149 results on '"Flakus, A"'
Search Results
2. Metrics of dose to highly ventilated lung are predictive of radiation-induced pneumonitis in lung cancer patients
- Author
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Flakus, Mattison J., primary, Kent, Sean P., additional, Wallat, Eric M., additional, Wuschner, Antonia E., additional, Tennant, Erica, additional, Yadav, Poonam, additional, Burr, Adam, additional, Yu, Menggang, additional, Christensen, Gary E, additional, Reinhardt, Joseph M., additional, Bayouth, John E., additional, and Baschnagel, Andrew M., additional
- Published
- 2023
- Full Text
- View/download PDF
3. An examination of the factor structure of the Goldfarb Fear of Fat Scale in clinical and non-clinical samples of Polish women
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Maria Flakus, Hanna Przybyła-Basista, and Krystyna Buszman
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Anorexia Nervosa ,Social Psychology ,Population ,Sample (statistics) ,Assessment ,Anorexia nervosa ,Factor structure ,Feeding and Eating Disorders ,Body Image ,medicine ,Humans ,Women ,Bulimia Nervosa ,education ,General Psychology ,Applied Psychology ,education.field_of_study ,Bulimia nervosa ,Fear ,medicine.disease ,Factorial structure ,Eating disorders ,Phobic Disorders ,Non clinical ,Scale (social sciences) ,Female ,Poland ,Fear of fat ,Psychology ,Clinical and non-clinical samples ,Clinical psychology - Abstract
Although associations between fear of fat and eating disorders (ED) have been frequently studied, it appears that the construct of fear of fat requires in-depth understanding to determine whether it is similar in individuals diagnosed with bulimia nervosa, anorexia nervosa, and individuals from the general population. The purpose of our study was to confirm the factor structure of the Goldfarb Fear of Fat Scale (GFFS) in clinical and non-clinical settings. This issue has not yet been investigated in the literature. Data were collected from 126 female patients diagnosed with ED and a total of 581 women from the general population. Our findings are highly consistent with the original single-factor structure of GFFS but only in the clinical sample. In the non-clinical sample, a good fit to the data has been achieved with a two-factor model composed of Fear of gaining weight and Fear of losing control over eating/weight. The Polish version of GFFS demonstrated good psychometric properties. It can be used as a fast screening tool to identify individuals with eating disorders and those at risk of developing such disorders. We recommend the two-factor model for non-clinical samples and the one-dimensional model for clinical samples for both research and practice.
- Published
- 2022
4. Dose to High Ventilating Lung Predicts Radiation-Induced Pneumonitis in Lung Cancer Patients
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Flakus, M.J., primary, Wallat, E., additional, Wuschner, A.E., additional, Tennant, E., additional, Yadav, P., additional, Burr, A., additional, Bayouth, J., additional, and Baschnagel, A.M., additional
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- 2022
- Full Text
- View/download PDF
5. Metrics of dose to highly ventilated lung are predictive of radiation-induced pneumonitis in lung cancer patients
- Author
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Mattison J. Flakus, Sean P. Kent, Eric M. Wallat, Antonia E. Wuschner, Erica Tennant, Poonam Yadav, Adam Burr, Menggang Yu, Gary E Christensen, Joseph M. Reinhardt, John E. Bayouth, and Andrew M. Baschnagel
- Subjects
Oncology ,Radiology, Nuclear Medicine and imaging ,Hematology - Published
- 2023
6. An examination of the factor structure of the Goldfarb Fear of Fat Scale in clinical and non-clinical samples of Polish women
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Przybyła-Basista, Hanna, primary, Buszman, Krystyna, additional, and Flakus, Maria, additional
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- 2022
- Full Text
- View/download PDF
7. Dose to High Ventilating Lung Predicts Radiation-Induced Pneumonitis in Lung Cancer Patients
- Author
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M.J. Flakus, E. Wallat, A.E. Wuschner, E. Tennant, P. Yadav, A. Burr, J. Bayouth, and A.M. Baschnagel
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Cancer Research ,Radiation ,Oncology ,Radiology, Nuclear Medicine and imaging - Published
- 2022
8. IR spectral density of the υS(Cl–H→) band in gaseous (CH3)2O…HCl complex: Phase decoherence due to the anharmonic coupling theory and the bending mode effects
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Saed Salman, Jamal Suleiman, Henryk T. Flakus, Umer Farooq, and Najeh Rekik
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Quantum decoherence ,010304 chemical physics ,Chemistry ,Anharmonicity ,Transition dipole moment ,General Physics and Astronomy ,H band ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,symbols.namesake ,Fourier transform ,Absorption band ,0103 physical sciences ,symbols ,Physical and Theoretical Chemistry ,Atomic physics ,Hamiltonian (quantum mechanics) ,Morse potential - Abstract
The elucidation of Fermi resonances impact on the IR spectral density (SD) of weak hydrogen bonded systems is still subject of an ongoing debate. We present, in this paper, a simple quantum approach that may illumine the contribution of Fermi resonances, resulting from the interaction between the high stretching and bending modes, on the SD of the υ S ( Cl – H → ) band in gaseous ( CH 3 ) 2 O … HCl Complex and address the question whether there is Fermi resonances phenomenon in such weak hydrogen bonded complexes. We analyzed the problem by considering a quantum approach taking into account the following hypotheses: (i) the low frequency stretching mode (slow mode) of the hydrogen bond is represented by a Morse potential, (ii) the high stretching mode (fast mode) is considered to harmonic, (iii) the υ S ( Cl – H → ) phase coherence is lost because of the coupling between the fast and slow modes, and because of the coupling between the fast and the bending mode, (iv) the SD is obtained within the framework of Kubo’s theory, according to which the SD is the Fourier transform of the transition dipole moment autocorrelation function which characterises the lineshape of the mid infrared υ S ( Cl – H → ) absorption band, (v) the direct relaxation mechanism of the υ S ( Cl – H → ) stretching band is incorporated by aid of the quantum treatment of Rosch and Ranter for which for the autocorrelation function decays exponentially on time, (vi) the indirect relaxation mechanism of the bending mode is introduced by aid of complex energy levels’ method for which the Hamiltonian eigenvalues of the H-bonded system, computed in the absence of damping, imaginary parts reflecting the irreversible influence of the medium on the bending mode. Using a set of physically reasonable parameters as input into the presented approach, the numerical experimentations have shown the capability of this simple model, which anharmonically couple the high stretching mode together with the slow and bending modes, to explain the main spectroscopic features of the υ S ( Cl – H → ) band in gaseous ( CH 3 ) 2 O … HCl Complexes. A good agreement between the simulated and experimental lineshapes is illustrated and a deep study of the role of each mechanism on the υ S ( Cl – H → ) band is elucidated.
- Published
- 2019
9. Are intelligent peers liked more? Assessing peer-reported liking through the network analysis
- Author
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Flakus, Maria, primary, Danieluk, Barnaba, additional, Baran, Lidia, additional, Kwiatkowska, Katarzyna, additional, Rogoza, Radosław, additional, and Schermer, Julie Aitken, additional
- Published
- 2021
- Full Text
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10. The structure of the Dark Triad traits: A network analysis
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Trahair, Cassidy, primary, Baran, Lidia, additional, Flakus, Maria, additional, Kowalski, Christopher Marcin, additional, and Rogoza, Radosław, additional
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- 2020
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11. A unified quantum model susceptible to elucidate the dissimilarity of IR spectral density of dicarboxylic acid crystals: Phthalic and terephthalic acid crystals cases
- Author
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Rekik, Najeh, primary, Alsaif, Norah A.M., additional, Flakus, Henryk T., additional, Farooq, Umer, additional, and Chand, Ram, additional
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- 2020
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12. Molecular docking studies, structural and spectroscopic properties of monomeric and dimeric species of benzofuran-carboxylic acids derivatives: DFT calculations and biological activities
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Sagaama, Abir, primary, Noureddine, Olfa, additional, Brandán, Silvia Antonia, additional, Jędryka, Anna Jarczyk-, additional, Flakus, Henryk T., additional, Ghalla, Houcine, additional, and Issaoui, Noureddine, additional
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- 2020
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13. How far the vibrational exciton interactions are responsible for the generation of the infrared spectra of oxindole crystals?
