Molecular structure, vibrational, UV and NBO analysis of 4-chloro-7-nitrobenzofurazan by DFT calculations

In the present work, we reported a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of 4-chloro-7-nitrobenzofurazan (NBD-Chloride). The FT-IR (400-4000 cm(-1)) and FT-Raman spectra (50-4000 cm(-1)) of NBD-Chloride were recorded. The molecular geometry, harmonic vibrational frequencies and bonding features of NBD-Chloride in the ground-state have been calculated by using the density functional B3LYP method with 6-311++G (d, p) as higher basis set. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) result in DMSO and CDCl3 solvents complements with each other. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Finally the calculation results were applied to simulate infrared and Raman spectra of the title compound which show good agreement with observed spectra.     

Crystal structure and vibrational spectra of AlVO4. A DFT study

We present periodic density functional calculations within the generalized gradient approximation (Perdew-Wang 91) on structure and vibrational properties of bulk AlVO(4). The optimized structure agrees well with crystallographic data obtained by Rietveld refinement (the mean absolute deviation of bond distances is 0.032 A), but the deviations are larger for the lighter oxygen atoms than for the heavier Al and V atoms. All observed bands in the Raman and IR spectrum have been assigned to calculated harmonic frequencies. Bands in the 1020-900 cm(-1) region have been assigned to V-O((2)) stretches in V-O((2))-Al bonds. The individual bands do not arise from vibrations of only one bond, not even from vibrations of several bonds of one VO(4) tetrahedron. The results confirm that vibrations around 940 cm(-1) observed for vanadia particles supported on thin alumina film are V-O-Al interface modes with 2-fold coordinated oxygen atoms in the V-O((2))-Al interface bonds.     

The specific vibrational modes of GTP in solution and bound to Ras: a detailed theoretical analysis by QM/MM simulations

The hydrolysis of guanosine triphosphate (GTP) in general, and especially by GTPases like the Ras protein, is in the focus of biological investigations. A huge amount of experimental data from Fourier-transformed infrared studies is currently available, and many vibrational bands of free GTP, GTP·Mg(2+), and Ras·GTP·Mg(2+) in solution have been assigned by isotopic labeling. In the Ras environment, bands between 800 cm(-1) and 1300 cm(-1) have already been assigned, but not those below 800 cm(-1). The combination of quantum and molecular mechanics (QM/MM) methods takes the quantum effects for selected relevant atoms into account. This provides structural details, vibrational frequencies and electron distributions of the region of interest. We therefore used MM and QM/MM simulations to investigate the normal vibrational modes of GTP, GTP·Mg(2+), and Ras·GTP·Mg(2+) in solution, and assigned the vibrational frequencies for each normal vibration mode. In this study, the quantum box contains the nucleoside and the Mg(2+). The comparison of calculated and experimental vibrational spectra provides a very good control for the quality of the calculations. Structurally, MM and QM/MM simulations reveal a stable tridentate coordination of the Mg(2+) by GTP in water, and a stable bidentate coordination by GTP in complex with Ras. For validation, we compare the calculated frequencies and isotopic shifts with the experimental results available in the range of 800 cm(-1) to 1300 cm(-1). For the first time we suggest band assignments of the vibrational modes below 800 cm(-1) by comparison of calculated and experimental spectra.     

Density-Functional Theory of Vibrations in Ni<Subscript>1−<Emphasis Type="Italic">x</Emphasis></Subscript>V<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript> Clusters

We have performed the calculation of the vibrational frequencies, Fermi energy and binding energy for several clusters of Ni and vanadium atoms by using the first principles. The calculations are performed by using the density-functional theory in the local-density approximation with spin polarized orbitals. The calculation of vibrational frequencies shows that some of the clusters have positive vibrational frequencies which describe the oscillations of the stable clusters. The negative vibrational frequencies indicate that these clusters are instable with respect to these vibrations when no energy of this frequency is supplied. We find that for vanadium concentration less than 11.1% the clusters of Ni and V atoms are not stable. Hence ferromagnetism in Ni is predicted below 11.1% vanadium. We find the vibrational frequencies of several clusters for which the vanadium concentration is more than 11.1%. We are able to find a phase transition by use of quantum mechanics alone without the use of classical mechanical variables or thermodynamic variables such as temperature.     

