IR Frequencies Research Articles

Vibrational spectra of phenyl acridine-9-carboxylates and their 10-methylated cations: A theoretical and experimental study

Infrared spectra of phenyl acridine-9-carboxylates and their 10-methylated cationic derivatives were recorded and discussed. Experimental data were compared with theoretically predicted transitions at the DFT level of theory (using the B3LYP functional and 6-31G** basis set) for optimized geometries of molecules. Substitution influences the values of the wavenumbers of characteristic stretching and bending modes, i.e. those corresponding to ester groups and fragments of molecules containing a heterocyclic nitrogen atom. The experimentally determined transitions of selected groups of atoms correlate well with the theoretically predicted values. Interdependences among some theoretically derived physicochemical features of the compounds and IR frequencies of selected bands are also discussed.

Molecular Structure and a Density Functional Theoretical Study on 2‐Nitroimino‐5‐Nitro‐Hexahydro‐1,3,5‐Triazine (NNHT)

Abstract2‐Nitroimino‐5‐nitro‐hexahydro‐1,3,5‐triazine (NNHT), was synthesized and its structure was determined by single‐crystal X‐ray diffraction. The crystal is monoclinic, space group P21/c with crystal parameters of a = 9.4031(13) Å, b = 8.5891(12) Å, c = 9.0200(13) Å, β = 91.213(2)°, V = 728.33(18) Å3, Z = 4, F(000) = 392, Dc = 1.734 g/cm3. The experimental geometry of NNHT was input to Gaussian‐03W program and optimized using DFT‐B3LYP/6‐311++G** method. The IR frequencies and NMR chemical shift were carried out and compared well with those of the experimental. The atomic net charges and the population analysis are discussed. The heat of formation (HOF) for NNHT was evaluated by designing an isodesmic reaction. The detonation velocity (D) and detonation pressure (P) were estimated by using the well known Kamlet‐Jacobs equation, based on the theoretical HOF.

Theoretical study of CO adsorption on the illuminated TiO 2 (0 0 1) surface

A quantum modeling of the CO adsorption on illuminated anatase TiO 2 (0 0 1) is presented. The calculated adsorption energy and geometries of illuminated case are compared with the ground state case. The calculations were achieved by using DFT formalism and the BH and HLYP. Upon photoexcitation, an electron–hole pair is generated. Comparing of natural population in the ground state and the exited state, shows that an electron is trapped in a Ti 4+ ion and a hole is localized in an oxygen ion. The photoelectron helps generation of a CO 2 molecule on the TiO 2 surface. As shown by optimization of these systems, the CO molecule adsorbed vertically on the TiO 2 (0 0 1) surface in the ground state case while the CO molecule made an angle of 134.3° to this surface at the excited state case. Based on the here used model the obtained adsorption energy was 0.36 eV which is in excellent agreement with the reported experimental value. In the present work the C–O stretch IR frequencies are calculated which are 1366.53 and 1423.16 cm −1. These results are in good agreement with the earlier reported works for the surface carbonaceous compounds, and oxygenated carbon species.

DFT study of N′-acetyl formohydrazide isomers

DFT calculations have been applied to find the optimized structures of N′-acetyl formohydrazide isomers (18 isomers) using B3LYP/6-311++G∗∗ and B3LYP/AUG-CC-PVTZ levels of theory. From outputs of these calculations, important molecular parameters, IR frequencies, and energetic results were extracted. The relative stabilities of isomers in the gas phase are found to be as 1, 2E, 2Z, 4Z, 4E, 6EE, 5, 6EZ, 6ZZ, 6ZE, 3E, 7E, 9E, 3Z, 7Z, 9Z, 8E, and 8Z. Moreover, the relative stabilities have been calculated in different solvents (acetone, chloroform, cyclohexane, and DMSO) at B3LYP/AUG-CC-PVTZ level of theory. The relative stabilities in solvents are similar to those in the gas phase except in 6EZ and 9E because these isomers have, respectively, the minimum and maximum average Δ G solvations among all isomers.