- Author
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Rekik, Najeh, primary, Flakus, Henryk T., additional, Hachula, Barbara, additional, Salman, Saed, additional, Alshoaibi, Adil, additional, and Farooq, Umer, additional
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- 2020
- Full Text
- View/download PDF
14. Are intelligent peers liked more? Assessing peer-reported liking through the network analysis
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Lidia Baran, Radosław Rogoza, Barnaba Danieluk, Maria Flakus, Julie Aitken Schermer, and Katarzyna Kwiatkowska
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Relation (database) ,Dynamics (music) ,Exponential random graph models ,Psychology ,Constant (mathematics) ,Social psychology ,General Psychology ,Network analysis ,Test (assessment) - Abstract
The current study examines whether intelligent adolescents are liked more by their peers, does this likeability assessment remains constant over time, and do intelligent adolescents like certain people or everyone? For this purpose, we recruited seven classes of adolescents at the beginning of the first school year. We administered an intelligence test and gathered peer-reported information regarding the liking relations. To examine the dynamics of such associations, we repeated the measurement three months and one year later. The results of the Temporal Exponential Random Graph Model revealed that intelligent adolescents are liked more. However, these highly intelligent adolescents did not reciprocate such relations, as they liked fewer people than those who were less intelligent. This finding was stable both across short- and long-term and could be explained by the fact that those who are intelligent, tend to only like other intelligent peers, representing a fewer number of individuals. Our results suggest that intelligence is important in the explanation of the relation of liking.
- Published
- 2021
15. 'Long-distance' H/D isotopic self-organization phenomena in scope of the infrared spectra of hydrogen-bonded terephthalic and phthalic acid crystals
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Barbara Hachuła, Faisal Abdulaziz Al-Agel, Najeh Rekik, Henryk T. Flakus, and Jakub T. Hołaj-Krzak
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Terephthalic acid ,Hydrogen ,Hydrogen bond ,Stereochemistry ,chemistry.chemical_element ,Infrared spectroscopy ,Aromaticity ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Analytical Chemistry ,Isotopomers ,chemistry.chemical_compound ,Crystallography ,Phthalic acid ,chemistry ,Molecule ,0210 nano-technology ,Instrumentation ,Spectroscopy - Abstract
This paper deals with the experimental and theoretical studies of abnormal properties of terephthalic acid (TAC) and phthalic acid (PAC) crystals manifested in the H/D isotopic exchange. The widely utilized deuteration routine appeared to be insufficiently effective in the case of the h 6 -TAC isotopomer. In the case of the d 4 -TAC derivative the isotopic exchange process occurred noticeably more effectively. In contrast, both isotopomers of PAC, h 6 and d 4 , appeared much more susceptible for deuteration. A theoretical model was elaborated describing “long-distance” dynamical co-operative interactions involving hydrogen bonds in TAC and PAC crystals. The model assumes extremely strong dynamical co-operative interactions of hydrogen bonds from the adjacent (COOH) 2 cycles. This leads to an additional stabilization of h 6 –TAC molecular chains. The interaction energies affect the chemical equilibrium of the H/D isotopic exchange. The model predicts a differentiated influence of the H and D atoms linked to the aromatic rings on to the process. In this approach the totally-symmetric C H bond stretching vibrations and the proton stretching totally symmetric vibrations couple with the π -electronic motions. It was also shown that identical hydrogen isotope atoms, H or D, in whole TAC molecules, noticeably enlarge the energy of the dynamical co-operative interactions in the crystals, in contrast to the case of different hydrogen isotopes present in the carboxyl groups and linked to the aromatic rings. The “long-distance” dynamical co-operative interactions in PAC crystals were found of a minor importance due to the electronic properties of PAC molecules.
- Published
- 2017
16. The structure of the Dark Triad traits: A network analysis
- Author
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Lidia Baran, Cassidy Trahair, Maria Flakus, Radosław Rogoza, and Christopher Marcin Kowalski
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Dark triad ,media_common.quotation_subject ,05 social sciences ,Psychopathy ,050109 social psychology ,medicine.disease ,050105 experimental psychology ,Facet (psychology) ,Narcissism ,medicine ,Trait ,Personality ,0501 psychology and cognitive sciences ,Optimal distinctiveness theory ,medicine.symptom ,Psychology ,Social psychology ,General Psychology ,Machiavellianism ,media_common - Abstract
Growing interest in the exploration of the dark side of personality recently led to the questions concerning the number, distinctiveness, and structural organization of its components. The main goal of the current study (N = 1012) is to explore the structure of the Dark Triad traits using the network approach. The results showed that all of the traits formed a single network forming two dimensions. However, agentic facets of narcissism were least related to Machiavellianism and psychopathy, which suggests the partial distinctiveness of the trait. Also, the antagonistic facet of narcissism mediated the relations between most of the agentic facets of narcissism and Machiavellianism and psychopathy. Finally, Machiavellianism and psychopathy were located in close proximity, which reflects their core status in the Dark Triad. The interpretation of the results and limitations of the study are further discussed.
- Published
- 2020
17. A unified quantum model susceptible to elucidate the dissimilarity of IR spectral density of dicarboxylic acid crystals: Phthalic and terephthalic acid crystals cases
- Author
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Henryk T. Flakus, Ram Chand, Norah A.M. Alsaif, Umer Farooq, and Najeh Rekik
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Terephthalic acid ,chemistry.chemical_classification ,Hydrogen bond ,Anharmonicity ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Resonance (chemistry) ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,Spectral line ,0104 chemical sciences ,Analytical Chemistry ,chemistry.chemical_compound ,Vibronic coupling ,Phthalic acid ,Dicarboxylic acid ,chemistry ,Chemical physics ,0210 nano-technology ,Instrumentation ,Spectroscopy - Abstract
Over the last decades, several approaches have been developed for elucidating the infrared spectral density of dicarboxylic acid crystals, which has been served as prototype for determining hydrogen bonds dynamics. These approaches differ in how accurately the simulated spectra can superimpose the experimental ones. In this study, we present a superdimer quantum approach susceptible to elucidate the infrared spectral properties of some particular dicarboxylic acid crystals using a newly proposed algorithm, which favors the rule of Davydov coupling in the generation of the spectra. The approach, which is herein effectively applied to terephthalic and phthalic acid dimer crystals, ascribes the non-conventional IR spectral properties of these particular acid crystals to the existence of superdimer structure in their lattices. In this superdimer structure, a strong vibronic coupling mechanism, namely Davydov coupling, takes place between the proton stretching vibrations in the (COOH)₂ cycles. This strong coupling exciton, generated by the resonance arising in the two coupled (COOH)₂ cycles of the aromatic rings of the superdimer, in conjunction with the strong anharmonic coupling between the fast and slow modes of each hydrogen bonds provide a strong support basis for a common explanation of the physical properties of these two different crystalline systems. The numerical simulations, involving the implications of the superdimer model, are systematically correlated with the experimental spectra. A decent agreement between the evaluated spectra and the experimental bandshapes of terephthalic and phthalic dicarboxylic acid crystals was obtained using a set of physically sound parameters as inputs in the theoretical formulation. The superdimer quantum approach thereby underscore the potential of the dynamical cooperative interactions between “Davydov coupling” and “strong anharmonic coupling” mechanisms in the generation of the spectral features of terephthalic and phthalic dicarboxylic acid crystals, suggesting that the congregated effects of these two mechanisms can be considered as the most reliable source of the non-conventional IR spectral properties observed. It is therefore expected that this novel algorithm reduces the discrepancies between the simulated spectra compared to the experimental one and simplify the computation of spectra in more complex hydrogen bonded systems.
- Published
- 2020
18. Davydov coupling as a factor influencing the H-bond IR signature: Computational study of the IR spectra of 3-thiopheneacrylic acid crystal
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Faisal Abdulaziz Al-Agel, Najeh Rekik, and Henryk T. Flakus
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Coupling ,Condensed matter physics ,Chemistry ,Hydrogen bond ,Anharmonicity ,General Physics and Astronomy ,Infrared spectroscopy ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Molecular physics ,0104 chemical sciences ,Davydov soliton ,Crystal ,Coupling parameter ,Physical and Theoretical Chemistry ,0210 nano-technology ,Doppler broadening - Abstract
In this work, we have studied the role played by Davydov coupling in the evolution of the fine structure of the IR spectra of 3-thiopheneacrylic acid dimer crystal. For this purpose, we took into account the linear dependence of the Davydov coupling on the position coordinate Qi(i = 1, 2) of the slow frequency O ← H … O → mode of the two H-bond bridges of the cyclic dimer. The Davydov coupling VD term was expanded up to first order with respect to the slow mode coordinate Qi. We have considered: V D ( Q 1 , Q 2 ) = V D 0 + Θ ( Q 1 + Q 2 ) . That leads to the anharmonic expression of the Davydov coupling parameter VD: V D Q g = V D 0 + 2 Θ Q g within the symmetrized coordinates. The effect of the second order parameter (Θ) of Davydov coupling on to the spectral density was undertaken. The numerical calculations clearly show that the crystal spectral properties of the infrared υO H stretching band remain in a close relation with the new anharmonic coupling parameter and provide a direct evidence of the increase of the level density and the spectral broadening.
