Structure and vibrational spectra of dicyclopentadienylzinc. A DFT study

The quantum-chemical DFT calculations of the Cp₂Zn structure confirm the conclusion made earlier from the vibrational spectra that the sandwich structure (⁵-C₅H₅)₂Zn (A) is not energetically favorable and more favorable are the close in energy -structure (⁵-C₅H₅)(¹-C₅H₅)Zn (B) and -structure (¹-C₅H₅)₂Zn (C). The vibrational spectra of structures B and C with the DFT-derived force fields were calculated. A comparison of the calculated spectra of the isolated Cp₂Zn molecules with the experimental data gives no way of deciding between the B and C structures. It is most likely that the molecule is nonrigid and experiences a strong influence from the nearest environment in solution or in the crystalline state.     

Crystal structure and vibrational spectra of pyridine-2,6-dithio-carbomethylamide

The crystal structure of Pyridine-2,6-dithio-carbomethylamide (PDTA) is described: C₉H₁₁N₃S₂, monoclinic, P2₁/c,Z=4,a=6.000 (1) Å,b=8.840 (1) Å,c=21.452 (1) Å, =105.47 (1)^o,d _x=1.47 gcm^–3. The structure was solved with direct methods and refined to a conventionalR-factor of 0.047. The molecule is nearly planar in the crystal. There are possibly weak intramolecular H-bonds between the two amide nitrogens and the pyridine nitrogen and intermolecular H-bonds between two amide nitrogens and one thioamide sulfur atom. The IR andRaman spectra ofPDTA and deuteratedPDTA are discussed.

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Kristallstruktur und Schwingungsspektren von Pyridin-2,6-dithiocarbomethylamid

Zusammenfassung Die Kristallstruktur von Pyridin-2,6-dithiocarbomethylamid (PDTA) wurde bestimmt: C₉H₁₁N₃S₂, monoklin, P2₁/c,Z=4,a=6,000 (1) Å,b=8,840 (1) Å,c=21,452 (1) Å, =105,47 (1)^o,d _x=1,47 gcm^–3. Das Phasenproblem wurde mittels direkter Methoden gelöst und die Struktur bis zu einemR-Faktor vonR=0,047 verfeinert. Das Molekül ist im Kristall nahezu planar. Das Vorliegen schwacher intramolekularer Wasserstoffbrücken zwischen den beiden Thioamid-Stickstoffatomen und dem Pyridinstickstoff sowie intermolekularer Wasserstoffbrücken zwischen Thioamid-Stickstoff- und Thioamid-Schwefelatomen wird postuliert. IR- undRaman-Spektren vonPDTA und deuteriertemPDTA werden diskutiert.

     

DFT and experimental studies of the structure and vibrational spectra of curcumin

The potential energy surface of curcumin [1,7‐bis(4‐hydroxy‐3‐methoxyphenyl)‐1,6‐heptadiene‐3,5‐dione] was explored with the DFT correlation functional B3LYP method using 6‐311G* basis. The single‐point calculations were performed at levels up to B3LYP/6‐311++G**//B3LYP/6‐311G*. All isomers were located and relative energies determined. According to the calculation the planar enol form is more stable than the nonplanar diketo form. The results of the optimized molecular structure are presented and compared with the experimental X‐ray diffraction. In addition, harmonic vibrational frequencies of the molecule were evaluated theoretically using B3LYP density functional methods. The computed vibrational frequencies were used to determine the types of molecular motions associated with each of the experimental bands observed. Our vibrational data show that in both the solid state and in all studied solutions curcumin exists in the enol form. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Crystal structure and vibrational spectra of piperazinium bis(4-hydroxybenzenesulphonate) molecular-ionic crystal

The piperazinium bis(4-hydroxybenzenesulphonate) crystallizes from water solution at room temperature in P2(1)/c space group of monoclinic system. The crystals are built up of doubly protonated piperazinium cations and ionized 4-hydroxybenzenesulphonate anions that interact through weak hydrogen bonds of O-H...O and N-H...O type. Mutual orientation of anions is determined by non-conventional hydrogen bonds of C-Hcdots, three dots, centeredpi type. Room temperature powder FT IR and FT Raman measurements were carried out. The vibrational spectra are in full agreement with the structure obtained from X-ray crystallography. The big single crystals of the title salt can be grown.     

DFT studies of the structure and vibrational spectra of 8-hydroxyquinoline N-oxide

The geometry, frequency and intensity of the vibrational bands of 8-hydroxyquinoline N-oxide (8-HQNO) and its deuterated derivative (8-DQNO) were obtained by the density functional theory (DFT) with the BLYP and B3LYP functionals and 6-31G(d,p) basis set. The optimized bond lengths and bond angles are in good agreement with the X-ray data. The IR and INS spectra of 8-HQNO and 8-DQNO computed at the DFT level reproduce the vibrational wavenumbers and intensities with an accuracy, which allows reliable vibrational assignments.     

