IR Frequency Shifts Research Articles

Mini-Review on Structure-Reactivity Relationship for Aromatic Molecules: Recent Advances.

Recent advances in quantifying nucleophilic reactivities in chemical reactions and intermolecular interactions of aromatic molecules are reviewed. This survey covers experimental (IR frequency shifts induced by hydrogen bonding) and theoretical (modeling of potential energy surfaces, atomic charges, molecular electrostatic potential) approaches in characterizing chemical reactivity. Recent advances in software developments assisting the evaluation of the reactive sites for electrophilic aromatic substitution are briefly discussed.

Tuning the Strength of Molecular Bonds in Oxygenates via Surface-Assisted Intermolecular Interactions: Atomistic Insights

Lateral interactions between coadsorbed hydrocarbon species play an important role in their chemical transformations on catalytic metal surfaces. In this report, we present a mechanistic study on mutual lateral interactions of the α-ketoester ethyl pyruvate adsorbed on a well-defined Pt(111) surface, resulting in a strong weakening of ester bonds. By employing a combination of surface-sensitive spectroscopic and microscopic techniques as well as theoretical calculations, we address the atomistic-level structure of surface assemblies containing several ethyl pyruvate species. We report formation of different types of surface oligomers comprising topologically different dimer, trimer, and tetramer species. Based on a combination of spectroscopic and microscopic observations, all species can be attributed to two large classes of oligomers exhibiting different types of intermolecular bonding. In the first class of species, the intermolecular interaction is realized via H-bonding between two acetyl groups of ethyl pyruvate, that is, a carbonyl and a methyl group of the neighboring molecules, while in the second type of species the bonding interaction involves the ester-O of one molecule and the acetyl group of a neighboring adsorbate. For the latter type of species, a strong IR frequency shift of the ester C–O vibration was observed pointing to a significant weakening of the related ester bonds, which might exert a strong impact on the chemical transformations involving this group. We demonstrate that the particular type of intermolecular interaction in ethyl pyruvate assemblies can be effectively tuned by controlling the adsorption parameters, such as surface coverage and the presence of coadsorbed hydrogen. Obtained results provide important insights into the details of lateral interactions of complex multifunctional molecules adsorbed on catalytically relevant surfaces. We show that the parameter space in a catalytic process involving ester compounds can be purposefully varied to tune the strength of the ester bond toward improving the catalytic performance.

Characterization of Acid and Basic Sites on Zirconia Surfaces and Nanoparticles by Adsorbed Probe Molecules: A Theoretical Study

Acid and basic sites on monoclinic and tetragonal zirconia were investigated at the DFT level by computing IR and NMR properties of adsorbed probe molecules. Regular and stepped ZrO2 surfaces as well as stoichiometric zirconia nanoparticles have been considered. Acidity and basicity were probed by the adsorption of carbon monoxide and pyrrole, respectively. CO adsorption shows a positive shift of the C–O stretching frequency in IR spectra while the C atom of CO is shielded and 13C chemical shifts moves to higher field as a function of the strength of the acid site. For the study of basic sites we used a pyrrole molecule, but the interaction between the pyrrole ring and the surface leads to adsorption modes that cannot be used to titrate the surface basicity. On the other hand, at high coverage the molecule assumes an upright position and the formation of a hydrogen bond of the pyrrole NH group with the oxygen atoms of the surfaces provides a proxy of the basic properties of these sites. In particular, we focus on changes of the N–H IR frequency, 1H, 15N, and 17O NMR chemical shifts and their correlations with the surface basicity. Among the correlations found, that between the N–H stretching frequency of adsorbed pyrrole and the 17O NMR chemical shift of the O ion where the molecule is bound show a nice linear correlation. These two properties can provide useful information about the basic character of various O sites on the surface of zirconia.Graphic

Effects of Halogen, Chalcogen, Pnicogen, and Tetrel Bonds on IR and NMR Spectra.