- Published
- 2016
19. IR spectral density of the υS(Cl–H→) band in gaseous (CH3)2O…HCl complex: Phase decoherence due to the anharmonic coupling theory and the bending mode effects
- Author
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Rekik, Najeh, primary, Salman, Saed, additional, Suleiman, Jamal, additional, Farooq, Umer, additional, and Flakus, Henryk T., additional
- Published
- 2019
- Full Text
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20. Photochromic supramolecular azopolyimides based on hydrogen bonds
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Joachim Stumpe, Katarzyna Bijak, Anna Sobolewska, Anna Jarczyk-Jedryka, Jolanta Konieczkowska, Mariola Siwy, Henryk T. Flakus, and Ewa Schab-Balcerzak
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chemistry.chemical_classification ,Materials science ,Hydrogen bond ,Organic Chemistry ,Supramolecular chemistry ,Chromophore ,Atomic and Molecular Physics, and Optics ,Electronic, Optical and Magnetic Materials ,Inorganic Chemistry ,Supramolecular polymers ,chemistry.chemical_compound ,Photochromism ,Azobenzene ,chemistry ,Polymer chemistry ,Electrical and Electronic Engineering ,Physical and Theoretical Chemistry ,Glass transition ,Spectroscopy ,Polyimide - Abstract
The approach of deriving new photoresponsive active supramolecular azopolymers based on the hydrogen bonds is described. Polymers with imide rings, i.e., poly(esterimide)s and poly(etherimide)s, with phenolic hydroxyl or carboxylic groups were applied as matrixes for the polymer–dye supramolecular systems. Supramolecular films were built on the basis of the hydrogen bonds between the functional groups of the polymers and various azochromophores, that is, 4-phenylazophenol, 4-[4-(6-hydroxyhexyloxy)phenylazo]benzene, 4-[4-(6-hexadecaneoxy)phenylazo]pyridine and 4-(4-hydroxyphenylazo)pyridine. The hydrogen bonding interaction in azo-systems were studied by Fourier transform infrared spectroscopy and for selected assembles by 1H NMR technique. The obtained polyimide azo-assembles were characterized by X-ray diffraction and DSC measurements. H-bonds allow attaching a chromophore to each repeating unit of the polymer, thereby suppressing the macroscopic phase separation except for the systems based on 4-[4-(6-hydroxyhexyloxy)phenylazo]benzene. H-bonds systems were amorphous and revealed glass transition temperatures lower than for the polyimide matrixes (170–260 °C). The photoresponsive behavior of the azo-assemblies was tasted in holographic recording experiment.
- Published
- 2015
21. The source of the differences in the IR spectral properties of the hydrogen bond in two isomeric thioamide crystals: Thioacetanilide and N-methylthiobenzamide
- Author
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Piotr Lodowski, Henryk T. Flakus, Barbara Hachuła, Wioleta Śmiszek-Lindert, Edyta Turek, and Anna Michta
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chemistry.chemical_classification ,Hydrogen bond ,Spectral properties ,Substituent ,General Physics and Astronomy ,Infrared spectroscopy ,Thioacetanilide ,N-methylthiobenzamide ,Molecular systems ,Photochemistry ,Crystallography ,chemistry.chemical_compound ,chemistry ,Physical and Theoretical Chemistry ,Thioamide - Abstract
This letter is devoted to the explanation of the differences between the IR spectral properties of hydrogen bond systems found in crystals of two isomeric thioamides, thioacetanilide (TACN) and N-methylthiobenzamide (NMTB). The magnitude of the temperature-dependent Davydov-splitting effects, the H/D isotopic ‘ self - organization ’ effects in the crystalline polarized IR spectra depend on the electronic properties of the two different associating molecular systems, which are affected by the methyl and phenyl substituent groups linked to the H N C S common structural fragments.
- Published
- 2015
22. Elucidating the Davydov-coupling mechanism in hydrogen bond dimers: Experimental and theoretical investigation of the polarized IR spectra of 3-thiopheneacetic and 3-thiopheneacrylic acid crystals
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Anna Jarczyk-Jedryka, Mohsen Daouahi, Peter G. Jones, Maria Nowak, Henryk T. Flakus, Faisal Abdulaziz Al-Agel, Najeh Rekik, and Joachim Kusz
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Quantitative Biology::Biomolecules ,Chemistry ,Hydrogen bond ,Exciton ,Dimer ,Infrared spectroscopy ,General Chemistry ,Crystal structure ,Condensed Matter Physics ,Molecular physics ,Spectral line ,Crystallography ,Vibronic coupling ,chemistry.chemical_compound ,Physics::Atomic and Molecular Clusters ,Molecule ,General Materials Science - Abstract
Monocrystals of the 3-thiopheneacetic and 3-thiopheneacrylic acid dimers were investigated by polarized IR spectroscopy at 77 and 293 K in the υO‒H and υO‒D band frequency ranges. We propose to elucidate the strong difference between spectra of the two individual systems, expressed by the corresponding band shapes and by the temperature effects characterizing the bands. The experimental results are compared to predictions obtained with theoretical calculations based on a model for a centrosymmetric hydrogen-bonded dimer that treats the high-frequency OH stretches harmonically and the low-frequency intermonomer stretches anharmonically. It was found that the vibronic coupling mechanism involving the hydrogen bond protons and the electrons on the π-electronic systems in the molecules determines the way in which the vibrational exciton coupling between the hydrogen bonds in the carboxylic acid dimers occurs.
- Published
- 2015
23. Inter-hydrogen bond coupling in crystals with molecular chains in their lattices investigated by polarized IR spectroscopy: 4-Bromo-3,5-dimethylpyrazole and 3,4-dimethoxyphenylacetic acid
- Author
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Anna Polasz, Henryk T. Flakus, and Barbara Hachuła
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Models, Molecular ,Halogenation ,Spectrophotometry, Infrared ,Hydrogen bond ,Chemistry ,Exciton ,Temperature ,Infrared spectroscopy ,Hydrogen Bonding ,Electronic structure ,Deuterium ,Atomic and Molecular Physics, and Optics ,Spectral line ,Analytical Chemistry ,Crystal ,Crystallography ,Computational chemistry ,Pyrazoles ,Molecule ,Crystallization ,Instrumentation ,Spectroscopy ,Phenylacetates - Abstract
We report the results of the experimental and theoretical studies of the polarized IR crystalline spectra of 4-bromo-3,5-dimethylpyrazole (4Br35DMPz) and 3,4-dimethoxyphenylacetic acid (34DMPAA) as well as the spectra of their deuterium-bonded analogues. The results of model calculations of the temperature impact exerted on to the band shapes measured in the X–H- and X–D bond stretching vibration regions, performed on the basis of the “ strong-coupling ” model, are also shown. These studies confirm a direct relationship between the spectral properties in IR and the electronic structure of the associating molecules in the crystals. Two different competing exciton coupling mechanisms involving hydrogen bonds, the “ tail-to-head ” (TH) in 4Br35DMPz and the “ side-to-side” coupling in 34DMPAA, were recognized. The molecular electronic structure determines the relative contribution of each individual vibrational exciton coupling mechanism in the spectra generation. It also strongly influences the temperature-induced evolution of the Davydov-splitting effects in the crystalline spectra. Dynamical co-operative interactions responsible for a non-random distribution of protons and deuterons in the crystal hydrogen bonds can also be identified in the investigated systems.
- Published
- 2014
24. Extremely strong temperature-dependent Davydow-splitting effects in the polarized IR spectra of the hydrogen bond: Pyrazole and quinolin-2(1H)-one crystals
- Author
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Anna Polasz, Aleksandra Tyl, Barbara Hachuła, and Henryk T. Flakus
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Range (particle radiation) ,chemistry.chemical_compound ,Proton ,Chemistry ,Hydrogen bond ,General Physics and Astronomy ,Physical chemistry ,Infrared spectroscopy ,Physical and Theoretical Chemistry ,Atmospheric temperature range ,Pyrazole ,Photochemistry ,Spectral line - Abstract
Polarized IR spectra were recorded in the spectral range of the νN–H and νN–D proton stretching vibration bands for the isotopically neat and isotopically diluted crystals of pyrazole (Pzl) and quinolin-2(1H)-one (2HQ). The spectra measured in the temperature range of 77–293 K have shown that temperature extremely strongly influenced the magnitude of the Davydow-splitting effects in the crystalline spectra. Two different competing vibrational Davydow-coupling mechanisms involving hydrogen bonds, i.e., the ‘tail-to-head’ and the ‘side-to-side’, were responsible for the generation of the temperature effects in the polarized spectra.
