Experimental IR Spectra Research Articles

Jahn-Teller effect versus spin-orbit coupling: The structure of the free molybdenum pentafluoride molecule

The complete active space self-consistent field (CASSCF) and multiconfigurational quasi-degenerate second-order perturbation (MCQDPT2) calculations have been used to study the ground and low-lying excited electronic states of MoF5. Scalar-relativistic effects and spin-orbit coupling (SOC) have been taken into account employing the third-order Douglas-Kroll-Hess (DKH) Hamiltonian and full Breit-Pauli operator, respectively. The optimization and the calculation of the Hessian matrix have been performed by non-routine procedure employing the symmetry coordinates for all considered (D3h, C2v and C4v) geometrical configurations. The trigonal bipyramidal D3h structure of molybdenum pentafluoride MoF5 possesses two-fold degenerate ground first excited electronic orbital state and undergoes Jahn-Teller distortion to the C2v configurations. Accounting of SOC quenches the JT effect. As a result the D3h structure of MoF5 is no longer the conical intersection of two adiabatic potential energy surfaces (APES) but two separated APES corresponding to ground (12E1/2) and nearest excited (12E3/2) spin-orbit states are appeared instead. The D3h trigonal bipyramidal structure in the ground spin-orbit state corresponds to the 2-nd order saddle point on APES and lies above the minima (C2v structure, 12E1/2 state) by 244 cm−1. The warping barrier (another C2v structure) in the trough of APES and the Berry pseudorotation barrier (C4v structure, ground spin-orbit state 2E3/2) are 19 and 310 cm−1, respectively. Therefore MoF5 molecule is characterized in the gas phase by a large-amplitude motion of fluorine atoms in the equatorial plane and non-rigid intramolecular rearrangement by Berry mechanism. Despite such non-rigid nuclei dynamic, the calculated harmonic frequencies of MoF5 molecule do not contradict to available experimental IR spectrum. The repeat refinement of MoF5 gas electron diffraction data has been carried out using static and pseudoconformer models based on the SO-MCQDPT2 results. Corresponding to only extreme points on APES the configurations have been included into the pseudoconformer model. The both models have been fitted to the experimental data by the same quality.

Synthesis, crystal structure, and properties of new compounds [NH4]4[SbF4]2[NbOF5], K4[SbF4]2[NbOF5], and [NH4]4[SbF4]2[SnF6

Three new isostructural complex compounds – [NH4]4[SbF4]2[NbOF5] (1), K4[SbF4]2[NbOF5] (2), and [NH4]4[SbF4]2[SnF6] (3) – have been synthesized, and their structures have been determined. The compounds have appeared to crystallize in a triclinic system, the spatial group P1¯. The structures of the compounds are built from anion layers of the composition [Sb2NbOF13]4–∞2 in 1, 2 and [Sb2SnF14]4–∞2 in 3. The anion layers alternate with the layers of potassium cations in 2 and with ammonium cations in 1, 3. The anion layers of [Sb2NbOF13]4–∞2 in 1, 2 and [Sb2SnF14]4–∞2 in 3 are formed by edge- and corner-sharing centrosymmetric Sb2F12 dimer groups and NbOF5 (for the 1 and 2) and SnF6 (for 3) distorted octahedra. The melting points of the compounds 1-3 along with K4[SbF4]2[SnF6] (4) have been determined: 454 K – for 1, 556 K – for 2, 463 K – for 3, 559 K – for 4. Based on quantum-chemical calculations of vibrational frequencies, the assignment of bands in the experimental IR and Raman spectra of the synthesized compounds have been performed.

Theoretical (DFT) and experimental (Raman and FTIR) spectroscopic study on communic acids, main components of fossil resins.