Complexes were formed pairing FX, FHY, FH2Z, and FH3T (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) with NH3 in order to form an A⋯N noncovalent bond, where A refers to the central atom. Geometries, energetics, atomic charges, and spectroscopic characteristics of these complexes were evaluated via DFT calculations. In all cases, the A–F bond, which is located opposite the base and is responsible for the σ-hole on the A atom, elongates and its stretching frequency undergoes a shift to the red. This shift varies from 42 to 175 cm−1 and is largest for the halogen bonds, followed by chalcogen, tetrel, and then pnicogen. The shift also decreases as the central A atom is enlarged. The NMR chemical shielding of the A atom is increased while that of the F and electron donor N atom are lowered. Unlike the IR frequency shifts, it is the third-row A atoms that undergo the largest change in NMR shielding. The change in shielding of A is highly variable, ranging from negligible for FSnH3 all the way up to 1675 ppm for FBr, while those of the F atom lie in the 55–422 ppm range. Although smaller in magnitude, the changes in the N shielding are still easily detectable, between 7 and 27 ppm.

Acid Gas Adsorption on Metal–Organic Framework Nanosheets as a Model of an “All-Surface” Material

To establish a model of metal-organic framework (MOF) surfaces and build an understanding of surface-specific ligand adsorption phenomena in MOFs, we present a computational study exploring multiple models of a series of MOF-2 nanosheet materials, "M-BDCs", with M = Zn, Cu, and Co and BDC = benzene-1,4-dicarboxylate. We study and assess the appropriateness of a series of models ranging from small clusters (18 atoms) to fully periodic sheet models. We additionally study the interactions of these models with acid gases and energy-relevant small molecules (CO, CO2, H2O, SO2, NO2, and H2S). We employ computational methods ranging from DFT with various exchange-correlation functionals to perturbative and coupled-cluster methods. For these systems, we present binding energies and enthalpies with the various ligands studied as well as IR frequency shifts for the normal modes of these ligands upon complexation with the open-metal sites of these materials. Our calculations lead to an understanding of phenomena unique to MOF surfaces and the importance of the periodicity in these materials in capturing surface-specific adsorption behaviors.

Vibrational Stark Effects of Carbonyl Probes Applied to Reinterpret IR and Raman Data for Enzyme Inhibitors in Terms of Electric Fields at the Active Site.

IR and Raman frequency shifts have been reported for numerous probes of enzyme transition states, leading to diverse interpretations. In the case of the model enzyme ketosteroid isomerase (KSI), we have argued that IR spectral shifts for a carbonyl probe at the active site can provide a connection between the active site electric field and the activation free energy (Fried et al. Science 2014, 346, 1510-1514). Here we generalize this approach to a much broader set of carbonyl probes (e.g., oxoesters, thioesters, and amides), first establishing the sensitivity of each probe to an electric field using vibrational Stark spectroscopy, vibrational solvatochromism, and MD simulations, and then applying these results to reinterpret data already in the literature for enzymes such as 4-chlorobenzoyl-CoA dehalogenase and serine proteases. These results demonstrate that the vibrational Stark effect provides a general framework for estimating the electrostatic contribution to the catalytic rate and may provide a metric for the design or modification of enzymes. Opportunities and limitations of the approach are also described.

Modeling the Adsorption of Oxalate onto Montmorillonite.

In this work, a multiscale modeling of the interaction of oxalate with clay mineral surfaces from macroscale thermodynamic equilibria simulations to atomistic calculations is presented. Previous results from macroscopic adsorption data of oxalate on montmorillonite in 0.01 M KNO3 media at 25 °C within the pH range from 2.5 to 9 have been used to develop a surface complexation model. The experimental adsorption edge data were fitted using the triple-layer model (TLM) with the aid of the FITEQL 4.0 computer program. Surface complexation of oxalate is described by two reactions: >AlOH + Ox(2-) + 2H(+) = >AlOxH + H2O (log K = 14.39) and >AlOH + Ox(2-) + H(+) = >AlOx(-) + H2O (log K = 10.39). The monodentate complex >AlOxH dominated adsorption below pH 4, and the bidentate complex >AlOx(-) was predominant at higher pH values. Both of the proposed inner-sphere oxalate species are qualitatively consistent with previously published diffuse reflectance FTIR spectroscopic results for oxalate on montmorillonite edge surface (Chem. Geol. 2014, 363, 283-292). Atomistic computational studies have been performed to understand the interactions at the molecular level between adsorbates and mineral surface, showing the atomic structures and IR frequency shifts of the adsorption complexes of oxalate with the edge surface of a periodic montmorillonite model.