- Published
- 2014
25. A complete assignment of the vibrational spectra of 2-furoic acid based on the structures of the more stable monomer and dimer
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Houcine Ghalla, María V. Castillo, Silvia Antonia Brandán, Henryk T. Flakus, and Noureddine Issaoui
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Models, Molecular ,Dimer ,Atoms in molecules ,Intermolecular force ,Molecular Conformation ,Spectrum Analysis, Raman ,Vibration ,Bond order ,Atomic and Molecular Physics, and Optics ,Analytical Chemistry ,chemistry.chemical_compound ,Crystallography ,chemistry ,Computational chemistry ,Ab initio quantum chemistry methods ,Spectroscopy, Fourier Transform Infrared ,Physics::Atomic and Molecular Clusters ,Molecule ,Density functional theory ,Physics::Chemical Physics ,Furans ,Dimerization ,Instrumentation ,Spectroscopy ,Natural bond orbital - Abstract
The structural and vibrational properties of cyclic dimer of 2-furoic acid (2FA) were predicted by combining the available experimental infrared and Raman spectra in the solid phase and ab initio calculations based on density functional theory (DFT) with Pople's basis sets. The calculations show that there are two cyclic dimers for the title molecule that have been theoretically determined in the gas phase, and that only one of them, cis conformer, is present in the solid phase. The complete assignment of the 66 normal vibrational modes for the cis cyclic dimer was performed using the Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology. Four strong bands in the infrared spectrum at 1583, 1427, 1126 and 887 cm(-1) and the group of bands in the Raman spectrum at 1464, 1452, 1147, 1030, 885, 873, 848, 715 and 590 cm(-1) are characteristic of the dimeric form of 2FA in the solid phase. In this work, the calculated structural and vibrational properties of both dimeric species were analyzed and compared between them. In addition, three types of atomic charges, bond orders, possible charge transfer, topological properties of the furan rings, Natural Bond Orbital (NBO) and Atoms in Molecules (AIM) theory calculations were employed to study the stabilities and intermolecular interactions of the both dimers of 2FA.
- Published
- 2014
26. Spectroscopic and molecular structure investigation of 2-furanacrylic acid monomer and dimer using HF and DFT methods
- Author
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Henryk T. Flakus, M. Govindarajan, Brahim Oujia, Noureddine Issaoui, M.H. Jamroz, and Houcine Ghalla
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Oscillator strength ,Chemistry ,Hydrogen bond ,Organic Chemistry ,Intermolecular force ,Analytical Chemistry ,Inorganic Chemistry ,Computational chemistry ,Polarizability ,Physics::Atomic and Molecular Clusters ,Molecule ,Physical chemistry ,Density functional theory ,Physics::Chemical Physics ,HOMO/LUMO ,Spectroscopy ,Natural bond orbital - Abstract
In the present work, we reported a combined experimental and theoretical study on molecular structure and vibrational spectra of 2-furanacrylic acid (abbreviated as 2FAA). The FT-IR and FT-Raman spectra of 2FAA have been recorded in the regions 4000–400 and 4000–100 cm −1 . The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The monomer and dimer structures of the title molecule have been obtained from Hartree–Fock (HF) and density functional theory (DFT) B3LYP methods with 6-311++G(d,p) as basis set calculations. The vibrational frequencies were calculated by DFT method and compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. Intermolecular O H⋯O hydrogen bonds are discussed in dimer structure of the molecule. The infrared and Raman spectra were also predicted from the calculated intensities. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. A study on the electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, are performed by time-dependent DFT (TD-DFT) approach. In addition, Milliken atomic charges, possible charge transfer, natural bond orbital (NBO) and AIM topological analysis were performed. Moreover, molecular electrostatic potential (MEP) and the thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase.
- Published
- 2014
27. Temperature, H/D isotopic and Davydov-splitting effects in the polarized IR spectra of hydrogen bond chain systems: 1,2,4-Triazole and 3-methyl-2-oxindole crystals
- Author
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Anna Polasz, Henryk T. Flakus, and Barbara Hachuła
- Subjects
Models, Molecular ,Indoles ,Spectrophotometry, Infrared ,Hydrogen ,Chemistry ,Hydrogen bond ,Exciton ,Temperature ,Infrared spectroscopy ,chemistry.chemical_element ,Hydrogen Bonding ,Triazoles ,Atomic and Molecular Physics, and Optics ,Spectral line ,Oxindoles ,Analytical Chemistry ,Vibronic coupling ,Delocalized electron ,Chemical physics ,Molecule ,Atomic physics ,Crystallization ,Instrumentation ,Spectroscopy - Abstract
The spectral properties of two different hydrogen-bonded crystalline systems, 1,2,4-triazole and 3-methyl-2-oxindole, containing molecular chains in their lattices, were examined by polarized IR spectroscopy, aided by the calculations utilizing the “strong-coupling” model. The experimental and theoretical approaches have shown that the individual crystal spectral properties in IR remain in a close relation with the electronic structure of the individual molecular systems. A vibronic coupling mechanism involving the hydrogen bond protons and the electrons occupying the π-electronic orbitals in the molecules determines the way in which the vibrational exciton coupling between the hydrogen bonds in the crystals occurs. For the associating systems, which molecules contain large delocalized π-electronic systems coupled directly with H-bonds, strong exciton interactions involving the vibrationally excited hydrogen bonds in the chains prefer a “tail-to-head”–type Davydov-coupling widespread via the π-electrons. A weak through-space exciton coupling involves two closely-spaced hydrogen bonds belonging to two different adjacent chains in the case, when large π-electronic systems in the molecules are absent. The relative contribution of each exciton coupling mechanism in the chain system spectra generation is temperature-dependent. The two competing individual Davydov-coupling mechanism are responsible for the appearance in the polarized spectra of temperature-dependent Davydov-splitting effects differentiating the spectral properties of the two crystalline systems. The H/D isotopic ‘‘self-organization’’ phenomenon, depending on a non-random distribution of protons and deuterons in the crystal hydrogen bridges was also analyzed.
- Published
- 2014
28. Electron-induced phase transition in hydrogen-bonded anhydrous solid state 4-pyridone
- Author
-
Aleksandra Tyl and Henryk T. Flakus
- Subjects
Crystal ,Phase transition ,Crystallography ,Hydrogen ,Hydrogen bond ,Chemistry ,Anhydrous ,Infrared spectroscopy ,chemistry.chemical_element ,Orthorhombic crystal system ,Spectroscopy ,Monoclinic crystal system - Abstract
Spectral studies of hydrogen bonded 4-pyridone crystal have demonstrated the existence of two anhydrous solid-state phases of the compound, namely the α and the β-phase. Hydrogen bonds in the high-temperature α-phase have been estimated to be 40% stronger than hydrogen bonds in the β-phase. It was proved that the crystals of the two polymorphs are identical with the crystals of the previously determined structures. The α polymorph is monoclinic while the β is orthorhombic. The mechanism of the phase transition 4-pyridone is proposed on the basis of the crystalline polarized IR spectra measured in the νO H and νO D band frequency ranges. It is connected with a partial change in the hydrogen bond nature, from the N+ H⋯O− in the α-phase, to the N H⋯O in the β-phase crystals. This involves small changes in the geometry of hydrogen bonds, which accompany the electron density redistribution in the hydrogen bonds during the phase transition.
- Published
- 2012
29. Effect of the resonance of the C–H and O–H bond stretching vibrations on the IR spectra of the hydrogen bond in formic and acetic acid
- Author
-
Barbara Hachuła and Henryk T. Flakus
- Subjects
Phase transition ,Formates ,Spectrophotometry, Infrared ,Chemistry ,Hydrogen bond ,Formic acid ,Temperature ,Infrared spectroscopy ,Hydrogen Bonding ,Photochemistry ,Vibration ,Atomic and Molecular Physics, and Optics ,Spectral line ,Analytical Chemistry ,chemistry.chemical_compound ,Acetic acid ,Vibronic coupling ,Molecule ,Physical chemistry ,Physics::Chemical Physics ,Instrumentation ,Spectroscopy ,Acetic Acid - Abstract
It is shown that the resonance of the O-H and C-H bond stretching vibrations is responsible for a noticeable intensity redistribution effect in the IR spectra of associated formic acid molecules in the gaseous phase. This effect is manifested by a considerably high growth in intensity of the νC-H band, which overlaps the νO-H band contour in the spectra. A vibronic coupling of the Herzberg-Teller-type expressed by the second order term in the perturbation theory is the most probable source of these spectral effects. The presented mechanism explains the variation of the effect magnitude accompanying the phase transitions. The proposed model also facilitates the understanding of the H/D isotopic effects in the spectra as well as the essential difference in the corresponding spectral properties between the formic and the acetic acid.