Observation of the lead carbonyls, PbnCO(n=1-4): reactions of lead atoms and small clusters with carbon monoxide in solid argon

Reactions of laser-ablated Pb atoms with CO molecules in solid argon lead to the formation of the lead carbonyls, PbnCO (n=1-4), using matrix-isolation infrared spectroscopy. Absorption at 2027.7 cm(-1) is assigned to C-O stretching mode of the PbCO product, which appears and increases on annealing, disappears on broadband irradiation, and recovers on further annealing. Small lead cluster mono-carbonyls PbnCO (n=2-4) are also observed in the present infrared spectra. Based on the results of stepwise annealing and the comparison with theoretical predictions, the absorptions at 1915.5, 1923.8, and 2042.8 cm(-1) are assigned to Pb2CO, Pb3CO, and Pb4CO, respectively. Bridging CO is found in Pb2CO or Pb3CO, whereas terminal CO in Pb4CO. The density functional theory calculations have been performed on these molecules and small naked lead clusters. The good agreement between experimental and calculated vibrational frequencies, relative absorption intensities, and isotopic shifts provides strong support for the identifications of these lead mono-carbonyls PbnCO (n=1-4). Furthermore, energetic analysis for the possible reactions of lead atoms with CO molecules is also given.     

DFT Calculations of Vibrational Frequencies of Carbon–Nitrogen Clusters: Raman Spectra of Carbon Nitrides

We have performed the calculation of structures of clusters containing carbon and nitrogen atoms. We determine the bond lengths in each case. We also calculate the vibrational frequencies of all of the clusters. We compare the calculated values of the vibrational frequencies with those measured by the Raman spectra of amorphous carbon nitrides. Some of the calculated frequencies are in agreement with those measured. We identity that linear structures and hence “back bones” are present in the glassy state.     

Hydrogen-bonded structures for self-aggregates of 2,5-dimethylpyrrole and its binary clusters with pyrrole studied by IR cavity ringdown spectroscopy

N-H···π hydrogen-bonded (H-bonded) structures were studied by applying vibrational spectroscopy to self-aggregate clusters of 2,5-dimethylpyrrole (DMPy) and its binary clusters with pyrrole (Py). The NH stretching vibrations of jet-cooled clusters were observed by IR cavity ringdown spectroscopy. A combination of experiments and density functional theory calculations revealed the stable structures, intermolecular binding energies, and harmonic vibrational frequencies. The IR spectrum of the DMPy self-aggregate clusters was very similar in spectral features to that of the Py clusters in a previous work. The observed NH stretching vibrations at 3505, 3420, 3371, and 3353 cm(-1) are simultaneously red-shifted by ～25 cm(-1) from the Py monomer, dimer, trimer, and tetramer, respectively. Based on a spectral analogy of DMPy with Py, and a consistency of the calculated harmonic frequencies with experiments, the H-bonded structures of the DMPy clusters were determined to be of a T-shape for a dimer and a cyclic for a trimer and a tetramer. For the DMPy-Py binary clusters, we discussed the stability and geometry of the N-H···π interactions in the T-shaped dimer and the cyclic trimer. The binary dimer showed the only single NH stretch at 3419 cm(-1) in the IR spectrum. A vibrational analysis of the H-bonded NH stretches as well as the calculated stabilization energies deduced that only the binary dimer by DMPy as an acceptor and Py as a donor can exist in a supersonic jet. For binary trimers, NH stretches were observed due to both (DMPy)(2)-(Py)(1) and (DMPy)(1)-(Py)(2). They were found to have different vibrational patterns from each other; the former showed three dispersed NH stretches, and the other had two quasi-degenerate NH stretches. Throughout this study, we also considered the intermolecular geometries, such as the H-bond distance and the angle in terms of the methyl group substitution effect.     

Vibrational spectroscopic (FT-IR and FT-Raman), first-order hyperpolarizablity, HOMO, LUMO, NBO, Mulliken charges and structure determination of 2-bromo-4-chlorotoluene

The FT-IR and FT-Raman spectra of 2-bromo-4-chlorotoluene (2B4CT) molecule have been recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. Optimized geometrical structures, harmonic vibrational frequencies, intensities, reduced mass, force constants and depolarization ratio have been computed by the B3 based (B3LYP) density functional methods using 6-31+G(d,p) and 6-311++G(d,p) basis sets. The observed FT-IR and FT-Raman vibrational frequencies are analysed and compared with theoretically predicted vibrational frequencies. The geometries and normal modes of vibration obtained from DFT method are in good agreement with the experimental data. The Mulliken charges, the natural bonding orbital (NBO) analysis, the values of electric dipole moment (μ) and the first-order hyperpolarizability (β) of the investigated molecule were computed using DFT calculations. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The influences of bromine atom, chlorine atom and methyl group on the geometry of benzene and its normal modes of vibrations have also been discussed.     

