ZIF-8 Vibrational Spectra: Peak Assignments and Defect Signals

Zeolitic imidazolate framework (ZIF-8) is a promising material for gas separation applications. It also serves as a prototype for numerous ZIFs, including amorphous ones, with a broader range of possible applications, including sensors, catalysis, and lithography. It consists of zinc coordinated with 2-methylimidazolate (2mIm) and has been synthesized with methods ranging from liquid-phase to solvent-free synthesis, which aim to control its crystal size and shape, film thickness and microstructure, and incorporation into nanocomposites. Depending on the synthesis method and postsynthesis treatments, ZIF-8 materials may deviate from the nominal defect-free ZIF-8 crystal structure due to defects like missing 2mIm, missing zinc, and physically adsorbed 2mIm trapped in the ZIF-8 pores, which may alter its performance and stability. Infrared (IR) spectroscopy has been used to assess the presence of defects in ZIF-8 and related materials. However, conflicting interpretations by various authors persist in the literature. Here, we systematically investigate ZIF-8 vibrational spectra by combining experimental IR spectroscopy and first-principles molecular dynamics simulations, focusing on assigning peaks and elucidating the spectroscopic signals of putative defects present in the ZIF-8 material. We attempt to resolve conflicting assignments from the literature and to provide a comprehensive understanding of the vibrational spectra of ZIF-8 and its defect-induced variations, aiming toward more precise quality control and design of ZIF-8-based materials for emerging applications.

Hydrogen-atom tunneling in small thioamides: N-methylthiourea, thiobenzamide and 2-cyanothioacetamide

The most stable thione tautomeric forms of N-methylthiourea, thiobenzamide and 2-cyanothioacetamide were isolated in low-temperature argon matrices. The higher-energy thiol tautomers of these compounds were generated upon irradiation of matrix-isolated monomers with UV (λ > 270 nm) light. For N-methylthiourea and thiobenzamide, kept in the dark at 3.5 K for a long period of time, a spontaneous thiol → thione hydrogen atom tunneling transformation occurred. Only the thiol isomers with the favorably oriented hydrogen atom of the imino group underwent these hydrogen-atom tunneling processes. The other thiol isomers, with the hydrogen atom of the imino group oriented towards the sulfur atom, did not undergo the thiol → thione conversion. For the photogenerated thiol forms of 2-cyanothioacetamide, no spontaneous thiol → thione tautomeric transformation was detected. Instead, only the spontaneous conformational change of one S-H rotamer of the thiol 2-cyanothioacetamide tautomer into the other S-H rotamer was observed.

Microstructural and Hydrophilic Properties of Polylactide Polymer Samples with Various 3D Printing Patterns

The aim of the work is to study the effect of the 3D printing process on the microstructural and hydrophilic properties of polylactic acid (PLA) samples with various model printing patterns obtained from the black filament PLA by sequentially applying polymer layers using the FDM (fused deposition modeling) method. X-ray phase analysis revealed the partial crystallization of PLA polymer chains in the printed samples, which occurs under thermal and mechanical action on the original amorphous PLA filament during 3D printing to varying degrees, depending on the geometry of the pattern and the morphology of its surface. At the same time, IR spectroscopy data indicate the preservation of all intrastructural chemical bonds of polylactide. Measured at the original installation, the values of the wetting edge angles on the surface of the printed samples are in the range φ = 50-60°, which is significantly less than the right angle. This indicates the hydrophilic properties of the whole sample's surface. At the same time, the influence of different geometries of model drawings in printed samples was found not only on the morphology of the sample's surface according to SEM data but also on its wettability.

Exploration of the Conformational Scenario for α-, β-, and γ-Cyclodextrins in Dry and Wet Conditions, from Monomers to Crystal Structures: A Quantum-Mechanical Study

Cyclodextrins (CDs) constitute a class of cyclic oligosaccharides that are well recognized and largely applied in the drug delivery field, thanks to their biocompatibility, low cost, and the possibility to be derivatized in order to tune and optimize the complexation/release of the specific drug. The conformational flexibility of these systems is one of their key properties and requires a cost-effective methodology to be studied by combining the accuracy of results with the possibility of exploring a large set of conformations. In the present paper, we have explored the conformational potential energy surface of the monomers and dimers of α-, β-, and γ-cyclodextrins (i.e., 6, 7, and 8 monomeric units, respectively) by means of fast but accurate semiempirical methods, which are then refined by state-of-the-art DFT functionals. Moreover, the crystal structure is considered for a more suitable comparison with the IR spectrum experimentally recorded. Calculations are carried out in the gas phase and in water environments, applying both implicit and explicit treatments. We show that the conformation of the studied molecules changes from the gas phase to the water, even if treated implicitly, thus modifying their complexation capability.

Composite Resins Impregnated by Phosphorus Organic Extractants for Separation of Rare Earth Elements from Nitrate-Based Leachate of Permanent Magnets

Composite resins impregnated by different organophosphorus extractants were developed and used for the extraction chromatography recovery of rare earth elements from nitrate-based leachate of NdFeB permanent magnets. The influence of different factors on recovery of Nd(III) and Fe(III), as the most difficult to separate elements, by developed resins was studied. The influence of extractant structure, the composition of feed solutions, and concentrations of HNO3 and NH4NO3 on the recovery of Fe(III) and Nd(III) by prepared resins were considered. The best recovery of Nd(III) was shown by resin impregnated with N,N-dioctyl (diphenylphosphoryl) acetamide. For this material, sorption characteristics (values of the distribution coefficient, capacity, and the Nd(III)/Fe(III) separation factor) were obtained, and the reproducibility of the loading-stripping process was evaluated. This resin and its precursors were characterized by IR spectroscopy. It was found that the developed resin is more efficient for Nd(III) recovery than resin impregnated with TODGA. An effective approach to the Nd(III)/Fe(III) separation with developed resin in nitrate solution was proposed. This approach was used for recovery of Pr(III), Nd(III), and Dy(III) from the nitrate-based leachate of NdFeB magnets by the developed resin. The final product contained 99.6% of rare earths.

Effects of Me-Solvent Interactions on the Structure and Infrared Spectra of MeTFSI (Me = Li, Na) Solutions in Carbonate Solvents-A Test of the GFN2-xTB Approach in Molecular Dynamics Simulations

We investigated the performance of the computationally effective GFN2-xTB approach in molecular dynamics (MD) simulations of liquid electrolytes for lithium/sodium batteries. The studied systems were LiTFSI and NaTFSI solutions in ethylene carbonate or fluoroethylene carbonate and the neat solvents. We focused on the structure of the electrolytes and on the manifestations of ion-solvent interactions in the vibrational spectra. The IR spectra were calculated from MD trajectories as Fourier transforms of the dipole moment. The results were compared to the data obtained from ab initio MD. The spectral shifts of the carbonyl stretching mode calculated from the GFN2-xTB simulations were in satisfactory agreement with the ab initio MD data and the experimental results for similar systems. The performance in the region of molecular ring vibrations was significantly worse. We also found some differences in structural data, suggesting that the GFN2-xTB overestimates interactions of Me ions with TFSI anions and Na+ binding to solvent molecules. We conclude that the GFN2-xTB method is an alternative worth considering for MD simulations of liquids, but it requires testing of its applicability for new systems.