Prediction among spectra data of 1H NMR, Raman and IR in aqueous solutions of ionic liquid

In order to make clear the relationship among different spectroscopic properties of aqueous solution of n-butylammonium nitrate (N4NO3) ionic liquid, the concentration-dependent 1H NMR chemical shifts, IR frequency, and Raman frequency shifts, were measured for aqueous solution of N4NO3 and the prediction among these spectroscopic properties were carried out using the local composition (LC) model. The satisfying results can be achieved with the help of the LC model, indicating that different spectroscopic properties may tell us the same story about the local environment involved in aqueous solutions of ionic liquids.

Estimating the Hydrogen Bond Energy

First, different approaches to detect hydrogen bonds and to evaluate their energies are introduced newly or are extended. Supermolecular interaction energies of 256 dimers, each containing one single hydrogen bond, were correlated to various descriptors by a fit function depending both on the donor and acceptor atoms of the hydrogen bond. On the one hand, descriptors were orbital-based parameters as the two-center or three-center shared electron number, products of ionization potentials and shared electron numbers, and the natural bond orbital interaction energy. On the other hand, integral descriptors examined were the acceptor-proton distance, the hydrogen bond angle, and the IR frequency shift of the donor-proton stretching vibration. Whereas an interaction energy dependence on 1/r(3.8) was established, no correlation was found for the angle. Second, the fit functions are applied to hydrogen bonds in polypeptides, amino acid dimers, and water cluster, thus their reliability is demonstrated. Employing the fit functions to assign intramolecular hydrogen bond energies in polypeptides, several side chain CH...O and CH...N hydrogen bonds were detected on the fly. Also, the fit functions describe rather well intermolecular hydrogen bonds in amino acid dimers and the cooperativity of hydrogen bond energies in water clusters.

Comparative study on formamide–water complex

AbstractThe hydrogen bonding of 1:1 complexes formed between formamide and water molecule have been investigated systematically using Hartree–Fock (HF), hybrid density functional theory (B3LYP), and post‐Hartree–Fock (MP2 and CCSD(T)) methods with range of basis sets 6‐31G(d), cc‐pVXZ (X = D, T, Q) and aug‐cc‐pVYZ (Y = D, T). Three stable structures are considered on the potential energy surface of formamide and water system. The optimized geometric parameters and interaction energies for various isomers at different levels are estimated. The IR frequencies, intensities, and frequency shifts are reported. This study shows that B3LYP/aug‐cc‐pVDZ method gives better performance for formamide‐water complexes. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010.

MP2 and DFT study of IR spectra of TCNE‐methylsubstituted benzene complexes: Is charge transfer important?

AbstractThe second‐order Møller–Plesset (MP2) and density functional theory (DFT; B3LYP, B3LYP‐D) approaches show that the CN (and also CC) stretching IR vibrations are relatively small but reproducibly shifted to lower frequencies in a series of methylbenzenes‐tetracyanoethylene (NMB‐TCNE, N = mono‐, di‐, … , hexa‐) complexes with increasing number of methyl groups (N). These CN stretching IR frequency shifts, ranging from 8 to 12 cm−1, are linearly dependent on number N but still 2‐4 times greater than recently published experimental data [Stires et al., Chem Commun, 2005, 28, 3532; Pawlukojc et al., Chem Phys, 2006, 327, 311]. An explanation of the shifts toward lower frequencies is in literature [Stires et al., Chem Commun, 2005, 28, 3532; Pawlukojc et al., Chem Phys, 2006, 327, 311] usually attributed to the magnitude of transferred electron charge ΔQ from a donor molecule to TCNE (mainly to its π LUMO [lowest unoccupied molecular orbital]). The LUMO has antibonding character on CN and CC bonds, and thus the respective CN and CC bond orders are, due to partial occupation in the complex, decreased. However, the difference by a factor of 2‐4 between our MP2 (and also B3LYP) calculations and experiment is probably also due to the effect of environment, i.e., intermolecular forces between complex and solvent molecules or crystal lattice. The calculated interplanar distance R, dipole moment μ, and transferred charge ΔQ are approximately linearly dependent on number of methyl groups N. However, between N = 2 and 3, the abrupt changes in the dependencies were observed. This is caused by the change of mutual (perpendicular) orientations between respective methyl benzenes and TCNE in the complexes as a consequence of preferred interaction between one of two degenerated or near degenerated π highest occupied molecular orbitals (being orthogonal) on NMB with π LUMO located mainly on TCNE. This fact is important for many properties (especially for electron excited states) of these complexes. A strong dependence of polarizability, namely of its αzz part, of the benzene‐TCNE (Be‐TCNE) complex on soft vibrations was found. The vibrational contribution to αzz value is almost as large as the electronic αzz contribution. Finally, MP2 and B3LYP studies indicate that inclusion of anharmonicity has small, if any, effect on calculated vibrational frequencies of Be‐TCNE. This theoretical finding is quite important especially because it holds also for soft vibrational modes, which are always present at weak intermolecular complexes. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

