In-plane vibrational modes of cytosine from an ab initio MO calculation

Harmonic force constants, in-plane vibrational frequencies, and in-plane vibrational modes of cytosine were calculated by an ab initio Hartree—Fock SCF MO method. The force contants were calculated by the use of an energy gardient method with the STO-3G basis set, and then they were corrected into “4-31G force constants” by the scaling factors given by us previously for the case of uracil. The corrected set of force constants can produce a calculated vibrational spectra of cytosine and cytosine-1,amino-d₃, that can be well corrected with the observed Raman and infrared spectra of these compounds, with little ambiguity. Thus, the assignments of all the in-plane vibrations are now practically established. The calculated vibrational modes, in addition, can account for the recently published resonance Raman effects of cytosine residue.     

Molecular geometry and vibrational spectroscopy of potassium O,O-diethyldithiophosphate

The aim of this work was to build a good theoretical and experimental basis for the further study of changes in structure and spectra of the O,O-diethyldithiophosphate anion upon its adsorption on the surfaces of transition metal sulfides.Infrared and Raman spectra of potassium O,O-diethyldithiophosphate were recorded. High level quantum chemical calculations were carried out to optimize the molecular geometry of both the potassium salt and its anion. Vibrational force constants were calculated from the second derivative of the molecular energy function with respect to the Cartesian coordinates of the atoms. With the aid of the optimized geometry and the calculated vibrational force constants a normal coordinate analysis was carried out to characterize the molecular vibrational modes and to assign the vibrational frequencies.     

Vibrational spectroscopy of resveratrol

In this article the authors deal with the experimental and theoretical interpretation of the vibrational spectra of trans-resveratrol (3,5,4'-trihydroxy-trans-stilbene) of diverse beneficial biological activity. Infrared and Raman spectra of the compound were recorded; density functional calculations were carried out resulting in the optimized geometry and several properties of the molecule. Based on the calculated force constants, a normal coordinate analysis yielded the character of the vibrational modes and the assignment of the measured spectral bands.     

Ab-initio molecular geometry and normal coordinate analysis of pyrrolidine molecule.

The molecular geometry of pyrrolidine was quantum mechanically calculated using the split valence 6-31G** basis set. Electron correlation energy has been computed employing MP2 method. The molecule showed an envelope form puckered structure with inter-plane angle of 36.4 degrees and has a total energy of -132976.80 kcal mol(-1) of which a -464.86 kcal mol(-1) electron correlation energy. The twist form of the molecule showed a twist angle of 10.2 degrees from planarity and has a total energy of -132976.05 kcal mol(-1) involving -464.097 kcal mol(-1) electron correlation energy. The normal coordinates of the molecule were theoretically analyzed on the basis of the Cs point symmetry of the envelope form. Using initial set of force constants obtained from the ab-initio calculations the fundamental vibrational frequencies were computed. The IR and laser Raman spectra of Pyrrolidine molecules were measured. All the observed vibrational bands including combination bands and overtones were assigned to normal modes with the aid of the potential energy distribution values obtained from normal coordinate calculations. The molecular force field was obtained by refining the initial set of force constants using the least square fit method. The molecular force field was determined by refining the initial set of force constants using the least square fit method instead of using the less accurate scaling factor methods. The determined molecular force field has produced simulated frequencies best match to the observed values. The low frequency molecular out-of-plane deformation modes were observed in both infrared and Raman spectra at 298 and 163 cm(-1). The barrier of ring twisting estimated from the observed ring out-of-plane vibrational mode at 163 cm(-1) was found 3.1 kcal mol(-1).     

Calculations of the structural and thermodynamic characteristics of copper carbonates by quantum-chemical methods

The possibility of using the PM5 semiempirical method and the LADY program for calculations of the vibrational properties and thermodynamic characteristics of copper carbonates, malachite and azurite, was considered. The infrared and Raman spectra of these minerals were calculated using the valence force field model of the theory of crystal lattice dynamics with varying force constants. The results closely agreed with the calorimetric and spectroscopic experimental data.     