Effect of Recombinant Spidroins Self-Assembly on Rheological Behavior of Their Dispersions and Structure of Electrospun Nanofibrous Materials

The effect of primary amino acid sequence in recombinant spidroins on their spatial organization is crucial for the fabrication of artificial fibers and fibrous materials. This study focuses on the rheological properties of aqueous and alcoholic solutions of recombinant analogs of natural spidroins (rS1/9 and rS2/12), as well as the structure of their films and nanofibrous materials. Non-Newtonian flow behavior of aqueous solutions of these proteins was observed at certain concentrations in contrast to their solutions in hexafluoroisopropanol. The secondary structure of recombinant spidroins was addressed by IR spectroscopy, whereas their self-organization in various solvents was studied by AFM and cryo-TEM. The influence of the solvent on the structure and properties of the films and nanofibrous materials produced by electrospinning has been established.

Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation

The investigation of the strong infrared (IR)-active amide I modes of peptides and proteins has received considerable attention because a wealth of detailed information on hydrogen bonding, dipole-dipole interactions, and the conformations of the peptide backbone can be derived from the amide I bands. The interpretation of experimental spectra typically requires substantial theoretical support, such as direct ab-initio molecular dynamics simulation or mixed quantum-classical description. However, considering the difficulties associated with these theoretical methods and their applications are limited in small peptides, it is highly desirable to develop a simple yet efficient approach for simulating the amide I modes of any large proteins in solution. In this work, we proposed a comprehensive computational method that extends the well-established molecular dynamics (MD) simulation method to include an unpolarized IR laser for exciting the CO bonds of proteins. We showed the amide I frequency corresponding to the frequency of the laser pulse which resonated with the CO bond vibration. At this frequency, the protein energy and the CO bond length fluctuation were maximized. Overall, the amide I bands of various single proteins and amyloids agreed well with experimental data. The method has been implemented into the AMBER simulation package, making it widely available to the scientific community. Additionally, the application of the method to simulate the transient amide I bands of amyloid fibrils during the IR laser-induced disassembly process was discussed in details.

The effects of conformation and intermolecular hydrogen bonding on the structure and IR spectra of flutamide; a study based on the matrix isolation technique, ab initio and DFT calculations

In this study, stable conformers of flutamide referred to as an anticancer drug were searched through a relaxed potential energy surface scan carried out at the B3LYP/6-31G(d) level of theory. This was followed by geometry optimization and thermochemistry calculations performed with the HF-SCF, MP2, B3LYP methods and the 6-31G(d), 6-311++G(d,p), aug-cc-pvTZ basis sets for each of the determined minimum energy conformers. The results revealed that flutamide has at least five stable conformers and two of them provide the major contribution to the observed matrix isolation infrared (IR) spectra of the molecule. The effects of conformational variety and intermolecular hydrogen bonding interactions on the observed IR spectra of flutamide were interpreted in the light of the vibrational spectral data obtained for the most stable monomer and dimer forms of the molecule at the same levels of theory. Pulay's "Scaled Quantum Mechanical-Force Field (SQM-FF)" method was used in the refinement of the calculated harmonic wavenumbers, IR intensities and potential energy distributions. This scaling method which proved its superiority to both anharmonic frequency calculations and other scaling methods helped us to correctly interpret the remarkable differences between the matrix IR spectra of flutamide in argon and the condensed phase IR spectra of the molecule in solvents such as KBr, H₂O, D₂O, ethanol and methanol.

DFT study of the conformation, hydrogen bonds, IR, Raman, and NMR spectra of 1,3-disubstituted p-tert-butylthiacalix[4]arenes

CONTEXT

The molecular design of spatially preorganized molecules is one of the critical issues in organic chemistry. Molecular recognition and multipoint binding define them. They organize nanoscale assemblies and devices and stably form host-guest inclusion complexes. Not only is this kind of research important in theory but it also has applications. They are used to create the basic elements of sensory devices: elements of cellular electronics, functional nanofilms and coatings, molecular switches, etc. Thiacalix[4]arenes are a useful molecular platform for constructing a wide range of preorganized receptor structures. This research aims to examine the structure and spectra of distally substituted para-tert-butylthiacalix[4]arene aliphatic (C1) and aromatic (C2) esters. The comparison of the spectra of C1, C2, and C3 makes it possible to reveal the structures and H-bonds of these compounds. The structures and H-bonds of these compounds can be seen by analyzing the spectra of C1, C2, and C3. Calculations were made for the spectra of various C1 and C2 molecule conformations. The most stable conformation for C1 and C2 molecules is a distorted cone 2 (DC2) with the same ester group orientation. The pinched cone (PC) conformation is the most unstable. Thiacalixarene molecules' cavities shrink from 3.61 to 3.57 Å when aromatic ester groups take the place of aliphatic ester groups. Two OH groups are linked to an oxygen atom in the DC1 and DC2 conformations of the C1 and C2 molecules. H-bonds in C1 and C2 molecules affect the supramolecular characteristics of these molecules. A drop in ionization energy and increases in electron affinity, chemical potential, softness, electrophilicity index, and dipole moment occur when aliphatic esters are replaced with aromatic ones.

METHODS

Disubstituted aliphatic and aromatic esters' IR, Raman, and NMR spectra have been investigated. The DFT/B3LYP/6-311G(d,p) method and the GAUSSIAN 09W software were used to determine the vibrational spectra of molecules and optimize their geometry. A gauge-independent (GIAO) approach was used to determine chemical shifts in the NMR spectra with respect to tetramethylsilane.

Structure and Vibrational Spectroscopy of C82 Fullerenol Valent Isomers: An Experimental and Theoretical Joint Study

Gd@C₈₂O_xH_y endohedral complexes for advanced biomedical applications (computer tomography, cancer treatment, etc.) were synthesized using high-frequency arc plasma discharge through a mixture of graphite and Gd₂O₃ oxide. The Gd@C₈₂ endohedral complex was isolated by high-efficiency liquid chromatography and consequently oxidized with the formation of a family of Gd endohedral fullerenols with gross formula Gd@C₈₂O₈(OH)₂₀. Fourier-transformed infrared (FTIR) spectroscopy was used to study the structure and spectroscopic properties of the complexes in combination with the DFTB3 electronic structure calculations and infrared spectra simulations. It was shown that the main IR spectral features are formed by a fullerenole C₈₂ cage that allows one to consider the force constants at the DFTB3 level of theory without consideration of gadolinium endohedral ions inside the carbon cage. Based on the comparison of experimental FTIR and theoretical DFTB3 IR spectra, it was found that oxidation of the C₈₂ cage causes the formation of Gd@C₈₂O₂₈H₂₀, with a breakdown of the integrity of the parent C₈₂ cage with the formation of pores between neighboring carbonyl and carboxyl groups. The Gd@C₈₂O₆(OOH)₂(OH)₁₈ endohedral complex with epoxy, carbonyl and carboxyl groups was considered the most reliable fullerenole structural model.