The objective of this work is to establish a spectral assignment of several communic acids. The most significant vibrational modes of three stereoisomers of communic acids [trans-, cis-, and iso- (or mirceo-)] are presented. They are showed throughout experimental Raman and IR spectra, and on the basis on calculations with Density Functional Theory (DFT) and the assignment of the spectral bands of different resins found in the literature. These three communic acids studied are the most important isomers present in the scaffold of the fossil resins Class I, as monomers or co-polymerized according to several authors. These kinds of terpenes are used as starting material, for example, for the synthesis of the fungicide and compounds bioactives. In a novel way, it is reported jointly the assignment of the experimental Infrared and Raman modes together with theoretical modes, since normally the authors tend to focus on one or another spectroscopic technique only. These results can be used as a reference for distinguishing amber from less matured resins as copal, determining the local origin of archaeological fossilized resins. Moreover, they will serve as help to differentiate between real and imitation ambers.

Experimental and theoretical study of Aspartic acid

The aim of this research is to detect zwittterionic structure of the aspartic acid and confirm the experimental spectra with quantum chemical calculations. The experimental IR and Raman spectra of aspartic acid powder show no vibrational bands of OH and NH stretching in expected spectral region. We assume that zwitterionic structure of aspartic acid is responsible for lowering the frequencies of these vibrations. An extensive experimental and computational research supports this assumption. Our DFT calculation strongly suggests the need for the dielectric environment in order to stabilize the zwitterionic structure of a single molecule. The network of intermolecular hydrogen bonding between aspartic acid molecules provides this dielectric environment. The DFT quantum mechanical calculations corroborate this assumption by optimizing a four-member group of molecules, which also gives an explanation of broad IR spectrum lines.

Vibrational properties of uranium fluorides

Multiphase mixtures of the uranium fluoride compounds UFx with x = 3, 4, 4.5, 5, whose local U–F bonding geometry is conserved, may result from UF6 reduction. One method for identifying multiphase mixtures is optical vibrational spectroscopy, but experimental Raman and IR spectra for UFx compounds are difficult to obtain. To supplement those experimental measurements, we use density functional perturbation theory (DFPT) with the on-site Coulomb correction (Hubbard + U) to calculate the phonon normal modes, their IR intensity, and their Raman activity for UF3, UF4, U2F9, and UF5. In addition, we use neutron spectroscopy to measure the phonon density of states of the most stable UF4. Our measurements on the Wide-Angular Range Chopper Spectrometer at the Spallation Neutron Source indicate that UF4 has a broad phonon spectrum centered at about 30 meV, but modeling of this spectrum indicates significant multiphonon scattering is present. DFPT calculations for U2F9, which shares structural features with UF4 and UF5, suggest a dynamic instability and we speculate that previous crystallographic measurements of this compound were possible only in multiphase mixtures. Analysis of the detailed atomic motions of phonons in UF5 indicate that a series of high energy modes (between 69 and 75 meV) are described by motion of single-coordinated F atoms (bonded to only one U atom). These single-coordinated F atoms are unique to the UF5 structure and those modes could be used to distinguish UF5 in a multiphase mixture using optical spectroscopy.

High-temperature “ion baseball” for enhancing concentrated solar power efficiency

Recent guidelines for the third generation of solar absorber coatings have shown an unavoidable necessity for low thermal emittance coatings for concentrated solar power tower technology to decrease the thermal loss at the absorber surface. By tuning the pigment spinel crystal structure, density or roughness of a coating, improved optical properties for the coating can be achieved. In this study, a high solar-radiation absorbing pigment CuMn1.5Fe0.5O4 was calcined with 3 wt % Al, Fe, Ni, Mo and Cr to study the optical property improvement of the absorber coating, which could increase the efficiency of concentrated solar power plants. The modified pigment particles were investigated and compared to the non-modified pigment by XRD, TEM and elemental mapping, which showed that the pigment was successfully doped with Fe, Ni, and Cr. In contrast, no spinel doping was observed when Al and Mo were used. The most likely final position of the migrating Cr atoms was determined by comparing the experimental IR spectrum of the Cr-doped spinel structure with the spectra of various structures calculated based on first principles density functional theory calculations. Furthermore, the prepared coatings were thermally aged for 1300 h at 800 °C in air, followed by repetitive optical measurements. Outstanding results were achieved for the aged coating, which was made from a Cr-doped black pigment. Its solar absorptance (>95%) and εT/αS ratio (0.94) after 1300 h of thermal ageing were better than that of a standard paint (εT/αS = 1). We estimated that it may be possible to save up to 300,000 €/year on a fully operating concentrated solar power (CSP) plant by replacing the standard absorber paint with the Cr-doped pigment due to its better absorption efficiency.