Dynamics of an [Fe4S4(SPh)4]2- cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using 36S substitution, DFT calculations, and empirical force fields

We have used four vibrational spectroscopies--FT-IR, FT-Raman, resonance Raman, and 57Fe nuclear resonance vibrational spectroscopy (NRVS)--to study the normal modes of the Fe-S cluster in [(n-Bu)4N]2[Fe4S4(SPh)4]. This [Fe4S4(SR)4]2- complex serves as a model for the clusters in 4Fe ferredoxins and high-potential iron proteins (HiPIPs). The IR spectra exhibited differences above and below the 243 K phase transition. Significant shifts with 36S substitution into the bridging S positions were also observed. The NRVS results were in good agreement with the low temperature data from the conventional spectroscopies.The NRVS spectra were interpreted by normal mode analysis using optimized Urey-Bradley force fields (UBFF) as well as from DFT theory. For the UBFF calculations, the parameters were refined by comparing calculated and observed NRVS frequencies and intensities. The frequency shifts after 36S substitution were used as an additional constraint. A D 2d symmetry Fe4S4S'4 model could explain most of the observed frequencies, but a better match to the observed intensities was obtained when the ligand aromatic rings were included for a D 2d Fe4S4(SPh)4 model. The best results were obtained using the low temperature structure without symmetry constraints. In addition to stretching and bending vibrations, low frequency modes between approximately 50 and 100 cm(-1) were observed. These modes, which have not been seen before, are interpreted as twisting motions with opposing sides of the cube rotating in opposite directions. In contrast with a recent paper on a related Fe4S4 cluster, we find no need to assign a large fraction of the low frequency NRVS intensity to 'rotational lattice modes'. We also reassign the 430 cm(-1) band as primarily an elongation of the thiophenolate ring, with approximately 10% terminal Fe-S stretch character. This study illustrates the benefits of combining NRVS with conventional Raman and IR analysis for characterization of Fe-S centers. DFT theory is shown to provide remarkable agreement with the experimental NRVS data. These results provide a reference point for the analysis of more complex Fe-S clusters in proteins.     

Quantum chemical calculation of infrared spectra of acidic groups in chabazite in the presence of water

The changes in the spectra of the acidic group in chabazite are studied by quantum chemical calculations. The zeolite is modeled by two clusters consisting of eight tetrahedral atoms arranged in a ring and seven tetrahedral atoms coordinated around the zeolite OH group. The potential energy and dipole surfaces were constructed from the zeolite OH stretch, in-plane and out-of-plane bending coordinates, and the intermolecular stretch coordinate that corresponds to a movement of the water molecule as a whole. Both the anharmonicities of the potential energy and dipole were taken into account by calculation of the frequencies and intensities. The matrix elements of the vibrational Hamiltonian were calculated within the discrete variable representation basis set. We have assigned the experimentally observed frequencies at approximately 2900, approximately 2400, and approximately 1700 cm(-1) to the strongly perturbed zeolite OH vibrations caused by the hydrogen bonding with the water molecule. The ABC triplet is a Fermi resonance of the zeolite OH stretch mode with the overtone of the in-plane bending (the A band) and the overtone of the out-of-plane bending (the C band). In the B band the stretch is also coupled with the second overtone of the out-of-plane bending. The frequencies at approximately 3700 and approximately 3550 cm(-1) we have assigned to the OH stretch frequencies of a slightly perturbed water molecule.     

Spectroscopic analysis of 2-(2,3-dihydro-1,5-dimethyl-3-oxo-2-phenyl-1H-pyrazol-4-ylimino)-2-(4-nitro-phenyl) acetonitrile

The optimized geometry and vibrational frequencies of 2-(2,3-dihydro-1,5-dimethyl-3-oxo-2-phenyl-1H-pyrazol-4-ylimino)-2-(4-nitro-phenyl) acetonitrile (DOPNA) were obtained by ab initio DFT/B3LYP level with complete relaxation in the potential energy surface using 6-31G and 6-311G basis sets. The Fourier-transform infrared (FT-IR) spectrum of DOPNA has been recorded in the region 4000-400 cm(-1). The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR spectrum. The calculated frequencies are in comparable agreement with the experimental frequencies. The calculated energy span between the HOMO and the LUMO of DOPNA is 2.94 and 2.87eV by B3LYP/6-31G and B3LYP/6-311G, respectively.     