Synthesis, crystal structure and thermal properties of tetra-kis-(3-methyl-pyridine-κN)bis-(thio-cyanato-κN)nickel(II)

Reaction of Ni(NCS)₂ with 3-methyl-pyridine in water leads to the formation of crystals of the title compound, [Ni(NCS)₂(C₆H₇N)₄]. All of them are of poor quality and non-merohedrally twinned but a refinement using data in HKLF-5 format leads to a reasonable structure model and reliability factors. The crystal structure of the title compound consists of discrete complexes, in which the nickel cations are sixfold coordinated by two terminal N-bonded thio-cyanate anions and four 3-methyl-pyridine ligands within slightly distorted octa-hedra. One of the 3-methyl-pyridine ligands is disordered and was refined using a split model. The discrete complexes are arranged into layers. X-ray powder diffraction proves that pure samples have been obtained, and in the IR spectrum, the CN stretching vibration is observed at 2072 cm^-1, in agreement with the presence of only terminally coordinated thio-cyanate anions. Comparing the calculated powder pattern with those of the residues obtained by solvent removal from several solvates already reported in the literature proves that, in each case, this crystalline phase is formed. Assessing the crystal structures of the solvates in comparison with that of the ansolvate reveals some similarities.

Liquid-Crystalline Order in the Phosphorus-Containing DenDrimers

The structure of phosphorus-containing dendrimers has been studied by IR spectroscopy and optical polarization microscopy. The repeating units of dendrimer molecules are mesogens. This property arises from the conjugation of the aromatic ring and the hydrazone group. An analysis of the IR spectra showed that, with an increase in the generation number, the width of the stretching vibration bands ν(PN) and ν(PO) increases. Difficulties in packing molecules of higher generations cause conformational diversity. The shape of the dendrimer molecules was determined by analyzing the increments of dipole moments. Additionally, the modeling of the stacking of repeating links was performed. The spherical model of molecules does not satisfy the experimental dipole moments of the dendrimers. The flat disk model is more suitable for explaining step changes in dipole moments. The liquid-crystalline ordering of dendrimers under the action of applied pressure was found. With simultaneous heating and uniaxial compression, optical anisotropy appears in dendrimers. It is associated with the formation of liquid-crystalline order. However, a thermodynamically stable liquid-crystalline phase is not formed in this case. Dendrimers most likely have disk-shaped molecules.

Radiative and Magnetically Stimulated Evolution of Nanostructured Complexes in Silicon Surface Layers

The effect of a weak magnetic field (B = 0.17 T) and X-irradiation (D < 520 Gy) on the rearrangement of the defective structure of near-surface p-type silicon layers was studied. It was established that the effect of these external fields increases the positive accumulated charge in the region of spatial charge (RSC) and in the SiO2 dielectric layer. This can be caused by both defects in the near-surface layer of the semiconductor and impurities contained in the dielectric layer, which can generate charge carriers. It was found that the near-surface layers of the barrier structures contain only one deep level in the silicon band gap, with an activation energy of Ev + 0.38 eV. This energy level corresponds to a complex of silicon interstitial atoms SiI+SiI. When X-irradiated with a dose of 520 Gy, a new level with the energy of Ev + 0.45 eV was observed. This level corresponds to a point boron radiation defect in the interstitial site (BI). These two types of defect are effective in obtaining charge carriers, and cause deterioration of the rectifier properties of the silicon barrier structures. It was established that the silicon surface is quite active, and adsorbs organic atoms and molecules from the atmosphere, forming bonds. It was shown that the effect of a magnetic field causes the decay of adsorbed complexes at the Si−SiO2 interface. The released hydrogen is captured by acceptor levels and, as a result, the concentration of more complex Si−H3 complexes increases that of O3−Si−H.

Role of zinc as an essential microelement for algal growth and concerns about its potential environmental risks

This work aims to measure the role of zinc as an essential micronutrient for algal growth and the effect of using different concentrations of this heavy metal on growth and essential metabolites of Dunaliella tertiolecta. The EC50 obtained was around 15 mg/l. The results obtained proved that lower concentrations of the element increased growth and the content of the measured metabolites (photosynthesis pigments, fatty acids, and protein) but with different responses. The increase in content of these metabolic products with low concentrations of the tested heavy metal may be attributed to inhibition to these metabolites' export out of cells by heavy metals. The obtained infrared peaks of the major cell constituents of the treated cells revealed the emergence of new peaks and the removal of others, indicating changes in cell constituents due to changing zinc concentrations.

An investigation on the structure and group vibrations of balenine molecule by matrix isolation IR spectroscopy, DFT and MP2 based calculations

Stable conformers of neutral balenine were scanned through molecular dynamics simulations and energy minimizations using Allinger's MM2 force field. For each of the found minimum-energy conformers, geometry optimization and thermochemistry calculations were performed by using B3LYP, MP2, G3MP2B3 methods, 6-31G(d), 6-311++G(d,p) and aug-cc-pvTZ basis sets. The calculation results have indicated that balenine has about twenty stable conformers whose relative energies are in the range of 0-9.5 kcal/mol. Three of these are thought to provide the major contribution to matrix isolation IR spectra of the molecule. Our solvent calculations using the polarized continuum model revealed the stable zwitterion structures which are predicted to dominate IR spectra of balenine in water and heavy water (D₂O) solvents. Pulay's SQM-FF method was used in scaling of the harmonic force constants and vibrational spectral data calculated for the neutral and zwitterion structures. These refined calculation data together with those obtained from anharmonic frequency calculations enabled us to correctly interpret the matrix isolation IR spectrum of balenine and the tautomerism-based changes observed in its KBr IR and solution (D₂O) IR spectra. The results revealed the crucial role of conformation and zwitterionic tautomerism on the structure and vibrational spectral data of the molecule.

A Computational Journey across Nitroxide Radicals: From Structure to Spectroscopic Properties and Beyond

Nitroxide radicals are characterized by a long-lived open-shell electronic ground state and are strongly sensitive to the chemical environment, thus representing ideal spin probes and spin labels for paramagnetic biomolecules and materials. However, the interpretation of spectroscopic parameters in structural and dynamic terms requires the aid of accurate quantum chemical computations. In this paper we validate a computational model rooted into double-hybrid functionals and second order vibrational perturbation theory. Then, we provide reference quantum chemical results for the structures, vibrational frequencies and other spectroscopic features of a large panel of nitroxides of current biological and/or technological interest.

Water-induced conformational changes in the powder and film of ε-poly(L)lysine studied by infrared and Raman spectroscopy

In this study, we have investigated the water absorption-induced structural changes and thermal behavior of ε-poly(L)lysine-hydrochloride (EPLHCl) in the powder and film samples using infrared (IR) and Raman spectroscopy. An X-ray diffraction measurement reveals that the crystal structure of ε-poly(L)lysine (EPL) is similar to that of the γ-crystal of nylon-6. The powder form of EPLHCl absorbs water from the air and solidifies into a film (18% water content). The film does not transform into the powder form with increasing temperature; it remains as a film, suggesting that the transformation from powder to film is irreversible. The IR spectra in the amide Ⅰ region of the powder and film are distinctly different, indicating that the secondary structure of EPLHCl changes upon water absorption. The position of the amide I band suggests that the powder form of EPLHCl has a β-sheet structure, while the film has two types of β-sheet structures. Raman spectra of EPLHCl in the region 1490-1440 cm^-1 indicate that the EPLHCl film has a trans amide structure, unlike its powder form. Hence, it is highly probable that the differences in the secondary structures of the EPLHCl powder and film originate due to the twisting of the amide group induced by water absorption.

