Finding the 3D structure of a molecule in its IR spectrum

 The labile iron(II) and iron(III) species are complexed directly in the sample solution with 1,10 phenanthroline and ferron (8-hydroxy-7-iodoquinoline-5-sulfonic acid), respectively. The complexes thus formed are mutually adsorbed and separated by solid phase extraction. The direct determination of iron(III) and iron(II) species with flame atomic absorption spectrometry (FAAS) follows the elution of the iron(III)-ferron complex adsorbed by an anion-exchange and an iron(II)-phenanthroline complex adsorbed by a non-polar RP-18 phase. In the case of indirect determination, the iron(II)-phenanthroline complex that passes through the anion-exchange phase, is measured, and the content of iron(III) is calculated by the difference of the iron(II) and the total iron content. A direct determination with this method has been applied to the iron species analysis in wine samples and the results are compared with those obtained for the determination with adsorptive stripping voltammetry (ASV) as reference method. Received: 17 August 1995/Revised: 12 February 1996/Accepted: 14 February 1996     

Simulation of IR and Raman spectral based on scaled DFT force fields: a case study of 2-amino 4-hydroxy 6-trifluoromethylpyrimidine, with emphasis on band assignment

This work deals with the vibrational spectroscopy of 2-amino 4-hydroxy 6-triflouromethylpyrimidine (AHFMP) by means of quantum chemical calculations. The mid and far FTIR and FT-Raman spectra were measured in the condensed state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6-31G* and B3LYP/6-311+G** method and basic set combinations. Normal co-ordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors yielding fairly good agreement between observed and calculated frequencies. Simulation of infrared and Raman spectra utilizing the results of these calculations led to excellent overall agreement with the observed spectral patterns. The SQM approach applying selective scaling of the DFT force field was shown to be superior to the uniform scaling method in its ability to allow for making modifications in the band assignment, resulting in more accurate simulation of IR and Raman Spectra.     

A problem in the structure assignment of acremolin C,which is most probably identical with acremolin B

With the help of chemical shifts computed with density functional theory (DFT), it is demonstrated that the reported experimental ¹³C NMR data of acremolin C are incompatible with the claimed structure of an N²,3-ethenoguanine with an isopropyl group at C-1'. An alternative structure, which is in agreement with both experimental and computed data, presents an isopropyl group at the C-2' position of an N²,3-ethenoguanine and leads to the conclusion that acremolin C is identical with acremolin B.     

Effects of microsolvation and aqueous solvation on the tautomers of histidine: a computational study on energy, structure and IR spectrum

Microsolvation and combined microsolvation-continuum approaches are employed to investigate the structures and energies of canonical and zwitterionic histidine conformers. The effect of hydration on the relative conformational stability is examined. The strategy of exploring singly and doubly hydrated structures and the possible microsolvation patterns are described. We find that bonding water molecule may significantly change the relative conformational stabilities. In gas phase, the singly and doubly hydrated canonical forms are more stable than their zwitterionic counterparts. In solution, the continuum solvent model shows that bare zwitterionic form is more stable than bare canonical form by 1.1 kcal/mol. This energy separation is increased to 2.2 and 3.4 kcal/mol with inclusion of one and two explicit water molecules, respectively. We have also observed that the doubly hydrated structures obtained by combining two water molecules simultaneously to the solute molecule are preferred over the stepwise hydration. Hydrogen bond energies for the most stable hydrated histidine tautomers are determined by the atoms in molecules theory. The infrared (IR) spectra for the most stable singly and doubly hydrated structures of both histidine tautomers in gas phase are characterized. The stretching frequencies for NH of imidazole ring and OH of COOH are red shifted due to the hydrations. The IR spectra for the most stable zwitterionic tautomers in solution are also presented and discussed in connection with the comparison to the experiments. The pKa values obtained for the ring protonated zwitterions with two explicit water molecules appear to be in good agreement with the experiments.     

An investigation on the structure,spectroscopy, and thermodynamic aspects of clusters: A combined Parallel tempering and DFT based study

The problem of identifying low-energy structures of (n = 1-6) was investigated, and the evaluation of important properties like heat capacity, solvation energy, and vertical detachment energy for each of the clusters was carried out. The problem was handled at two different theoretical levels. First, an adequately chosen empirical potential energy surface was used to account for the major interactions between the constituents of the cluster studied. Once the surface was chosen, the Parallel tempering algorithm was employed to search out the low-energy critical points on this surface, which gave geometries at this level. To refine the structures further, these pre-optimized structures were used as inputs for quantum chemical evaluation to complete the final refinement. To check whether the structures found were reasonable, sensitive properties like heat capacity, solvation energy, and vertical detachment energy were calculated. Then, an effort was made to understand and explain the variations in these properties with change in the cluster size. To understand the process of cluster formation further, thermodynamic aspects like △H (298.15 K), △G (298.15 K), and heat capacity (C_v) changes were also evaluated. Infrared spectroscopic features were also studied to see whether the introduction of the ion caused reasonable shifts compared to a pure water cluster.     

