Molecular structure and vibrational spectra analysis of diethylsilanediol by IR and Raman spectroscopies and DFT calculations

A thorough theoretical analysis (DFT/B3LYP) of the potential energy surface of diethylsilanediol (DESD) allowed finding ten stable conformations of the molecule, differing on the relative arrangement of both ethyl and hydroxyl groups. The Boltzmann??s population analysis allowed establishing their stability order that was justified in terms of the anomeric effect analyzed by means of the Natural Bond Orbitals methodology. Besides, DESD was synthesized and characterized using FT-IR and Raman spectroscopies data, firstly reported in this work, combined with DFT calculations (B3LYP/aug-ccpVTZ). Finally some of the main structural and vibrational features of this and other closely related alkylsilanediols, i. e. DMSD and EMSD, have been put together in order to establish some trends that can allow a better understanding of the chemistry of these compounds.     

Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphate

We present an experimental and quantum chemical NMR study of the mononucleotide cyclic uridine monophosphate in water. Spectral parameters ((1)H and (13)C chemical shifts and (1)H--(1)H, (13)C--(1)H, (31)P--(13)C and (31)P--(1)H spin-spin coupling constants) have been carefully obtained experimentally and calculated using DFT methods including the solvent effect and the conformational flexibility of the solute. This study confirms that the (1)H and (13)C spectra of polar, flexible molecules in aqueous solution can be predicted with a high level of accuracy, comparable to that obtained for less complex systems.     

The conversion of phenylpropanedinitrile (phenylmalononitrile) into the carbanion, followed by IR spectra, ab initio and DFT force field calculations

The spectral and structural changes, caused by the conversion of phenylpropanedinitrile (phenylmalononitrile) into the carbanion, have been followed by IR spectra, ab initio HF, MP2 and DFT BLYP force field calculations. In agreement between theory and experiment, the conversion is accompanied with strong frequency decreases (with 114 cm(-1), mean value) of the cyano stretching bands nu(C triple bond N), dramatic increases in the corresponding integrated intensities (136-fold, total value), strong enhancement of the nu(C triple bond N) vibrational coupling and other essential spectral changes. According to the calculations, the strongest structural changes take place at the carbanionic center: (i) shortenings of the Cz-Ph and Cz-CN bonds with 0.064-0.092 A, and increases in the corresponding bond orders with 0.14-0.21 U; (ii) simultaneous enlargements of the bond angles at the same carbon atom with 7.6 degrees -9.7 degrees, as from tetrahedral its configuration becomes trigonal. The carbanionic charge is distributed between the two cyano groups (0.44-0.52 e(-)), phenyl ring (0.31-0.34 e(-)) and carbanionic center (0.14-0.25 e(-)). The formation of moderately strong (CH(3))(2)S=O...H-C(CN)(2)C(6)H(5) hydrogen bonds has been found experimentally.     

Examination of small molecule losses in 5‐methylpyranopelargonidin MS/MS CID spectra by DFT calculations

Pyranoanthocyanins are formed during food treatment and maturation (e.g. wine, juices), and they can be considered a natural alternative to artificial food colorants. Tandem mass spectrometry (MS/MS) is perhaps the most important technique in analysis of anthocyanin dyes. Knowledge of fragmentation pattern is a key aspect of their successful structural characterization. Polyphenolic compounds are known to lose small molecules during collision‐induced dissociation (CID) in MS/MS experiments. However, the specific positions where such losses occur preferentially are unknown. The aim of this communication is to investigate the energetically most preferred places for H₂O and CO losses during the fragmentation of 5‐methylpyranopelargonidin molecule by the means of computational chemistry (employing density functional theory) combined with CID MS/MS experiments and infrared multiphoton dissociation spectroscopy. Mechanisms responsible for the fragmentations were investigated, and optimal geometries and transition states were obtained. Cleavage of water as well as carbon monoxide occurs preferentially from the C‐ring of flavonoid skeleton. In the most stable structure of 5‐methylpyranopelargonidin, B‐ring was found to be tilted with respect to the rest of the molecule. Planarization effort of the parent molecule contributes both to its decarbonylation and dehydration. Copyright © 2014 John Wiley & Sons, Ltd.     

Ion-pair charge transfer complexes with intense near IR absorption: Syntheses,crystal structures,electronic spectra and DFT calculations

Five ion-pair complexes, consisting of R-benzylidene-1-aminopyridinium derivatives and [Ni(mnt)₂]²⁻ (R = p-nitro (1), p-methyl (2), p-bromo (3), p-chloro (4) and m-nitro (5); mnt²⁻ = maleonitriledithiolate), were synthesized and structurally characterized. As for 1, it is interesting to observe a large deviation from square-planar coordination geometry for the Ni atom, while no deviation is observed in the other four complexes. In the solid state, UV–Vis–NIR spectra of 2–5 show similar properties with intense absorption in the 200–750 nm and moderate near IR absorption in the 750–1000 nm region, whereas 1 exhibits an intense absorption from UV/Visible to near-IR region (200–1100 nm). This unique spectral feature of 1 is attributed to its distinctive structural differences from 2 to 5, namely the strong intermolecular packing interactions between anions and cations, as well as a significant deviation from the planarity of the anion. Based on DFT and TDDFT calculations, near-IR absorbance bands in 1–5 were assigned to combined transitions of d–d, MLCT and π–π^∗ in the [Ni(mnt)₂]²⁻ anion as well as the ion-pair charge transfer (IPCT) from the anionic HOMO to the cationic LUMO. The IPCT band position in acetonitrile is independent of the substituent group feature in benzene ring of cations for 1–5, which could be interpreted that the substituent group in benzene ring only has a minor contribution to the cationic LUMO.     