Structural-Spectroscopic Properties and Antioxidant Activity Studies of Naringenin in Solvent Media

In this study, solvent effects on the structural and spectroscopic properties of the naringenin have been investigated. Geometric parameters were calculated and were compared with the experimental X-ray crystallographic data. In addition, optimized structures were obtained in solvent media and the solvents effects on geometric parameters were determined. Vibrational modes obtained in the vacuum and in solvent environments were compared with the experimental IR spectrum. Furthermore, the HOMO-LUMO energies and chemical reactivity were also determined. Antioxidant activity of naringenin has been investigated with hydrogen atom abstraction from −OH groups. The bond dissociation enthalpies have been calculated and it is determined that this process should be the main mechanism for the antioxidant activity of naringenin. According to the calculation results, surprisingly, it has been found that in DMSO, BDE values of naringenin are significantly reduced and thus antioxidant activity is increased compared to other media.

Doping of molecular materials based on ferrocene and the study of their properties as organic semiconductors for their application in optoelectronic devices

The present study refers to the chemical doping of ferrocene materials from the reaction with 2,6-Dihydroxyanthraquinone and 2,6-Diaminoanthraquinone. Thin films of the doped molecular materials were prepared by vacuum evaporation and the morphology and structure of films were studied using SEM, EDS and IR spectroscopy. Theoretical calculations were carried out by means Gaussian16 software and all the involved species were geometrically optimized. The IR spectrum, the HOMO-LUMO energy and the bandgaps from these calculations were achieved. The theoretical and experimental IR spectra were compared in order to verify the presence of the main functional groups of the molecular materials. The theoretical bandgap of each film was also compared with that obtained by UV–vis spectroscopy, showing similar results in the range of 2–2.9 eV. These bandgap values place the synthesized materials within the so-called organic semiconductors. Additionally from the calculations of HOMO-LUMO and bandgap results, it has been suggested that the synthesized materials can be used as a semiconductor p-type. The films were evaluated in their p-type semiconductor behavior by means of unipolar devices. In the material synthesized from ferrocene and 2,6-Dihydroxyanthraquinone a virtually ohmic I-V ratio was obtained, while the compound constituted by 2,6-Diaminoanthraquinone behaved as an insulator. In order to improve the p-type behavior of the synthesized semiconductors, unipolar devices were given a hole-injecting layer between the anode and the synthesized materials: glass/ITO/CuPc/synthesized material/Ag. Its I-V electrical behavior was evaluated by the effect of influencing electromagnetic radiation in the range of the electromagnetic spectrum between the IR and the UV passing through the visible spectrum. The results for both devices have shown that the one manufactured from ferrocene and 2,6-Dihydroxyanthraquinone exhibited a behavior similar to that of a Schottky diode, while the one prepared from ferrocene and 2,6-Diaminoanthraquinone behaves like a resistor.

Study of conformation and hydrogen bonds in the p-1-adamantylcalix[8]arene by IR spectroscopy and DFT

The hydrogen bonds and the conformations of calix[8]arene molecules with p-tert-butyl and p-1-adamantyl substituents were studied by infrared spectroscopy in different states. The conformations, the reactivity, the charge distribution and the IR spectra of the calixarenes were calculated by the DFT method with the PBE functional and a TZVP basis set. We compare the IR spectra of calix[8]arene molecules in the conformation of the pleated loop and the chair. The optimized geometry of the molecules reproduces the experimental X-ray data. The conformation chair is 20 kcal/mol less preferable than the conformation pleated loop. The conformation of a pleated loop is the most stable in the solid state and solution. Hydrogen bonds determine the stability of this structure. In the p-1-adamantylcalix[8]arene, stronger hydrogen bonds are realized compared to p-tert-butylcalix[8]arene. The observed IR spectra were interpreted using the calculated potential energy distribution with the quantum-chemical force constants. The theoretical absorption curves calculated for the pleated loop conformation correspond to the experimental IR spectra of the calix[8]arenes.