- Published
- 2011
30. The source of similarity of the IR spectra of acetic acid in the liquid and solid-state phases
- Author
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Henryk T. Flakus and Barbara Hachuła
- Subjects
Quantitative Biology::Biomolecules ,Formic acid ,Hydrogen bond ,Inorganic chemistry ,Infrared spectroscopy ,Spectral line ,Crystal ,chemistry.chemical_compound ,Acetic acid ,Crystallography ,chemistry ,Yield (chemistry) ,Isotopologue ,Spectroscopy - Abstract
This paper explains the problem of the fair similarity of the ν O–H band contour shapes in the spectra of liquid and crystal samples of hydrogen-bonded acetic acid, in contrast to the corresponding spectral properties of formic acid. It has been proven that regardless of the relative arrangement of hydrogen bonds in each phase, the hydrogen-bonded dimeric systems decide about the profile of the bands. Moreover, the model dimers of different symmetry, i.e., the C i or C 2v one of the “ side-to - side ” type arrangement of moieties, yield nearly identical spectra. Qualitatively similar spectral properties in the ν O–D band frequency range were found for deuterium-bonded formic and acetic acid isotopologues.
- Published
- 2011
31. The hydrogen bond IR spectra of indole-3-carboxaldehyde and 3-acetylindole crystals – The reason behind their similarity
- Author
-
Barbara Hachuła, Henryk T. Flakus, and Aleksandra Pyzik
- Subjects
Indole test ,Crystallography ,Deuterium ,Chemistry ,Hydrogen bond ,Exciton ,Analytical chemistry ,General Physics and Astronomy ,Infrared spectroscopy ,Molecule ,Physical and Theoretical Chemistry ,Dichroic glass ,Spectral line - Abstract
This paper presents the investigation results of the polarized IR spectra of indole-3-carboxaldehyde and 3-acetylindole crystals. Analysis of the results concerned the linear dichroic, H/D isotopic and temperature effects, observed at the frequency ranges of the vN–H and the vN–D bands, respectively. The main spectral properties of the crystals were interpreted in terms of the “strong-coupling” theory on the basis of the hydrogen bond dimeric model. The spectra revealed that the strongest vibrational exciton coupling involved the closely spaced hydrogen bonds, each belonging to a different chain of associated molecules. The paper explains why almost identical shapes of the vN–H and of the vN–D bands characterize these two different crystalline systems. Moreover it is proved that a non-random distribution of protons and deuterons takes place in the lattices of the isotopically diluted crystals. A specific mechanism of the isotopic recognition is the source of this phenomenon.
- Published
- 2011
32. Effects of dynamical couplings in hydrogen bond systems in the polarized IR spectra of 3-hydroxybenzaldehyde and 4-hydroxybenzaldehyde crystals
- Author
-
Barbara Hachuła and Henryk T. Flakus
- Subjects
Hydrogen ,Hydrogen bond ,Exciton ,Analytical chemistry ,General Physics and Astronomy ,chemistry.chemical_element ,Infrared spectroscopy ,Spectral line ,chemistry.chemical_compound ,chemistry ,Deuterium ,Physical chemistry ,Molecule ,3-Hydroxybenzaldehyde ,Physical and Theoretical Chemistry - Abstract
This paper presents the investigation results of the polarized IR spectra of 3-hydroxybenzaldehyde and 4-hydroxybenzaldehyde crystals measured at 293 and 77 K. Analysis of the results concerned the linear dichroic, H/D isotopic and temperature effects observed in the spectra of the hydrogen and deuterium bond at the frequency ranges of the ν O–H and the ν O–D bands, respectively. The main spectral properties of the crystals were interpreted in terms of the “ strong - coupling ” theory on the basis of the hydrogen bond dimer model. The spectra revealed that the strongest vibrational exciton coupling involved the closely-spaced hydrogen bonds, each belonging to a different chain of associated molecules. The reason for two different crystalline systems, are characterized by almost identical ν O–H and ν O–D band shapes, is explained. It was proved that a random distribution of the protons and deuterons took place in the lattices of the isotopically diluted crystals.
- Published
- 2010
33. Effects of strong inter-hydrogen bond dynamical couplings in the polarized IR spectra of adipic acid crystals
- Author
-
Henryk T. Flakus, Aleksandra Tyl, and Magdalena Jabłońska
- Subjects
Adipic acid ,Hydrogen ,Hydrogen bond ,Analytical chemistry ,General Physics and Astronomy ,Infrared spectroscopy ,chemistry.chemical_element ,Dichroic glass ,Spectral line ,chemistry.chemical_compound ,Dipole ,chemistry ,Deuterium ,Physical chemistry ,Physical and Theoretical Chemistry - Abstract
This paper presents the results of the re-investigation of polarized IR spectra of adipic acid and of its d 2 , d 8 and d 10 deuterium derivative crystals. The spectra were measured at 77 K by a transmission method using polarized light for two different crystalline faces. Theoretical analysis concerned linear dichroic effects and H/D isotopic effects observed in the spectra of the hydrogen and deuterium bonds in adipic acid crystals at the frequency ranges of the ν O–H and the ν O–D bands. The two-branch fine structure pattern of the ν O–H and ν O–D bands and the basic linear dichroic effects characterizing them were ascribed to the vibronic mechanism of vibrational dipole selection rule breaking for IR transitions in centrosymmetric hydrogen bond dimers. It was proved that for isotopically diluted crystalline samples of adipic acid, a non-random distribution of protons and deuterons occurs in the dimers (H/D isotopic “ self-organization ” effect). This effect results from the dynamical co-operative interactions involving the dimeric hydrogen bonds.
- Published
- 2009
34. An anomalous linear dichroic effect in the polarized IR spectra of 2-furancarboxylic acid crystals: Proton transfer induced by co-operative interactions involving hydrogen bonds
- Author
-
Magdalena Jabłońska-Czapla, Joachim Kusz, Magdalena Jabłońska, and Henryk Flakus
- Subjects
Crystal ,chemistry.chemical_compound ,Crystallography ,chemistry ,Hydrogen bond ,Dimer ,Lattice (order) ,Infrared spectroscopy ,Dichroic glass ,Spectroscopy ,Spectral line ,Excitation - Abstract
The polarized IR spectra of the hydrogen bond systems were studied in crystals of 2-furancarboxylic acid C 4 H 3 O–COOH as well as in crystals of its deuterium-bonded derivative. The spectra were measured by a transmission method at room temperature and at 77 K. Theoretical analysis of the results concerned the linear dichroic effects, the H/D isotopic and the temperature effects observed in the solid-state IR spectra at the frequency ranges of the ν O–H and the ν O–D bands, respectively. The main spectral properties of the crystals can be quantitatively interpreted in terms of the “ strong-coupling ” theory for a hydrogen bond dimer model. This model explains satisfactorily not only the two-branch structure of the ν O–H and the ν O–D bands, the temperature-induced evolution of the crystalline spectra, but also the basic linear dichroic effects observed in the band frequency ranges. A vibronic mechanism, responsible for promotion of the symmetry-forbidden transition in the IR and for the excitation of the totally symmetric proton stretching vibrations in centrosymmetric hydrogen bond dimers was also taken into the account. An excess of fine linear dichroic effects, accompanying the splitting of the spectral lines in the crystalline spectra, appeared for the crystal with only one dimer in a unit cell. This fact suggests that the existence of a specific co-operative interaction effect in the lattice, depending on the stimulated rearrangement of the proton positions in the hydrogen bond dimers, occurring in the nearest surrounding of an individual dimer in the lattice. Therefore, regardless of the published X-ray P 1 ¯ space-symmetry of the lattice, the effective unit cell for explaining the crystalline spectra behaved as if it contained two nonequivalent dimers. Re-examination of the crystal X-ray structure supported the hypothesis concerning the lattice transformation predicted by the IR spectroscopic studies.
- Published
- 2009
35. Inter-hydrogen bond dynamical coupling effects in polarized IR spectra of N-methylacetamide single crystals
- Author
-
Henryk T. Flakus and Anna Michta
- Subjects
Hydrogen ,Hydrogen bond ,Exciton ,Dimer ,Infrared spectroscopy ,chemistry.chemical_element ,Spectral line ,Crystallography ,chemistry.chemical_compound ,Deuterium ,chemistry ,Molecule ,Physics::Atomic Physics ,Atomic physics ,Spectroscopy - Abstract
This article presents the investigation results of polarized IR spectra of the hydrogen bond in N -methylacetamide (NMA) crystals measured in the frequency range of the proton and deuteron stretching vibration bands, ν N–H and ν N–D . A similar study was also performed for crystals of the deuterium isotopomers of the compound, D 7 -NMA (CD 3 CONDCD 3 ) and D 6 -NMA (CD 3 CONHCD 3 ). On the basis of the analysis of the linear dichroic and temperature effects, the two-branch structure of the ν N–H bands in the spectra was ascribed to centrosymmetric hydrogen bond pairs in the lattice. Each hydrogen bond in such a dimeric system belonged to another chain of the associated molecules. The exciton interactions involving the dimer hydrogen bonds were considered to be responsible for the band shape generation. For the deuterium-bonded crystals the exciton interactions were found to be weaker since the ν N–D bands were less split. Within an individual hydrogen or deuterium bond chain the in-chain exciton couplings involving hydrogen bonds were estimated as considerably weaker than the inter-chain ones. The exciton dilution retains the two-branch fine structure pattern of the “ residual ” ν N–H and ν N–D bands. This means that the inter-chain couplings involving hydrogen bonds do not change, when the in-chain couplings vanish. These results are the evidence of the influence of non-conventional co-operative interactions occurring in the hydrogen bond systems on the spectra. These co-operative interactions are responsible for the non-random distribution of the hydrogen isotope atoms in the hydrogen bridge lattices, namely for the grouping of identical hydrogen isotope atoms in the dimers. The proposed interpretation of the IR spectra of the hydrogen bond in N -methylacetamide (NMA) crystals casts light on the spectra generation mechanisms and gives a new meaning to the traditional nomenclature applied for describing the ν N–H band structure pattern in IR spectra of amides.
