Experimental IR Research Articles

Density Functional Theory Calculations for Interpretation of Infra-Red Spectra of Liquid Crystalline Chiral Compound

The experimental IR spectra of (S)-4′-(1-methylheptyloxycarbonyl) biphenyl-4-yl 4-[2-(2,2,3,3,4,4,4-heptafluorobutoxy) ethyl-1-oxy]-2-fluorobenzoate in the crystal phase are analyzed with the help of dispersion-corrected density functional theory (DFT+D3) calculations for isolated molecular monomer and dimer models, and a periodic model computed at the extended density functional tight-binding (xTB) level of theory. It is found that the frequency scaling coefficients obtained with the results of the molecular calculations are good matches for the crystal phase, being close to 1. The molecular and periodic models both confirm that varied intra- and intermolecular interactions are crucial in order to reproduce the broadened shape of the experimental band related to C=O stretching; the key factors are the conjugation of the ester groups with the aromatic rings and the varied intermolecular chemical environments, wherein the C=O group that bridges the biphenyl and F-substituted phenyl groups seems particularly sensitive. The C=O stretching vibrations are investigated as a function of temperature, covering the range of the crystal, smectic CA*, smectic C* and isotropic liquid phases. The structure changes are followed based on the X-ray diffraction patterns collected in the same temperatures as the IR spectra. The experimental and computational results taken together indicate that the amount of weak C=O…H-C hydrogen bonds between the molecules in the smectic layers decreases with increasing temperature.

Surface oxygen vacancies induced by cu-doping in hexagonal ZnMn2O4 nanoplates for high efficiency photothermocatalytic oxidation of toluene

The exploitation of efficient and stable photothermal catalyst for the deep mineralization of volatile organic compounds (VOCs) is crucial and challenging. Herein, a photothermal catalyst with abundant oxygen defects was prepared for the first time via Cu-doped ZnMn2O4 hexagonal nanoplate. Experimental characterization results reveal that Cu doping enhances not only the ZnMn2O4 defect contents but also the light absorption and thermal conversion ability of ZnMn2O4. Compared to the undoped ZnMn2O4 (ZMO), the ZnMn2O4 with optimal Cu doping amount (ZMO-4Cu) exhibits excellent photothermal catalytic performance (94% toluene conversion and 87% toluene mineralization) and good resistance to low concentration SO2 under full-spectrum light irradiation. Experimental characterizations and theoretical calculations jointly demonstrated that the oxygen vacancies of ZMO-4Cu surface are more conducive to the adsorption of O2, effectively reduce the oxygen dissociation energy of ZMO-4Cu, thus generating abundant active oxygen species and improving the photothermal catalytic activity for toluene oxidation. In situ IR experiments disclosed that photothermal catalysis is more conducive to the toluene deep oxidation than thermal catalysis. This work provides new insights for the design of high efficiency photothermal catalysis for the deep oxidation of VOCs.

Au⋅⋅⋅H-X (X=N or C) Intramolecular Interactions in Gold (I)-NHC Carbene Complexes with Potential Anticancer Properties: A Quantum Mechanical Study with Two Basis Sets.

Three cationic Gold(I)-NHC complexes with potential anticancer properties were studied using DFT with B3LYP functional in combination with two basis sets, LanL2DZ and SDD. Obtained equilibrium geometries and computed IR spectra were found in excellent agreement with previously reported x-ray structures and experimental IR spectral data. NBO population analysis showed gold(I) has a charge deficiency of 0.26-0.30 e. All three complex cations are polar, with dipole moment values ranging from 6.8 to 7.4 Debye. Regardless of some structural differences in their co-ligands, all three complex cations have remarkably similar HOMO-LUMO energy gaps, with values ranging from 5.2 to 5.4 eV, confirming they are chemically stable and that they share an almost identical stability. Long-range intramolecular interactions Au ⋅⋅⋅H-X (X=N or C) in all three cationic complexes were identified. Both basis sets employed in this study were found equally effective in producing reliable results.