Experimental and theoretical investigation of the molecular and electronic structure of anticancer drug camptothecin

The Fourier Transform Infrared spectrum of (S)-4 ethyl-4-hydroxy-1H-pyrano [3',4':6,7]-indolizino-[1,2-b-quinoline-3,14-(4H,12H)-dione] [camptothecin] was recorded in the region 4000-400 cm(-1). The Fourier Transform Raman spectrum of camptothecin (CPT) was also recorded in the region 3500-50 cm(-1). Quantum chemical calculations of geometrical structural parameters and vibrational frequencies of CPT were carried out by MP2/6-31G(d,p) and density functional theory DFT/B3LYP/6-311++G(d,p) methods. The assignment of each normal mode has been made using the observed and calculated frequencies, their IR and Raman intensities. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. Most of the computed frequencies were found to be in good agreement with the experimental observations. The isotropic chemical shifts computed by (13)C and (1)H NMR analysis also show good agreement with experimental observations. Comparison of calculated spectra with the experimental spectra provides important information about the ability of computational method to describe the vibrational modes of large sized organic molecule.     

End-cap effects on vibrational structures of finite-length carbon nanotubes

Vibrational structures of C60-related finite-length nanotubes, C(40+20n) and C(42+18n) (1 < or = n < or = 4), in which n is, respectively, the number of cyclic cis- and trans-polyene chains inserted between fullerene hemispheres, are analyzed from density functional theory (DFT) calculations. To illuminate the end-cap effects on their vibrational structures, the corresponding tubes terminated by H atoms C(20n)H20 and C(18n)H18 (1 < or = n < or = 5) are also investigated. DFT calculations show a broad range of vibrational frequencies for the finite-size nanotubes: high-frequency modes (1100-1600 cm(-1)) containing oscillations along tangential directions (tangential modes), medium-frequency modes (700-850 cm(-1)) whose oscillations are located on the edges or end caps, and low-frequency modes (300-600 cm(-1)) involving oscillations along the radial directions (radial modes). Broadening of the calculated frequencies is due to the number of nodes in the standing waves of normal modes in the finite-size tubes. In the capped tubes, calculated vibrational frequencies are insensitive to the number of chains (n), whereas in the uncapped tubes, most vibrational frequencies change significantly with an increase in tube length. The discrepancy in the size dependency is reasonably understood by their C-C bonding networks; the capped tubes have similar bond-length alternation patterns within the polyene chains irrespective of n, whereas the uncapped tubes have various bond-deformation patterns. Thus, DFT calculations illuminate that the edge effects have strong impacts on the vibrational frequencies in the finite-size nanotubes.     

Infrared spectra and ab initio calculations for the Cl--(CH4)n (n = 1-10) anion clusters

In an effort to elucidate their structures, mass-selected Cl--(CH4)n (n = 1-10) clusters are probed using infrared spectroscopy in the CH stretch region (2800-3100 cm(-1)). Accompanying ab initio calculations at the MP2/6-311++G(2df,2p) level for the n = 1-3 clusters suggest that methane molecules prefer to attach to the chloride anion by single linear H-bonds and sit adjacent to one another. These conclusions are supported by the agreement between experimental and calculated vibrational band frequencies and intensities. Infrared spectra in the CH stretch region for Cl--(CH4)n clusters containing up to ten CH4 ligands are remarkably simple, each being dominated by a single narrow peak associated with stretching motion of hydrogen-bonded CH groups. The observations are consistent with cluster structures in which at least ten equivalent methane molecules can be accommodated in the first solvation shell about a chloride anion.     

Infrared spectroscopy of Li(+)(CH4)1Ar(n), n = 1-6, clusters

Infrared predissociation (IRPD) spectra of Li(+)(CH(4))(1)Ar(n), n = 1-6, clusters are reported in the C-H stretching region from 2800 to 3100 cm(-1). The Li(+) electric field perturbs CH(4) lifting its tetrahedral symmetry and gives rise to multiple IR active modes. The observed bands arise from the totally symmetric vibrational mode, v(1), and the triple degenerate vibrational mode, v(3). Each band is shifted to lower frequency relative to the unperturbed CH(4) values. As the number of argon atoms is increased, the C-H red shift becomes less pronounced until the bands are essentially unchanged from n = 5 to n = 6. For n = 6, additional vibrational features were observed which suggested the presence of an additional conformer. By monitoring different photodissociation loss channels (loss of three Ar or loss of CH(4)), one conformer was uniquely associated with the CH(4) loss channel, with two bands at 2914 and 3017 cm(-1), values nearly identical to the neutral CH(4) gas-phase v(1) and v(3) frequencies. With supporting ab initio calculations, the two conformers were identified, both with a first solvent shell size of six. The major conformer had CH(4) in the first shell, while the conformer exclusively present in the CH(4) loss channel had six argons in the first shell and CH(4) in the second shell. This conformer is +11.89 kJ/mol higher in energy than the minimum energy conformer at the MP2/aug-cc-pVDZ level. B3LYP/6-31+G* level vibrational frequencies and MP2/aug-cc-pVDZ level single-point binding energies, D(e) (kJ/mol), are reported to support the interpretation of the experimental data.     

FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular geometry of butylated hydroxy toluene

The FT-IR spectrum of 2,6-di-tert-butyl-4-methylphenol [butylated hydroxy toluene] was recorded in the region 4000-400 cm(-1). The FT-Raman spectrum of butylated hydroxy toluene was also recorded in the region 3500-50 cm(-1). The molecular structure and vibrational frequencies of butylated hydroxy toluene (BHT) have been investigated with combined experimental and theoretical study. Two stable conformers of the title compound were obtained from the result of geometry optimizations of these possible conformers. The conformer 1 is (approximately 2.6 kcal/mol) more stable than conformer 2. Geometry optimizations and vibrational frequency calculations were performed by BLYP and B3LYP methods using 6-31G(d), 6-31G(d,p) and 6-31+G(d,p) as basis sets. The scaled frequencies were compared with experimental spectrum and on the basis of this comparison; assignments of fundamental vibrational modes were examined. Comparison of the experimental spectra with harmonic vibrational wavenumbers indicates that B3LYP/6-31G(d) results are more accurate. Predicted electronic absorption spectra of BHT from TD-DFT calculation have been analyzed and compared with the experimental UV-vis spectrum. The calculated HOMO and LUMO energies show that the charge transfer occurs within the molecule.     

The Creutz-Taube complex revisited: DFT study of the infrared frequencies

The structural parameters, electronic properties, and infrared frequencies of three binuclear ruthenium complexes, [(NH(3))(5)Ru(pyrazine)Ru(NH(3))(5)](n+), n = 4-6, have been investigated with density functional theory. Structural analysis demonstrates that the structure of the mixed-valence 5+, or [II,III], is not an intermediate of the reduced 4+, or [II,II], and the oxidized 6+, or [III,III], compounds. Electronic structure comparison shows that the Ru d(yz) antibonding orbital is empty when n = 5 and 6 and occupied, when n = 4. The infrared frequencies have been calculated for a sequence of models with increasingly detailed accounts of counterions, ranging from the free Creutz-Taube 5+ ion, over jellium embedded, COnductor-like Screening MOdel (COSMO), to the experimental structure of the triclinic [II,III](tos)(5).4H(2)O (tos = p-toluenesulfonate) crystal. Analysis of the Ru vibrations shows that the spectra for the two symmetry-inequivalent Ru atoms are essentially the same. We find that Ru-Ru modes exist near three well-defined frequencies in the solid: at 145, 285, and 345 cm(-1). Similar results are also obtained for the simplified jellium and COSMO models. The spectral properties of these vibrational correlations testify to the existence of two coupled Ru atoms in the same charge state.     

Vibrational spectral analysis and first hyperpolarizability studies of 1-bromonaphthalene based on ab initio and DFT methods

In this work, the experimental and theoretical vibrational spectra of 1-bromonaphthalene (1-BN) were studied. FTIR and FT Raman spectra were recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The structural and spectroscopic data of the molecule in the ground state were calculated by using ab initio Hartree-Fock and density functional method (B3LYP) with the 6-311++G(d,p) basis set. The vibrational frequencies were calculated and scaled values were compared with experimental FTIR and FT Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The optimized geometric parameters were calculated. The predicted first hyperpolarizability also shows that the molecule might have a reasonably good nonlinear optical (NLO) behaviour. The calculated HOMO-LUMO energy gap reveals that charge transfer occurs within the molecule.     

InnNa和InnNa+(n=2-8)的团簇结构和电子性质

在密度泛函理论B3LYP水平上, 对InnNa和InnNa+(n=2-8)团簇进行了结构优化和振动频率计算. 计算结果表明, InnNa(n=2、3、4、6)最稳定结构中的对称性分别为C2v、C3v、C4v和C2v, 而InnNa(n=5、7、8)的最稳定结构的对称性为C1点群. 从InnNa(n=4-8)的最稳定结构可以看出, Na原子均位于四个In原子形成的四边形面上. 对于InnNa+(n=2-8), 除了In2Na+、In4Na+和In7Na+, 其它结构都与其中性结构相似. 进一步计算InnNa(n=2-8)团簇的平均结合能、能量的二阶差分以及绝热电离能表明, InnNa(n=2-8)团簇能量的二阶差分呈现奇偶交替特征, In4Na和In6Na较其它团簇更为稳定, 而且理论计算得到的绝热电离能和实验结果吻合得很好.