- Published
- 2009
36. Strong vibrational exciton coupling effects in polarized IR spectra of the hydrogen bond in 2-thiopyridone crystals
- Author
-
Henryk T. Flakus and Aleksandra Tyl
- Subjects
Crystal ,Deuterium ,Hydrogen ,Computational chemistry ,Chemistry ,Hydrogen bond ,Exciton ,Anharmonicity ,Infrared spectroscopy ,chemistry.chemical_element ,Molecular physics ,Spectroscopy ,Spectral line - Abstract
This paper presents the results of investigation on polarized IR spectra of the hydrogen bond in 2-thiopyridone crystals. The spectra were measured in the frequency range of the N H and N D bond stretching vibrations, for two different crystalline forms, having developed ab or bc crystal faces. The spectra exhibited extremely strong vibrational exciton coupling effects characterized by a large Davydov-splitting (correlation field splitting), whose existence was confirmed by a strong difference between the polarized spectra of the two forms of 2-thiopyridone crystals. It was shown that extremely strong exciton interactions involving the translationally non-equivalent hydrogen bonds in the unit cell are responsible for these effects. Isotopic dilution in the crystals caused the disappearance of the spectral effects, ascribed to the inter-dimer exciton couplings, and the simultaneous retaining of the dimeric character of the “residual” νN H and νN D bands. This spectral behavior of the isotopically diluted crystals was interpreted as the result of the dynamical co-operative interactions involving the hydrogen bonds in the lattice. These interactions lead to a non-random distribution of the protons and deuterons in the cyclic hydrogen bond dimeric systems and in consequence to the so-called H/D isotopic “self-organization” effects in the crystal spectra. The fine structure of the “residual” νN H and νN D bands is also influenced by such non-conventional spectral effects as the selection rule breaking for IR transitions, as well as the “reversal” exciton coupling effect for centrosymmetric hydrogen bonded dimers. This statement is supported by model calculations of the analyzed band shapes. They are performed in terms of the “strong-coupling” theory which assumes a strong anharmonic coupling involving different frequency hydrogen bond normal vibrations in the dimers, namely the high-frequency N H stretching and the low-frequency νN⋯S hydrogen bond stretching vibrations.
- Published
- 2008
37. Effects of 'excessive' exciton interactions in polarized IR spectra of the hydrogen bond in 2-butynoic acid crystals: Proton transfer induced by dynamical co-operative interactions involving hydrogen bonds
- Author
-
Barbara Hachuła and Henryk T. Flakus
- Subjects
Proton ,Hydrogen ,Hydrogen bond ,Stereochemistry ,Dimer ,Exciton ,General Physics and Astronomy ,Infrared spectroscopy ,chemistry.chemical_element ,chemistry.chemical_compound ,Crystallography ,chemistry ,Deuterium ,Molecule ,Physical and Theoretical Chemistry - Abstract
In this article, we present the results of our study of polarized IR spectra of the hydrogen bond in crystals of 2-butynoic acid (CH3C CCOOH) as well as in crystals of its deuterium derivative (CH3C CCOOD). 2-Butynoic acid can exist in two polymorphous crystalline forms: in the “α” form, based on a classic dimer motif and in the “β” form, based on the catamer pattern of the hydrogen bond arrangement. By cooling the melted substance crystals of the “β” phase were obtained selectively. The polarized IR spectra of the hydrogen bond in the “β” form of 2-butynoic acid crystals were measured at room temperature and at the temperature of liquid nitrogen in the νO–H and νO–D band frequency ranges. In terms of the “strong-coupling” theory the fine structure patterns of the νO–H and νO–D polarized bands were quantitatively explained along with the dichroic and the H/D isotopic effects in the spectra. To interpret the main properties of the spectra the existence of a non-conventional effect concerning a self-stimulated concerted proton position rearrangements in the neighboring cells in the lattice had to be assumed. On the basis of the spectra of isotopically diluted crystalline samples of 2-butynoic acid it was suggested that a random distribution of protons and deuterons occurred in the open chains of the hydrogen bonded molecules. However, coordination in the mutual arrangement of protons and deuterons in the neighboring hydrogen bonds from the closely spaced molecular chains was found to be non-random. This fact was ascribed to dynamical co-operative interactions, most strongly involving hydrogen bonds from different chains in the modified lattice. These non-conventional interactions were responsible for appearance of the so-called H/D “self-organization” isotopic effects in the spectra.
- Published
- 2008
38. Experimental FTIR and FT-Raman and theoretical studies on the molecular structures of monomer and dimer of 3-thiopheneacrylic acid
- Author
-
Issaoui, N., primary, Ghalla, H., additional, Brandán, Silvia Antonia, additional, Bardak, F., additional, Flakus, H.T., additional, Atac, A., additional, and Oujia, B., additional
- Published
- 2017
- Full Text
- View/download PDF
39. Combined experimental and theoretical studies on the molecular structures, spectroscopy, and inhibitor activity of 3-(2-thienyl)acrylic acid through AIM, NBO,FT-IR, FT-Raman, UV and HOMO-LUMO analyses, and molecular docking
- Author
-
Issaoui, N., primary, Ghalla, H., additional, Bardak, F., additional, Karabacak, M., additional, Aouled Dlala, N., additional, Flakus, H.T., additional, and Oujia, B., additional
- Published
- 2017
- Full Text
- View/download PDF
40. “Long-distance” H/D isotopic self-organization phenomena in scope of the infrared spectra of hydrogen-bonded terephthalic and phthalic acid crystals
- Author
-
Flakus, Henryk T., primary, Hachuła, Barbara, additional, Hołaj-Krzak, Jakub T., additional, Al-Agel, Faisal A., additional, and Rekik, Najeh, additional
- Published
- 2017
- Full Text
- View/download PDF
41. Polarized IR spectra of the hydrogen bond in acetic acid crystals
- Author
-
Henryk T. Flakus and Aleksandra Tyl
- Subjects
Hydrogen ,Hydrogen bond ,Dimer ,General Physics and Astronomy ,chemistry.chemical_element ,Infrared spectroscopy ,Photochemistry ,Spectral line ,Isotopomers ,chemistry.chemical_compound ,chemistry ,Deuterium ,Physical chemistry ,Molecule ,Physics::Atomic Physics ,Physical and Theoretical Chemistry - Abstract
The paper presents the results of our investigations of the polarized IR spectra of the hydrogen bond in crystals of acetic acid, CH3COOH, as well as in crystals of three deuterium isotopomers of the compound: CH3COOD, CD3COOH and CD3COOD. The spectra were measured at 283 K and at 77 K by a transmission method using polarized light. Theoretical analysis of the results concerned the linear dichroic effects, together with the H/D isotopic and temperature effects observed in the solid-state IR spectra of the hydrogen and of the deuterium bond at the frequency ranges of the νO–H and the νO–D bands, respectively. Basic spectral properties of the crystals can be interpreted satisfactorily in terms of one of the quantitative theories of the IR spectra of the hydrogen bond, i.e. the “strong-coupling” theory or the “relaxation” theory when a hydrogen bond dimer model is used. From the spectra obtained it resulted that the strongest exciton coupling involved the closely spaced hydrogen bonds, belonging to different chains of associated acetic acid molecules. These results contradict the former explanation of the spectra within a model, which assumed a strong vibrational exciton coupling between four hydrogen bonds in a unit cell. On analyzing the spectra of isotopically diluted crystalline samples of acetic acid it has been proved that a non-random distribution of the protons and deuterons takes place in the hydrogen bond lattices. This non-conventional isotopic effect is a result of dynamical co-operative interactions involving hydrogen bonds in the system. Simultaneously it has been also found that in an individual hydrogen bonded chain in the crystals, distribution of the hydrogen isotope atoms H and D was fully random. The H/D isotopic “self-organization” mechanism most probably involves a pair of hydrogen bonds from each unit cell where each hydrogen bond belongs to a different chain.