Looking for heteroaromatic rings and related isomers as interstellar candidates

Finding complex organic molecules in the interstellar medium (ISM) is a major concern for understanding the possible role of interstellar organic chemistry in the synthesis of prebiotic species. The present interdisciplinary report is a prospective study aimed at helping detection of heteroaromatic compounds or at least of some of their isomers in the ISM. The thermodynamic stabilities of the C(4)H(5)N, C(4)H(4)O, C(4)H(4)S families were calculated using density functional theory (DFT). It was found that pyrrole, furan and thiophene are unambiguously the most stable isomers at the 10-50 K temperatures of the ISM. Several of the less stable isomers were synthesized and flash vacuum thermolysis experiments were performed on these species. Although the detection of pyrrole in the pyrolysis of many compounds has been reported in the literature, we observed that none of its isomers led to pyrrole in these conditions, which suggests that other formation routes are to be considered. On the other hand, these three aromatic compounds present a very high stability, few % been decomposed at 1500 K by flash vacuum thermolysis; these experiments also show a great stability of crotonitrile that is the most stable compound that can be formed in these conditions. The rotational constants, dipole moments and IR frequencies of the low-lying isomers are given to encourage laboratory experiments on these prototype molecules.

Intermolecular Hydrogen Bonding and Vibrational Analysis of N,N-Dimethylformamide Hexamer Cluster

Hexamer cluster of N,N-dimethylformamide(DMF) based on the crystal structure was investigated for the equilibrium structure, the stabilization energies, and the vibrational properties in the density functional force field. The geometry (point group <TEX>$C_i$</TEX>) of fully optimized hexamer clustered DMF shows quite close similarity to the crystal structure weakly intermolecular hydrogen bonded each other. Stretching force constants for intermolecular hydrogen bonded methyl and formyl hydrogen atoms with nearby oxygen atom, methyl C–H<TEX>${\cdots}$</TEX>O and formyl C–H<TEX>${\cdots}$</TEX>O, were obtained in 0.055 <TEX>$\sim$</TEX> 0.11 and <TEX>$\sim$</TEX> 0.081 mdyn/<TEX>$\AA$</TEX>, respectively. In-plane bending force constants for hydrogen bonded methyl hydrogen atoms were in 0.25 <TEX>$\sim$</TEX> 0.33, and for formyl hydrogen <TEX>$\sim$</TEX> 0.55 mdynÅ. Torsion force constants through hydrogen bonding for methyl hydrogen atoms were in 0.038 <TEX>$\sim$</TEX> 0.089, and for formyl hydrogen atom <TEX>$\sim$</TEX> 0.095 mdynÅ. Calculated Raman and infrared spectral features of single and hexamer cluster represent well the experimental spectra of DMF obtained in the liquid state. Noncoincidence between IR and Raman frequency positions of stretching C=O, formyl C–H and other several modes was interpreted in terms of the intermolecular vibrational coupling in the condensed phase.

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.

Growth and characterization of large CdSiP 2 single crystals

Large, optically transparent crystals of CdSiP 2 (CSP) have been grown for the first time from a stoichiometric melt. The material is a high temperature analog to ZnGeP 2 with promising characteristics for IR frequency conversion. Crystals are birefringent and are transparent from 0.5 to 9 μm. Polycrystalline charges were successfully synthesized from high purity elemental starting materials by two-temperature vapor transport despite the very high equilibrium vapor pressure (∼22 atm) at the melting point of CdSiP 2 (1133 °C). Single crystals were grown using the horizontal gradient freeze (HGF) technique in high-temperature transparent furnaces. Over the course of several growth runs, the material proved to be prone to cracking and to twinning along (1 1 2) planes. Twinning was eliminated by seeded growth along directions normal to the 112 planar boundaries. Further modifications to growth conditions resulted in high optical quality, crack- and twin-free single crystals 70×25×8 mm 3. The largest CdSiP 2 single crystals previously reported in the literature were grown through either halogen assisted vapor transport or from a molten Sn flux and measured 2×2×0.2 mm 3. The HGF growth of large CdSiP 2 crystals has allowed several bulk properties to be measured for the first time, including the thermal expansion coefficients, thermal conductivity, and wavelength dependent birefringence and dispersion. Measurements of the optical and thermal properties reveal this to be an extremely promising material for 1-, 1.5-, and 2 μm-pumped mid-IR lasers.