Molecular structure, IR and Raman spectra as well as DFT chemical calculations for alkylaminoacetylureas: vibrational characteristics of dicarbonylimide bridge

The present work reports room temperature IR and Raman study of R-NH-CH2-CO-NH-CO-NH2 alkylaminoacetylureas (R=C3H7, C4H9, C5H11, C6H13, C7H15, C8H17, C9H19, C10H21, C12H25, C14H29, C16H33 and C18H37). The experimental energy levels have been compared to those obtained from DFT chemical quantum calculations performed with the use of B3LYP/6-31G (d,p) basis for the R=C3H7 derivative. Energies of 66 vibrational states have been calculated for this molecule. Its molecular symmetry was taken as C1 and was optimized in the both quantum models applied. The role of the hydrogen bond in the stabilization of the structure has been analyzed.     

Structures and EPR spectra of binary sulfur-nitrogen radicals from DFT calculations

The scattered electron paramagnetic resonance (EPR) spectroscopic data for binary sulfur-nitrogen (S,N) radicals have been compiled and critically assessed.Many of these are inorganic rings or cages.For each species, possible equilibrium structures in the gas phase and the EPR hyperfine coupling (hfc) constants have been calculated with DFT using the B3LYP functional and basis sets of triple-ζ (or better) quality.Good agreement is obtained between calculated and measured values for the well characterized [S₃N₂]⁺, a planar π-radical for which the s-component of the orbitals is likely to be reasonably independent of minor geometrical changes between gas-phase and condensed-phase states.The cage compounds [S₄N₄]⁻ and [S₄N₅]⁻², for which reliable experimental EPR spectra have been reported, show larger variation between calculated and measured hfc, as a consequence of the dependence of the s orbital content of the molecular orbitals on small structural changes.The very large disagreements between the DFT calculated and experimentally claimed hfc constants for [NS], [SNS] and [S₄N₄]⁻³ in condensed phases lead us to question their assignment.Among binary S,N radicals, ³³S hfc data has only been reported for [S₃N₂]⁺ (through isotopic enrichment).These values were essential for the correct identification of the EPR spectra of this important radical, which previously was misassigned to other species.Our results suggest that ³³S data will be equally important for the correct identification of the EPR spectra of other binary S,N species, many of which are cyclic systems, e.g.[S₃N₃], [S₄N₃] and[S₄N₅].     

Quantum-chemical calculations of the IR absorption spectra of modified polytetrafluoroethylene forms

DFT(B3LYP) (basis set 6–31 + G(d)) and HF (basis set 6–31G) calculations were performed to determine the geometric structure and vibrational spectra of the C_nF_2n and C_nF_2n O molecules (n = 3–13). The IR spectra of chain C_nF_2n O molecules with the terminal carbonyl group (-COF) were found to contain a band at 1885 cm^?1. The C=C and C=O stretching vibrations of the-CF=CF₂ and COF terminal groups were independent, and there was no mutual influence of their frequencies starting with the seven-fragment molecule. In the presence of chain branching, the sensitivity of the ν(C=C) and ν(C=O) frequencies in the olefin and carbonyl groups depended on where branching occurred. The chain configuration was found to be energetically favorable compared with branched structures.     

Structural analysis of electrolyte solutions for rechargeable Mg batteries by stereoscopic means and DFT calculations

We present a rigorous analysis of unique, wide electrochemical window solutions for rechargeable magnesium batteries, based on aromatic ligands containing organometallic complexes. These solutions are comprised of the transmetalation reaction products of Ph(x)MgCl(2-x) and Ph(y)AlCl(3-y) in different proportions, in THF. In principle, these reactions involve the exchange of ligands between the magnesium and the aluminum based compounds, forming ionic species and neutral molecules, such as Mg(2)Cl(3)(+)·6THF, MgCl(2)·4THF, and Ph(y)AlCl(4-y)(-) (y = 0-4). The identification of the equilibrium species in the solutions is carried out by a combination of Raman spectroscopy, multinuclear NMR, and single-crystal XRD analyses. The association of the spectroscopic results with explicit identifiable species is supported by spectral analyses of specially synthesized reference compounds and DFT quantum-mechanical calculations. The correlation between the identified solution equilibrium species and the electrochemical anodic stability window is investigated. This study advances both development of new nonaqueous solution chemistry and possible development of high-energy density rechargeable Mg batteries.     