The adsorption of 1,3-butadiene on Ag(1 1 1): A TPD/IRAS study and importance of lateral interactions

Temperature programmed desorption (TPD) and infrared reflection absorption spectroscopy (IRAS) have been used to study the adsorption, desorption, molecular orientation and conformation of 1,3-butadiene on Ag(1 1 1) at 80 K. Butadiene adsorbs weakly as an s-trans conformer with the first layer oriented parallel to the silver surface and desorbs without decomposition. A very narrow line shape of the out-of-plane modes at low submonolayer coverage indicates molecular ordering within the diluted adsorbed layer, presumably through weak π-bonding interaction with the surface and intermolecular repulsive interaction. Compression within the first layer at coverages above 0.5 ML is driven by repulsive interaction as seen in both TPD and IRAS data. The IR intensity rollover and peak broadening, together with a significant shift in the TPD peak to lower temperature, indicate a reorientation of the butadiene molecule. Adsorption in the second- and multilayer is characterized by distinct IR frequency shifts and crystal field splitting effects similar to those reported for solid butadiene.

Miscibility and specific interactions in blends of poly[(styrene)-co-(cinnamic acid)] with poly(methyl methacrylate) and modified poly(methyl methacrylate)

The miscibility behavior of poly(styrene-co-cinnamic acid) (PSCA) with poly(methyl methacrylate) (PMMA), poly((methyl methacrylate)-co-(4-vinylpyridine)) (PMMA4VP) and poly((methyl methacrylate)-co-(2-vinylpyridine)) (PMMA2VP) was studied. DSC measurements indicated that PSCA23 containing 23 mol% of carboxylic acid units was miscible with PMMA, PMMA2VP and PMMA4VP as established from the observation of a single composition dependent glass transition temperature. Miscibility was induced via hydrogen bonding as evidenced by IR frequency shifts of the hydroxyl stretching vibrations of the acid copolymer in the blends. Interpolymer hydrogen bonding formation within the binary systems was also investigated by viscosimetric study of dilute solutions in toluene. For PMMA/PSCA5 blends the viscosity of the mixtures was close to the weight average viscosities of the individual polymer while for blend solutions of PSCA5 with PMMA2VP and PMMA4VP, the interactions were sufficiently strong to form interpolymer complexes with a decrease in viscosity in comparison to the additivity rule.

Spectroscopic identification of adsorption properties of Zn2+ ions at cationic positions of high-silica zeolites with distant placing of aluminium ions

For Zn2+ cations in ZnZSM-5 zeolite unusual type of cationic positions, formed by two distantly placed framework aluminium atoms, is considered. Some extent of structural destabilization of cations in these cationic positions in comparison with traditional localization should result in promoted Lewis activity and adsorption activity of these sites. The last ones are manifested in the significantly increased IR low frequency shifts for adsorbed molecules and in their ability for heterolytic dissociation at elevating temperature. DFT cluster quantum chemical modeling of light alkane adsorption on Zn2+ in ZnZSM-5 zeolites confirms these conjectures in full agreement with recent experiments. Similar to the previously considered dihydrogen and methane molecule adsorption, we present here the calculations of ethane molecular and dissociative adsorption on these sites. It is shown that the unusually large ethane IR frequency shift recently observed in ZnZSM-5 zeolite can result from adsorptive interaction of C2H6 with Zn2+ stabilized in a cationic position with distantly placed aluminium ions. The dissociative adsorption of ethane molecules with the formation of bridged hydroxyl group and Zn–C2H5 structure is considered and an activation energy of ethylene formation from the alkyl fragment is evaluated.

