Normal Mode Vibrational Frequencies Research Articles

Gas phase H+, H3O+ and NH4+ affinities of oxygen-bearing volatile organic compounds; DFT calculations for soft chemical ionisation mass spectrometry.

Quantum chemistry calculations were performed using the density functional theory, DFT, to understand the structures and energetics of organic ions relevant to gas phase ion chemistry in soft chemical ionisation mass spectrometry analytical methods. Geometries of a range of neutral volatile organic compound molecules and ions resulting from protonation, the addition of H3O+ and the addition of NH4+ were optimised using the B3LYP hybrid DFT method. Then, the total energies and the normal mode vibrational frequencies were determined, and the total enthalpies of the neutral molecules and ions were calculated for the standard temperature and pressure. The calculations were performed for several feasible structures of each of the ions. The proton affinities of several benchmark molecules agree with the accepted values within ±4 kJ mol-1, indicating that B3LYP/6-311++G(d,p) provides chemical accuracy for oxygen-containing volatile organic compounds. It was also found that the binding energies of H3O+ and NH4+ to molecules correlate with their proton affinities. The results contribute to the understanding of ligand switching ion-molecule reactions important for secondary electrospray ionisation, SESI, and selected ion flow tube, SIFT, mass spectrometries.

A detailed kinetic study on the tautomerization reactions of barbituric acid: A combined DFT-QTAIM analysis

A detailed kinetic study on the tautomerization reactions of barbituric acid (BA) at elevated temperatures from 270 K up to 1000 K was performed in this work. The B3LYP/6-311 + G(3df,2p) density functional theory (DFT) calculations were performed to evaluate the rate constants of transition states (TS) conversions of the tautomerization reactions. The connections from a given TS to the corresponding local minima of the reactant and product sides were confirmed by means of employing the intrinsic reaction coordinate (IRC) method. Moreover, the quantum theory of atoms in molecules (QTAIM) approach was employed to analyze the molecular mechanisms of reactions. The effects of vibrational normal mode frequencies of the reactant and TS were investigated on the curvature of the corresponding Arrhenius plot in the presence and absence of the tunneling effect. For each tautomerization reaction, the investigated reaction was partitioned into three different stages and four zones. The obtained results were plotted along with the corresponding reaction coordinates for each reaction considering and comparing different factors in agreement with already affirmed concepts. As a consequence, details of performed kinetic study on the tautomerization reactions of BA were successfully provided in this work.

First-principles electronic structure in second-moment calculation of mode frequencies: Failure of quasiharmonic approximation in silicon

Using first-principles electronic structure calculations (local density approximation), we present second-moment calculations of the temperature dependence of the vibrational normal mode frequencies in Si up to 1500 K . The method is based on simple ensemble averages of displacements and forces and is easy to implement. These efficient calculations incorporate all interactions nonperturbatively, implicitly including all high order force constants, in contrast to typical perturbative approaches. Also in this work, we propose and apply to our classical calculations an estimated quantum correction that could be used for classical approaches other than the moments method. We compare our results to available experiments, including recent inelastic neutron scattering data and conclude that the second-moment gives the frequency shift to within a factor of 2 in contrast to quasiharmonic approaches that fail by an order of magnitude to predict the anharmonic shift. Noting the relative simplicity and speed of the calculations, we conclude that the second-moment approximation reasonably accounts for anharmonicity in a system that has been very closely studied experimentally and may reliably be applied in an exploratory way to more complex systems. We suggest that further improvement on the results could be obtained by incorporating the fourth moment, which can be implemented with little additional cost.

Structural, vibrational and electronic spectroscopic study of 6-hydroxycoumarin using experimental and theoretical methods.

Understanding the photochemical behavior of structural isomers of hydroxycoumarin (HC) having different properties of consequence in biological activities demand spectroscopic information of this class of compounds. Barring 6-hydroxycoumarin (6-HC), other isomers of HC's are well studied spectroscopically. To understand and compare the photochemical activity of 6-HC with other isomers, a detailed study of this molecule has been taken up. For this purpose, electronic, vibrational and structural properties of 6-HC have been studied using ultraviolet absorption and Infrared spectroscopy techniques. Quantum chemical calculations have been performed at DFT/B3LYP level of theory to get the optimized geometry and vibrational frequencies of normal modes to support and analyze experimental data. The detailed vibrational assignments were made on the basis of potential energy distributions. Chemical activity, molecular orbital energies, band gap and hyper-polarizability information have been computed from quantum chemical simulations. NBO analysis helped in understanding the stability of the molecule arising from hyper-conjugative interaction and charge delocalization. UV-Visible spectrum of the compound was recorded in the region 300-600nm helped in obtaining band gap data of the compound. Molecular Electrostatic Potentials (MESP) were plotted and the respective centers of electrophilic and nucleophilic attacks were predicted with the help of Fukui functions calculations. Further, it was observed that the negative electrostatic potential regions are mainly localized over the oxygen atoms and the positive regions are localized over the benzene ring. Details of the results and analysis of experimental and theoretical spectroscopy studies are presented in this paper.