A DFT analysis of the vibrational spectra of nitrobenzene

Raman and FTIR, spectra of nitrobenzene, nb, and its isotopomers, nb-¹⁵N, nb-¹³C₆ and nb-d₅, were obtained and the fundamental vibrational modes assigned with the aid of a B3LYP/6-311+G** calculation, without the need for scaling of the force constants. The changes in vibrational coupling between the nitro and benzene groups upon certain isotopic substitutions are well modelled by the calculation, which is able to reproduce the isotopic shifts in frequencies for the nitro vibrations, as well as changes in IR intensities.     

A DFT study of the vibrational spectra of 1-, and 2-nitrotriphenylene

The infrared (IR) and Raman spectra, and intensities of triphenylene, 1-, and 2-nitrotriphenylene were investigated by the density functional theory (DFT, B3LYP method) with 6-311+G** basis set. Normal mode assignments are proposed with particular emphasis on the nitro group vibrations. Compared to 2-nitrotriphenylene (2-NTRP) 1-nitrotriphenylene (1-NTRP) is predicted to show asymmetric nitro stretches at higher frequencies. Through the vibrational study, the structure–spectroscopic relationships of these nitro polycyclic aromatic hydrocarbons (nitro-PAHs) are made, and possible insights into their differential mutagenic potencies correlated. The geometrical distortions of the TRP structure upon nitro group substitution and correlations between structural parameters and vibrational data as well as structure–function relationships related to the mutagenicity of this important class of polycyclic aromatic hydrocarbons are discussed.     

DFT study of vibrational circular dichroism spectra of D-lactic acid-water complexes

This paper presents a discussion of the interaction energies, conformations, vibrational absorption (VA, harmonic and anharmonic) and vibrational circular dichroism (VCD) spectra for conformers of monomeric chiral d(-)-lactic acid and their complexes with water at the DFT(B3LYP)/aug-cc-pVDZ and DFT(B3LYP)/aug-cc-pVTZ levels. A detailed analysis has been performed principally for the two most stable complexes with water, differing by lactic acid conformation. The VCD spectra were found to be sensitive to conformational changes of both free and complexed molecules, and to be especially useful for discriminating between different chiral forms of intermolecular hydrogen bonding complexes. In particular, we show that the VCD modes of an achiral water molecule after complex formation acquire significant rotational strengths whose signs change in line with the geometry of the complex. Using the theoretical prediction, we demonstrate that the VCD technique can be used as a powerful tool for structural investigation of intermolecular interactions of chiral molecules and can yield information complementary to data obtained through other molecular spectroscopy methods.     

Triangular halogen trimers. A DFT study of the structure, cooperativity, and vibrational properties

Triangular halogen trimers (RX)3, where X = Br, I and R represents H, H3C, H2FC, HF2C, F3C, CH2=CH, CH[triple bond]C, and Ph, have been investigated using the density functional theory in the Perdew, Burke, and Ernzerhof method. We report herein the optimized geometries of the stable structures, their vibrational frequencies, and binding energies with the two- and three-body terms. All trimer structures possess a cyclic array of halogen atoms in the type II approach by virtue of the nonspherical atomic charge distribution around the halogens. The Br...Br interactions in trimers are very weak, whereas the I...I interactions in trimers are relatively stronger. While all bromine trimers and most of iodine trimers are predicted to be noncooperative, three of iodine trimers show weak cooperativity. The analysis of vibration modes reveals that all halogen trimers exhibit no especially remarkable frequency shifts. It is also shown that the electrostatic contribution plays a major role in the halogen...halogen interactions in halogen trimers. In contrast to bromine trimers, the relative contribution of charge-transfer component to the halogen...halogen interactions becomes more important for iodine trimers.     

A coupled-cluster study of the structure and vibrational spectra of pyrazole and imidazole

Harmonic force fields were calculated at the corresponding optimized geometries for pyrazole and imidazole at the HF, B3LYP, MP2, CCSD and CCSD(T) levels using the 6-31G* basis set and at the HF and B3LYP levels using the cc-pVTZ basis set. The agreement between the calculated and experimental geometries by the CCSD and CCSD(T) methods was generally similar to that obtained with the B3LYP and MP2 methods. The force fields were scaled using one-scale-factor (1SF), 3SF and 7SF scaling schemes. The scale factors were varied with respect to the experimental frequencies. Using 7SF scaling, the root-mean-square (RMS) deviation of the calculated frequencies from the experimental frequencies by the HF, B3LYP, MP2, CCSD and CCSD(T) methods and the 6-31G* basis set was 16, 7, 13, 11 and 11 cm(-1), respectively. This shows that the B3LYP method is preferred for force field calculations over the perturbative MP2, CCSD and CCSD(T) methods. Using 1SF scaling, the CCSD(T) scale factor was 0.931, the highest among the five methods used but close to that obtained with the B3LYP method and the cc-pVTZ basis set with lower RMS deviation.     