Theoretical models for the description of the IR frequency shifts of carbon monoxide interacting with silanol groups

Several theoretical models were tried to reproduce the nearly equal values of blue and red shifts of the CO vibrational frequency of surface species formed by the CO adsorption on silica and which were ascribed to SiOH⋯CO and SiOH⋯OC complexes. The adequacy of the theoretical methods applied was assessed on frequency shifts for the analogous complexes of CO with water and methanol. B3LYP has the advantage over MP2 in the reproduction of these shifts due to a better description of the CO dipole moment. However, B3LYP predictions for CO complexes with silanols R 3SiOH (R = H,F,OH) give the 2:1 ratio of shifts, in contrast to the 1:1 ratio observed for surface species. The high red shift observed for surface species with SiOH⋯OC bonding may be reproduced only in the cases when the interaction of CO with atoms imitating lattice oxygens is present.

Possible molecular structure of promoted Lewis acidity sites in ZnZSM‐5

AbstractIt is suggested that the abnormal methane IR frequency shift observed in ZnZSM‐5 zeolites is caused by adsorptive interaction of CH4 with particularly strong Zn2+ Lewis sites. Various molecular structures of zinc ion species in high‐silica zeolites are discussed, and it is concluded that increased Lewis acidity of a site is associated with decreased structural stability. It is shown that Zn2+ in zeolite cationic position with distantly placed A1 ions can produce observed shift of vibrational frequencies for adsorbed methane molecule. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004

Theoretical and experimental studies of IR spectra of 4-aminopyridine metal(II) complexes

In this study FT-IR spectra of M(L) 2Ni(CN) 4 {where M=Fe or Zn, L=4-aminopyridine} complexes are reported for the first time in the 400–4000 cm −1 range. The spectral features suggest that the compounds are similar in structure to the Hofmann-type complexes with infinite polymeric layers formed with Ni(CN) 4 −2 ions bridged by M(L) 2 +2 cations. IR frequency shifts, upon formation of coordination compound are reliable indicators of the coordination mode of 4-aminopyridine. It is concluded that the ring nitrogen and not the amino nitrogen is involved in complex formation. In order to investigate metal–ligand coupling peculiarities, the vibrational wavenumbers of free and coordinated 4-aminopyridine have been calculated by a force field refinement method. The results indicated that the force field of free 4-aminopyridine should be altered in complex formation in order to represent the experimental data.

Determination of the basicity of alkali-exchanged molecular sieves

A procedure is proposed to quantify the basicity of zeolite oxygen centers by estimating the proton affinity (PA) of these centers, employing measured IR frequency shifts of the stretching and deformation modes of the OH group of adsorbed methanol. The PA scale is established with the help of density functional theory (DFT) calculated PA values of selected zeolites calibrated to the experimental gas phase PA of small oxygen-containing molecules. The reliability of the method is increased by combining two experimental parameters.

An enthalpic scale of hydrogen‐bond basicity, part 1: halogenoalkanes

AbstractHydrogen bond enthalpies ΔH° for the interaction of 4‐fluorophenol with 18 fluoro‐, chloro‐, bromo‐, and iodo‐alkanes in CCl4 solution have been determined through the temperature variation of hydrogen‐bond equilibrium constants. A statistical analysis of the ΔH°–ΔS° correlation shows that this extrathermodynamic relationship is valid for the family of halogenoalkanes. The enthalpic data are also used to test the correlation of ΔH° versus Δν(OH), the IR frequency shifts of the OH band of 4‐fluorophenol caused by the hydrogen bonding (the Badger–Bauer relationship). This relationship is family dependent, and, for fluoroalkanes and iodoalkanes, does not pass through the origin. These findings allow a safer use of the Badger–Bauer relationship to predict hydrogen‐bond enthalpies accurately. Copyright © 2001 John Wiley & Sons, Ltd.

Parity Violation in Fluorooxirane

In contrast to what has been accepted, electroweak quantum chemistry predicts the heats of formation, the structures, the microwave and infrared spectra of enantiomers of chiral molecules to be different. The R enantiomer of fluoroxirane is calculated to be more stable than the S enantiomer by the minute amount of 2×10−12 J mol−1, and the relative IR frequency shifts are ≤10−18 (see scheme). Nevertheless, this recently synthesized compound may prove useful for fundamental experimental tests and calculations of parity violation in chiral molecules because of its particularly simple rovibrational spectrum and its rigid cyclic structure composed of light atoms.