Vibrational signatures of curcumin's chelation in copper(II) complexes: An appraisal by IRMPD spectroscopy.

Curcumin (Cur) is a natural polyphenol with a wide spectrum of biological activities and appealing therapeutic potential. Herein, it has been delivered by electrospray ionization as gaseous protonated species, [Cur + H]+, and as a Cu(ii) complex, [Cu(Cur - H)]+, a promising antioxidant and radical scavenger. The gas phase structures were assayed by infrared multiple photon dissociation (IRMPD) spectroscopy in both the fingerprint (800-2000 cm-1) and hydrogen stretching (3100-3750 cm-1) ranges. Comparison between the experimental features and linear IR spectra of the lowest energy structures computed at the B3LYP/6-311+G(d,p) level reveals that bare [Cu(Cur - H)]+ exists in a fully planar and symmetric arrangement, where the metal interacts with the two oxygens of the syn-enolate functionality of deprotonated Cur and both OCH3 groups are engaged in H-bonding with the ortho OH. The effect of protonation on the energetic and geometric determinants of Cur has been explored as well, revealing that bare [Cur + H]+ may exist as a mixture of two close-lying isomers associated with the most stable binding motifs. The additional proton is bound to either the diketo or the keto-enol configuration of Cur, in a bent or nearly planar arrangement, respectively.

STUDY OF STRUCTURAL ORGANIZATION OF SYSTEMS ON BASIS OF p-n-PROPYLOXICINNAMIC ACID AND NONMESOGENES OF Ph–X–Ph TYPE

The variants of structural organization in the systems “mesogen – nonmesogen” are considered. The systems contain p-n-propyloxycinnamic acid (A), as a mesogenic component, and nonmesogenic Ph–X–Ph compounds: phenyl benzoate (B, where X = –COO–), azobenzene (C, where X = –N=N–) and N-benzylideneaniline (D, where X = –CH=N–). Quantum-chemical modeling of possible structural units in such systems has been performed. It was shown that all assumed A∙∙∙X(Ph)2 H-complexes do not have electronic and geometric anisotropy and have a lower intermolecular interaction energy than the cyclic dimer of acid A∙∙∙A. The calculated values of the Gibbs free energy of complexation reactions also indicate a low probability of the formation of A∙∙∙X(Ph)2 type H-complexes. It is noted that the “length” of the A∙∙∙A dimer is comparable with the doubled “length” of Ph–X–Ph molecules, which, like the acid dimer, have a rod-like structure favorable for the formation of nematic and smectic LC phases. Based on the analysis of the quantum chemical calculations, it was assumed that Ph–X–Ph can be embedded between acid cyclic dimers A∙∙∙A and can facilitate reduce intermolecular interactions in the system, which reduces the temperature of Cr–LC transitions. The proposed structural organization of systems A: Ph–X–Ph is confirmed by an experimental IR spectrum for a similar system, in which the bands corresponding to the vibrational frequencies of the acid dimer and to individual molecules of alkyloxy substituted phenyl benzoate B are recorded.