Chemical components with biological activities in the roots of Ilex pubescens

Two new triterpenoids, ilexsaponin U (1) and ilexsaponin V (2), and three new phenylpropanoids, pubescenoside S (3), pubescenoside T (38), and pubescenoside U (39), along with thirty-four existing compounds were isolated from the roots of Ilex pubescens. The elucidation of their structures involved comprehensive spectroscopic techniques, including IR, UV, HR-ESI-MS, and NMR experiments. The anti-inflammatory effects of almost all the compounds were evaluated in LPS-induced RAW264.7 cells. Among these, compounds 1, 4, 8, 11, 12, 26, 27, 29 and 33 exhibited varying degrees of inhibition of inflammatory factors. Notably, compounds 1, 4 and 8 significantly inhibited the mRNA levels of iNOS, IL-6, IL-1β and TNFα, comparable to or exceeding the effect of the positive control (dexamethasone, DEX). We also evaluated the cardioprotective effects of these compounds in OGD/R-induced H9c2 cells. The results revealed that compounds 2, 3, 7, 8, 26, 35, 36 and 37 at 20 μM significantly increased cell viability by 24.9 ± 3.4%, 28.0 ± 0.3%, 37.6 ± 0.2%, 44.86 ± 0.5%, 9.47 ± 2.1%, 23.9 ± 0.4%, 39.5 ± 3.1% and 28.2 ± 0.1%, respectively. Some of them exhibited effects equal to or greater than that of the positive control (diazoxide, DZ) at 100 μM, showing a 21.9 ± 3.0% increase.

Investigation of coverage dependence of the stretching frequency of CO adsorbed on Pd surfaces at low coverage limits

The stretching frequency of the CO bond is a sensitive probe of the local environment of a surface-bound CO molecule, including the adorption site and density, i.e. surface coverage. In this work, we extend our analysis beyond the frequency shift due to differences in adsorption configurations. Using density functional theory (DFT) calculations, we directly explore the correlations between surface coverage and the stretching frequency of adsorbed CO on Pd surfaces. We also perform constant pressure infrared reflection absorption measurements of CO on Pd(111) and use existing relations between pressure and coverage to derive coverage dependency. Both results are compared to previously reported experimental data. Our derived correlations of peak frequency and area with surface coverage can help interpret experimental IR spectra in real time and extract time-dependent concentration data from transient kinetic experiments.

Investigation of infra-red spectra of three chiral liquid crystalline compounds with different fluorosubstitution of benzene ring

The IR spectra of three liquid crystalline compounds, differing only by the number of fluorine atoms in the molecular core, are investigated. The DFT+D3/BLYP-def2SVP calculations for isolated molecules are applied for the band assignments of the experimental IR spectra collected in the crystal phase. Additional DFT calculations, including the B3LYP exchange-correlation functional and def2TZVPP basis set, are also performed for the compound without the fluorine atoms in the molecular core. The scaling factors between the experimental and calculated peak positions, obtained at different levels of theory, are compared. For all compounds, the absorption bands assigned to the C=O stretching vibrations are analyzed as a function of temperature in the isotropic liquid, smectic phases, and crystal phase. The formation of hydrogen bonding involving the C=O groups during crystallization is inferred. The differences in the crystallization temperature of three compounds and the presence of the hexatic smectic phase for only one compound are discussed.

Polyvinyl alcohol covalently grafted perylene imide for high-performance light-conversion film

To suppress the aggregation caused quenching of perylene diimide (PDI) derivatives, and improve photostability of PDI derivatives, a polyvinyl alcohol grafted copolymer (PVA-PDIE) was prepared by transesterification of a perylene imide derivative (PDIE) and polyvinyl alcohol (PVA). PDIE was characterized by H-NMR and HR-MS, and PVA-PDIE was confirmed by IR, water resistance, and control experiments. PVA-PDIE film showed high quantum yield (0.75), and matching emission maxima (620 nm). More importantly, PVA-PDIE film had excellent thermal stability and photostability, high transmittance and light conversion quality. Furthermore, the decomposition temperature of PVA-PDIE film was up to 240 °C, while emission intensity maintained at 95 % and 96 % of the initial value in turn after intensified ultraviolet radiation of 40 h and sunlight radiation of 40 days. Compared with the PVA blank film, photosynthetic photon flux density (PFD) of PVA-PDIE film increased by 25 % and 34 % for red orange light and near-infrared light respectively, and decreased by 39 %, 27 %, and 24 % for ultraviolet light, blue violet light, and yellow-green light in sequence, indicating outstanding light conversion performance. Meanwhile, PVA-PDIE film had excellent transparency.

