A theoretical study on three conformational structures of 2,6‐distyrylpyridine

Ab initio methods at the levels HF/cc‐pVDZ, HF/6‐31G(d,p), MP2/cc‐pVDZ, and MP2/6‐31G(d,p), as well as methods based on density functional theory (DFT) employing the hybrid functional B3LYP with the basis sets cc‐pVDZ and 6‐31G(d,p), have been applied to study the conformers of 2,6‐distyrylpyridine. Bond distances, bond angles, and dihedral angles have been calculated at the B3LYP level. The calculated values were in good agreement with those measured by X‐ray diffraction analysis of 2,6‐distyrylpyridine. The values calculated using the Hartree‐Fock method and second‐order perturbation theory (MP2) were inconsistent. The optimized lowest‐energy geometries were calculated from the reported X‐ray structural data by the B3LYP/cc‐pVDZ method. Three conformations, A, B, and C, were proposed for 2,6‐distyrylpyridine. Calculations at the three levels of theory indicated that conformation A was the most stable structure, with conformations C and B being higher in energy by 1.10 and 2.57 kcal/mol, respectively, using the same method and basis function. The same trend in the relative energies of the three possible conformations was observed at the two levels of theory and with the different basis sets employed. The reported X‐ray data were utilized to optimize total molecular energy of conformation A at the different calculation levels. The bond lengths, bond angles, and dihedral angles were then obtained from the optimized geometries by ab initio methods and by applying DFT using the two basis functions cc‐pVDZ and 6‐31G(d,p). The values were analyzed and compared. The calculated total energies, the relative energies of the molecular orbitals, the gap between them, and the dipole moment for each conformational structure proposed for 2,6‐distyrylpyridine are also reported. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Enamines. II. A theoretical and photoelectron spectroscopic study of the molecular and electronic structures of aliphatic enamines

Comparison of PE. spectroscopic data for four series of enamines (including azetidine and some aziridine derivatives) for studying the influence of amine-ring size on electronic structure show the pyrrolidino group to exhibit the strongest amine/double bond coupling in sterically unconstrained enamines. However, the azetidino group accommodates best steric congestion due to dialkyl substitution at the β-position of the enamine unit. Quantum-chemical calculations of equilibrium structures and energy profiles for amine rotations in model enamines by the PRDDO SCF method agree satisfactorily with experimental results. Notable exceptions are pyrrolidine derivatives for which PRDDO overestimates the amount of N-pyramidality.     

Enamines. III. A theoretical and photoelectron spectroscopic study of the molecular and electronic structures of aziridine enamines

The photoelectron (PE.) spectra of N-vinylaziridine ( 1 ) and some methyl and ethyl substituted derivatives are discussed in the light of quantum-chemical model calculations using the PRDDO SCF method. All aziridine enamines are found to exist as equilibrium mixtures of variable compositions, with an enamine-type conformation ( I ) generally as the major and a trans-bisected form (II) as the minor component.     

A theoretical study of conformational properties of N-methyl azapeptide derivatives

The conformational properties of azapeptide derivatives, Ac-azaGly-NHMe (1), Ac-azaAla-NHMe (2), Ac-NMe-azaGly-NHMe (3), Ac-NMe-azaAla-NHMe (4), Ac-azaGly-NMe(2) (5), Ac-azaAla-NMe(2) (6), Ac-NMe-azaGly-NMe(2) (7), and Ac-NMe-azaAla-NMe(2) (8), were systematically examined by using ab initio MO and DFT methods. Structural perturbations in azapeptides resulting from cyclic substitution of a methyl group at three N-positions of an azaamino acid were studied on the basis of the structure of the simplest model azapeptide, 1. Potential energy surfaces were generated at the HF/6-31G level for 1-4 and at the HF/6-31G//HF/3-21G level for 5-8 by rotating two key dihedral angles (phi, psi) in increments of 30 degrees. The backbone (phi, psi) angles of the minima for 1-4 are observed at the i + 2 position to form the betaI(I')-, betaII(II')-, betaVI-turns or the polyproline II structure according to the orientation of the acetyl group and the positions of the N-methyl groups. Compounds 5-8 coupled to a secondary amine were found to preferentially adopt polyproline II, betaI(III)-turn, or alpha-helical structure or even extended conformations depending on the orientation of the acetyl group and the positions of the N-methyl groups. Furthermore, N-methyl groups, depending on their positions, were found to affect the orientation of the amide group in the lowest energy conformations, the pyramidality of the N2 atom, and the bond length in azapeptide derivatives. These unique theoretical conformations of N-methyl azapeptide derivatives could be utilized in the definite design of secondary structure for peptides and proteins, and in the development of new drugs and molecular machines.     