Multinuclear NMR spectra and GIAO/DFT calculations of N-benzylazoles and N-benzylbenzazoles

The ¹H, ¹³C, and ¹⁵N chemical shifts of almost the whole series of N-benzyl azoles and benzazoles, with the exception of the unknown 1-benzyl-1H-pentazole (10) and the very unstable 2-benzyl-2H-isoindole (12), have been measured. In addition, the X-ray crystal structure of 1-benzyl-1H-indazole (14) was solved (monoclinic, space group P2₁/n), its geometry being very close to that used for the calculations. The absolute chemical shieldings were calculated at the gauge-independent atomic orbital (GIAO)/Becke, 3-parameter, Lee-Yang-Parr (B3LYP)/6-311++G(d,p) level and then transformed with very robust empirical equations into chemical shifts of the three nuclei showing an excellent agreement with the 313 experimental values.

     

Structural studies of methyl brevifolincarboxylate in solid state by means of NMR spectroscopy and DFT calculations

Methyl brevifolincarboxylate isolated from the herb of Potentilla argentea L. (Rosaceae) is a representative of the naturally occurring polyphenols. The compound is of pharmaceutical interest mainly because of its antiviral and antioxidant properties. ¹³C NMR spectra were recorded for solution and solid phase. ¹³C CPMAS spectra were assigned by comparison with solution data, dipolar dephasing and short contact time experiments. The correctness of assignments was verified by GIAO DFT calculations of shielding constants. The differences between the solution and solid state chemical shift values were explained in terms of orientation of OH groups and intramolecular hydrogen bonds. The splitting of the C1O resonance shows that there exists a polymorphism in the solid phase, which might be due to the formation of intramolecular hydrogen bond involving carbonyl or methoxy oxygen (i.e. C10OH⋯OC or C10OH⋯OCH₃).     

FT-IR,FT-Raman,NMR spectra and DFT calculations on 4-chloro-N-methylaniline

In this work, the vibrational spectral analysis was carried out by using FT-IR and FT-Raman spectroscopy in the range 400–4000 and 50–3500 cm^?1 respectively, for the title molecule. The structural and spectroscopic data of the molecule in the ground state were calculated by using density functional method using 6-311++G(d,p) basis set. The vibrational frequencies were calculated and scaled values were compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete assignments of all the vibrational mode were performed on the basis of the total energy distributions (TED). ¹³C and ¹H NMR chemical shifts results were given and are in agreement with the corresponding experimental values. The theoretically constructed FT-IR and FT-Raman spectra exactly coincides with experimental one.     

Comparison of DFT methods for molecular structure and vibration spectra of ofloxacin calculations

Comparison of the performance of different density functional theory (DFT) methods at various basis sets in predicting molecular and vibration spectra of ofloxacin was reported. The methods employed in this study comprise six functionals, namely, mPW1PW91, HCTH, LSDA, PBEPBE, B3PW91 and B3LYP. Different basis sets including LANL2DZ, SDD, LANL2MB, 6-31g, 6-311g and 3-21g were also examined. Comparison between the calculated and experimental data indicates that the mPW1PW91/6-311g level afford the best quality to predict the structure of ofloxacin. The results also indicate that B3LYP/LANL2DZ level show better performance in the vibration spectra prediction of ofloxacin than other DFT methods.     

Modeling of NMR spectra and signal assignment using real-time DFT/GIAO calculations

An automated algorithm for fast quantum chemical modeling of NMR spectra within the framework of the density functional theory was developed. High accuracy of calculations of NMR parameters achieved for various classes of organic compounds including heterocyclic compounds, carbohydrates, steroids, and peptides is comparable with the accuracy of experimental determination. The efficiency of computing the NMR chemical shifts using the high-performance PBE/PRIRODA method was demonstrated.     

DFT calculations of vibrational spectra and nonlinear optical properties for MgO nanotube clusters

The IR and Raman spectra, nonlinear optical properties of MgO nanotube clusters are studied by density-functional theory at B3LYP/6-31G(d) level. The IR spectra are match closely to those in the corresponding MgO cluster and bulk materials. The strongest peaks of the IR spectra are located in the range from 650 to 750 cm⁻¹. The Raman spectra are very sensitive to structural variations in MgO clusters, and redshift of vibrational frequency is observed in Raman spectra as increasing cluster length. The motion of the strongest peaks in spectra is discussed. The total dipole moment and the first hyperpolarizabilities oscillate between zero and a constant when the layer is grown for the layer dependence of symmetry in MgO nanotube clusters.     

The hydrogen bonding and conformations of p-tert-butylcalix[4]arene as studied by IR spectroscopy and by DFT calculations

IR and far IR spectra of p-tert-butylcalix[4]arene were recorded at various temperatures between 16 and 180 degrees C and spectra of solutions and crystalline solids were obtained. Ab initio density functional calculations gave vibrational frequencies and infrared intensities for four conformers: cone, partial cone, 1,2- and 1,3-alternate. Complete assignments were made for experimental IR spectra of the cone conformer. The bands characteristic for each conformation were defined. It was revealed that O--H stretching low-frequency shift Deltanu in the cone conformation exceeds Deltanu shifts for other conformers. The effect was stipulated by a cooperative interaction of cyclic hydrogen bonds. The obtained spectra-structure correlation can be used for characteristic of calixarenes conformation.