Study of the conformation and hydrogen bonds of the p-tetrasulfonatothiacalix[4]arene pentasodium salt by vibrational spectroscopy and DFT

The vibrational spectra of the p-tetrasulfonatothiacalix[4]arene pentasodium salt (TCAS) and tert-butylthiacalix[4]arene (BuTCA) were studied. Comparison of the TCAS and BuTCA IR spectra allows us to isolate the bands of tert-butyl and sulfonate groups. Geometry, IR and Raman spectra were calculated for conformation cone, partial cone, 1,2-, and 1,3-alternate. The most stable conformation of the TCAS is the cone. Characteristic bands were determined for each of the possible conformations. In the case of the TCAS molecule, four ions of sodium are coordinated with the oxygen atoms of sulfonate groups, and the fifth ion interacts with the oxygen and sulfur atoms of the macrocycle. Under the influence of sodium ions, the distribution of electron density in the TCAS molecule and its ability to supramolecular interactions change.

Adsorption/Desorption Behaviors and SERS Chemical Enhancement of 6-Mercaptopurine on a Nanostructured Gold Surface: The Au20 Cluster Model

Computational approaches are employed to elucidate the binding mechanism and the SERS phenomenon of 6-mercaptopurine (6MP) adsorbed on the tetrahedral Au20 cluster as a simple model for a nanostructured gold surface. Computations are carried out in both vacuum and aqueous environments using a continuum model. In the gaseous phase and neutral conditions, interaction of 6MP with the gold cluster is mostly dominated by a covalent Au-S bond and partially stabilized by the Au⋅⋅⋅H-N coupling. However, in acidic solution, the nonconventional Au⋅⋅⋅H-S hydrogen-bond becomes the most favorable binding mode. The 6MP affinity for gold clusters decreases in the order of vacuum > neutral solution > acidic medium. During the adsorption, the energy gap of Au20 substantially declines, leading to an increase in its electrical conductivity, which can be converted to an electrical noise. Moreover, such interaction is likely a reversible process and triggered by either the low pH in sick tissues or the presence of cysteine residues in protein matrices. While N-H bending and stretching vibrations play major roles in the SERS phenomenon of 6MP on gold surfaces in neutral solution, the strongest enhancement in acidic environment is mostly due to an Au⋅⋅⋅H-S coupling, rather than an aromatic ring-gold surface π overlap as previously proposed.

Inactivation of Acanthamoeba Cysts in Suspension and on Contaminated Contact Lenses Using Non-Thermal Plasma

Water suspensions of cysts of a pathogenic clinical isolate of Acanthamoeba sp. were prepared, and the cysts were inactivated either in suspension or placed on the surface of contact lenses by the non-thermal plasma produced by the DC corona transient spark discharge. The efficacy of this treatment was determined by cultivation and the presence of vegetative trophozoites indicating non-inactivated cysts. The negative discharge appeared to be more effective than the positive one. The complete inactivation occurred in water suspension after 40 min and on contaminated lenses after 50 min of plasma exposure. The properties of lenses seem to not be affected by plasma exposure; that is, their optical power, diameter, curvature, water content and infrared and Raman spectra remain unchanged.

Theoretical Prediction of Structures, Vibrational Circular Dichroism, and Infrared Spectra of Chiral Be4B8 Cluster at Different Temperatures

Lowest-energy structures, the distribution of isomers, and their molecular properties depend significantly on geometry and temperature. Total energy computations using DFT methodology are typically carried out at a temperature of zero K; thereby, entropic contributions to the total energy are neglected, even though functional materials work at finite temperatures. In the present study, the probability of the occurrence of one particular Be4B8 isomer at temperature T is estimated by employing Gibbs free energy computed within the framework of quantum statistical mechanics and nanothermodynamics. To identify a list of all possible low-energy chiral and achiral structures, an exhaustive and efficient exploration of the potential/free energy surfaces is carried out using a multi-level multistep global genetic algorithm search coupled with DFT. In addition, we discuss the energetic ordering of structures computed at the DFT level against single-point energy calculations at the CCSD(T) level of theory. The total VCD/IR spectra as a function of temperature are computed using each isomer's probability of occurrence in a Boltzmann-weighted superposition of each isomer's spectrum. Additionally, we present chemical bonding analysis using the adaptive natural density partitioning method in the chiral putative global minimum. The transition state structures and the enantiomer-enantiomer and enantiomer-achiral activation energies as a function of temperature evidence that a change from an endergonic to an exergonic type of reaction occurs at a temperature of 739 K.

Computational studies on binding, solvent, and pH effects on (S)-propranolol and methacrylic acid complex

Density functional theory methods have been applied to understand binding of (s)-propranolol, a template, to a methacrylic acid molecule acting as a functional monomer using basic 1:1 model. The model has been expanded to study the effect of various pH by adding hydronium and hydroxide ions solvated by water molecules to the template-monomer system, to mimic acidic and basic environments, respectively. This could be considered a model study towards a potential use of molecular imprinting method for the design of a transdermal patch for a topical and direct delivery of (s)-propranolol to hemangiomas. In addition, this study provides detailed binding site analysis of the template and functional monomer verified by the theoretical IR spectra analysis, as well as solvent and pH effects on template-monomer binding energy.

Experimental and DFT investigation of structure and IR spectra of H-bonded associates of p-(3-carboxy-1-adamantyl)thiacalix[4]arene

The IR spectra of p-(3-carboxy-1-adamantyl)thiacalix[4]arene (1-AdCOOHTC4A) have been studied. IR spectra of crystalline 1-AdCOOHTC4A obtained at room temperature or upon heating to 250 °C or its dilute solutions lack bands of free hydroxyl groups. The frequency of hydroxyl groups at 3377 cm^-1 indicates the formation of an intramolecular H-bond along the lower rim of the 1-AdCOOHTC4A molecule. On the top edge of thiacalixarene, the carboxyl groups form dimeric or cyclic tetrameric complexes via intermolecular H-bonds. The conformation of the cone persists, but there is a mutual influence of H-bonds along the upper and lower rims of the thiacalix[4]arene molecule. The structure with dimer H-bonds between carboxyl groups is 31.9 KJ/mol less preferable than the conformation with tetramer cyclic H-bonds for 1-AdCOOHTC4A. Comparison of the absorption band of νOH alcohol hydroxyl groups in the IR spectra of 1-AdCOOHTC4A at 3377 cm^-1, with the corresponding band of 1-AdTC4A at 3372 cm^-1, suggests that the presence of the second system of H-bonds of carboxyl groups in the first molecule does not affect the H-bond of alcohol hydroxyl groups.

Subcritical water extraction of organic acids from chicken manure

BACKGROUND

Chicken manure waste has a wide range of organic substances and mineral elements. This enriched source has stimulated great scientific interest in finding cleaner and more environmentally benign nutrient recovery options. This study aimed to determine an effective and eco-friendly method (i.e. subcritical water extraction) for processing fresh poultry manure.

RESULTS

The high content of total organic carbon, including humic acids carbon and fulvic acids carbon, in extract was found to release under subcritical conditions. The organic compounds obtained by extraction with subcritical water correspond to humic acid in composition because of the presence in the sample of all the functional groups: polymer bonded by molecular hydrogen bond (3400 cm^-1 ), the presence of CH₂ and CH₃ groups (2870 cm^-1 ), the presence of carboxyl groups (1720 cm^-1 ) and quinones (1640-1680 cm^-1 ). The solid phase left over was characterized by a high content of organic carbon, phosphorus, potassium, and microelements. The maximum extraction of humic acid and fulvic acid carbon was found between 210 and 250 °C at a pressure of 50-60 atm, and the content was a maximum of 3647.2 × 10^-6 g kg^-1 at an extraction temperature of 250 °C.