A theoretical study of spectroscopic properties and transition moments of HBr

Relativistic configuration interaction calculations are performed for twelve electronic states of the HBr molecule. Ground-state spectroscopic properties and electronic dipole moment function are calculated and compared with theoretical and experimental data. Electric dipole moments for eleven excited states are presented and discussed. Electronic transition moments between the ground state and seven excited states are presented in the intermediate coupling scheme.     

DFT study of conformational and spectroscopic properties of yatakemycin

Molecular structure and conformational preferences of yatakemycin, a novel and exceptionally potent antitumor agent, have been investigated using the density functional theory (DFT) formalism. From the relative stability of various possible conformations, it is found that two conformers are nearly isoenergetic and markedly more stable than the others in the gas phase. To test the effect of polar mediums, the relative energies have been recalculated using the self-consistent reaction field method. Thus, the most stable conformer of the isolated molecule in the gas phase is expected to be still more preferred in solution. The molecular structure of yatakemycin has also been studied by means of its spectroscopic properties. The DFT results satisfactorily reproduce the experimental data and corroborate the reliability of the structural characterization advanced for yatakemycin. The lowest-energy electronic transitions have been interpreted with time-dependent DFT calculations. Notably, the strong IR band observed at 2852 cm(-1) is unambiguously assigned to the O-H stretching of the (C7)O-H...O(C12) fragment, linked by a strong intramolecular H-bond, and may be viewed as a distinctive fingerprint of yatakemycin. Furthermore, the calculated set of NMR chemical shifts of carbonyl carbon atoms and indole protons, the most sensitive to stereoelectronic factors, is consistent with experiment. The effects of both protonation and oxidation on the geometry of the most stable conformer have also been studied. With reference to yatakemycin's DNA alkylation properties, the structure of the yatakemycin-adenine adduct has been theoretically modeled and found to be consistent with experimental spectroscopic evidence.     

A theoretical conformational analysis of morpholine

The CNDO and INDO methods were used for a theoretical conformational analysis of morpholine. The agreement between the methods is very satisfactory. Some results are also compared with the available experimental data.     

Isomeric structures of protonated ozone: A theoretical study

Ab initio molecular orbital calculations have been used to determine the structure of protonated ozone. Four stable minima were found on the O₃H⁺ singlet potential energy surface. Three forms correspond to ozone protonated at the central oxygen (C_2v) or at the terminal oxygen (two C_s isomers, E and Z). The fourth isomer (C_s) is a derivative of trioxirane. The most stable structure is the planar E form I. The proton affinity of ozone (to give I) is given as 123.6 kcal/mole (MP2/6-31G*//4-31G). The energy difference between I and protonated trioxirane VI is greater than that between ozone and trioxirane.     

Barbituric and thiobarbituric acids: a conformational and spectroscopic study

A conformational study on Barbituric (BA) and Thiobarbituric (TBA) acids was performed at ab initio MP2/6-31G** level on the neutral, protonated, mono- and di-anionic forms. Acid-base equilibria were studied by comparing the electronic transitions evaluated for the most stable conformations and the experimental spectra at different pH values. The electronic transitions were obtained through the ZINDO approach.     