A general study of actinyl hydration by molecular dynamics simulations using ab initio force fields.

A set of new ab initio force fields for aqueous [AnO2]2+/+ (An = Np(vi,v), Pu(vi), Am(vi)) has been developed using the Hydrated Ion (HI) model methodology previously used for [UO2]2+. Except for the non-electrostatic contribution of the HI-bulk water interaction, the interaction potentials are individually parameterized. Translational diffusion coefficients, hydration enthalpies, and vibrational normal mode frequencies were calculated from the MD simulations. Physico-chemical properties satisfactorily agree with experiments validating the robustness of the force field strategy. The solvation dynamics and structure for all hexavalent actinoids are extremely similar and resemble our previous analysis of the uranyl cation. This supports the idea of using the uranyl cation as a reference for the study of other minor actinyls. The comparison between the NpO2 2+ and NpO2 + hydration only provides significant differences in first and second shell distances and second-shell mean residence times. We propose a single general view of the [AnO2]2+/+ hydration structure: aqueous actinyls are amphiphilic anisotropic solutes which are equatorially conventional spherically symmetric cations capped at the poles by clathrate-like water structures.

Crystallography, vibrational, electronic and optical analysis of 4-Bromo-2-(2,5-dichloro-phenylimino)-phenol

This work reports synthesis and characterization of a novel compound, 4-Bromo-2-(2,5-dichloro-phenylimino)-phenol (BDP). The crystal structure of this Schiff base is determined and compared with DFT calculations. Density functional theory (DFT) and time dependent density functional theory (TD-DFT) is applied to study the optical, electronic properties, vibrational frequencies and optimized structure of 4-Bromo-2-(2,5-dichloro-phenylimino)-phenol by B3LYP, M06–2X, and ab initio (HF) methods and 6–311++G (d,p) basis set. The geometry and electronic properties, thermodynamic functions and atomic charges of the title compound are reported too. Finally, the calculated normal mode vibrational frequencies provide thermodynamic properties through the principle of statistical mechanics. A natural bond orbital (NBO) analysis was carried out to explain the charge transfer or delocalization of charge due to intra-molecular interactions.

Synthesis, spectral, structural and DFT studies of novel dialkylfluorene decorated phenothiazine-3-carbaldehyde

A novel conjugated alkylfluorene decorated phenothiazine carbaldehyde, 10-(9,9-diethyl-9H-fluoren-2-yl)-10H-phenothiazine-3-carbaldehyde (FPTZC) was synthesized and fully characterized by spectroscopic, elemental and single crystal XRD analyses. The geometry and electronic structures were arrived using B3LYP/6-31G++(d,p) calculations. The geometrical parameters, resulted from single crystal XRD, are in accord with the computed ones. FT-IR and NMR spectra of the title molecule have been investigated computationally. The theoretical NMR results are found to be similar with the experimental ones. The calculated vibrational frequencies of normal modes were matched well with the experimental values. These studies provide insights into their molecular geometry and electronic structures.

DFT Analyses of Reaction Pathways and Temperature Effects on various Guaiacol Conversion Reactions in Gas Phase Environment

AbstractGuaiacol component represents the phenolic fraction of bio‐oil. In this numerical study, six reaction pathways originating from guaiacol and yielding anisole, phenol, cyclopentanone and cyclohexanone as the major end products with various intermediates, are carried out. The transition state optimizations, normal mode vibrational frequencies, and intrinsic reaction coordinate calculations are performed under the density functional theory (DFT) framework at B3LYP/6‐311+g(d,p) level of theory. The thermochemistry calculations are carried out at 1 atm pressure and at a wide range of temperature between 298–898 K with an interval temperature of 100 K. Results indicate that all six reactions are both exothermic and spontaneous at each temperature point, however, pathways 1, 2, and 3 show increase in exothermicity and spontaneity with increase in temperature but pathways 4, 5, and 6 show the increase in exothermicity only with increase in temperature while decrement in reaction free energies with increasing temperature.