CONCLUSION

Given the high content of humic acid found in the extracted medium, the proposed subcritical extraction opens up new opportunities for nutrients recovery in the poultry industry. © 2020 Society of Chemical Industry.

Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be6B11- Flux-Ional Cluster

The starting point to understanding cluster properties is the putative global minimum and all the nearby local energy minima; however, locating them is computationally expensive and difficult. The relative populations and spectroscopic properties that are a function of temperature can be approximately computed by employing statistical thermodynamics. Here, we investigate entropy-driven isomers distribution on Be₆B₁₁⁻ clusters and the effect of temperature on their infrared spectroscopy and relative populations. We identify the vibration modes possessed by the cluster that significantly contribute to the zero-point energy. A couple of steps are considered for computing the temperature-dependent relative population: First, using a genetic algorithm coupled to density functional theory, we performed an extensive and systematic exploration of the potential/free energy surface of Be₆B₁₁⁻ clusters to locate the putative global minimum and elucidate the low-energy structures. Second, the relative populations’ temperature effects are determined by considering the thermodynamic properties and Boltzmann factors. The temperature-dependent relative populations show that the entropies and temperature are essential for determining the global minimum. We compute the temperature-dependent total infrared spectra employing the Boltzmann factor weighted sums of each isomer’s infrared spectrum and find that at finite temperature, the total infrared spectrum is composed of an admixture of infrared spectra that corresponds to the spectra of the lowest-energy structure and its isomers located at higher energies. The methodology and results describe the thermal effects in the relative population and the infrared spectra.

From Infrared Spectra to Macroscopic Mechanical Properties of sH Gas Hydrates through Atomistic Calculations

The vibrational characteristics of gas hydrates are key identifying molecular features of their structure and chemical composition. Density functional theory (DFT)-based IR spectra are one of the efficient tools that can be used to distinguish the vibrational signatures of gas hydrates. In this work, ab initio DFT-based IR technique is applied to analyze the vibrational and mechanical features of structure-H (sH) gas hydrate. IR spectra of different sH hydrates are obtained at 0 K at equilibrium and under applied pressure. Information about the main vibrational modes of sH hydrates and the factors that affect them such as guest type and pressure are revealed. The obtained IR spectra of sH gas hydrates agree with experimental/computational literature values. Hydrogen bond’s vibrational frequencies are used to determine the hydrate’s Young’s modulus which confirms the role of these bonds in defining sH hydrate’s elasticity. Vibrational frequencies depend on pressure and hydrate’s O···O interatomic distance. OH vibrational frequency shifts are related to the OH covalent bond length and present an indication of sH hydrate’s hydrogen bond strength. This work presents a new route to determine mechanical properties for sH hydrate based on IR spectra and contributes to the relatively small database of gas hydrates’ physical and vibrational properties.

A simple approach for determination of the phase transition temperature using infrared temperature-induced isosbestic points

The appearance and formation of an isosbestic point in the temperature-dependent IR spectra can be used to reveal a phase transition at a certain temperature. This conclusion was made by a thorough investigation of the IR (transmission and ATR) spectra of methylammonium iodide (MAI) and formamidinium iodide (FAI) recorded in a wide temperature range starting from -170 to +200 °C. By investigating the isosbestic points, it was found that MAI undergoes two phase transitions at -110 and +146 °C. The results obtained for FAI also showed two phase transitions at 73 and 115 °C. Furthermore, it was found that the shift of certain bands that are provoked by the phase change could be used to calculate the transition temperature. So far, according to the literature data, no attempts have been made to reveal the exact temperature of phase transitions using IR spectroscopic techniques.

[Spectroscopic studies of the changes occurring in the molecular composition of oral fluid in people with multiple caries]

The changes in molecular composition of mixed saliva (oral fluid) were analyzed with the use of spectroscopic techniques for the patients with multiple caries. Using Fourier-transform infrared spectroscopy studies including synchrotron radiation for the excitation certain features were detected in the IR-spectra of the oral fluid. Mineral-organic, carbon-phosphate, AmidII/AmidI and protein/thiocyanate ratios were calculated for the groups of patients with multiple caries and patients of the control group. Complex analysis of the obtained experimental data enabled to determine that in the oral fluid of the persons with multiple caries as compared with the control group content of the mineral groups and complexes is reduced while the share of organic component is increased. Content of thiocyanate increases by more than two times and there appear carboxyl groups of esters, lipids and carbohydrates. The detected features in IR-spectra of mixed saliva as well as the changes found in its molecular composition based on the calculated ratios between organic and inorganic components can be used as biomarkers of cariogenic condition in the oral cavity. It can be used as a diagnostic criterion in the analysis of the oral fluid samples taken from the patients.

Hydrated Sodium Ion Clusters [Na+(H2O)n (n = 1-6)]: An ab initio Study on Structures and Non-covalent Interaction

Structural, thermodynamic, and vibrational characteristics of water clusters up to six water molecules incorporating a single sodium ion [Na⁺(H₂O)_n (n = 1–6)] are calculated using a comprehensive genetic algorithm combined with density functional theory on global search, followed by high-level ab initio calculation. For n ≥ 4, the coordinated water molecules number for the global minimum of clusters is 4 and the outer water molecules connecting with coordinated water molecules by hydrogen bonds. The charge analysis reveals the electron transfer between sodium ions and water molecules, providing an insight into the variations of properties of O–H bonds in clusters. Moreover, the simulated infrared (IR) spectra with anharmonic correction are in good agreement with the experimental results. The O–H stretching vibration frequencies show redshifts comparing with a free water molecule, which is attributed to the non-covalent interactions, including the ion–water interaction, and hydrogen bonds. Our results exhibit the comprehensive geometries, energies, charge, and anharmonic vibrational properties of Na⁺(H₂O)_n (n = 1–6), and reveal a deeper insight of non-covalent interactions.

Density functional theory studies on the structures and vibrational spectroscopic characteristics of nickel, copper and zinc naphthalocyanines

Molecular geometries and electronic structure calculations and spectroscopic assignments for metallonaphthalocyanines NiNc, CuNc and ZnNc are performed on the optimized geometries at B3LYP/6-31G* level. The order of the bond lengths of the NM bonds is computed to be NiNc < CuNc < ZnNc. The Mulliken atomic charges of the central M vary in the same order as the bond lengths. The metal dependent frequencies of IR-active and Raman-active vibrational modes decrease in the order of NiNc > CuNc > ZnNc, which is in reverse sequence of the N-M bond length. The strongest Raman lines predicted at 1570 (NiNc), 1546 (CuNc) and 1525 (ZnNc) cm^-1 are highly sensitive to the metal ion. Comparison of the calculated properties of MNcs and MPcs (metallphthalocyanines) compounds reveals some interesting and meaningful results due to extension of the conjugated systems.

On the ability of pnicogen atoms to engage in both σ and π-hole complexes. Heterodimers of ZF2C6H5 (Z = P, As, Sb, Bi) and NH3

When bound to a pair of F atoms and a phenyl ring, a pyramidal pnicogen (Z) atom can form a pnicogen bond wherein an NH₃ base lies opposite one F atom. In addition to this σ-hole complex, the ZF₂C₆H₅ molecule can distort in such a way that the NH₃ approaches on the opposite side to the lone pair on Z, where there is a so-called π-hole. The interaction energies of these π-hole dimers are roughly 30 kcal/mol, much larger than the equivalent quantities for the σ-hole complexes, which are only 4-13 kcal/mol. On the other hand, this large interaction energy is countered by the considerable deformation energy required for the Lewis acid to adopt the geometry necessary to form the π-hole complex. The overall energetics of the complexation reaction are thus more exothermic for the σ-hole dimers than for the π-hole dimers.