Experimental and theoretical study of the conformational analysis of hydrochlorothiazide

Hydrochlorothiazide was characterized in order to determine the possible structural modifications at different temperatures due to its importance as a drug to control heart diseases and a diuretic. This compound could present conformers due to the rotation of the NH₂ group, which was studied by using different techniques such as Thermal Analysis, IR spectroscopy, X-Ray Diffraction and complemented by theoretical calculations. The theoretical and experimental results point to the conclusion that no polymorphic forms are present in the compound under study. The calculations confirm the apparent difference in values between theory and experiment for the vibration frequencies explained by the hydrogen bonds between near molecules.     

A theoretical, spectroscopic, and photophysical study of 2,7-carbazolenevinylene-based conjugated derivatives

A combined theoretical and experimental study of the structure, optical, and photophysical properties of four 2,7-carbazolenevinylene-based derivatives in solution is presented. Geometry optimizations of the ground states of PCP, PCP-CN, TCT, and TCT-CN were carried out using the density functional theory (DFT/B3LYP/6-31G*). It is found that PCP and TCT are nearly planar in their ground electronic states (S0), whereas the cyano derivatives are more twisted. The nature and the energy of the first singlet-singlet electronic transitions have been obtained from time-dependent density functional theory (TDDFT) calculations performed on the optimized geometries. For all the compounds, excitation to the S1 state corresponds mainly to the promotion of one electron from the highest-occupied molecular orbital to the lowest-unoccupied molecular orbital, and the S1 <-- S0 electronic transition is strongly allowed and polarized along the long axis of the molecular frame. The optimization (relaxation) of the first singlet excited electronic state (S1) has been done using the restricted configuration interaction (singles) (RCIS/6-31G*) approach. It is observed that all four investigated compounds become more planar in their S1 relaxed excited state. Electronic transition energies from the relaxed excited states have been obtained from TDDFT calculations performed on the S1-optimized geometries. The absorption and fluorescence spectra of the carbazolenevinylenes have been recorded in chloroform. A good agreement is obtained between TDDFT vertical transitions energies and the (0,0) absorption and fluorescence bands. The change from phenylene to thiophene rings as well as the incorporation of cyano substituents induce bathochromic shifts in the absorption and fluorescence spectra. From the analysis of the energy of the frontier molecular orbitals, it is believed that thiophene rings and CN substituents induce some charge-transfer character to the first electronic transition, which is responsible for the red shifts observed. Finally, the fluorescence quantum yield and the lifetime of the compounds in chloroform have been obtained. In sharp contrast with many oligothiophenes, it is observed that TCT possesses a high fluorescence quantum yield. On the other hand, the CN-containing derivatives exhibit much lower fluorescence quantum yields, probably due to the combined influence of steric effects and charge-transfer interactions caused by the cyano groups.     

Vibrational structure of titanium silicate catalysts. A spectroscopic and theoretical study.