Chemoselective synthesis, spectral and computational studies of 2-amino-3-cyano-4-aryl-4H-chromen-7-yl alkyl carbonates

Abstract A series of 2-amino-3-cyano-4-aryl-4H-chromen-7-yl alkyl carbonates (4–13) was synthesised in just two steps via a one-pot multicomponent reaction and consequent nucleophilic substitution reaction. The structures of newly synthesized compounds were established on the basis of FT−IR, 1H NMR, 13C NMR, 1H 13C COSY and HMBC spectral techniques. FT−IR, and NMR spectra of compound 11 has been investigated by computational method using DFT B3LYP with 6-311++G(d, p) basis set. The calculated vibrational frequencies of normal modes were matched well with the experimental values.

Theoretical investigations of absorption and fluorescence spectra of protonated pyrene.

The equilibrium geometry and 75 vibrational normal-mode frequencies of the ground and first excited states of protonated pyrene isomers were calculated and characterized in the adiabatic representation by using the complete active space self-consistent field (CASSCF) method. Electronic absorption spectra of solid neon matrixes in the wavelength range 495-415 nm were determined by Maier et al. and they were analyzed using time-dependent density functional theory calculations (TDDFT). CASSCF calculations and absorption and emission spectra simulations by one-photon excitation equations were used to optimize the excited and ground state structures of protonated pyrene isomers. The absorption band was attributed to the S0 → S1 electronic transition in 1H-Py(+), and a band origin was used at 20580.96 cm(-1). The displaced harmonic oscillator approximation and Franck-Condon approximation were used to simulate the absorption spectrum of the (1) (1)A' ← X[combining tilde](1)A' transition of 1H-Py(+), and the main vibronic transitions were assigned for the first ππ* state. It shows that the vibronic structures were dominated by one of the eight active totally symmetric modes, with ν15 being the most crucial. This indicates that the electronic transition of the S1((1)A') state calculated in the adiabatic representation effectively includes a contribution from the adiabatic vibronic coupling through Franck-Condon factors perturbed by harmonic oscillators. The present method can adequately reproduce experimental absorption and fluorescence spectra of a gas phase.

Synthesis, spectroscopic investigation and computational study of 3-(1-(((methoxycarbonyl)oxy)imino)ethyl)-2H-chromen-2-one

The molecular structure and vibrational modes of 3-acetylcoumarin oxime carbonate (abbreviated as 3-ACOC) have been investigated by FT-IR, FT-Raman, NMR spectra and also by computational methods using HF and B3LYP with 6-311++G(d,p) basis set. The optimized geometric parameters (bond lengths, bond angles and dihedral angles) were in good agreement with the corresponding experimental values of 3-ACOC. The calculated vibrational frequencies of normal modes from DFT method matched well with the experimental values. The complete assignments were made on the basis of the total energy distribution (TED) of the vibrational modes. NMR (1H and 13C) chemical shifts were calculated by GIAO method and the results were compared with the experimental values. The other parameters like dipole moment, polarizability, first order hyperpolarizability, zero-point vibrational energy, EHOMO, ELUMO, heat capacity and entropy have also been computed.

Calculated Vibrational Properties of Ubisemiquinones

Density functional theory has been used to calculate harmonic normal mode vibrational frequencies for unlabeled and isotope-labeled ubisemiquinones in both the gas phase and in several solvents. It is shown that four methoxy group conformations are likely to be present in solution at room temperature. Boltzmann weighted infrared and Raman spectra for the four conformers were calculated, and composite spectra that are the sum of the Boltzmann weighted spectra were produced. These composite spectra were compared to experimental FTIR and resonance Raman spectra, and it is shown that the calculated band frequencies, relative band intensities, and C13 and O18 isotope-induced band shifts are in excellent agreement with experiment. The calculations show that the C=O and C=C modes of ubisemiquinone strongly mix with methoxy methyl CH bending vibrations, and that the degree of mixing is altered upon isotope labeling, resulting in complicated changes in mode frequencies, intensities, and composition upon isotope labeling. Upon consideration of the calculated potential energy distributions of the normal modes of ubisemiquinone, and how they change upon isotope labeling, an explanation of some puzzling features in previously published Raman spectra is provided.

Ab initio calculations of the thermodynamic parameters of lithium, sodium, and potassium oxides under pressure

The parameters of the equation of state and Gruneisen parameters for lithium, sodium, and potassium oxides have been calculated in the generalized gradient approximation of the density functional theory using a linear combination of atomic orbitals with the CRYSTAL09 software package. The frequencies of long-wavelength normal mode vibrations have also been calculated and the dependence of these frequencies on the pressure has been established. The Debye temperature has been determined from the elastic characteristics of the compounds. The dependences of the Debye temperature, compressibility, thermodynamic potential, entropy, specific heat, thermal expansion coefficient, and thermal conductivity coefficient on the pressure in the range from −3 to −15 GPa and on the temperature have been calculated in the quasi-harmonic Debye model. The results obtained are in satisfactory agreement with the available reference and experimental data.