Structural and vibrational spectroscopic analysis of two Au(I) − NHC carbene complexes potential anticancer agents with intramolecular aurophilic interactions: A DFT study

Structural, electronic, and vibrational spectroscopic analysis using DFT/B3LYPD with LanL2DZ and SDD basis of two novel cationic gold(I) complexes with potential anticancer application exhibiting intramolecular aurophilic Au···H–N interactions, ranging from 2.74 to 2.84 Å. Both basis sets yielded equilibrium geometries and computed IR spectra in excellent agreement with X-ray structures and experimental IR spectra data. Despite structural differences in the thione co-ligand, both cationic complexes have remarkably similar dipole moments ranging from 6.4 to 6.6 D and HOMO-LUMO energy gaps, ranging from 5.0 to 5.3 eV, indicating that both possess almost identical solubility and similar chemical stability. Solvation free energies ranging from −35.9 to −39.0 kcal/mol were calculated using the implicit solvation SMD model, suggesting solvent effects play a significant role.

Green synthesis of a novel bis-Schiff base derived from 4-N, N-dimethylaminobenzaldehyde and hexamethylenediamine: DFT study

The study focuses on the green synthesis of a novel bis-Schiff base (EE) derived from 4-N, N-dimethylaminobenzaldehyde, and hexamethylenediamine. The structural properties of the bis-Schiff base were investigated using experimental methods such as IR, 1HNMR, 13CNMR, and elemental analyses (CHN). Computer simulation using Gaussian03 software at DFT/B3LYP/6–311 G (d, p) level of theory was also used to identify the structural parameters, geometrical isomers, conformational analysis, Mulliken charges, optical properties, frontier orbitals, electrostatic potential map and chemical reactivity descriptors of the bis-Schiff base. The formation mechanism of EE and its geometrical isomers were studied. The study compares theoretical and experimental IR, 1HNMR, and 13CNMR spectra, highlighting the importance of green chemistry in reducing toxic organic solvents and chemicals.

Role of Longitudinal Temperature Gradients in Eliminating Interleaving Inclusions in Casting of Monocrystalline Silicon Ingots

Infrared analysis reveals the presence of interwoven inclusions, primarily comprised of silicon nitride and silicon carbide, in the casting process of monocrystalline silicon ingots. This study investigates how the longitudinal temperature gradient affects the removal of inclusions during the casting of monocrystalline silicon ingots through simulations and comparative experiments. Two monocrystalline silicon ingots were cast, each using different longitudinal temperature gradients: one employing smaller gradients and the other conventional gradients. CGSim (Version Basic CGSim 23.1) simulation software was utilized to analyze the melt flow and temperature distribution during the growth process of quasi–monocrystalline silicon ingots. The findings indicate that smaller longitudinal temperature gradients lead to a more robust upward flow of molten silicon at the solid–liquid interface, effectively carrying impurities away from this interface and preventing their inclusion formation. Analysis of experimental photoluminescence and IR results reveals that although inclusions may not be observed, impurities persist but are gradually displaced to the top of the silicon melt through a stable growth process.

Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers.

Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.

Hierarchical Self-Assembly of Nano- and Microstructures of Zinc Oxide in Combined Sol-Gel Systems

Using the methods of optical spectrometry and IR spectroscopy, the processes of self-assembly of nano- and microstructures of zinc oxide in combined sol-gel systems obtained by mixing film-forming sols with different maturation times were studied. Characteristic bands and absorption peaks in the IR spectra were established, demonstrating an unambiguous relationship between the IR transmittance — radiation and maturation time for different volumetric ratios of mixed sols. It has been shown that experimental IR spectroscopy data correlate with optical spectrometry data in the visible and UV radiation range. The correspondence of ZnO films formed on the basis of combined sol-gel systems to the tasks of nanostructural engineering has been demonstrated.