Preparation and photoelectron spectrum of the glycine molecular anion: assignment to a dipole-bound electron species with a high-dipole moment, non-zwitterionic form of the neutral core

We report the gas-phase preparation of negatively charged glycine as well as the Gly(H(2)O)(1,2) (-) complexes by entrainment of the neutral precursor into an ionized supersonic expansion tuned to optimize the (H(2)O)(n) (-)Ar(m) clusters. The photoelectron spectrum of Gly(-) displays the signature of a dipole-bound species, with sufficient vibrational fine structure to characterize the core neutral as a higher energy, non-zwitterionic isomer of the amino acid.     

Chiral self-dimerization of vanadium complexes on a SiO2 surface for asymmetric catalytic coupling of 2-naphthol: structure, performance, and mechanism

Vanadium monomers with chiral tridentate Schiff-base ligands were supported on SiO(2) through a chemical reaction with surface silanols, where we found a new chirality creation by the self-dimerization of the vanadyl complexes on the surface. The chiral self-dimerization and the role of surface silanols in the self-assembly were investigated by means of X-ray absorption near-edge structure (XANES), extended X-ray absorption fine structure (EXAFS), diffuse-reflectance ultraviolet/visible (DR-UV/VIS), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FT-IR), electron spin resonance (ESR), and density functional theory (DFT) calculations. The surface vanadyl complexes had a distorted square-pyramidal conformation with a V=O bond. FT-IR spectra revealed that the Ph-O moiety of Schiff-base ligands was converted to Ph-OH by a surface-concerted reaction between the vanadium precursors and surface SiOH groups. The Ph-OH in an attached vanadyl complex interacted with a COO moiety of another vanadyl complex by hydrogen bonding to form a self-dimerized structure at the surface. The interatomic distance of V-V in the surface self-assembly was evaluated to be 0.40 +/- 0.05 nm by ESR after O(2) adsorption. The self-dimerized V structure on SiO(2) was modeled by DFT calculations, which demonstrated that two vanadium monomers with Ph-OH linked together by two hydrogen bonds and their V=O groups were directed opposite to each other. The surface self-dimerization of the vanadium precursors fixes the direction of the V=O bond and the plane of the Schiff-base ligand. Thus, a new chiral reaction field was created by two types of chirality: the chiral Schiff-base ligand and the chiral V center. We have also found that the chiral self-dimerized vanadyl complexes exhibit remarkable catalytic performance for the asymmetric oxidative coupling of 2-naphthol: 96% conversion, 100% selectivity to 1,1'-binaphthol (BINOL), and 90% enantiomeric excess (ee). Increasing the vanadium loading on SiO(2) caused a dramatic swell of enantioselectivity, and the maximum 90% ee was observed on the supported catalyst with the full coverage of the vanadyl complex (3.4 wt % vanadium). This value is equivalent to the maximum ee reported in homogeneous catalysis for the coupling reaction. Furthermore, the supported vanadium dimers were reusable without loss of the catalytic performance. To our knowledge, this is the first heterogeneous catalyst for the asymmetric oxidative coupling of 2-naphthol.     

DFT and experimental study on the IR spectra and structure of 2-hydroxy-3-methoxybenzaldehyde (o-vanillin) and its oxyanion

The structure of o-vanillin molecule and its oxyanion have been studied by density functional theory (DFT), employing the B3LYP functional and 6-311++G** basis set. All conformational isomers of o-vanillin and of its anion have been located and their relative energies have been determined. The IR spectral changes, caused by the conversion of the molecule into the corresponding oxyanion have been studied. In a general agreement between theory and experiment, the conversion causes a frequency decrease of the carbonyl stretching band ν(CO) and essential intensity increases of the aromatic skeletal bands as well as methyl stretching band ν(CH₃). According to the NBO electric charge analysis, the oxyanionic center bears 60% of the whole anionic net charge.     

Rule-based mass spectrum prediction and ranking: Applications to structure elucidation of novel marine sterols

A novel, computer aided approach to the interpretation of mass spectra is documented by its application to a series of recently isolated marine sterols. The method consists of construction of biosynthetically plausible candidate structures, prediction of their major mass spectral fragmentation paths using class-specific rules derived from a training set of known compounds, and a system of ranking candidate structures based on a comparison of the predicted and observed spectra.     

An alternative route for Carboni-Lindsey reaction: N,N cycloaddition of an alkene to s-tetrazine

Quantum mechanical calculations show that N,N cycloaddition of alkenes and alkynes to s-tetrazines is possible as an alternative to the well-known C,C cycloaddition (Carboni-Lindsey reaction). Formation of 1,2,4-triazole derivatives (formal product of N,N cycloaddition) along with the pyrazole (formal product of C,C cycloaddition) corroborates this theoretical prediction.     