Analysis of the excited-state absorption spectral bandshape of oligofluorenes

We present ultrafast transient absorption spectra of two oligofluorene derivatives in dilute solution. These spectra display a photoinduced absorption band with clear vibronic structure, which we analyze rigorously using a time-dependent formalism of absorption to extract the principal excited-state vibrational normal-mode frequencies that couple to the electronic transition, the configurational displacement of the higher-lying excited state, and the reorganization energies. We can model the excited-state absorption spectrum using two totally symmetric vibrational modes with frequencies 450 (dimer) or 400 cm(-1) (trimer), and 1666 cm(-1). The reorganization energy of the ground-state absorption is rather insensitive to the oligomer length at 230 meV. However, that of the excited-state absorption evolves from 58 to 166 meV between the oligofluorene dimer and trimer. Based on previous theoretical work [A. Shukla et al., Phys. Rev. B 67, 245203 (2003)], we assign the absorption spectra to a transition from the 1B(u) excited state to a higher-lying mA(g) state, and find that the energy of the excited-state transition with respect to the ground-state transition energy is in excellent agreement with the theoretical predictions for both oligomers studied here. These results and analysis permit profound understanding of the nature of excited-state absorption in pi-conjugated polymers, which are the subject of general interest as organic semiconductors in the solid state.

Anharmonic Franck−Condon Simulation of the Absorption and Fluorescence Spectra for the Low-Lying S1 and S2 Excited States of Pyridine

Anharmonic effects of the absorption and fluorescence spectra of pyridine molecule are studied and analyzed for the two-low lying singlet excited states S(1)((1)B(1)) and S(2)((1)B(2)). The complete active space self-consistent field (CASSCF) method is utilized to compute equilibrium geometries and all 27 vibrational normal-mode frequencies for the ground state and the two excited states. The present calculations show that the frequency differences between the ground and two excited states are small for the ten totally symmetric vibrational modes so that the displaced oscillator approximation can be used for spectrum simulations. The Franck-Condon factors within harmonic approximation basically grasp the main features of molecular spectra, but simulated 0-0 transition energy position and spectrum band shapes are not satisfactorily good for S(1)((1)B(1)) absorption and fluorescence spectra in comparison with experiment observation. As the first-order anharmonic correction added to Franck-Condon factors, both spectrum positions and band shapes can be simultaneously improved for both absorption and fluorescence spectra. It is concluded that the present anharmonic correction produces a significant dynamic shifts for spectrum positions and improves spectrum band shapes as well. The detailed structures of absorption spectrum of S(2)((1)B(2)) state observed from experiment can be also reproduced with anharmonic Franck-Condon simulation, and these were not shown in the harmonic Franck-Condon simulation with either distorted or Duschinsky effects in the literature.

Correlation Between Energy Transfer Rate and Atomization Energy of Some Trinitro Aromatic Explosive Molecules

An assumptive theoretical relationship is suggested to describe the property of molecular atomization energy and energy transfer rate in the initiation of explosions. To investigate the relationship between atomization energy and energy transfer rate, the number of doorway modes of explosives is estimated by the theory of Dlott and Fayer in which the rate is proportional to the number of normal mode vibrations. It was evaluated frequencies of normal mode vibrations of eight molecules by means of density functional theory (DFT) at the b3p86/6-31G(d,p) level. It is found that the number of doorway modes shows a linear correlation to the atomization energies of the molecules, which were also calculated by means of the same method. A mechanism of this correlation is discussed. It is also noted that in those explosives with similar molecular structure and molecular weight, the correlation between the atomization energy and the number of doorway modes is higher.