X-ray, optical, vibrational, electrical, and DFT study of the polymorphic structure of ethylenediammonium bis iodate α-C2H10N2(IO3)2 and β-C2H10N2(IO3)2

The interaction of ethylenediamine with iodic acid by the slow evaporation method at room temperature gives rise to the crystals of α-C2H10N2(IO3)2 and β-C2H10N2(IO3)2 denoted as α-EBI and β-EBI, respectively. The acentric crystal structures of both polymorphs that consist of [C2H10N2]2+ cations and [IO3]− anions connected together by N–H…O hydrogen bonds are discussed and compared. The optical properties of both polymorphs were determined using UV-vis diffuse reflectance spectroscopy (DRS) showing a wide transparency windows. The DFT calculations using the mixed B3PW91/[6–31 + (d, p), LanL2Dz] basis set of optimized geometries, dipole moment (μ), polarizability (α), first static hyperpolarizability (β), and population analysis were also reported. The experimental and theoretical IR and Raman spectra were compared, and the careful and complete assignment of the vibrational motions of both compounds was undertaken with the aid of potential energy distribution (PED) analysis. DSC and AC conductivity analysis revealed that α-C2H10N2(IO3)2 and β-C2H10N2(IO3)2 undergo a first-order phase transition around 360 K. The electrical σtot (ω, T) conductivity obeyed to Jonscher’s power law and the temperature dependence of the S(T) parameter showed that the electrical conductivity of both polymorph phases might be treated using the correlated barrier hopping (CBH) model.

IRMPD action spectroscopy, ER-CID experiments, and theoretical approaches investigate intrinsic L-thymidine properties compared to D-thymidine: Findings support robust methodology

L-Thymidine (L-dThd) is the enantiomer of D-thymidine (dThd), a naturally-occurring pyrimidine nucleoside found within DNA nucleic acids. L-dThd, also known as Telbivudine, does not occur naturally, but in the last decade has found successful application as an antiviral medication for hepatitis B virus infection. In this work, the gas-phase conformers of the protonated and sodium cationized forms of L-dThd, [L-dThd+H]+ and [L-dThd + Na]+, are investigated using infrared multiple photon dissociation (IRMPD) action spectroscopy complemented by electronic structure calculations performed at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory. Comparisons between the experimental IRMPD spectra and theoretical linear IR spectra elucidate the stable low-energy conformations adopted by these L-dThd complexes generated by electrospray ionization. Minor 2,4-dihydroxy tautomers (T) and O2 protonated conformers contribute to the experimental [L-dThd+H]+ population, whereas conformers involving tridentate binding of Na+ to the O2, O4′, and O5′ atoms primarily contribute to the experimental [L-dThd + Na]+ population. Theory predicts a tautomer as the protonated ground conformer of [L-dThd+H]+ with thymine in an anti orientation and a tridentate (O2O4′O5′) sodium cationized ground conformer with a syn thymine orientation, consistent with theoretical predictions for [dThd+H]+ and [dThd + Na]+, respectively. Both protonated and sodium cationized L-dThd and dThd illustrate highly parallel IRMPD spectral features as expected. Survival yield analyses of data from energy-resolved collision-induced dissociation experiments elucidate the relative stabilities of [L-dThd+H]+ and [L-dThd + Na]+ as compared to the corresponding enantiomeric systems. Identical results are exhibited in the survival yield analyses as anticipated for enantiomeric complexes to simple cations. This work employs the same robust methodology that has provided structural characterization and energetic insight for similar systems preceding it to validate the parallel theoretical and experimental behaviors expected for enantiomers.

Structural analysis and charge transfer properties of a novel pyrazoline derivative: potential energy scan, XRD, DFT and molecular docking studies

The title molecule, 1-[3-(6-bezyloxy-2-hydroxy-4-methyl-cyclohexa-2, 4-dienyl)-5-phenyl-4, 5-dihydro-pyrazol-1-yl]-propan-1-one was synthesized and characterized by FTIR, 1H NMR, 13C NMR and single-crystal X-ray diffraction technique. The optimized geometry is calculated using density functional theory (DFT). A good linear correlation was observed between experimental data and theoretical structural parameters (DFT). Predicted vibrational frequencies were assigned and compared with the experimental IR spectra and they support each other. To determine conformational flexibility and hence to predict the stable geometry, potential energy scan of the molecule was obtained with respect to selected degree of freedom about O18–C19 torsional angle varied from − 180° to + 180° in steps 20°. NBO analysis was carried out for the molecule to check possible hydrogen bond interactions to correlate with those of X-ray data. Molecular stability is mainly due to weak but collective contributions of significant nonconventional C–H…π, π–π and C–H…O-type hydrogen bond interactions and those interactions also quantified by Hirshfeld surface analysis. The thermal stability of the compound was determined with the aid of thermo-gravimetric analysis and differential thermal analysis. The molecular docking study was carried out against the title molecule with 5DBM protein receptor active sites.

