Vibrational spectra and scaled quantum-mechanical molecular force fields

Toward Elimination of Discrepancies between Theory and Experiment: Anharmonic Rotational-Vibrational Spectrum of Water in Solid Noble Gas Matrices

Rotational–vibrational spectroscopy of water in solid noble gas matrices has been studied for many decades. Despite that, discrepancies persist in the literature about the assignment of specific bands. We tackle the involved rotational–vibrational spectrum of the water isotopologues H₂¹⁶O, HD¹⁶O, and D₂¹⁶O with an unprecedented combination of experimental high-resolution matrix isolation infrared (MI-IR) spectroscopy and computational anharmonic vibrational spectroscopy by vibrational configuration interaction (VCI) on high-level ab initio potential energy surfaces. With VCI, the average deviation to gas-phase experiments is reduced from >100 to ≈1 cm^–1 when compared to harmonic vibrational spectra. Discrepancies between MI-IR and VCI spectra are identified as matrix effects rather than missing anharmonicity in the theoretical approach. Matrix effects are small in Ne (≈1.5 cm^–1) and a bit larger in Ar (≈10 cm^–1). Controversial assignments in Ne MI-IR spectra are resolved, for example, concerning the ν₃ triad in HDO. We identify new transitions, for example, the ν₂ 1₀₁ ← 1₁₀ transition in D₂O and H₂O or the ν₃ 0₀₀ ← 1₀₁ transition in D₂O, and reassign bands, for example, the band at 3718.9 cm^–1 that is newly assigned as the 1₁₀ ← 1₁₁ transition. The identification and solution of discrepancies for a well-studied benchmark system such as water prove the importance of an iterative and one-hand combination of theory and experiment in the field of high-resolution infrared spectroscopy of single molecules. As the computational costs involved in the VCI approach are reasonably low, such combined experimental/theoretical studies can be extended to molecules larger than triatomics.

The molecular structure and vibrational spectra of N-(3-tert-butyl-2-hydroxybenzylidene)-2,6-diphenyl-4-hydroxyaniline

The molecular structure, vibrational frequencies and intensities of N-(3-tert-butyl-2-hydroxybenzylidene)-2,6-diphenyl-4-hydroxyaniline were calculated by the Density Functional Theory methods (BLYP, B3PW91 and B3LYP) using the 6-31G(d,p) basis set. The calculated geometric parameters were compared to the corresponding X-ray structure of the title compound. The comparison of the theoretical and experimental geometry of the title compound shows that the X-ray parameters fairly well reproduce the geometry of optimized by B3LYP method (r=0.9825). The harmonic vibrations computed for this compound by the B3LYP/6-31G(d,p) method are in good agreement with the observed IR and Raman spectral data. The root mean square values error of the observed and calculated IR bands are found to be 9.80, 9.40 and 8.42 for B3LYP, B3PW91 and BLYP/6-31G(d,p) methods, respectively. Theoretical vibrational spectra of the title compound were interpreted by means of PEDs using the SQM 2.0 program. A general better performance of the investigated methods was calculated by PAVF 1.0 program.

Molecular structure and vibrational study of diprotonated guanazolium using DFT calculations and FT-IR and FT-Raman spectroscopies

The purpose of this manuscript is to discuss our investigations of diprotonated guanazolium chloride using vibrational spectroscopy and quantum chemical methods. The solid phase FT-IR and FT-Raman spectra were recorded in the regions 4000-400cm(-1) and 3600-50cm(-1) respectively, and the band assignments were supported by deuteration effects. Different sites of diprotonation have been theoretically examined at the B3LYP/6-31G level. The results of energy calculations show that the diprotonation process occurs with the two pyridine-like nitrogen N2 and N4 of the triazole ring. The molecular structure, harmonic vibrational wave numbers, infrared intensities and Raman activities were calculated for this form by DFT/B3LYP methods, using a 6-31G basis set. Both the optimized geometries and the theoretical and experimental spectra for diprotonated guanazolium under a stable form are compared with theoretical and experimental data of the neutral molecule reported in our previous work. This comparison reveals that the diprotonation occurs on the triazolic nucleus, and provide information about the hydrogen bonding in the crystal. The scaled vibrational wave number values of the diprotonated form are in close agreement with the experimental data. The normal vibrations were characterized in terms of potential energy distribution (PED) using the VEDA 4 program.