Application of DFT Method for Determination of IR Frequencies and Electrochemical Properties of 1,4-dihydroxy-9,10-anthraquinone-2-sulphonate

Application of DFT Method for Determination of IR Frequencies and Electrochemical Properties of 1,4-dihydroxy-9,10-anthraquinone-2-sulphonate

Surface Modification of Fe3O4and FePt Magnetic Nanoparticles with Organometallic Complexes

Hexane solutions of Fe3O4 and FePt nanoparticles (NPs) having both oleylamine and oleic acid as surfactants were surface modified by treatment with a DMSO solution of [(η6-hydroquinone)Mn(CO)3]BF4, which is readily deprotonated by the oleylamine to [(η5-semiquinone)Mn(CO)3]. The latter complex binds to the NP by replacing the protonated oleylamine, which likely forms a bilayer with the alkyl chains of the oleic acid on the NP surface. The resulting surface-modified assembly is soluble in DMSO. With FePt nanoparticles, [(η5-semiquinone)Mn(CO)3] coordinates to the Pt atoms and the IR frequency of the tricarbonyls differs from that obtained with Fe3O4 nanoparticles, in which coordination is to the iron.

Computational study to assign structure, tautomerism, E/ Z and s- cis/ s- trans isomerism, π-delocalization, partial aromaticity, and the ring size of 1,3-thiazolidin-4-ones and 1,3-thiazin-4-ones formed from thiosemicarbazides

A set of structures encompassing 1-(9-acridinyl)thiosemicarbazide and its 2-methyl derivative together with their various tautomeric structures; the 5-membered ring 1,3-thiazolidin-4-one products resulting from the reaction of 1-(9-acridinyl)thiosemicarbazide and its 2-methyl derivative with dimethyl acetylenedicarboxylate (DMAD) together with the alternative 6-membered ring isomeric reaction products as well as other potential isomeric structures; and the 6-membered ring 1,3-thiazin-4-one product resulting from the reaction of 2-methyl-1-(9-acridinyl)thiosemicarbazide with methyl propiolate (MP) together with the alternative 5-membered ring isomeric reaction product were all extensively studied by molecular modeling calculations using DFT at the B3LYP/6-31G(d,p) level of theory. The ring-chain tautomerism of the thiosemicarbazides, the regio- and stereoselectivity of the reactions, the adopted conformations and E/ Z configurations of the products, the prototropic tautomerism of all the compounds, and the reasons for the predominance of the s- cis conformation of the Z configuration of the 1,3-thiazolidin-4-one product in particular were all extensively analyzed. Comparison of the modeled structures were also made to the 1,3-thiazolidin-4-one and 1,3-thiazin-4-one structures of the methyl derivative as well as 1-(9-acridinyl)thiosemicarbazide available from X-ray crystallographic analysis. Tactics utilizing spectroscopic methods {IR frequencies ( ν) and NMR chemical shifts ( δ), scalar coupling constants ( J), and NOEs ( η)} in conjunction with molecular modeling calculations of the spectral parameters {frequency calculations ( ν) and NMR δ using the GIAO method and J by calculation of the Fermi contact term} were evaluated in terms of proving 5- or 6-membered ring formation.

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

Femtosecond Measurements of Vibrational Circular Dichroism and Optical Rotatory Dispersion Spectra

Heterodyne-detected spectral interferometry with fs IR pulses measures vibrational optical activity free-induction-decay fields. By utilizing Brewster's angle germanium polarizers with ultimate extinction ratio over almost the entire IR frequency range, the complex vibrational optical activity susceptibility of small organic chiral molecules in the CC stretching mode region is characterized (see picture). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Novel hexacoordinate organosilicon(IV) complexes of diethylenetriamine Schiff base with SiO2N3 skeleton

Some novel hexacoordinate silicon(IV) complexes with a SiO2N3 skeleton were synthesized by using potentially pentadentate ligand N,N'-diethylenetriamine-bis(salicylideneimine). The aforesaid ligand, obtained by the condensation of diethylenetriamine and salicylaldehyde, contains two N of azomethine C=N group, two O of phenolic -OH group and one N of -NH- group capable of coordination. The ligand reacts with RSiCl3 (R = CH3, C6H5, C2H5, CH=CH2) in the presence of triethylamine to yield hexacoordinate silicon complexes 1-4. The resulting complexes were characterized by IR spectroscopy, 1 H, 13 C, 29 Si NMR spectroscopy and elemental analysis. The geometry and hexacoordination was confirmed by comparing the experimental results with computational studies by using GAUSSIAN 03 series of programs. The IR frequencies and 29 Si NMR shifts calculated for isomer B with Density Functional Theory (B3LYP-3-21+G* basis set) correlate with experimental values and suggested the geometry of synthesized complexes. Total energies, dipole moment and bond lengths were calculated from the geometries optimized with semi-empirical methods.