Structural And Vibrational Studies on Isomers of Antiviral Ribavirin Drug in Gas and Aqueous Environmental by Using The SQM Approach

Five stable isomers of antiviral ribavirin agent were theoretically determined in gas and aqueous solution by using the hybrid B3LYP/6-31G* method. Here, the solvent effects were studied with the self consistent reaction field (SCRF) methodology employing the polarized continuum (PCM) and the universal solvation model (SM). Structural, electronic and topological properties were reported for all isomers while the vibrational analyses were performed only for those two polymorphic structures experimentally observed in the solid phase by X-ray diffraction. Calculations have evidenced that C2 correspond to the polymorphic V1 structure while C5 to the polymorphic V2 structure. The high dipole moment values predicted for C2 and C5 in both media could probably explain their presences in the solid. Experimental available IR and Raman spectra of ribavirin in the solid state and normal internal coordinates were employed together with the scaled quantum mechanical force field (SQMFF) approach to perform the complete vibrational assignments in both media. Here, the 81 vibration modes expected for C2 and C5 in both media were completely assigned. The frontier orbitals studies reveal that C5 is the less reactive in both media. Here, the gap value observed for C5 is in agreement with the value recently reported for ribavirin by using B3LYP/6-311++G** calculations.

Enhanced NLO activity of organic 2-methyl-5-nitroaniline crystal: Experimental and computational investigation with and without silver addition

The nonlinear optical (NLO) material, 2-methyl-5-nitroaniline (M5NA), is synthesized and the crystals are grown by slow evaporation technique. The theoretical vibrational spectral analyses are done for the first time for M5NA using B3LYP computational method with the basis set cc-pVTZ. Natural Bond Orbital (NBO) and Atoms In Molecules (AIM) analyses are carried out for obtaining the charge transfer interactions and the Hirshfeld surface analysis with the fingerprint plot is performed for finding out the intermolecular interaction sites of the molecule. Using the theoretical and experimental IR and Raman spectra, the vibrations of M5NA are estimated. Changes in the linear and nonlinear optical properties with the addition of silver nanoparticles are studied from the UV–vis absorption spectra and the Z-Scan curves. A comparison of the hyperpolarizability values is done with pure and silver-added M5NA.

Tetrakis(1,2,5-thiadiazolo)porphyrazines. 9. Synthesis and spectral and theoretical studies of the lithium(i) complex and its unusual behaviour in aprotic solvents in the presence of acids.

The template cyclotetramerization of 1,2,5-thiadiazolo-3,4-dicarbonitrile in the presence of lithium n-butoxide in n-butanol leads to the Li(i) complex of tetrakis(1,2,5-thiadiazolo)porphyrazine. Various possible structures of dilithium and monolithium complexes have been considered by DFT/B3LYP molecular modelling using the cc-pvtz basis set, and their theoretical IR and UV-VIS spectra have been calculated. The experimental 7Li NMR, IR and UV-VIS spectra measurements show that the complex contains two inequivalent lithium atoms - one is coordinated to the macrocyclic dianion to form the anionic lithate complex [TTDPaLi]-, while the other forms the solvated countercation [Li(Solv)4]+. The lithate complex is stable in protic solvents, such as methanol, and is soluble in water to give aggregated solutions. Its demetallation occurs in the presence of acids (CH3COOH, CF3COOH, H2SO4). In aprotic solvents (DMF, DMSO), the acid-catalyzed formation of the [TTDPa]2- dianion is observed which is followed by the formation of the meso-protonated form {H[TTDPa]}- at higher acid concentrations. Both processes can be reversed by the addition of a lithium salt excess or neutralization of the acid. The fluorescence quantum yield for the lithate complex [TTDPaLi]- is much higher than that for the [TTDPa]2- dianion (0.34 and 0.01 in DMSO), and this can be used for detecting low concentrations of acids and Li+ in aprotic solvents (10-6-10-5 M). The first reversible reduction of the macrocycle in the anionic lithate complex (-0.94 V vs. SCE in DMSO) is ∼0.5 V more difficult than that in the complexes with divalent metals [TTDPaM] (M = MgII, ZnII, CuII).