Normal coordinate and infrared band intensities of trichloronitromethane and trichloroacetate ions

Laser Raman and IR spectra in the region 50–3000 cm⁻¹ for trichloronitromethane and trichloroacetate ions were recorded. All observed vibrational bands have been assigned to normal modes. Normal coordinate analyses of these molecules have been carried out in the valence force-field approximation. A set of force constants was obtained leading to good agreement between observed and calculated frequencies. The relative displacements of the atoms resulting from normal coordinate calculations were used to compute the IR band intensity of each mode by the CNDO/2-MO procedure. The intensity calculations confirmed the assignments and supported the calculated force constants.     

Vibrational analysis of ethyl and n-propyl fluorides

Infrared spectra of n-propyl fluoride in the gas and solid states were obtained that confirm the presence of two molecular conformations in the gas and unannealed solid. Only one conformation identified as the gauche form is present in the annealed solid. Raman spectra were obtained for the solid. Normal coordinate calculations were made simultaneously for ethyl fluoride, gauche n-propyl fluoride, and trans n-propyl fluoride, and the resulting force constants and vibrational assignments are given.     

Determination of the thermodynamic functions of lead carbonate on the basis of the calculation of vibrational states

The force constants of bond angles and bonds and parameters of the interatomic potential for the natural carbonate cerussite were determined from the valence force field calculation of the vibrational states of its crystal structure. The initial force constants were calculated by the semiempirical PM5 method using the MOPAC quantum-chemical program package. As the criterion of adequacy of calculations, the consistency between the simulated IR and Raman spectra and the experimental spectra of the compound was used. The heat capacity of lead carbonate as a function of temperature was calculated based on the theory of crystal lattice dynamics and by quantum-chemical methods. The best fit to the experimental data was provided by the semiempirical PM5 method. From the calculated heat capacities, the entropy values of the compound were found.     

Theoretical study on the vibrational spectra of methoxy- and formyl-dihydroxy-trans-stilbenes and their hydrolytic equilibria

Compounds formed by exchanging one of the resveratrol hydroxy groups to methoxy or formyl groups are biologically important. Quantum chemical DFT calculations were applied for the simulation of some of their properties. Their optimized structures and charge distributions were computed. Based on the calculated vibrational force constants and optimized molecular structure infrared and Raman spectra were calculated. The characteristics of the vibrational modes were determined by normal coordinate analysis. Applying the calculated thermodynamic functions also for resveratrol, methanol, formaldehyde and water, thermodynamic equilibria were calculated for the equilibria between resveratrol and its methyl and formyl substituted derivatives, respectively.     

Ab Initio Equilibrium Geometry and Vibrational Spectroscopic Study of 25,26,27,28-tetrahydroxycalix[4]arene

The aim of this work was to present a comprehensive vibrational spectroscopic study of 25,26,27,28-tetrahydroxycalix[4]arene. For this purpose, quantum chemical calculations were carried out at the ab initio HF/4-31G* level, as a consequence of the great size of the molecule. In the frame of these calculations, the symmetry of the molecule was investigated. Trying C 4v , C 2v , and C s symmetries as input, the geometry optimization, however, pointed to the C 2 configuration. In the latter case, all the calculated vibrational frequencies were greater than zero, and therefore the equilibrium geometry could be identified. Medium and far infrared as well as Raman spectra of the compound were measured. On the basis of the calculated force constants and geometric parameters, normal coordinate analysis was applied for the interpretation of the experimental vibrational spectra. Problems arose with the choice of the internal coordinates of the molecule, which are important from the point of view of the internal macrocycle ("lower rim") of the molecule. On the basis of the theory of redundant coordinates, a program was written for choosing the coordinates of this 16-membered cycle. Full interpretation of the vibrational fundamentals of the compound is presented. Several force constant matrix elements have surprisingly high values. As a result of the normal coordinate analysis, the relative rigidity of the lower rim was concluded. Ab initio calculations and assignment of the vibrational spectra of 25,26,27,28-tetrahydroxycalix[4]arene based on the calculations are presented.     