Computational Study on the Conformation and Vibration Frequencies of β-Sheet of ε-Polylysine in Vacuum

Two oligomers, each containing 3 l-lysine residues, were used as model molecules for the simulation of the β-sheet conformation of ɛ-polylysine (ɛ-PLL) chains. Their C terminals were capped with ethylamine and N terminals were capped with α-l-aminobutanoic acid, respectively. The calculations were carried out with the hybrid two-level ONOIM (B3LYP/6-31G:PM3) computational chemistry method. The optimized conformation was obtained and IR frequencies were compared with experimental data. The result indicated that the two chains were winded around each other to form a distinct cyclohepta structure through bifurcated hydrogen bonds. The groups of amide and α-amidocyanogen coming from one chain and the carbonyl group from the other chain were involved in the cyclohepta structure. The bond angle of the bifurcated hydrogen bonds was 66.6°. The frequency analysis at ONIOM [B3LYP/6-31G (d):PM3] level showed the IR absorbances of the main groups, such as the amide and amidocyanogen groups, were in accordance with the experimental data.

Trifluoromethyl Fluoroformyl Trioxicarbonate, CF3OC(O)OOOC(O)F: The First Nonsymmetric Acyl Trioxide

This paper reports for the first time the synthesis and characterization of trifluoromethyl fluoroformyl trioxicarbonate, CF(3)OC(O)OOOC(O)F. The new trioxide is obtained from the gas-phase photolytic reaction of CF(3)C(O)OC(O)CF(3) and FC(O)C(O)F at 223-228 K. It is a very thermally labile molecule that decomposes at room temperature by rupture of either of the CF(3)OC(O)O-O-OC(O)F bonds. These bonds are nonequivalent, and a branching ratio of 0.8 for fragmentation through the CF(3)OC(O)OO-OC(O)F bond was obtained. Unambiguous identification was possible through reaction of the trioxide with an excess of NO(2). Potential-energy surfaces (PES) of the different rotamers were studied by the B3LYP/6-311+G* method, and analysis of the IR frequency of the possible mixture of rotamers agrees excellently with the experimental IR spectrum. This molecule is the first nonsymmetric acyl trioxide reported in the literature.

Effect of ortho substituents on carbonyl carbon 13C NMR chemical shifts in substituted phenyl benzoates

Abstract13C NMR spectra of 37 ortho‐, meta‐, and para‐substituted phenyl benzoates, containing substituents in benzoyl and phenyl moiety, 4 ortho‐substituted methyl and 5 ethyl benzoates as well as 9 R‐substituted alkyl benzoates have been recorded. The influence of the ortho substituents on the carbonyl carbon 13C NMR chemical shift, δCO, was found to be described by a linear multiple regression equation containing the inductive, σI, resonance, σ°R, and steric, E, or υ substituent constants. For all the ortho‐substituted esters containing substituents in the acyl part as well as the phenyl part, the substituent‐induced reverse inductive effect (ρI &lt; 0), the normal resonance effect (ρR &gt; 0), and the negative steric effect (δortho &lt; 0) with the E were observed. In the case of ortho substituents in the phenyl part, the resonance effect was negligible. Due to inductive effect, the ortho electron‐withdrawing substituents showed an upfield shift or shielding of the carbonyl carbon, while the electron‐donating substituents had an opposite effect. Because of the sterical consequences, ortho substituents revealed a deshielding effect on the 13C NMR chemical shift of the carbonyl carbon. For all the meta‐ and para‐substituted esters, the reverse substituent‐induced inductive and resonance effects (ρI &lt; 0, ρR &lt; 0) were found to be significant. In alkyl benzoates, the alkyl substituents showed the reverse inductive and steric effects. The log k values for the alkaline hydrolysis in water, aqueous 0.5 M Bu4NBr and 2.25 M Bu4NBr, and the IR frequencies, νCO, for the ortho‐, meta‐, and para‐substituted phenyl benzoates and alkyl benzoates were correlated nicely with the corresponding 13C NMR substituent chemical shifts, ΔδCO. Copyright © 2009 John Wiley &amp; Sons, Ltd.