Three New Copper (II) Complexes with CHIRAL SCHIFF BASES: Synthesis, Characterization, DNA Binding and DNA-Cleavage Studies

New mononuclear copper (II) complexes (1, 2 and 3) were synthesized from Schiff bases (H2L) of chiral amino alcohols. The structures of the copper complexes were proposed by a combination of elemental analyses, FTIR, LCMS, magnetic susceptibility and molar conductance measurement methods. Spectroscopic and analytical data of the complexes suggest four-coordinated structures. Geometry optimization carried out with DFT/6-31G (d,p) were proposed to be distorted square planar geometry for the complexes. The similarity between experimental and theoretical IR spectra confirms the proposed structures. The interaction of copper (II) complexes with calf thymus (CT-DNA) was investigated using absorption titration method. The results suggest that the complex 1 and 2 can bind to DNA by intercalation. Binding constants Kb were found to be 2.46and#215;105 for 1, 5.41and#215;105 for 2 and 7.00and#215;104 for 3. Moreover, agarose gel electrophoresis assay demonstrates that all complexes were found to cleavage of plasmid pentry/d-topo plasmid DNA. Complex 2 shows the best cleavage activity (5 and#181;M).

Conformational assignment of gas phase peptides and their H-bonded complexes using far-IR/THz: IR-UV ion dip experiment, DFT-MD spectroscopy, and graph theory for mode assignment.

The combined approach of gas phase IR-UV ion dip spectroscopy experiments and DFT-based molecular dynamics simulations for theoretical spectroscopy reveals the 3D structures of (Ac-Phe-OMe)1,2 peptides using their far-IR/THz signatures. Both experimental and simulated IR spectra are well-resolved in the 100-800 cm-1 domain, allowing an unambiguous assignment of the conformers, that could not be achieved in other more congested spectral domains. We also present and make proofs-of-principles for our newly developed theoretical method for the assignment of (anharmonic) vibrational modes from MD simulations based on graph theory coupled to APT-weighted internal coordinates velocities DOS spectra. The principles of the method are reviewed, applications to the simple gas phase water and NMA (N-methyl-acetamide) molecules are presented, and application to the more complex (Ac-Phe-OMe)1,2 peptidic systems shows that the complexity in assigning vibrational modes from MD simulations is reduced with the graphs. Our newly developed graph-based methodology is furthermore shown to allow an easy comparison between the vibrational modes of isolated monomer(s) and their complexes, as illustrated by the (Ac-Phe-OMe)1,2 peptides.

Structural and spectroscopic properties of posaconazole – Experimental and theoretical studies

The paper compares the experimental FT-IR, UV–vis and 1H NMR spectra of posaconazole with the DFT calculations using five different functionals. The results were compared with previously reported data related to its analogue – itraconazole. Owing to the lack of crystallographic data, the IR analysis for posaconazole was performed for the rotamer optimized at the B3LYP/6-311++G(d,p) level of theory. This analysis shows good accordance with the experimental IR spectrum. The best compatibility between the experimental and theoretical UV spectra was observed with the use of CAM-B3LYP/6-31G(d,p) method for both conazoles. The reason for the difference in the UV–vis spectra of posaconazole and itraconazole was discussed based on linear response time-dependent DFT and natural bond orbital methods. The calculated 1H NMR spectrum shows that the DFT formalism, particularly the B3LYP functional, gives an accurate description of the posaconazole chemical shifts.