- Published
- 2007
42. 'Reversal' exciton coupling effect in the IR spectra of the hydrogen bond cyclic dimers; polarized IR spectra of 3-hydroxy-4-methyl-2(3H)-thiazolethione crystals
- Author
-
Joachim Kusz, Aleksandra Pyzik, Anna Michta, and Henryk T. Flakus
- Subjects
Hydrogen ,Hydrogen bond ,Exciton ,Dimer ,Infrared spectroscopy ,chemistry.chemical_element ,Spectral line ,Crystal ,Crystallography ,chemistry.chemical_compound ,Nuclear magnetic resonance ,chemistry ,Deuterium ,Spectroscopy - Abstract
This paper presents the results of our investigation of the polarized IR spectra of the hydrogen bond in crystals of 3-hydroxy-4-methyl-2(3H)-thiazolethione. These spectra were measured at room temperature and at 77 K by a transmission method using polarized light. The spectral studies were preceded by re-determination of the crystal X-ray structure. Theoretical analysis of the results concerned linear dichroic effects, the H/D isotopic and temperature effects observed in the solid-state IR spectra of hydrogen and deuterium bonds at frequency ranges of the νO H and the νO D bands, respectively. Basic spectral properties of the crystals can be interpreted satisfactorily in terms of the “strong-coupling” theory, when based on a hydrogen bond dimer model. This model sufficiently explains not only the two-branch structure of the νO H and the νO D bands and the temperature-induced evolution of the crystalline spectra, but also the linear dichroic effects observed in the band frequency ranges. A vibronic mechanism responsible for promotion of the symmetry forbidden transition in the IR for the totally symmetric proton stretching vibrations in centrosymmetric hydrogen bond dimers was analyzed. The crystal spectral properties were successfully interpreted on assuming a “reversal” Davydow-splitting effect expressed by changing of the vibrational exciton interaction energy sign for hydrogen bond dimers in the lattice. These effects were ascribed to a considerable elongation of the dimeric O H ⋯ S bonds in the crystal due to the large atomic radius of sulfur determining the dimer geometry.
- Published
- 2007
43. A systematic study of polarized IR spectra of the hydrogen bond in formic acid crystals
- Author
-
Henryk T. Flakus and Barbara Stachowska
- Subjects
Hydrogen ,Formic acid ,Stereochemistry ,Hydrogen bond ,General Physics and Astronomy ,Infrared spectroscopy ,chemistry.chemical_element ,Linear dichroism ,Spectral line ,chemistry.chemical_compound ,Deuterium ,chemistry ,Physical chemistry ,Molecule ,Physical and Theoretical Chemistry - Abstract
In this paper, we present the results of our investigation of the polarized IR spectra of the hydrogen bond in formic acid crystals, as well as in crystals of the three deuterium derivatives of the compound: DCOOH, HCOOD, and DCOOD. These spectra were measured by a transmission method, using polarized light at 273 K and also at the temperature of liquid nitrogen for the “ bc ” crystalline face. Our studies mainly focused on spectral effects corresponding to the intensity distribution, the influence of temperature, the linear dichroism, and isotopic substitution of deuterium in formic acid molecules measured in the frequency range of the proton and the deuterium stretching vibration bands, ν O–H and ν O–D , respectively. The basic spectral properties of the hydrogen bond IR spectra of formic acid crystals were interpreted in a quantitative way in terms of the “strong-coupling” theory. On the basis of this theoretical model, we succeeded in explaining the fine structure patterns of the ν O–H and ν O–D polarized sub-bands, the temperature, the dichroic, and the H/D isotopic effects in the spectra. The spectra were interpreted as a result of vibrational exciton interactions involving two adjacent hydrogen bonds in one chain of the associated molecules. The hydrogen bonds from one unit cell belonging to different chains were found uncoupled. In the spectra of isotopically diluted crystalline samples of HCOOH and DCOOH we found no characteristic changes in the “residual” ν O–H band shapes, which could be attributed to a random distribution of protons and deuterons in open chains of the hydrogen bonded molecules. This fact proves the existence of strong dynamical co-operative interactions in the hydrogen bond chain system in the formic acid crystal lattices responsible for a non-random distribution of protons and deuterons in the chains.
- Published
- 2006
44. Study of polarized IR spectra of the hydrogen bond system in crystals of styrylacetic acid
- Author
-
Peter G. Jones, Magdalena Jabłońska, and Henryk T. Flakus
- Subjects
Models, Molecular ,Chemical Phenomena ,Spectrophotometry, Infrared ,Hydrogen ,Dimer ,Infrared spectroscopy ,chemistry.chemical_element ,Crystal structure ,Crystallography, X-Ray ,Spectrum Analysis, Raman ,Photochemistry ,Vibration ,Analytical Chemistry ,Fatty Acids, Monounsaturated ,chemistry.chemical_compound ,Molecule ,Methylene ,Instrumentation ,Spectroscopy ,Molecular Structure ,Chemistry, Physical ,Hydrogen bond ,Temperature ,Hydrogen Bonding ,Atomic and Molecular Physics, and Optics ,Crystallography ,Deuterium ,chemistry ,Crystallization - Abstract
We have investigated the polarized IR spectra of the hydrogen bond system in crystals of trans-styrylacetic acid C(6)H(5)CHCHCH(2)COOH, and also in crystals of the following three deuterium isotopomers of the compound: C(6)H(5)CHCHCH(2)COOD, C(6)H(5)CHCHCD(2)COOH and C(6)H(5)CHCHCD(2)COOD. The spectra were measured at room temperature and at 77K by a transmission method. The spectral studies were preceded by determination of the X-ray crystal structure. Theoretical analysis of the results concerned linear dichroic effects, the H/D isotopic and temperature effects, observed in the solid-state IR spectra of the hydrogen and of the deuterium bond, at the frequency ranges of the nu(OH) and the nu(OD) bands, respectively. Basic spectral properties of the crystals can be interpreted satisfactorily in terms of the "strong-coupling" theory, when based on a hydrogen bond dimer model. This model sufficiently explained not only a two-branch structure of the nu(OH) and the nu(OD) bands, and temperature-induced evolution of the crystalline spectra, but also the linear dichroic effects observed in the band frequency ranges. A vibronic mechanism was analyzed, responsible for promotion of the symmetry-forbidden transition in the IR for the totally symmetric proton stretching vibrations in centrosymmetric hydrogen bond dimers. It was found to be of minor importance, when compared with analogous spectral properties of arylcarboxylic acid, or of cinnamic acid crystals. These effects were ascribed to a substantial weakening of electronic couplings between the hydrogen bonds of the associated carboxyl groups and the styryl radicals, associated with the separation of these groups in styrylacetic acid molecules by methylene groups in the molecules.
- Published
- 2006
45. H/D isotopic 'self-organization' effects in the infrared spectra of cyclic tetramers of hydrogen bonds: Polarized spectra of 7-azaindole crystals
- Author
-
Aleksandra Pyzik and Henryk T. Flakus
- Subjects
Hydrogen ,Chemistry ,Hydrogen bond ,Analytical chemistry ,Infrared spectroscopy ,chemistry.chemical_element ,Electronic structure ,Spectral line ,Crystal ,Crystallography ,Deuterium ,Molecule ,Physics::Atomic Physics ,Spectroscopy - Abstract
This paper presents the results of our investigation of the polarized IR spectra of the hydrogen bond in the 7-azaindole crystals. These spectra were measured at room temperature and at 77 K by a transmission method, using polarized light. Theoretical analysis of the results concerned linear dichroic effects, and the H/D isotopic and temperature effects, observed in the solid-state IR spectra of the hydrogen and of the deuterium bond, at the frequency ranges of the ν N–H and the ν N–D bands, respectively. Basic spectral properties of the crystals can be interpreted satisfactorily in a quantitative way in terms of the “ strong-coupling ” theory. This model sufficiently explains a two-branch structure of the ν N–H and the ν N–D bands in the crystalline spectra, but also some of the isotopic dilution effects, observed in the band frequency ranges, in the spectra of 7-azaindole crystals. Within the scope of our studies, the mechanism of the H/D isotopic “ self-organization ” processes in the crystal hydrogen bonds was also recognized. When working with spectra of isotopically diluted crystalline samples of 7-azaindole, it was proved that a non-random distribution of the protons and deuterons occurs in the cyclic tetramers of hydrogen-bonded molecules. In isotopically diluted crystalline samples, in one four-membered hydrogen bond ring of associated 7-azaindole, only four identical hydrogen isotope atoms can stable exist. The electronic structure of these compounds was considered as responsible for relatively strong dynamical inter-hydrogen bond co-operative interactions, which was the reason of appearance of the H/D isotopic “ self-organization ” effects in the hydrogen bond IR spectra.