Tautomeric purine forms of 2-amino-6-chloropurine (N9H10 and N7H10): structures, vibrational assignments, NBO analysis, hyperpolarizability, HOMO-LUMO study using B3 based density functional calculations

Two purine tautomers of 2-amino-6-chloropurine (ACP), in labeled as N(9)H(10) and N(7)H(10), were investigated by vibrational spectroscopy and quantum chemical method. The FT-IR and FT-Raman spectra of ACP have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The measured spectra were interpreted by aid of a normal coordinate analysis following DFT full geometry optimization and vibrational frequency calculations at B3LYP/6-311++G(d,p) level. First-order hyperpolarizability, HOMO and LUMO energies were calculated at same level of theory. The calculated molecular geometry has been compared with the X-ray data. The observed and calculated frequencies were found in good agreement. The obtained NBO data and second-order perturbation energy values to elucidate the Lewis and non-Lewis types of bonding structures in the purine tautomer N(9)H(10), have indicated the presence of an intramolecular hyperconjucative interaction between lone pair N and N-C bond orbital.

Molecular geometry and vibrational studies of 3,5-diamino-1,2,4-triazole using quantum chemical calculations and FT-IR and FT-Raman spectroscopies

The 3,5-diamino-1,2,4-triazole (guanazole) was investigated by vibrational spectroscopy and quantum methods. The solid phase FT-IR and FT-Raman spectra were recorded in the region 4000-400 cm(-1) and 3600-50 cm(-1) respectively, and the band assignments were supported by deuteration effects. The results of energy calculations have shown that the most stable form is 1H-3,5-diamino-1,2,4-triazole under C1 symmetry. For this form, the molecular structure, harmonic vibrational wave numbers, infrared intensities and Raman activities were calculated by the ab initio/HF and DFT/B3LYP methods using 6-31G* basis set. The calculated geometrical parameters of the guanazole molecule using B3LYP methodology are in good agreement with the previously reported X-ray data, and the scaled vibrational wave number values are in good agreement with the experimental data. The normal vibrations were characterized in terms of potential energy distribution (PEDs) using VEDA 4 program.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, trimethylgermyl, trimethylstannyl and trimethylplumbyl derivatives of 3,3-dimethylcyclopropene. XII. 1,2-Di-tert-butyl-3,3-dimethylcyclopropene

The synthesis of 1,2-di-tert-butyl-3,3-dimethylcyclopropene (I) is performed and its IR and Raman spectra are measured. Optimized geometries of I are obtained at the HF/6-31G* and CCSD/cc-pVDZ levels. The ab initio calculated spectra are used for the assignments of the experimental spectral data. The results obtained are compared with the corresponding data for 3,3-dimethylbut-1-ene and 3,3-dimethylcyclopropene. These experimental data and the total vibrational analysis of I supplement the information obtained in the series of investigations of tert-butyl, trimethylsilyl, trimethylgermyl, trimethylstannyl, and trimethylplumbyl derivatives of 3,3-dimethylcyclopropene.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, trimethylgermyl, trimethylstannyl and trimethylplumbyl derivatives of 3,3-dimethylcyclopropene. XI. Secondary periodicity

Regularities of changes in the structural parameters and vibrational wavenumbers for certain moieties of the title compounds are presented. The optimized geometrical parameters and the force fields of the di- and monosubstituted 3,3-dimethylcyclopropenes were determined at the HF/3-21G* and HF/DDAll pseudopotential levels, respectively. These theoretical levels were chosen because of peculiarities of Gaussian 03 suite of programs for the Sn and Pb atoms. The theoretical vibrational wavenumbers were calculated using the corresponding scaled force fields. The regularities obtained in the form of zigzag lines for the properties as a function of the period number of X in the Mendeleyev Periodic Table are analogous to regularities that are characteristic of properties of the atoms of the 14 (IVA) group. This is known as the secondary periodicity phenomenon.

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.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, trimethylgermyl, trimethylstannyl, and trimethylplumbyl derivatives of 3,3-dimethylcyclopropene X. Some regularities

The changes in the vibrational frequencies of 1-tert-butyl and 1,2-di-tert-butyl derivatives of 3,3-dimethylcyclopropene brought about by substitution of the central carbon atom (X) of the tert-butyl moieties by Si, Ge, Sn, or Pb atoms are examined. The most important decrease in the vibrational frequencies implicating the X(CH(3))(3) moieties is noted for substitution of X=C by Si. The substitutions of Si by Ge or Ge by Sn or Sn by Pb are not accompanied by the pronounced frequency shifts observed for the C-->Si transition. An explanation is given for trends in these vibrational frequencies for the transitions X=C-->Si-->Ge-->Sn-->Pb. It is concluded that there are lower limiting values of the vibrational frequencies of a molecular moiety which are approached when the mass of its isovalent atom is increased. This leads to the formation of cluster regions in the vibrational spectra for the frequencies of the SnC(3) and PbC(3) moieties.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, trimethylgermyl, trimethylstannyl, and trimethylplumbyl derivatives of 3,3-dimethylcyclopropene IX. 3,3-Dimethyl-1-(trimethylplumbyl)cyclopropene