Towards accurate infrared spectral density of weak H-bonds in absence of relaxation mechanisms

Following the previous theoretical developments to completely reproduce the IR spectra of weak hydrogen bond complexes within the framework of the linear response theory (LRT), the quantum theory of the high stretching mode spectral density (SD) of weak H-bonds is reconsidered. Within the LRT theory, the SD is the one sided Fourier transform of the autocorrelation function (ACF) of the high stretching mode dipole moment operator. In order to provide more accurate theoretical bandshapes, we have explored the equivalence between the SDs given in previous studies with respect to a new quantum one, and revealed that in place of the basic equations used in the precedent works for which the SD I_Old(ω)=2Re∫₀^∞G_Old(t)e^-iωtdt where the ACF G_Old(t) = ⟨μ(0)μ(t)⁺⟩ = tr {ρ {μ(0)} {μ(t)}⁺}, one can use a new expression for the SD, given by I_New(ω)=2ωRe∫₀^∞G_New(t)e^-iωtdt where G_New(t)=μ(0)μ(t)⁺=1βtrρ_B∫₀^βμ(0)μ(t+iλℏ)⁺dλ. Here ρ_B is the Boltzmann density operator, μ(0) the dipole moment operator at initial time and μ(t) the dipole moment operator at time t in the Heisenberg picture, ℏ is the Planck constant, β is the inverse of the Boltzmann factor k_BT where T is the absolute temperature and k_B the Boltzmann constant. Using this formalism, we demonstrated that the new quantum approach gives the same final SD as used by previous models, and reduces to the Franck-Condon progression appearing in the Maréchal and Witkowski's pioneering approach when the relaxation mechanisms are ignored. Results of this approach shed light on the equivalence between the quantum and classical IR SD approaches for weak H-bonds in absence of medium surroundings effect, which has been a subject of debate for decades.

Carbon Materials with Zigzag and Armchair Edges

Carbon materials such as graphene and graphene nanoribbon with zigzag and armchair edges have attracted much attention because of various applications such as electronics, batteries, adsorbents, and catalyst supports. Preparation of carbon materials with different edge structures at a large scale is essential for the future of carbon materials, but it is generally difficult and expensive because of the necessity of organic synthesis on metal substrates. This work demonstrated a simple preparation method of carbon materials with zigzag and armchair edges with/without nonmetallic silica supports from aromatic compounds such as tetracene with zigzag edges and chrysene with armchair edges and also determined the edge structures in detail by three types of analyses such as (1) reactive molecular dynamic simulation with a reactive force field, (2) Raman and infrared (IR) spectra combined with calculation of spectra, and (3) reactivity analyzed by oxidative gasification using thermogravimetric analysis. Two different types of carbon materials with characteristic Raman and IR spectra could be prepared. These carbon materials with different edge structures also clearly showed different tendency in oxidative gasification. This work did not only show the simple preparation method of carbon materials with different edge structures, but also contributes to the development of detailed analyses for carbon materials.

Crystal structures of racemic and enantiopure synephrine correlated with physicochemical properties from IR spectroscopy and thermal analysis

The proto-alkaloid synephrine {SYN; systematic name: 4-[1-hydroxy-2-(methylamino)ethyl]phenol}, C₉H₁₃NO₂, is found to crystallize as a neutral molecule in the racemate and as a zwitterion in the pure enantiomer, in which the phenolic H atom has been transferred to the amino group. In the racemate crystal, an enantiomeric pair on an inversion centre is weakly linked by alcoholic O-H and N-H groups into an R₂²(10) ring. The trigonal pyramidal amino group is also linked to the phenolic and alcoholic groups to form a C(6) chain. In the enantiopure crystal, the deprotonated phenolic O atom is involved in trifurcated hydrogen bonding to two quaternary ammonium groups and an alcoholic O-H group to form a fused R₂⁴(11) ring and a C(7) chain. From the results of the crystal structure analysis, thermal analyses and DFT calculations validated from FT-IR spectra, a different tautomer was found in the racemic molecule (RS-SYN) versus the enantiopure molecule (R-SYN).

Vibrational spectroscopic investigation of the gold complexation within the cascade structure of phosphorus-containing dendrimer

The interaction of the phosphoric dendrimer with gold was performed by means of vibrational spectroscopy and quantum chemistry. Stable complexes are formed with a PN-PS linkage, whereas with an isolated PS bond this does not occur. The change in geometric parameters and delocalization of electric charge under the influence of gold was discovered. The classification of bands in the experimental vibrational spectra of the dendrimer and its complex was carried out. HOMO of molecule of the dendrimer is localized on the SPNP linkage, whereas the LUMO is located on the terminal group. In the SPNP linkage there is a noticeable delocalization of the charge which leads to a change in the reactivity of this group. Interaction energy was estimated as the difference between the energies of the complex and the energies of the molecules of the dendrimer G'₀ and two molecules AuCl and is equal to 25.2 eV. The ionization energy IE and electron affinity EA for AuCl are higher than for dendrimer, therefore, when the complex is formed, these quantities increases. Chemical potential and the electrophilicity index in the complex also increases.

Co-Tetraphenylporphyrin (co-TPP) in TM-TPP (TM = Fe, Co, Ni, Cu, and Zn) series: a new optical material under DFT

A detailed investigation of the structure, electronic, spectroscopic, and optical properties of a series of transition metal-doped tetraphenylporphyrins (TM-TPP; TM = Fe, Co, Ni, Cu and Zn) is performed under density functional framework. The structure and stability of tetraphenylporphyrin (TPP) and TM-TPPs are understood with HOMO-LUMO gap, chemical hardness, and binding energies of the transition metals to the compound. Optical properties of TPP and TM-TPP series are assessed with relevant optical absorption spectra. A couple of visible active compounds, viz. Co-TPP and Ni-TPP, are reported for the first time for future opto-electronic applications. To gain insight on the possible synthesis of these compounds, we have analyzed frontier molecular orbitals (FMOs) as well as infra-red spectra. Graphical abstract Optical absorption spectra of TPP and TM-TPPs, and infrared spectra of TPP merged with Co-TPP.

Elucidation of the molecular and electronic structures of some magic silver clusters Agn (n = 8, 18, 20)

Density functional theory (DFT) calculations were carried out to explore the geometric, spectroscopic, and electronic properties of three magic silver clusters Ag_n (n = 8, 18, and 20) in detail. The computed results show that the global minima of these clusters are compact, near-spherical structures, while other low-lying isomers exhibit oblate or prolate shapes. Vertical ionization energies for the low-lying isomers were also computed and assigned with respect to available experimental values. Although several isomers were predicted to have similar energies, their electronic and vibrational signatures were quite distinctive, meaning that they could be used as fingerprint signals to distinguish between isomers. In addition, the electronic structures of these systems were explored using the phenomenological shell model. Calculations for the coinage metal clusters M₂₀ (M = Cu, Ag, Au) indicated that the structures and properties of the Ag cluster are similar to those of the Cu cluster in that both Cu₂₀ and Ag₂₀ prefer a compact structure whereas Au₂₀ prefers to adopt a tetrahedral form. Graphical abstract Shell Orbitals of Ag₈ Cluster.