DFT studies of the structure, vibrational and NMR spectra of 2-amino-pyridine betaine monohydrate

Four of the most stable conformers of 2-amino-pyridine betaine (1-carboxymethyl-2-amino-pyridinium inner salt) monohydrates, 2-NH₂PB·H₂O, and one anhydrous were analyzed by the B3LYP/6-31G(d,p) calculations and compared with the X-ray data. Two types of optimized conformers can be distinguished: (a) with NH₂ and COO groups and (b) an imino tautomer with NH and COOH groups. A common feature of the optimized molecules are intramolecular hydrogen bonds between the COO⁻ and H₂N or COOH and HN groups. In the crystal both NH₂ and COO groups participate in intermolecular hydrogen bonds. The probable assignments of the anharmonic experimental solid state vibrational frequencies of 2-NH₂PB·H₂O and 2-ND₂PB·D₂O (conformer 2) based on the calculated B3LYP/6-31G(d,p) harmonic frequencies have been made. Correlations between experimental chemical shifts for 2-NH₂PB, its hydrochloride and 1-carboxyethyl-2-amino-pyridinium inner salt (¹³C and ¹H in D₂O) and GIAO/B3LYP/6-31G(d,p) calculated isotropic shielding constants, δ_exp=a+bσ_calc, are reported. Good linear regression between experimental and theoretical results for ¹³C was obtained. Only in 2-NH₂PB the hydrogen at -position is outside the linear correlation.     

Structural parameters and vibrational spectra of a series of zinc meso-phenylporphyrins: A DFT and experimental study

The influences of meso-phenyl substitution on the geometric structure and vibrational spectra have been studied by DFT calculation (B3LYP/6-31G(d)) and experiment on a series of zinc porphyrins (ZnTPP: zinc 5,10,15,20-tetraphenylporphyrin; ZnTrPP: zinc 5,10,15-triphenylporphryin; ZnDPP: zinc 5,15-dipenylporphyirn; ZnMPP: zinc 5-monophenylporphyrin; ZnP: zinc porphine). Calculation indicates that meso-phenyl substitution gives rise to slight out-of-plane distortion but significant in-plane distortion, especially for the configuration around C_m atom, to zinc porphyrin. The assignment of experimental vibrational spectra was proposed mainly on the basis of calculation. Different shifting tendency upon meso-phenyl substitution is observed for different structure-sensitive bands, such as the shifting of ν₂, ν₃, ν₆, and ν₈ modes toward higher frequencies and ν₄ and ν₂₈ modes toward lower frequencies, upon meso-phenyl substitution. This is attributed primarily to in-plane nuclear reorganization effect (IPNR), though the contribution from out-of-plane distortion cannot be excluded completely. Analysis on vibrational structure reveals that asymmetric meso-phenyl substitution, especially the 5,15-diphenyl substitution of ZnDPP, brings about asymmetric vibrational displacement, or even splitting of vibrational structure to normal modes involving mainly the motion of meso-C_m. This is ascribed to the reduction of symmetry of porphyrin skeleton caused by asymmetric meso-phenyl substitution.     

DFT studies and vibrational spectra of isoquinoline and 8-hydroxyquinoline

The geometry, frequency and intensity of the vibrational bands of isoquinoline (IQ) and 8-hydroxyquinoline (8-HQ) were obtained by the density functional theory (DFT) calculations with the B3LYP functional and 6-31 G* basis set. The vibrational spectral data obtained from the solid phase mid and far FT-IR and FT-Raman spectra of IQ and 8-HQ are assigned based on the results of the normal coordinate calculations. The observed and the calculated spectra are found to be in good agreement.     

Ab Initio study of the structure and vibrational spectra of ZrF n 4-n systems

The optimal geometry and vibrational spectra of a series of [ZrF_n]^4-n clusters (n = 4–8) are calculated in a nonrelativistic approximation of the Hartree-Fock-Roothaan method. The calculated frequencies of the totally symmetric stretching vibrations v_s are in satisfactory agreement with the experimental data. The values of v_s are very sensitive to minor changes in cluster geometry and to the outerspheric environment. The high stability of the [ZrF₆]²⁻ ion was confirmed in an MP2 calculation.     

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.     