The geometrical parameters and quantum mechanical force fields (QMFF's) of 3,3-dimethyl-1-(trimethylplumbyl)cyclopropene (I), 3,3-dimethyl-1-(t-butyl)cyclopropene (II), 3,3-dimethyl-1-(trimethylsilyl)cyclopropene (III), 3,3-dimethyl-1-(trimethylgermyl)cyclopropene (IV), and 3,3-dimethyl-1-(trimethylstannyl)cyclopropene (V) were calculated at the pseudopotential (HF/SDDAll) level. Analysis of the optimised geometrical parameters was performed. The set of scale factors for correction of the pseudopotential QMFF of III was determined using its earlier well-characterised vibrational spectrum. Transferral of the set of scale factors obtained for III to the QMFF's of I, II, IV and V was followed by calculation of the fundamental vibrational frequencies. Analysis of the results for these molecules revealed some peculiarities in the vibrational frequencies obtained at the pseudopotential level.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, trimethylgermyl, and trimethylstannyl derivatives of 3,3-dimethylcyclopropene VII. 3,3-Dimethyl-1-(trimethylstannyl) cyclopropene

The quantum mechanical force fields (QMFF's) of 3,3-dimethyl-1-(tert-butyl)cyclopropene (I), 3,3-dimethyl-1-(trimethylsilyl)cyclopropene (II), 3,3-dimethyl-1-(trimethylgermyl)cyclopropene (III), and 3,3-dimethyl-1-(trimethylstannyl)cyclopropene (IV) were calculated at the HF/3-21G*//HF/3-21G* level. The set of scale factors for the correction of HF/3-21G*//HF/3-21G* QMFF of II was determined using its well-characterised vibrational spectrum. Transferral of the set of scale factors obtained for II to the QMFF's of I, III and IV and calculation of the fundamental frequencies resulted in good agreement between the calculated and previously assigned experimental frequencies of III. This again demonstrates the feasibility of transferral of a set of scale factors obtained for the correction of the QMFF of a molecule to others containing heteroatoms from the same column of the Mendeleyev Periodic Table. Thus the calculations performed permitted the accurate assignment of the fundamental vibrational frequencies in the experimental IR spectrum of IV. The vibrational frequencies of 3,3-dimethyl-1-(tert-butyl)cyclopropene (I) were also calculated from the HF/6-31G*//HF/6-31G* QMFF, scaled by the set of scale factors used previously for the HF/6-31G*//HF/6-31G* QMFF's of II and III. Regularities in the trends of some vibrational frequencies with increasing atomic number of the heteroatom are observed.

s-trans-1,3-Butadiene and Isotopomers: Vibrational Spectra, Scaled Quantum-Chemical Force Fields, Fermi Resonances, and C−H Bond Properties

Quadratic quantum-chemical force fields have been determined for s-trans-1,3-butadiene using B3LYP and MP2 methods. Basis sets included 6-311++G, cc-pVTZ, and aug-cc-pVTZ. Scaling of the force fields was based on frequency data for up to 11 isotopomers, some of these data being original. A total of 18 scale factors were employed, with, in addition, an alteration to one off-diagonal force constant in the A(u) species. MP2 calculations without f functions in the basis perform badly in respect of out-of-plane bending mode frequencies. Centrifugal distortion constants and harmonic contributions to vibration-rotation constants (alphas) have been calculated. Existing experimental frequency data for all isotopomers are scrutinized, and a number of reassignments and diagnoses of Fermi resonance made, particularly in the nu(CH) region. The three types of CH bond in butadiene were characterized in terms of bond length and isolated CH stretching frequency, the latter reflecting data in the nu(CD) region. Broad agreement was achieved with earlier results from local mode studies. Differences in CH bond properties resemble similar differences in propene. A simplified sample setup for recording FT-Raman spectra of gases was applied to four isotopomers of butadiene.