Exploration of electronic and vibrational properties of sulfanilic acid through periodic and non-periodic DFT calculations.

The electronic, discrete water solvation, and vibrational properties of zwitterionic sulfanilic acid were thoroughly investigated using periodic and non-periodic DFT approaches. The periodic-DFT results, obtained by employing the PBE-TS functional (Perdew-Burke-Ernzerhof (PBE) functional with the Tkatchenko and Scheffler (TS) dispersion correction) were first presented in order to analyze the band structures of the studied crystal. An attentive reading of the predicted band structures has shown three lowest gap energies calculated at 4.23, 4.24, and 4.29eV arising from the Γ→Γ, Γ→Z, and Γ→S transitions, respectively. Then, non-periodic calculations were carried out, at the B3LYP-D3 level of theory (B3LYP functional with the D3 Grimme dispersion correction) in order to optimize the sulfanilic acid-(H2O)10 complex. Starting from the optimized structure, non-covalent interaction calculations were performed and the H-bonding, van der Waals, and steric effect interactions were identified. Finally, the PBE-TS calculations were strengthened by conducting anharmonic B3LYP-D3 calculations in order to achieve a complete decryption of the experimental IR spectrum of sulfanilic acid. The spectral analysis is not limited only to the interpretation of both the NH/CH stretching and fingerprint regions but also extended to the 1800-2600cm-1 region, which is characterized by a strong anharmonic effect. In the latter wavenumber region, the large experimental IR band centered at 1937cm-1 is reproduced theoretically employing the anharmonic B3LYP-D3 calculations. The similarity of this band with those usually considered as a fingerprint of zwitterionic amino acids is observed, and its origin is elucidated theoretically. In the vibrational spectroscopy field, the calculations presented in this study are probably the most appropriate for achieving vast analysis and accurate assignments of vibrational spectra of hydrogen bonding compounds recorded in the solid state. The periodic and non-periodic calculations were conducted within the Density Functional Theory (DFT) using the Generalized Gradient Approximation (GGA) at the PBE-TS level of theory and B3LYP-D3 functional with the 6-311++G(d,p) basis set, respectively. The PBE-TS and B3LYP-D3/6-311++G(d,p) calculations were performed using the CASTEP and Gaussian 09 programs, respectively. In addition, The non-covalent interactions were calculated by the Multiwfn 3.8 software. The obtained results for different calculations were visualized by employing the visualization tools in Materials Studio, GaussView, VMD, and Gnuplot programs.

A Scalable Robust Microporous Al-MOF for Post-Combustion Carbon Capture.

Herein, a robust microporous aluminum tetracarboxylate framework, MIL-120(Al)-AP, (MIL, AP: Institute Lavoisier and Ambient Pressure synthesis, respectively) is reported, which exhibits high CO2 uptake (1.9mmol g-1 at 0.1bar, 298 K). In situ Synchrotron X-ray diffraction measurements together with Monte Carlo simulations reveal that this structure offers a favorable CO2 capture configuration with the pores being decorated with a high density of µ2-OH groups and accessible aromatic rings. Meanwhile, based on calculations and experimental evidence, moderate host-guest interactions Qst (CO2) value of MIL-120(Al)-AP (-40kJ mol-1) is deduced, suggesting a relatively low energy penalty for full regeneration. Moreover, an environmentally friendly ambient pressure green route, relying on inexpensive raw materials, is developed to prepare MIL-120(Al)-AP at the kilogram scale with a high yield while the Metal- Organic Framework (MOF)is further shaped with inorganic binders as millimeter-sized mechanically stable beads. First evidences of its efficient CO2/N2 separation ability are validated by breakthrough experiments while operando IR experiments indicate a kinetically favorable CO2 adsorption over water. Finally, a techno-economic analysis gives an estimated production cost of ≈ 13 $ kg-1, significantly lower than for other benchmark MOFs. These advancements make MIL-120(Al)-AP an excellent candidate as an adsorbent for industrial-scale CO2 capture processes.