Theoretical Raman and infrared spectra, and vibrational assignment for para-halogenoanilines: DFT study

The theoretical IR and Raman spectra of para-halogenoanilines, 4-XC(6)H(4)NH(2) (X=F, Cl and Br) were calculated by using the density functional B3LYP method with the 6-311++G(df,pd) basis set. The theoretical spectra show very good agreement with experiment. The rigorous normal coordinate analyses have been performed, and the detailed vibrational assignment has been made on the basis of the calculated potential energy distributions (PEDs). Several ambiguities and contradictions in the previously reported vibrational assignments have been clarified. The "marker bands" and the effects of the halogen substituent on the characteristic aniline bands in the IR and Raman spectra are discussed.     

An ab initio and DFT study of structure and vibrational spectra of disiloxane H3SiOSiH3 conformers. Comparison to experimental data

The structural and vibrational properties of siloxane monomers may account in the physical and chemical properties of silicone polymers. Because disiloxane (H(3)SiOSiH(3)) is the smallest molecule in the set which runs through small siloxanes like hexamethyldisiloxane (CH(3))3SiOSi(CH(3))3 to silicone polymers, its energetic, structural and vibrational features have been investigated in detail using density functional theory (B3LYP), post Hartree-Fock methods (MP2 and CCSD(T)) and basis sets up to spdfg quality. Five conformations were considered: three bent structures with C2v (double staggered, SS, and double eclipsed, EE, conformations) and Cs symmetries, and two linear forms with D3d and D3h symmetries. At all levels of theory, the relative stability was C2v(SS) approximately C2v(EE)>Cs>D3h>D3d. The difference of energy between the two C2v conformers is lower than 0.04 kcal/mol. At the highest level of theory (CCSD(T)/cc-pVQZ), the barrier to linearisation from C(2v) to D(3h) conformers was calculated at 0.43 kcal/mol, which is extremely low. Most of the structural and vibrational features of the disiloxane do not depend on the conformation of the molecule but are strongly influenced by the SiOSi angle. Anharmonic calculations allowed, without any scaling factor, an exhaustive reinvestigation of the assignments of observed wavenumbers in the infrared and Raman spectra of gaseous disiloxane. Particularly, in the gas phase spectrum, the SiOSi symmetric and antisymmetric stretches have been assigned at 599 and 1105, 596 and 1060, 527 and 1093 cm(-1) for H(3)SiOSiH(3), H(3)Si(18)OSiH(3) and D(3)SiOSiD(3), respectively. The experimental wavenumber splitting of SiOSi symmetric and antisymmetric stretches of H(3)SiOSiH(3) gave an estimation of the SiOSi angle at around 145 degrees . Ab initio methods were revealed more accurate for structural parameters, when DFT/B3LYP was enough for spectral assignments, even at the harmonic level using a single scaling factor.     

X-Ray, MP2 and DFT studies of the structure and vibrational spectra of homarinium chloride

The effects of hydrogen bonding, inter- and intramolecular electrostatic interactions on the structure of homarinium chloride, HOMH·Cl, in the crystal and its isolated molecule have been studied by X-ray diffraction, FT-IR, Raman, ¹H and ¹³C NMR spectroscopies, and by the MP2 and DFT theoretical methods. In the crystal, the Cl⁻ anion is connected with protonated homarine via the O–HCl⁻ hydrogen bond of the length of 2.937(4) Å, and two N⁺Cl⁻ intermolecular electrostatic interactions. In the isolated molecule, according to the MP2 and B3LYP calculations, the Cl⁻ anion is engaged in a shorter hydrogen bond (O–HCl⁻ of 2.811–2.861 Å) and in one type of intramolecular electrostatic interactions. The calculated bond lengths and bond angles at the MP2 and B3LYP levels of theory are in good agreement with the X-ray data, except the conformation of the COOH group, which is cis (syn) in the crystal and trans (anti) in the isolated molecule. The tentative assignments for the experimental solid state vibrational spectra of HOMH·Cl and HOMD·Cl have been made on the basis of the B3LYP/6-31G(d,p) calculated frequencies and intensities. The effect of quaternization of picolinic acid on the chemical shifts of the ring protons and carbons is analyzed.     

FTIR, FT-Raman spectra and ab initio DFT vibrational analysis of 2-bromo-4-methyl-phenylamine

The FTIR and FT-Raman spectra of 2-bromo-4-methyl-phenylamine (BMP) have been recorded. From the standard geometrical parameters the geometry of BMP was optimized at ab initio and DFT levels of theory with complete relaxation in the potential energy surface using 6-311+g(d,p) and 6-311+g(2df,2p) basis sets. Several thermodynamic parameters were also calculated for the minimum energy conformer at ab initio and DFT level of theories. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. Majority of the computed wavenumbers were found to be in good agreement with the experimental observations. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.