Spectroscopic studies of fly ash-based geopolymers

In the present work fly-ash based geopolymers with different contents of alkali-activator and water were prepared. Alkali-activation was conducted with sodium hydroxide (NaOH) at the SiO₂/Na₂O molar ratio of 3, 4, and 5. Water content was at the ratio of 30, 40, and 50wt% in respect to the weight of the fly ash. Structural and microstructural characterization (FT-IR spectroscopy, ²⁹Si and ²⁷Al MAS NMR, X-ray diffraction, SEM) of the specimens as well as compressive strength and apparent density measurements were carried out. The obtained geopolymers are mainly amorphous due to the presence of disordered aluminosilicate phases. However, hydroxysodalite have been identified as a crystalline product of geopolymerization. The major band in the mid-infrared spectra (at about 1000cm^-1) is related to SiO(Si,Al) asymmetric stretching vibrations and is an indicator of the geopolymeric network formation. Several component bands in this region can be noticed after the decomposition process. Decomposition of band at 1450cm^-1 (vibrations of CO bonds in bicarbonate group) has been also conducted. Higher NaOH content favors carbonation, inasmuch as the intensity of the band then increases. Both water and alkaline activator contents have an influence on compressive strength and microstructure of the obtained fly-ash based geopolymers.

Complexes of O=C=S with Nitrogen Bases: Chalcogen Bonds, Tetrel Bonds, and Other Secondary Interactions

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate chalcogen-bond formation through the σ-hole at S and tetrel-bond formation through the π-hole at C in complexes of OCS with a series of nitrogen bases. The binding energies of chalcogen- and tetrel-bonded complexes with the sp-hybridized bases correlate exponentially with the N-S and N-C distances, respectively. The presence of secondary interactions between an N-H or C-H group of an sp2 -hybridized base and OCS in chalcogen-bonded complexes decreases the correlation between binding energies and the N-S distance. These secondary interactions are stronger in the tetrel-bonded complexes with the sp2 bases, particularly in the isomers of OCS:imidazole and OCS : N2 H2 , where they may be described as distorted N-H⋅⋅⋅O or N-H⋅⋅⋅S hydrogen bonds. Charge-transfer interactions are consistent with the nature of the primary and secondary interactions in these complexes. The in-plane OCS bending frequencies are blue-shift in the chalcogen-bonded complexes, and red-shifted in the tetrel-bonded complexes. EOM-CCSD spin-spin coupling constants 1c J(N4-S) across chalcogen bonds have absolute values less than 9.0 Hz, while the two-bond coupling constants 2c J(N4-C) do not exceed 4.0 Hz. These are greater in absolute value that the one-bond coupling constants 1t J(N4-C) across tetrel bonds that are less than 0.5 Hz at much shorter N-C distances.

Complexes of CO₂ with the Azoles: Tetrel Bonds, Hydrogen Bonds and Other Secondary Interactions

Ab initio MP2/aug’-cc-pVTZ calculations have been performed to investigate the complexes of CO₂ with the azoles pyrrole, pyrazole, imidazole, 1,2,3- and 1,2,4-triazole, tetrazole and pentazole. Three types of complexes have been found on the CO₂:azole potential surfaces. These include ten complexes stabilized by tetrel bonds that have the azole molecule in the symmetry plane of the complex; seven tetrel-bonded complexes in which the CO₂ molecule is perpendicular to the symmetry plane; and four hydrogen-bonded complexes. Eight of the planar complexes are stabilized by Nx···C tetrel bonds and by a secondary interaction involving an adjacent Ny-H bond and an O atom of CO₂. The seven perpendicular CO₂:azole complexes form between CO₂ and two adjacent N atoms of the ring, both of which are electron-pair donors. In three of the four hydrogen-bonded complexes, the proton-donor Nz-H bond of the ring is bonded to two C-H bonds, thereby precluding the planar and perpendicular complexes. The fourth hydrogen-bonded complex forms with the strongest acid pentazole. Binding energies, charge-transfer energies and changes in CO₂ stretching and bending frequencies upon complex formation provide consistent descriptions of these complexes. Coupling constants across tetrel bonds are negligibly small, but ^2hJ(Ny-C) across Nz-H···C hydrogen bonds are larger and increase as the number of N atoms in the ring increases.

Vibrational spectroscopic study of cationic phosphorus dendrimers with aminoethylpiperidine terminal groups

Two generations of phosphoric dendrimers with piperidine functional groups were synthesized for use in biology and medicine. Neutral samples are soluble in organic solvents but after protonation these dendrimers become water soluble and can be used for biological experiments. The FTIR and FT Raman spectra of two generations of dendrimers G_i constructed from the cyclotriphosphazene core, repeating units OC₆H₄CHNN(CH₃)P(S)< and aminoethylpiperidine end groups NH(CH₂)₂C₅NH₁₁ were recorded. The study of the IR spectra shows that the NH groups form hydrogen bonds. The calculation of the molecular structure and vibrational spectra of the first generation dendrimer was performed by the method of DFT. This molecule has flat, repeating units and a plane of symmetry passing through the core. The calculation of the distribution of potential energy made it possible to classify the bands in the experimental spectra of dendrimers. Amine groups are manifested in the form of a band of NH stretching vibrations at 3389 cm^-1 in the IR spectrum of G₁. NH⁺ stretching bands located at 2646 and 2540 cm^-1 in the IR spectrum of G₂. The stretching vibrations of NH⁺ groups are noticeably shifted to low frequencies due to the formation of a hydrogen bond with the chlorine atom. The line at 1575 cm^-1 in the Raman spectrum of G₁ is characteristic for repeating units.

Electronic properties of the polypyrrole-dopant anions ClO4- and MoO42-: a density functional theory study

The conductive properties of polypyrrole chains doped with ClO₄^- or MoO₄^2- anions and the existence of polarons and bipolarons in these doped polypyrrole chains were investigated by performing computational calculations based on density functional theory (DFT). Doping with these anions was found to decrease the band gap of the polypyrrole. Theoretical calculations revealed that changing the type of oxidative agent applied does not affect the conversion of polypyrrole into a conducting polymer, but the conductivity of the doped polypyrrole does depend on the ratio of oxidant to polypyrrole.

Cyclic cooperative intramolecular hydrogen bond in p-tert-butylcalix[6]arene according to FTIR spectroscopy and DFT studies

This article describes a comparative research of IR spectra and H-bonds in the p-tert-butylcalix[6]arene (TB6) and calix[6]arene (C6). IR spectra were computed for compressed cone conformation by DFT method. The assignment of the bands in the IR spectra of the TB6 and C6 was made. The effect of the bulky tert-butyl substituents on the structure and H-bonding in TB6 was established. Our research has shown that in TB6 and C6 the cyclic H-bond is realized, which ensures the existence of a compressed cone conformation. Introduction of tert-butyl substituents in TB6 leads to hardening of H-bonds. Examination of IR spectra showed that when heated TB6 remains in a compressed cone conformation. In a molecule of TB6 and C6 oxygen atoms are in a "boat" conformation.