Normal-mode analysis of FeCl4- and Fe2S2Cl42- via vibrational mössbauer, resonance Raman, and FT-IR spectroscopies

[NEt(4)][FeCl(4)], [P(C(6)H(5))(4)][FeCl(4)], and [NEt(4)](2)[Fe(2)S(2)Cl(4)] have been examined using (57)Fe nuclear resonance vibrational spectroscopy (NRVS). These complexes serve as simple models for Fe-S clusters in metalloproteins. The (57)Fe partial vibrational density of states (PVDOS) spectra were interpreted by computation of the normal modes assuming Urey-Bradley force fields, using additional information from infrared and Raman spectra. Previously published force constants were used as initial values; the new constraints from NRVS frequencies and amplitudes were then used to refine the force field parameters in a nonlinear least-squares analysis. The normal-mode calculations were able to quantitatively reproduce both the frequencies and the amplitudes of the intramolecular-mode (57)Fe PVDOS. The optimized force constants for bending, stretching, and nonbonded interactions agree well with previously reported values. In addition, the NRVS technique also allowed clear observation of anion-cation lattice modes below 100 cm(-1) that are nontrivial to observe by conventional spectroscopies. These features were successfully reproduced, either by assuming whole-body motions of point-mass anions and cations or by simulations using all of the atoms in the unit cell. The advantages of a combined NRVS, Raman, and IR approach to characterization of Fe-S complexes are discussed.     

Structure and vibrational frequencies of 1-naphthaldehyde based on density functional theory calculations

The mid and far FTIR and Raman spectra were measured in the liquid state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) and standard B3LYP/6-311+G** basis set combination. The vibrational spectra were interpreted, with the aid of normal coordinate analysis based on a scaled quantum mechanical (SQM) force field. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. Unambiguous vibrational assignment of all the fundamentals was made using the total energy distribution (TED).     

Vibrational analysis of substituted nitrobenzenes. I—Vibrational spectra,normal coordinate analysis and transferability of force constants of some chlorinated nitrobenzenes

The Raman and Fourier transform infrared spectra of 2,3-dichloro-, 2,4-dichloro-, 2,5-dichloro-, 3,4-dichloro-, 3,5-dichloro-, 2,3,4-trichloro-, 2,4,5-trichloro-, 2,4,6-trichloro-, 2,3,5,6-tetrachloro- and pentachloronitrobenzene were recorded. Raman polarization measurements were made wherever possible. A normal coordinate analysis was carried out for both the in-plane and out-of-plane vibrations of these molecules using a 59-parameter modified valence force field. The force constants were refined using an Overlay least-squares technique employing 352 frequencies of 10 molecules. The reliability of the force constants so obtained was tested by making a zero-order calculation for p-, m- and o-dinitrobenzenes, 1-fluoro-, 1-chloro- and 1-bromo-, 2,4-dinitrobenzenes, 2,4-difluoro- and 2,5-difluoro- and 2,5-dibromonitrobenzenes. Unambiguous vibrational assignments of all the fundamentals were made using the potential energy distribution and eigen vectors.     

Vibrational analysis of mononitro substituted benzamides, benzaldehydes and toluenes. Part I. Vibrational spectra, normal coordinate analysis and transferability of force constants of nitrobenzamides, nitrobenzaldehydes and nitrotoluenes

The Raman and Fourier transform infrared (FTIR) spectra of p-, m- and o-nitrobenzamides, p-, m- and o-nitrobenzaldehydes and p-, m- and o-nitrotoluenes were recorded. Raman polarisation measurements were made for the liquid samples. A normal coordinate analysis was carried out for both in-plane and out-of-plane vibrations of these molecules using 111-parameter modified valence force field. The force constants were refined using 316 frequencies of nine molecules in an overlay least-square technique. The reliability of the force constants was tested by making a zero-order calculation for nine related molecules. Unambiguous vibrational assignments of all the fundamentals were made by using the potential energy distributions and eigen vectors.     

Vibration-Spectroscopic Studies on Solid Compounds

Considerably improved possibilities are now available for the investigation of the optical vibrations in lattice compounds by Raman and IR spectroscopy. These spectra can be interpreted on the basis of the models and findings of molecular vibration spectroscopy. For simple lattice types simple frequency equations are found for the optical lattice vibrations with in-phase vibration motions in all unit cells (wave vector k = 0). As an approximation, the force constants that occur in these equations may be interpreted as stretching force constants. For typical ionic lattices, the influence of Coulomb forces due to the lattice polarization that occurs during the vibrational motion must be taken into account. As is shown by the example of some spinels, the assignment of lattice vibrations can be facilitated by model calculations.     

