms in the anions is apparent in the interplanar angles of the carboxylate or carboxylic groups. In all of the structures, there are intermolecular N–H···N, N–H···Oacid, N–H···Owater, Owater–H···Oacid and Owater–H···Owater hydrogen-bonds of moderate strength. The most common graph set motif, R 2 2(8), describes the arrangement of the involved carboxylic as well as of the primary- and secondary-amine groups. There is a growing complexity of arrangement of water molecules in the structures with longer anionic molecules. In 4,6-diaminopyrimidinium(1+) hydrogen malonate monohydrate, there is an intramolecular Oacid–H···Oacid bond, and the conformation of the hydrogen malonate ions with non-parallel carboxylic and carboxylate groups is not often observed. The structural parameters of the carboxylic or carboxylate groups in the dicarboxylic acids or their derivatives found in the Cambridge Structural Database (CSD) are compared with the title structures.

First fluoridoaluminate salt of amino acids

We report the synthesis, structural and vibrational spectroscopic characterization of the first salt of the amino acids containing a fluoridoaluminate anion, namely, GlyH(Gly⋯GlyH)AlF5(H2O)·H2O (I). Compound (I) is the first fluoridoaluminate salt of amino acids with an aquapentafluoridoaluminate anion and is a new member of salts with a so-called triglycine sulfate type cation, AH+(A⋯AH+)Y2−.

Vibrational spectroscopic characterization of arylisoquinolines by means of Raman spectroscopy and density functional theory calculations.

Promising new antimalarial agents were investigated using FT-NIR and deep-UV resonance Raman spectroscopy. The Raman spectra of the seven arylisoquinolines (AIQ) were calculated with the help of density functional theory (DFT). Very good agreement with the experimental data was achieved and a convincing mode assignment was performed with the help of the calculated potential energy distribution (PED). For the non-resonant Raman spectra the most prominent bands were assigned to ν(C[double bond, length as m-dash]C) stretching modes of the isoquinoline system. To differentiate between substances with similar structures, deep-UV resonance Raman spectra were recorded. Raman bands in the range between 1250 and 1210 cm-1 were assigned to ν(C[double bond, length as m-dash]C) stretching vibrations in combination with δ(HCC) deformation vibrations of the aryl rests. These vibrations of the aryl part of the molecules were selectively enhanced, which, thus, enabled the differentiation of similar active agents from each other. For λexc = 257 nm excitation, strong ν(C[double bond, length as m-dash]C) vibrations of the isoquinoline (benzo-) part dominate the Raman spectrum in the range between 1685 and 1585 cm-1 and for λexc = 244 nm the Raman signals between 1430 and 1350 cm-1 were enhanced and assigned to ν(C[double bond, length as m-dash]C) of the isoquinoline (pyridino-) system.

Cobalt(II) and nickel(II) complexes with N-benzyl- and N-(p-nitrobenzyl)iminodiacetic acids. Structural and vibrational spectroscopic characterization and DFT study

The reactions of N-benzyliminodiacetic acid (BnidaH2) and N-(para-nitrobenzyl)iminodiacetic acid (p-NO2BnidaH2) with cobalt(II) and nickel(II) acetate in aqueous solutions were performed. Three new complexes [Co(Bnida)(H2O)3]·H2O (1a·H2O), [Co(p-NO2Bnida)(H2O)3]·½H2O (2a·½H2O) and [Ni(p-NO2Bnida)(H2O)3]·½H2O (2b·½H2O) were prepared and characterized by infrared spectroscopy and thermal analysis (TG/DTA). The molecular and crystal structures of 1a·H2O and 2b·½H2O were determined by X-ray crystallography. The octahedral coordination environments around the Co(II) ion in 1a and Ni(II) ion in 2b consist of an O,N,O′-tridentate N-arylalkyliminodiacetate ion and three water molecules, resulting in the formation of fac-isomers in both cases. The molecular geometry and infrared spectra of these three complexes, together with previously synthesized and characterized complex [Ni(Bnida)(H2O)3]·H2O (1b·H2O) are studied by DFT calculations using BP86/6-311G(d,p) and mPW1PW91/6-311G(d,p) computational model.