FTIR, FT-Raman spectra and ab initio DFT vibrational analysis of 2-amino-5-chloropyridine

The FTIR and FT-Raman spectra of 2-amino-5-chloropyridine (ACP) has been recorded in the region 4000-400 and 3500-100 cm-1, respectively. The optimized geometry, frequency and intensity of the vibrational bands of ACP were obtained by the ab initio and density functional theory (DFT) levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311+G(2df,2p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

Density functional theory study on the structure and vibrational spectra for cyanuric chloride

The molecular structure and vibrational spectra of cyanuric chloride have been investigated by density functional theory (DFT) using standard B3LYP/6-31G* and B3LYP/6-311+G** method and basis set combinations. The DFT force field transformed to natural internal coordinates was corrected by a well-established set of scale factors that were found to be transferable to the title compound. Both the calculated structural parameters and vibrational frequencies are in good agreement with the available experimental data.

Vibrational spectra and potential energy distributions for 4,5-dichloro-3-hydroxypyridazine by density functional theory and normal coordinate calculations

The solid phase FT-IR and FT-Raman spectra of 4,5-dichloro-3-hydroxypyridazine have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The spectra were interpreted with the aid of normal coordinate analysis following a full structure optimization and force field calculations based on the density functional theory (DFT) using the standard B3LYP/6-31G* and B3LYP/6-311+G** method and basis set combinations. The DFT force field transformed to natural internal coordinates was corrected by a well-established set of scale factors that were found to be transferable to the title compound. The IR and Raman spectra were predicted theoretically and compared with the experimental spectra.

Analysis of vibrational spectra of 5-fluoro, 5-chloro and 5-bromo-cytosines based on density functional theory calculations

The geometry, frequency and intensity of the vibrational bands 5-fluoro, 5-chloro and 5-bromo-cytosines (5-FC, 5-ClC and 5-BrC) were obtained by the density functional theory (DFT) calculations with Becke3-Lee-Yang-Parr (B3LYP) functional and 6-31G* basis set. The effects of fluorine, chlorine and bromine substituents on the vibrational frequencies of cytosines have been investigated. The assignments have been proposed with the aid of the results of normal coordinate analysis. The observed and the calculated spectra are found to be in good agreement.

Density functional theory calculations and vibrational spectra of 3,5-dibromopyridine and 3,5-dichloro-2,4,6-trifluoropyridine

The solid phase mid FTIR and FT-Raman spectra of 3,5-dibromopyridine (3,5-DBP) and 3,5-dichloro-2,4,6-trifluoropyridine (3,5-DCTFP) have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The spectra were interpreted with the help of normal coordinate analysis (NCA) following full structure optimisation and force field calculations based on the density functional theory (DFT) using the standard B3LYP/6-31G( *) method and basis set combination. The results of the calculations are applied to stimulate infrared and Raman spectra of the title compounds which showed excellent agreement with the observed spectra.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethylcyclopropene. VI: Application of observed trends to stannyl derivatives

The effects of substitution of X = C by Si or Ge in X(CH(3))(3) moieties attached to the formal double bond of 3,3-dimethylcyclopropene are examined. Regularities in observed trends of vibrational frequencies implicating the moieties containing the X atom, as the X atomic mass is increased, are extrapolated to X = Sn. The results of this extrapolation made it possible to assign the known experimental vibrational frequencies of 3,3-dimethyl-1-(trimethylstannyl)cyclopropene and 3,3-dimethyl-1,2-bis(trimethylstannyl)cyclopropene.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethyl cyclopropene V. 3,3-dimethyl-1-(trimethylgermyl)cyclopropene

3,3-dimethyl-1-(trimethylgermyl)cyclopropene (I) was synthesised using a standard procedure. The IR and Raman spectra of I in the liquid phase were measured. The molecular geometry of I was optimised completely at the HF/6-31G* level. The HF/6-31G*//HF/6-31G* force field was calculated and scaled using the set of scale factors transferred from those determined previously for scaling the theoretical force fields of 3,3-dimethylbutene-1 and 1-methyl-, 1,2-dimethyl-, and 3,3-dimethylcyclopropene. The assignments of the observed vibrational bands were performed using the theoretical frequencies calculated from the scaled HF/6-31G*//HF/6-31G* force field and the ab initio values of the IR intensities, Raman cross-sections and depolarisation ratios. The theoretical spectra are given. The completely optimised structural parameters of I and its vibrational frequencies are compared with corresponding data of related molecules.