A thorough analysis of the vibrational features of the titanium silicalite-1 (TS-1) catalyst is presented, based on quantitative IR measurements, Raman and resonant Raman experiments, quantitative XANES, and quantum chemical calculations on cluster and periodic models. The linear correlation of the intensity of the IR and Raman bands located at 960 and 1125 cm(-1) and the XANES peak at 4967 eV with the amount of tetrahedral Ti are quantitatively demonstrated. Raman and resonant Raman spectra of silicalite and TS-1 with variable Ti content are presented, showing main features at 960 and 1125 cm(-1) associated with titanium insertion into the zeolite framework. The enhancement of the intensity of the 1125 cm(-1) feature and the invariance of the 960 cm(-1) feature in UV-Raman experiments, are discussed in terms of resonant Raman selection rules. Quantum chemical calculations on cluster models Si[OSi(OH)(3)](4) and Ti[OSi(OH)(3)](4) at the B3LYP/6-31G(d) level of theory provide the basis for the assignment of the main vibrational contributions and for the understanding of Raman enhancement. The resonance-enhanced 1125 cm(-1) mode is unambiguously associated with a totally symmetric vibration of the TiO(4) tetrahedron, achieved through in-phase antisymmetric stretching of the four connected Ti-O-Si bridges. This vibration can also be described as a totally symmetric stretching of the four Si-O bonds pointing toward Ti. The resonance enhancement of this feature is explained in terms of the electronic structure of the Ti-containing moiety. Asymmetric stretching modes of TO(4) units show distinct behavior when (i) T is occupied by Si as in perfect silicalite, (ii) T is occupied by Ti as in TS-1, or (iii) the oxygen atom belongs to an OH group, such as in terminal tetrahedra of cluster models and in real defective zeolites. Asymmetric SiO(4) and TiO(4) stretching modes appear above and below 1000 cm(-1), respectively, when they are achieved through antisymmetric stretching of the T-O-Si bridges, and around 800 cm(-1) (in both SiO(4) and TiO(4)) when they involve symmetric stretching of the T-O-Si units. In purely siliceous models, the transparency gap between the main peaks at 800 and 1100 cm(-1) contains only vibrational features associated with terminal Si-OH groups, while in Ti-containing models it contains also the above-mentioned asymmetric TiO(4) modes, which in turn are strongly coupled with Si-OH stretching modes. Calculations on periodic models of silicalite and TS-1 free of OH groups using the QMPOT embedding method correctly reproduce the transparency gap of silicalite and the appearance of asymmetric TiO(4) vibrations at 960 cm(-1) in TS-1. Finally, we demonstrate, for the first time, that the distortion of the tetrahedral symmetry around Ti caused by water adsorption quenches the UV-Raman enhancement of the 1125 cm(-1) band.     

A structural and spectroscopic study on para-aminohippuric acid with experimental and theoretical approaches

In this work, the molecular conformation, vibrational and electronic analysis of para-aminohippuric acid (pAHA, C(9)H(10)N(2)O(3)) were presented for the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. FT-IR and FT-Raman spectra were recorded in the regions of 400-4000cm(-1) and 50-4000cm(-1), respectively. The UV absorption spectra of the compound that dissolved in ethanol and water solution were recorded in the range of 190-400nm. Potential energy curve was computed by means of scanning NCCO torsion angle. The geometry optimization and the energies associated possible four conformers (C1-C4) were computed. The computational results diagnose the most stable conformer of pAHA as the C1 form. Optimized structure of compound was interpreted and compared with the earlier reported experimental values. The complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. A study on the electronic properties, such as frontier molecular energies, absorption wavelengths and oscillator strengths, were predicted by time-dependent DFT (TD-DFT) approach, while taking solvent effects into account. To investigate non-linear optical properties: polarizability, anisotropy of polarizability and molecular first hyperpolarizability of molecule were computed. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures were calculated.     

A theoretical study of conformational flexibility,magnetic properties,and polarizabilities of trimethylnaphthalenes

For almost all trimethylnaphthalenes (TMNs), the transition from a planar equilibrium ring conformation to a nonplanar conformation characterized by the torsional angle of 20° results in an energy increase of less than 2.5 kcal/mol. For some of them, it is less than 1.6 kcal/mol, which indicates that these molecules can change their conformation easily through intermolecular interactions. The results of the calculations reveal a linear relationship between the averaged rigidity constant and the relative energy for all planar TMNs. The changes of rings deformational energy imposed on π‐electron systems of TMNs by medium polarity are negligible (less than 0.05 kcal/mol). The aromaticity indices, based on nucleus‐independent chemical shifts, indicate aromatic character of TMNs. The α substitution increases the ring area more than the β substitution. The increase of anisotropy of dipole polarizabilities with the decrease of the area of rings for all planar TMNs, dimethylnaphthalenes and methylnaphthalenes is noticed. © 2013 Wiley Periodicals, Inc.     