Synthesis, Spectroscopic, Computational, and Biological Evaluation of Pyrazole mono azo dyes

In the present work, a series of new dispersed mono azo dyes (3) were synthesized through conventional diazo-coupling reaction between 4-hydroxy-phenylacetamide with pyrazole derivatives at low temperature. All the synthesized mono azo compounds were characterized by various spectroscopic methods like IR, NMR, electronic spectral, LC-MS, and fluorescence spectral studies. The experimental IR data was compared with that of the theoretical data and it has been observed that, the experimental IR spectral values are found to be lower than that of the theoretical values. The quantum chemical calculations were also carried out to understand the chemical reactivity of the compounds by using B3LYP method in conjugation with 6-311++G (d, p) basis set. The compounds were screened for anti-tuberculosis properties against M. tuberculosis and the compound 7 was found to exhibit a significant inhibitory effect with MIC value of 12.5μg/mL. The anti-microbial studies were carried for synthesized mono azo compounds. Further, the in silico molecular docking study was carried out to know the significant interaction of the synthesized compounds against VEGFR2 target protein.

SERS analysis, DFT, and solution effects regarding the structural and optical characteristics of folic acid biomolecule adsorbed on a Cu3 metal cluster

The optical characteristics of folic acid (ABP) and metal clusters of copper (Cu3) at various locations were investigated by means of density functional theory (DFT) computations. Mulliken charge analysis and molecular electrostatic potential (MEP) surface show how charge moves from Cu3 to ABP through the various groups. The peak in the UV–Vis spectra of ABP-Cu3 is caused by bonding and anti-bonding orbitals. In both vacuum and aqueous conditions, the polarizability values of ABP-Cu3 cluster are significantly higher than those of pure ABP, indicating a possible enhancement of the nonlinear optical (NLO) effect. Our research investigates the possibility of using ABP adsorbed metal clusters for NLO materials. Surface enhanced Raman scattering (SERS) in the ABP adsorbed metal clusters enhances the vibrational modes of ABP. Adsorption energies are found to be in the range −17.08 to −58.52 kcal/mol in vacuum and −53.34 to −93.44 kcal/mol in aqueous medium for the different configurations for ABP-Cu3. It indicates that metal clusters adsorbed by ABP are stable in the aqueous media. Experimental IR and UV–Vis of ABP is in agreement with theoretically predicted ones.

Matrix-isolation FTIR spectroscopic study and quantum chemical calculations of 1:1 adduct of CHCl3 and C2H5OH in N2 matrix

[▪-▪] mixture is a common binary solvent used in industries, organic synthesis, lipid extraction, drug extraction, etc. The purpose of this study is to have a molecular level understanding of the interaction of ▪ with ▪. The experiments have been carried out in low temperature ▪ matrix using Fourier Transform Infrared spectroscopy. Electronic structure calculations have been performed to identify the possible binding motifs between ▪ and ▪. Three minima have been obtained on the dimer potential energy surface stabilised by ▪ and ▪ hydrogen bond, and ▪ halogen bond interactions. Formation of more than one complexes have been confirmed using the experimental and simulated IR spectra. Energy decomposition analysis and Natural bond orbital analysis have been performed to understand the nature of interaction and the driving force for complexation. This is one of the first reports where separate complexes have been identified between ▪ and anti and gauche conformers of ▪ in the low temperature matrix.

How much freedom does an effectiveness metric really have?