The dependence on ammonia pretreatment of N-O activation by Co(II) sites in zeolites: a DFT and ab initio molecular dynamics study

This work is focused on the donor properties of cobalt-exchanged cationic sites in zeolites. It is based on cluster and periodic density functional theory modeling for relevant {[Co(II)(NH3)n]-NO} adducts, where Co(II) means a cobalt cation embedded either in a periodic model of chabasite (CHA) zeolite or in model clusters. NO stretching frequencies were derived from MD trajectories and compared to harmonic values from cluster calculations. By relating calculated NO frequencies to experimental FTIR spectra, it was shown that the forms of {Co(II)-NO} adducts comprising three or four ammonia co-ligands dominate the spectrum taken in ammonia-saturation conditions while forms with two NH3 ligands prevail under intermediate ammonia saturation. Finally, this work confirms the critical dependence of Co(II) activation ability towards NO upon the center donor properties, reinforced by ligation of strong donor ammonia ligands. However, strongly bound ligands appear also to compete with interaction of the center with the electron-rich framework, and a balance must be observed to maintain optimal activation ability. Graphical abstract A snapshot from MD trajectory showing a fragment of periodic framework with twoCo(II)-NO centers, bound to one framework oxygen and strongly coordinating three ammonia ligands with four others forming the second coordination sphere.

IR Spectra of Different O2-Content Hemoglobin from Computational Study: Promising Detector of Hemoglobin Variant in Medical Diagnosis

IR spectra of heme and different O₂-content hemoglobin were studied by the quantum computation method at the molecule level. IR spectra of heme and different O₂-content hemoglobin were quantificationally characterized from 0 to 100 THz. The IR spectra of oxy-heme and de-oxy-heme are obviously different at the frequency regions of 9.08-9.48, 38.38-39.78, 50.46-50.82, and 89.04-91.00 THz. At 24.72 THz, there exists the absorption peak for oxy-heme, whereas there is not the absorption peak for de-oxy-heme. Whether the heme contains Fe-O-O bond or not has the great influence on its IR spectra and vibration intensities of functional groups in the mid-infrared area. The IR adsorption peak shape changes hardly for different O₂-content hemoglobin. However, there exist three frequency regions corresponding to the large change of IR adsorption intensities for containing-O₂ hemoglobin in comparison with de-oxy-hemoglobin, which are 11.08-15.93, 44.70-50.22, and 88.00-96.68 THz regions, respectively. The most differential values with IR intensity of different O₂-content hemoglobin all exceed 1.0 × 10⁴ L mol^-1 cm^-1. With the increase of oxygen content, the absorption peak appears in the high-frequency region for the containing-O₂ hemoglobin in comparison with de-oxy-hemoglobin. The more the O₂-content is, the greater the absorption peak is at the high-frequency region. The IR spectra of different O₂-content hemoglobin are so obviously different in the mid-infrared region that it is very easy to distinguish the hemoglobin variant by means of IR spectra detector. IR spectra of hemoglobin from quantum computation can provide scientific basis and specific identification of hemoglobin variant resulting from different O₂ contents in medical diagnosis.

Photoacoustic Spectroscopy for the Determination of Lung Cancer Biomarkers-A Preliminary Investigation

With 1.6 million deaths per year, lung cancer is one of the leading causes of death worldwide. One reason for this high number is the absence of a preventive medical examination method. Many diagnoses occur in a late cancer stage with a low survival rate. An early detection could significantly decrease the mortality. In recent decades, certain substances in human breath have been linked to certain diseases. Different studies show that it is possible to distinguish between lung cancer patients and a healthy control group by analyzing the volatile organic compounds (VOCs) in their breath. We developed a sensor based on photoacoustic spectroscopy for six of the most relevant VOCs linked to lung cancer. As a radiation source, the sensor uses an optical-parametric oscillator (OPO) in a wavelength region from 3.2 µm to 3.5 µm. The limits of detection for a single substance range between 5 ppb and 142 ppb. We also measured high resolution absorption spectra of the biomarkers compared to the data currently available from the National Institute of Standards and Technology (NIST) database, which is the basis of any selective spectroscopic detection. Future lung cancer screening devices could be based on the further development of this sensor.

Influence of microhydration on the structures and proton-induced charge transfer in RNA intermediates

Solvation effects are of major interest in the context of radiation damage, due to their potential applications in cancer therapy. Reliable modeling of the solvent is, however, quite challenging, and numerous studies have been devoted to isolated biomolecules and stepwise-hydrated molecules in which the amount of solvent is controlled one molecule at a time. The influence of stepwise hydration on radiation damage is investigated here using the example of proton-induced charge transfer in two biomolecular targets. Uracil has been widely investigated both experimentally and theoretically in this context, and 2-aminooxazole was recently shown to be a potentially important intermediate in prebiotic chemistry. Focusing here on doubly hydrated biomolecules, stable structures and infrared spectra were obtained by combining the results of molecular dynamics simulations with those of quantum chemistry calculations performed at the density-functional theory level with the double hybrid M06-2X functional. The charge-transfer cross-sections upon proton impact were obtained from ab initio molecular calculations and after applying a semi-classical approach to investigate the collision. Our results suggest a significant relationship between the detailed hydration structure and the efficacy of proton-induced charge transfer, highlighting the competing roles of inter- and intramolecular hydrogen bonding.

Structure, IR and Raman spectra of phosphotrihydrazide studied by DFT

The FTIR and FT Raman measurements of the phosphotrihydrazide (S)P[N(Me)-NH2]3 have been performed. This compound is a zero generation dendrimer G0 with terminal amine groups. Structural optimization and normal mode analysis were obtained for G0 by the density functional theory (DFT). Optimized geometric bond length and angles obtained by DFT show good agreement with experiment. The amine terminal groups are characterized by the well-defined bands at 3321, 3238, 1614cm(-1) in the experimental IR spectrum and by bands at 3327, 3241cm(-1) in the Raman spectrum of G0. The experimental frequencies of asymmetric and symmetric NH2 stretching vibrations of amine group are lower than theoretical values due to intramolecular NH⋯S hydrogen bond. This hydrogen bond is also responsible for higher experimental infrared intensity of these bands as compared with theoretical values. Relying on DFT calculations a complete vibrational assignment is proposed for the studied dendrimer.

Sorption-desorption of fipronil in some soils, as influenced by ionic strength, pH and temperature

BACKGROUND

The sorption-desorpion of fipronil insecticide is influenced by soil properties and variables such as pH, ionic strength, temperature, etc. A better understanding of soil properties and these variables in sorption-desorption processes by quantification of fipronil using liquid chromatography may help to optimise suitable soil management to reduce contamination of surface and groundwaters. In the present investigation, the sorption-desorption of fipronil was studied in some soils at varying concentrations, ionic strengths, temperatures and pH values, and IR specta of fipronil sorbed onto soils were studied.

RESULT

The sorption of fipronil onto soils conformed to the Freundlich isotherm model. The sorption-desorption of fipronil varied with ionic strength in each of the soils. Sorption decreased but desorption increased with temperature. Sorption did not change with increasing pH, but for desorption there was no correlation. The cumulative desorption of fipronil from soil was significantly and inversely related to soil organic carbon content. IR spectra of sorbed fipronil showed the involvement of amino, nitrile, sulfone, chloro and fluoro groups and the pyrazole nucleus of the fipronil molecule.

CONCLUSION

The sorption of fipronil onto soils appeared to be a physical process with the involvement of hydrogen bonding. An increase in soil organic carbon may help to reduce desorption of fipronil. High-temperature regimes are more conducive to the desorption. © 2015 Society of Chemical Industry.