Biological and Biomedical Applications of Two-Dimensional Vibrational Spectroscopy: Proteomics, Imaging, and Structural Analysis

In the last 10 years, several forms of two-dimensional infrared (2DIR) spectroscopy have been developed, such as IR pump-probe spectroscopy and photon-echo techniques. In this Account, we describe a doubly vibrationally enhanced four-wave mixing method, in which a third-order nonlinear signal is generated from the interaction of two independently tunable IR beams and an electron-polarizing visible beam at 790 nm. When the IR beams are independently in resonance with coupled vibrational transitions, the signal is enhanced and cross-peaks appear in the spectrum. This method is known as either DOVE (doubly vibrationally enhanced) four-wave mixing or EVV (electron-vibration-vibration) 2DIR spectroscopy. We begin by discussing the basis and properties of EVV 2DIR. We then discuss several biological and potential biomedical applications. These include protein identification and quantification, as well as the potential of this label-free spectroscopy for protein and peptide structural analysis. In proteomics, we also show how post-translational modifications in peptides (tyrosine phosphorylation) can be detected by EVV 2DIR spectroscopy. The feasibility of EVV 2DIR spectroscopy for tissue imaging is also evaluated. Preliminary results were obtained on a mouse kidney histological section that was stained with hematoxylin (a small organic molecule). We obtained images by setting the IR frequencies to a specific cross-peak (the strongest for hematoxylin was obtained from its analysis in isolation; a general CH(3) cross-peak for proteins was also used) and then spatially mapping as a function of the beam position relative to the sample. Protein and hematoxylin distribution in the tissue were measured and show differential contrast, which can be entirely explained by the different tissue structures and their functions. The possibility of triply resonant EVV 2DIR spectroscopy was investigated on the retinal chromophore at the centre of the photosynthetic protein bacteriorhodopsin (bR). By putting the visible third beam in resonance with an electronic transition, we were able to enhance the signal and increase the sensitivity of the method by several orders of magnitude. This increase in sensitivity is of great importance for biological applications, in which the number of proteins, metabolites, or drug molecules to be detected is low (typically pico- to femtomoles). Finally, we present theoretical investigations for using EVV 2DIR spectroscopy as a structural analysis tool for inter- and intramolecular interaction geometries.

Fourier transform infrared (FTIR) spectroscopy

Fourier transform infrared (FTIR) spectroscopy probes the vibrational properties of amino acids and cofactors, which are sensitive to minute structural changes. The lack of specificity of this technique, on the one hand, permits us to probe directly the vibrational properties of almost all the cofactors, amino acid side chains, and of water molecules. On the other hand, we can use reaction-induced FTIR difference spectroscopy to select vibrations corresponding to single chemical groups involved in a specific reaction. Various strategies are used to identify the IR signatures of each residue of interest in the resulting reaction-induced FTIR difference spectra. (Specific) Isotope labeling, site-directed mutagenesis, hydrogen/deuterium exchange are often used to identify the chemical groups. Studies on model compounds and the increasing use of theoretical chemistry for normal modes calculations allow us to interpret the IR frequencies in terms of specific structural characteristics of the chemical group or molecule of interest. This review presents basics of FTIR spectroscopy technique and provides specific important structural and functional information obtained from the analysis of the data from the photosystems, using this method.

A THEORETICAL STUDY ON SOME (1,4)CYCLOPHANES

(1, 4)cyclophanes having either two butadiene bridges, or a butadiene bridge and a cyclobutene ring or two cyclobutene rings at the bridge positions have been considered for restricted Hartree-Fock, MP2 and DFT (B3LYP/6-31G(d,p)) level type calculations. Various molecular orbital energies, thermodynamic properties, IR frequencies etc. have been obtained and discussed. Also NICS calculations for the phane decks have been performed.