DENSITY FUNCTIONAL THEORY STUDY OF THE ENERGY TRANSFER RATES, MOLECULAR SIZE, AND ATOMIZATION ENERGIES OF SOME SECONDARY EXPLOSIVE MOLECULES

In this paper, we suggested a theoretical relationship between the property of molecular atomization energy and energy transfer rate in explosive detonation. According to the theory of Dlott and Fayer (J Chem Phys92(6):3798, 1990) some explosives are stable molecules with large energy barriers to chemical reaction in shock or impact initiation, so, a sizable amount of phonon energy must be converted to the molecular internal higher vibrations by multiphonon up pumping. To investigate the relationship between atomization energies and energy transfer rate, the number of doorway modes of explosives is estimated by their theory in which the rate is proportional to the number of normal mode vibrations. We evaluated frequencies of normal mode vibrations of TNB, TNAP, TNA, DATB, TATB, 2,4,6-trinitro-benzylalcohol ( C 7 H 5 N 3 O 7), and TNR by means of density functional theory (DFT) at the B3P86/6-31G(d, p) level. It is found that the number of doorway modes shows a linearly correlation to the atomization energies also calculated by means of DFT at the B3P86/6-31G(d, p) level. Besides, we studied the relation between the number of atoms and atomization energies for these molecules, and confirmed that for those secondary explosives molecules with similar molecular structure and similar molecular weight, the correlation between the atomization energy and the number of doorway modes is higher. This relationship is beneficial to the understanding of the property of explosive in detonation.

Energy transfer rates and impact sensitivities of two classes nitramine explosives molecules

Some explosives are stable molecules with large energy barriers to chemical reaction, and in shock or impact initiation, a sizable amount of phonon energy must be converted to the molecular internal higher vibrations by multiphonon up pumping. To investigate the relationship between impact sensitivities and energy transfer rates, the number of doorway modes of explosive molecules is estimated by a simple theory in which the rate is proportional to the number of normal mode vibrations. We evaluated frequencies of normal mode vibrations of 13 explosive molecules which are CHNO nitramine-contained and have not been analyzed previously. The number of doorway modes in the regions of 200–700 cm−1 was evaluated by the direct counting method. For more clear investigation of the relationship we have classified these 13 nitramine explosive molecules, by the number of nitramine group they contained, into two groups. There are eight molecules that contained one nitramine group and five molecules that contained poly-nitramine groups. It is found that the number of doorway modes shows a linearly correlation to the impact sensitivities derived from drop hammer tests. This result is in agreement with that of several previous works. Besides, it is also noted in our study that in those nitramine explosives molecules with similar molecular structure (similar number nitramine group they contained) and similar molecular weight, the correlation between the sensitivity and the number of doorway modes is higher. We found that the vibrational frequency of ω corresponds to nitro group motions of every molecule is contributed to the number of doorway modes in the regions of 200–700 cm−1.

Laser Induced Fluorescence Spectroscopy of a Mixed Dimer between 2-Pyridone and 7-Azaindole

We report here the laser induced fluorescence excitation (FE) and dispersed fluorescence (DF) spectra of a 1:1 mixed dimer between 7-azaindole (7AI) and 2-pyridone (2PY) measured in a supersonic free jet expansion of helium. Density functional theoretical calculation at the B3LYP/6-311++G** level has been performed for predictions of the dimer geometry and normal mode vibrational frequencies in the ground electronic state. A planar doubly hydrogen-bonded structure has been predicted to be the most preferred geometry of the dimer. In the FE spectrum, sharp vibronic bands are observed only for excitation of the 2PY moiety. A large number of low-frequency vibronic bands show up in both the FE and DF spectra, and those bands have been assigned to in-plane hydrogen bond vibrations of the dimer. Spectral analyses reveal Duschinsky-type mixing among those modes in the excited state. No distinct vibronic band structure in the FE spectrum was observed corresponding to excitations of the 7AI moiety, and the observation has been explained in terms of nonradiative electronic relaxation routes involving the 2PY moiety.

Correlation between normal mode vibrations and impact sensitivities of some secondary explosives

Because secondary explosives are stable molecules with large energy barriers to chemical reaction, in shock or impact initiation, a sizable amount of phonon energy must be converted to the molecular internal higher vibrations by multiphonon up pumping. To investigate the relationship between impact sensitivities and energy transfer rate, the number of doorway modes of explosives is estimated by a simple theory in which the rate is proportional to the number of normal mode vibrations. We evaluated frequencies of normal mode vibrations of 2,4,6-trinitro- m-cresol (C 7H 5N 3O 7), picric acid, TNB, TNAP, TNT, TNA, TBN, DATB, and TATB by means of density functional theory (DFT) at the b3p86/6-31g (d,p) level. The number of doorway modes in the regions of 200–700 cm −1 was evaluated by the direct counting method. It is found that the number of doorway modes shows a linearly correlation to the impact sensitivities derived from drop hammer tests. This result is in agreement with several previous works. Besides, it is also noted in our study that in those secondary explosives with similar molecular structure and similar molecular weight, the correlation between the impact sensitivity and the number of doorway modes is very high.