IR spectrum of CH3CN-BF3 in solid neon: matrix effects on the structure of a Lewis acid-base complex

We have observed several IR bands of CH3CN-BF3 in neon and nitrogen matrices. For the 11B isotopomer in neon matrices, we observed the BF3 symmetric deformation band (nu7) as a doublet at 600 and 603 cm(-1), the BF3 symmetric stretching band (nu6) as a doublet at 833 and 838 cm(-1), the BF3 asymmetric stretching mode (nu13) at 1281 cm(-1) (partially obscured), and the C-N stretching mode (nu2) as a doublet at 2352 and 2356 cm(-1). The nitrogen matrix data are largely consistent with those reported recently, though we do propose a refinement of one band assignment. Comparisons of the frequencies of a few key, structurally sensitive vibrational modes either observed in various condensed-phase environments or calculated for two minimum-energy gas-phase structures indicate that inert matrix media significantly alter the structural properties of CH3CN-BF3. Specifically, the B-N dative bond compresses relative to the gas phase and other concomitant changes occur as well. Furthermore, the frequency shifts depict structural changes that occur across the various matrix hosts in a manner that largely parallels the degree of stabilization offered by these inert media.     

A quantitative reconstruction of the amide I contour in the IR spectra of globular proteins: from structure to spectrum

The Amide I contours of six globular proteins of varied secondary structure content along with a peptide model for collagen and pulmonary surfactant protein C have been simulated very closely by using a modified GF matrix method. The starting point for the method uses the three-dimensional structure as obtained from the Protein Data Bank. Elements of the interactions between peptide groups (e.g., transition dipole coupling) are very sensitive to tertiary structure, thus the current formalism demonstrates that the Amide I contour may be useful for a more detailed probe of 3-D conformation that goes beyond the traditional use of this band to probe the percentages of particular elements of secondary structure. For example, postulated changes to a known structure can be tested by comparing the new simulated band to the experimental band. A number of refinements to the transition dipole interaction calculation have been made. Most of the important interactions between the C=O oscillators that define the Amide I mode appear to have been identified, including through space transition dipole coupling, through valence bond and through hydrogen bond coupling. The eigenvector matrix produced by the method permits the contribution of each peptide group to the spectrum to be precisely determined. Analysis of the results shows that the often-used structure-frequency correlations are at best approximate and at worst misleading. The subbands from helices, sheets, turns, and loops are much broader and more overlapped than has been commonly assumed. Furthermore, the traditional alpha-helical marker band may be substantially distorted in short segments. Difference spectra based on isotope editing, a technique thought capable of revealing the spectral contributions of individual peptide groups, are shown to be prone to misinterpretation.     

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.     

A DFT study on a mutipathways,one product reaction: Initially divergent radical reactions reconverge to form a single product

The mechanism for initially divergent radical reactions reconverging to form a single product is studied using density functional theory calculations. The calculation results suggest that there are six possible pathways from reactants to products. The free energy barriers of the rate‐determining steps of each pathway are almost equal. Thus, different from usual reaction, the selectivity of this reaction is determined by the relative value of free energy barriers of the two competitive reactions, that is, cyclization and bimolecular trapping, rather than that of rate‐determining steps. In all reaction pathways, cyclization reaction is more competitive than bimolecular trapping reaction due to its low free energy barrier. In addition, the free energy barriers of bimolecular trapping reaction between Bu₃SnH and reactants are all lower than that of NC? C₆H₁₁. However, Bu₃SnH is not always suitable due to its large steric repulsion. © 2014 Wiley Periodicals, Inc.     

Palladium-catalysed [3+2] cycloaddition of alk-5-ynylidenecyclopropanes to alkynes: a mechanistic DFT study

The mechanism of the palladium-catalysed [3+2] intramolecular cycloaddition of alkylidenecyclopropanes to alkynes has been computationally explored at DFT level. The energies of the reaction intermediates and transition states for different possible pathways have been calculated in a model system that involves the use of PH3 as a ligand. The results obtained suggest that the most favourable reaction pathway involves the initial C--C oxidative addition of the cyclopropane to a Pd0 complex to give an alkylidenepalladacyclobutane, which isomerises to a methylenepalladacyclobutane intermediate. Subsequent cyclisation by alkyne carbometallation, followed by reductive elimination affords the final product. An alternative mechanism consisting of a palladaene-type rearrangement is less probable in terms of Gibbs energy, but cannot be fully discarded because it is competitive if one considers electronic energies. For substrates that present an ester group at the terminal position of the triple bond we have found an alternative, more favourable mechanistic route that explains why the [3+2] cycloaddition of these types of systems does not lead to the expected cycloadducts.     

Synthesis,antioxidant, antibacterial,and DFT study on a coumarin based salen-type Schiff base and its copper complex

Synthesis of new efficient compounds is becoming urgent due to the resistance of organisms to drugs. Salen derivatives have interesting therapeutic and industrial applications. A coumarin based derivative of salen, 7-hydroxy-8-((E)-((2-((E)-((7-hydroxy-5-methyl-2-oxo-3,8a-dihydro-2Hchromen-8-yl)methylene)amino)-4-methylphenyl)imino)methyl)-5-methyl-2H-chromen-2-one (L), and its copper complex, CuL, have been synthesized and characterized. Antibacterial and antioxidant activity of these compounds have been evaluated and electronic, optical and molecular properties have been calculated using density functional theory (DFT) with B3LYP. The results were correlated with the biological activity and reactivity of the compounds. Experimental and theoretical calculations indicate that the studied copper complex has the potential to function as a drug.