Vibrational analysis of substituted phenols: part I. Vibrational spectra,normal coordinate analysis and transferability of force constants of some formyl-, methoxy-, formylmethoxy-, methyl- and halogeno-phenols

The Raman (including FT-Raman) and Fourier transform infrared (FTIR) spectra of 1,3-dihydroxybenzene, 1,4-dihydroxybenzene, 2-hydroxybenzaldehyde, 2-hydroxy-3-methoxybenzaldehyde, 4-hydroxy-3-methoxybenzaldehyde, 1,2-dihydroxy-3-methoxybenzene, 2,5-dihydroxytoluene, 2,6-dihydroxytoluene, pentachlorophenol and pentabromophenol were measured. Raman polarisation measurements were made wherever possible. A normal coordinate treatment was carried out for both the in-plane and out-of-plane vibrations of these molecules using a 123-parameter-modified valence force field. An overlay least-squares technique was employed to refine the force constants using 347 frequencies of 10 molecules. The reliability of these force constants was tested by making a zero-order calculation for 10 related molecules. Unambiguous vibrational assignments of all the fundamentals were made using the potential energy distributions and eigenvectors.     

Simulation of IR and Raman spectra of p-hydroxyanisole and p-nitroanisole based on scaled DFT force fields and their vibrational assignments

This work deals with the vibrational spectroscopy of p-hydroxyanisole (PHA) and p-nitroanisole (PNA) by means of quantum chemical calculations. The mid and far FT-IR and FT-Raman spectra were recorded in the condensed state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6-31G* method and basis set combination and were scaled using various scale factors which yield a good agreement between observed and calculated frequencies. The vibrational spectra were interpreted with the aid of normal coordinate analysis based on scaled density functional force field. The results of the calculations were applied to simulate infrared and Raman spectra of the title compounds, which showed excellent agreement with the observed spectra.     

Vibrational spectroscopic analysis of 2-bromobenzoic and anthranilic acids: a combined experimental and theoretical study

In this work, the vibrational spectral analysis was carried out by using Raman and infrared spectroscopy in the range 100-4000 cm(-1) and 50-4000 cm(-1) respectively, for the title molecules. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on Hartee-Fock (HF) and density functional theory (DFT) method and different basis sets combination. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The scaled B3LYP/6-311++G(d,p) results show the best agreement with the experimental values over the other methods. The effects due to the substitutions of amino group and halogen bond were investigated. The results of the calculations were applied to simulate spectra of the title compounds, which show excellent agreement with observed spectra.     

Simulation of IR and Raman spectral based on scaled DFT force fields: a case study of 2-amino 4-hydroxy 6-trifluoromethylpyrimidine, with emphasis on band assignment

This work deals with the vibrational spectroscopy of 2-amino 4-hydroxy 6-triflouromethylpyrimidine (AHFMP) by means of quantum chemical calculations. The mid and far FTIR and FT-Raman spectra were measured in the condensed state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6-31G* and B3LYP/6-311+G** method and basic set combinations. Normal co-ordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors yielding fairly good agreement between observed and calculated frequencies. Simulation of infrared and Raman spectra utilizing the results of these calculations led to excellent overall agreement with the observed spectral patterns. The SQM approach applying selective scaling of the DFT force field was shown to be superior to the uniform scaling method in its ability to allow for making modifications in the band assignment, resulting in more accurate simulation of IR and Raman Spectra.     

Low-energy vibrations of the group 10 metal monocarbonyl MCO (M = Ni, Pd, and Pt): rotational spectroscopy and force field analysis

The rotational spectra of NiCO and PdCO in the ground and ν(2) excited vibrational states were observed by employing a source-modulated microwave spectrometer. The NiCO and PdCO molecules were generated in a free space cell by the sputtering reaction of nickel and palladium sheets, respectively, lining the inner surface of a stainless steel cathode with a dc glow plasma of CO and Ar. The molecular constants of NiCO and PdCO were determined by least-squares analysis. By force field analysis for the molecular constants of not only NiCO and PdCO but also of PtCO as previously reported, the harmonic force constants were determined for these three group 10 metal monocarbonyls. The vibrational wavenumbers derived for the lower M-C stretching vibrations were in good agreement with those obtained from the IR spectra in noble gas matrices and those predicted by several quantum chemical calculations published in the past. The bending vibrational wavenumbers derived by the force field analysis were also consistent with most quantum chemical calculations previously reported, but showed systematic discrepancies from the matrix IR values by about 40 cm(-1), even after reassignment (ν(2) band → 2ν(2) band) of the matrix IR spectra of PdCO and PtCO.