AbstractIt is tempting to assume that because effectiveness metrics have free choice to assign scores to search engine result pages (SERPs) there must thus be a similar degree of freedom as to the relative order that SERP pairs can be put into. In fact that second freedom is, to a considerable degree, illusory. That is because if one SERP in a pair has been given a certain score by a metric, fundamental ordering constraints in many cases then dictate that the score for the second SERP must be either not less than, or not greater than, the score assigned to the first SERP. We refer to these fixed relationships as innate pairwise SERP orderings. Our first goal in this work is to describe and defend those pairwise SERP relationship constraints, and tabulate their relative occurrence via both exhaustive and empirical experimentation. We then consider how to employ such innate pairwise relationships in IR experiments, leading to a proposal for a new measurement paradigm. Specifically, we argue that tables of results in which many different metrics are listed for champion versus challenger system comparisons should be avoided; and that instead a single metric be argued for in principled terms, with any relationships identified by that metric then reinforced via an assessment of the innate relationship as to whether other metrics are likely to yield the same system‐versus‐system outcome.

Experimental and Theoretical Studies on the Reactions of Aliphatic Imines with Isocyanates.

In the context of a project aiming at the replacement of the 3-substituted β-lactam ring in classical β-lactam antibiotics by an N(3)-acyl-1,3-diazetidinone moiety, we have investigated the reaction of isocyanates with imines derived from allyl glycinate and differently substituted propionaldehydes. Imines of aromatic aldehydes with anilines have been reported to react with acyl isocyanates to give 1,3-diazetidinones or 2,3-dihydro-4H-1,3,5-oxadiazin-4-ones, via [2+2] or [4+2] cycloaddition, respectively. However, neither of these products was formed with imines derived from allyl glycinate and 2-(mono)methyl propionaldehydes. α,α-Dimethylation of the imine enabled the [4+2] cycloaddition pathway, but the desired 1,3-diazetidinone products were not observed. Surprisingly, the imines obtained from thioesters of 2,2-dimethyl 3-oxo propionic acid reacted with aryl isocyanates or with benzyl isocyanate to give 5,5-dimethyl-2,4-dioxo-6-(aryl-/alkylthio)tetrahydropyrimidines, via thiol displacement and re-addition to a putative six-membered iminium intermediate. These experimental results obtained for the reactions could be rationalized by DFT calculations. In addition, we have shown that N(3)-acyl-1,3-diazetidinone and 2,3-dihydro-4H-1,3,5-oxadiazin-4-one products can be distinguished based on experimental IR data in combination with theoretical reference spectra employing the IR spectra alignment (IRSA) algorithm. This discrimination was not possible by means of 1 H, 13 C, or 15 N NMR spectroscopy.

Geometry optimization and energy parameter calculations using density-functional theory method and molecular docking of anticonvulsant therapeutic metal complexes of gabapentin

This work aims to give computational studies of Mn(II), Co(II), Ni(II) and Cu(II) complexes of gabapentin (Gpn), formulized as [M(Gpn)(H2O)3(Cl)].nH2O complexes (where n = 2-6), using DFT method. They were previously synthesized and characterized. DFT calculations are in good agreement with practical studies. Bond lengths of metal complexes reduced or increased rather than that of ligand due to complexation. Bond angles of complexes predict the octahedral environment around the central metal ions predicting sp3d2 or d2sp3hybridization. The calculated energy parameters are negative indicating stability of metal complexes. The small energy band gap of compounds predicts the higher biological activity and high tendency of electron transfer. The comparable frequencies of theoretical and experimental IR may be attributed to different phases of measurement. The induced fit docking SP G-score of the molecular interactions of drug (Gpn) and its metal(II) complexes show that all investigated compounds have a good interaction towards sertonine receptor 5-HT2C and D2 dopamine receptor proteins. Co(II)-Gpn interacts with active site residues of sertonine receptor 5-HT2C with an excellent dock score of -7.370 kcal/mol and RMSD = 1.581 Å. On the other hand, Ni(II)-Gpn has the best dock score of -6.638 kcal/mol and RMSD = 1.995 Å with D2 dopamine receptor.
 KEY WORDS: Gabapentin, Transition metals, DFT-method, molecular docking
 Bull. Chem. Soc. Ethiop. 2024, 38(2), 511-526. 
 DOI: https://dx.doi.org/10.4314/bcse.v38i2.18