Aplicaciones de los métodos computacionales al estudio de la estructura y propiedades de polímeros

En este trabajo se revisan las técnicas de simulación molecular más habituales y potentes para la descripción de los polímeros a escala atómica y molecular, las cuales se han clasificado en cuánticas o clásicas dependiendo de cómo se describen las interacciones entre las partículas. Se presentan asimismo diversas aplicaciones de dichas metodologías, realizadas en nuestro laboratorio, en el contexto del estudio de la estructura y propiedades de polímeros. En particular, se muestran aplicaciones de las técnicas clásicas a la determinación de estructuras cristalinas, a estudio del plegamiento lamelar de los nylons, a la estabilidad de las estructuras supramoleculares observadas en algunos complejos tensioactivo·polielectrolito y a la difusión de gases en matrices poliméricas, mientras que el uso de técnicas cuánticas se ha ilustrado presentando estudios dedicados a la predicción de efectos cooperativos, interacciones específicas y parámetros espectroscópicos.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethylcyclopropene II. 3,3-Dimethyl-1,2-bis(trimethylsilyl)cyclopropene

The IR and Raman spectra of 3,3-dimethyl-1,2-bis(trimethylsilyl)cyclopropene (I) (synthesised using standard procedures) were measured in the liquid phase. Total geometry optimisation was performed at the HF/6-31G* level. The HF/6-31G*//HF/6-31G* quantum mechanical force field (QMFF) was calculated and used to determine the theoretical fundamental vibrational frequencies, their predicted IR intensities, Raman activities, and Raman depolarisation ratios. Using Pulay's scaling method and the theoretical molecular geometry, the QMFF of I was scaled by a set of scaling factors used previously for 3,3-dimethyl-1,2-bis(tert-butyl)cyclopropene (17 scale factors for a 105-dimensional problem). The scaled QMFF obtained was used to solve the vibrational problem. The quantum mechanical values of the Raman activities were converted to differential Raman cross sections. The figures for the experimental and theoretical Raman and IR spectra are presented. Assignments of the experimental vibrational spectra of I are given. They take into account the calculated potential energy distribution and the correlation between the estimations of the experimental IR and Raman intensities and Raman depolarisation ratios and the corresponding theoretical values (including Raman cross sections) calculated using the unscaled QMFF.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethylcyclopropene III. 3,3-Dimethyl-1-(trimethylsilyl)cyclopropene

The experimental Raman and IR vibrational spectra of 3,3-dimethyl-1-(trimethylsilyl)cyclopropene in the liquid phase were recorded. Total geometry optimisation was carried out at the HF/6-31G* level and the HF/6-31G*//HF/6-31G* force field was computed. This force field was corrected by scale factors determined previously (using Pulay's method) for correction of the HF/6-31G*//HF/6-31G* force fields of 3,3-dimethylbutene-1, 1-methyl-, 1,2-dimethyl-, and 3,3-dimethylcyclopropene. The theoretical vibrational frequencies calculated from the scaled quantum mechanical force field and the theoretical intensities obtained from the quantum mechanical calculation were used to construct predicted spectra and to perform the vibrational analysis of the experimental spectra.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethylcyclopropene IV. 3,3-dimethyl-1,2-bis(trimethylgermyl)cyclopropene

The infrared (IR) and Raman spectra of 3,3-dimethyl-1,2-bis(trimethylgermyl)cyclopropene (I) were measured in the liquid phase. Total geometry optimisation was performed at the HF/6-31G* level. The HF/6-31G*//HF6-31G* quantum mechanical force field (QMFF) was calculated and used to determine the theoretical fundamental vibrational frequencies, their predicted IR intensities, Raman activities, and Raman depolarisation ratios. Using Pulay's scaling method and the theoretical molecular geometry, the QMFF of I was scaled by a set of scaling factors comprised of elements transferred from the sets used to correct the QMFF's of 3,3-dimethylbutene-1, and 1-methyl-, 1,2-dimethyl-, and 3,3-dimethylcyclopropene (17 scale factors for a 105-dimensional problem). This set of scale factors was used previously to correct the QMFF of 3,3-dimethyl-1,2-bis(tert-butyl)cyclopropene and 3,3-dimethyl-1,2-bis(trimethylsilyl)cyclopropene. The scaled QMFF obtained was used to solve the vibrational problem. Differential Raman cross-sections were calculated using the quantum mechanical values of the Raman activities. The appropriate theoretical spectrograms for the Raman and IR spectra of I were constructed. Assignments of the experimental vibrational spectra of I are given. They take into account the calculated potential energy distributions and the correlation between the estimations of the experimental IR and Raman intensities and Raman depolarisation ratios and the corresponding theoretical values calculated using the unscaled QMFF.