Matrix isolation FTIR spectroscopic and theoretical study of dimethyl sulfite

The preferred conformations of dimethyl sulfite and their vibrational spectra were studied by matrix-isolation Fourier transform infrared spectroscopy and theoretical methods (density functional theory (DFT) and Moller-Plesset (MP2), with basis sets of different sizes, including the quadruple-zeta, aug-cc-pVQZ basis). Five minima were found at these levels of theory. At the MP2/6-31++G(d,p) and DFT/B3LYP/aug-cc-pVQPZ levels, the GG conformer (where the O-S-O-C dihedral angles are 73.2 and 70.8 degrees ) resulted in the conformational ground state. At the highest level of theory used, the GT conformer (O-S-O-C = +68.5 and -173.2 degrees ) is 0.83 kJ mol(-1) higher in energy than the GG form, while conformer GG' (O-S-O-C = +85.7 and -85.7 degrees ) has a relative energy of 1.18 kJ mol(-1). The remaining two conformers (G'T and TT) are high-energy forms and not experimentally relevant. In consonance with the theoretical predictions, conformer GG was found to be the most stable conformer in the gaseous phase as well as in the low-temperature matrices. Annealing of the argon matrices first promotes the GG'-->GT isomerization, which is followed by conversion of GT into the most stable conformer. There is no evidence of occurrence of GG'-->GG direct conversion in the low-temperature matrices. On the other hand, during deposition of the xenon matrices conformer GG' totally converts to conformer GT. Two observations demonstrated this fact: no evidence of bands corresponding to GG' were observed in xenon matrices and the GG/GT intensity ratio became similar to the GG/(GT + GG') intensity ratio observed in argon matrices. All these results could be explained by taking into account the relative values of the theoretically predicted energy barriers for the different isomerization processes: GG'-->GT, 1.90 kJ mol(-1); GT-->GG, 9.64 kJ mol(-1); and GG'-->GG, 19.46 kJ mol(-1).     

A theoretical study of conformational properties of dendritic block copolymers of first generation

Conformational properties of a dendritic block copolymer of the first generation are studied by means of an analytic calculation and dimensionality techniques. The polymer can have different functionalities and branch lengths in the interior region and the exterior shell. Three parameters are included in order to describe the intensity of the interactions between the same or different monomeric units. Based on the average end to end distances of the branches effective angles are defined in order to study how the microscopic parameters control the position and activity of the end groups, but also the hollowness in the internal region and the tweezing ability of the external shell of the macromolecule.     

A theoretical approach to molecular conformational analysis

The application of ab initio molecular orbital theory to the study of molecular conformational analysis is discussed. Examples presented include methyl rotational barriers, internal rotation in 1,2-dihalogenoethanes, $\text{cis-trans}$ isomerism in 1,2-dihalogenoethylenes, rotational barriers in substituted acetones and conformational preferences in substituted hydrazines.     

A theoretical study of electronic structures and intermolecular magnetic interactions for spiro-biphenalenyls

In order to inquire into the mechanism of the change in the magnetism of spiro-biphenalnyls, intermolecular magnetic interaction has been investigated in terms of the effective exchange integral of the Heisenberg model for dimeric pairs of diethyl-substituted spiro-biphenalenyl. Variation of the magnetic interaction with respect to temperature has been evaluated for X-ray crystallographic structures at several temperature points by Kohn–Sham hybrid-DFT. The intermolecular magnetic interactions have been calculated for the π-dimers to be antiferromagnetic at each temperature, which has decreased by approximately 30% in the magnitude from 100 to 173 K. In addition, the interactions have been almost none at 100 and 173 K except for one pair and the remaining pair had ferromagnetic interaction. Therefore, it has been found that the change in their magnetism is understood by the formation of a ferromagnetic dimer-pair at 173 K. Moreover, the natural orbital analysis for the electronic structure of diethyl-substituted spiro-biphenelenyl has shown our solutions are essentially identified to Haddon’s proposal in terms of the valence bond picture.