- Published
- 2006
46. Vibronic model for H/D isotopic 'self-organization' effects in hydrogen bond cyclic trimeric systems: 4-Bromopyrazole crystal IR spectra
- Author
-
Aleksandra Pyzik and Henryk T. Flakus
- Subjects
Proton ,Hydrogen ,Chemistry ,Hydrogen bond ,General Physics and Astronomy ,Infrared spectroscopy ,chemistry.chemical_element ,Trimer ,Ring (chemistry) ,Crystal ,Crystallography ,Deuterium ,Computational chemistry ,Physics::Atomic and Molecular Clusters ,Physics::Atomic Physics ,Physical and Theoretical Chemistry - Abstract
In this paper, a theoretical model has been proposed, aiming to explain a new kind of H/D isotopic effects concerning hydrogen bond systems, i.e. the H/D isotopic “self-organization” effects, recently deduced from the IR spectra of molecular crystals. The problem of existence of these kinds of co-operative effects was considered in the limits of a vibronic model in the Herzberg–Teller approximation, for cyclic trimeric systems of hydrogen bonds. It was shown that non-conventional attraction forces between three identical hydrogen isotope atoms, resulting from the vibronic mechanism, are responsible for excess stabilization energy of cyclic hydrogen bond trimers. The H/D “self-organization” effects were deduced to be negligible in the case of non-symmetric HDD, or HHD-type trimers, containing both, hydrogen and deuterium bonds in one ring trimer. The symmetric trimers of the HHH and of the DDD-type should be more stable, when compared with the HDD, or the HHD-type trimer properties. This thermodynamic effect explains the IR spectral properties of molecular crystals containing cyclic trimers of hydrogen bonds in their lattices, accompanying to isotopic dilution. The results of the theoretical considerations were confronted with the IR spectra of 4-bromopyrazole crystals, which were measured in a wide temperature range (from 298 to 77 K), using polarized light, in the frequency ranges of the proton or deuterium stretching vibrations bands.
- Published
- 2006
47. Theoretical interpretation of the infrared lineshape of liquid and gaseous acetic acid
- Author
-
Mohamed El-Amine Benmalti, Olivier Henri-Rousseau, Paul Blaise, and Henryk T. Flakus
- Subjects
Coupling ,Infrared ,Hydrogen bond ,Chemistry ,Computational chemistry ,Phase (matter) ,Excited state ,Anharmonicity ,General Physics and Astronomy ,Infrared spectroscopy ,Physical and Theoretical Chemistry ,Atomic physics ,Quantum - Abstract
We have applied a model used recently [P. Blaise, M.J. Wojcik, O. Henri-Rousseau, J. Chem. Phys. 122 (2005) 64306] to unpolarized ν X–H infrared lineshapes of cyclic (CH 3 COOH) 2 in liquid and gaseous phases and (CD 3 COOH) 2 in gaseous phase and taking into account the IR A g forbidden transition. This model incorporates (i) the anharmonic coupling between the high frequency mode and the H-bond bridge, (ii) the Davydov coupling between the excited states of the two moieties, (iii) the quantum direct and indirect dampings. The approach reproduces satisfactorily the main features of the experimental lineshapes by using a minimum number of independant parameters.
- Published
- 2006
48. Strong coupling effects in the polarized IR spectra of the chain hydrogen bond systems in 3-pyridinealdoxime and 4-pyridinealdoxime crystals: H/D isotopic self-organization effects in the IR spectra
- Author
-
Anna Michta and Henryk T. Flakus
- Subjects
Hydrogen ,Chemistry ,Hydrogen bond ,Dimer ,Organic Chemistry ,Analytical chemistry ,Infrared spectroscopy ,chemistry.chemical_element ,Electronic structure ,Spectral line ,Analytical Chemistry ,Inorganic Chemistry ,Crystallography ,chemistry.chemical_compound ,Deuterium ,Molecule ,Physics::Atomic Physics ,Spectroscopy - Abstract
This paper presents the results of our investigation with the polarized IR spectra of the hydrogen bond in the 3-pyridinealdoxime and 4-pyridnealdoxime crystals, and also in the crystals of the deuterium derivatives of these two compounds. In each case these spectra were measured for the two different crystalline faces at room temperature and at 77 K by a transmission method, using the polarized light. Theoretical analysis of the results concerned linear dichroic effects, and the H/D isotopic and temperature effects, observed in the solid-state IR spectra of the hydrogen and the deuterium bond, at the frequency ranges of the ν O–H and the ν O–D bands. Basic spectral properties of the crystals can be interpreted in a satisfactory quantitative way for a hydrogen bond linear dimer model in terms of the ‘ strong-coupling ’ theory. This model explains not only a two-branch structure of the ν O–H and the ν O–D bands in the crystalline spectra, but also some essential linear dichroic effects in the band frequency ranges, for isotopically diluted crystals. Within the scope of our studies, the mechanism of the H/D isotopic self-organization processes (which take place in the crystalline hydrogen bond lattices) was also recognized. It was proved that for isotopically diluted crystalline samples of 3-pyridinealdoxime and 4-pyridnealdoxime, a non-random distribution of the protons and deuterons occurs exclusively in some restricted fragments (i.e. domains) of open chains of the hydrogen bonded molecules. Nevertheless, these co-operative interactions between the hydrogen bonds do not concern the adjacent fragments of the neighboring hydrogen bond chains in the lattice. The electronic structure of these compounds was considered as responsible for such co-operative effects of the hydrogen bonds.
- Published
- 2005
49. Strong coupling effects in the polarized IR spectra of the chain hydrogen bond systems in imidazole crystals: H/D isotopic ‘self-organization’ effects in the IR spectra of isotopically diluted imidazole single crystals
- Author
-
Anna Michta and Henryk T. Flakus
- Subjects
Hydrogen ,Stereochemistry ,Hydrogen bond ,Organic Chemistry ,chemistry.chemical_element ,Infrared spectroscopy ,Spectral line ,Analytical Chemistry ,Inorganic Chemistry ,Crystal ,Crystallography ,chemistry.chemical_compound ,chemistry ,Deuterium ,Imidazole ,Molecule ,Spectroscopy - Abstract
This paper presents the investigation results of the polarized IR spectra of H1245 imidazole crystals and of D1H245, D1245 and H1D245 imidazole deuterium derivative crystals. The spectra were measured using polarized light at the room temperature and at 77 K by a transmission method, for two different crystalline faces. Theoretical analysis of the results concerned linear dichroic effects, H/D isotopic and temperature effects, observed in the spectra of the hydrogen and of the deuterium bonds in imidazole crystals, at the frequency ranges of ν N–H and ν N–D bands. The basic crystal spectral properties can be satisfactorily interpreted in a quantitative way for a hydrogen bond linear dimer model. Such a model explains not only a two-branch structure of the ν N–H and ν N–D bands in crystalline spectra, but also some essential linear dichroic effects in the band frequency ranges, for isotopically diluted crystals. Model calculations, performed within the limits of the strong-coupling model, allowed for quantitative interpretation and for understanding of the basic properties of the hydrogen bond IR spectra of imidazole crystals, H/D isotopic, temperature and dichroic effects included. The results allowed verification of theoretical models proposed recently for the imidazole crystal spectra generation mechanisms. In the scope of our studies, the mechanism of H/D isotopic self-organization processes, taking place in the crystal hydrogen bond lattices, was also recognized. It was proved that for isotopically diluted crystalline samples of imidazole, a non-random distribution of protons and deuterons exclusively occurs in some restricted fragments (domains) of open chains of the hydrogen-bonded molecules. Nevertheless, these co-operative interactions between the hydrogen bonds do not concern adjacent fragments of neighboring hydrogen bond chains in the lattice. Analysis of the isotopic self-organization effects in the spectra of imidazole crystals delivered crucial arguments for understanding of the nature of the hydrogen bond spectra generation mechanisms.
- Published
- 2004
50. Study of hydrogen bond polarized IR spectra of cinnamic acid crystals
- Author
-
Magdalena Jabłońska-Czapla, Henryk Flakus, and Magdalena Jabłońska
- Subjects
Hydrogen ,Hydrogen bond ,Dimer ,Organic Chemistry ,Infrared spectroscopy ,chemistry.chemical_element ,Photochemistry ,Spectral line ,Analytical Chemistry ,Inorganic Chemistry ,Crystal ,chemistry.chemical_compound ,Crystallography ,chemistry ,Deuterium ,Ab initio quantum chemistry methods ,Spectroscopy - Abstract
This paper presents the results of investigation of the polarized IR spectra of cinnamic acid and of its deuterium derivative crystals. The spectra were measured by a transmission method, using polarized light, at the room temperature and at 77 K, for two different crystalline faces. Theoretical analysis of the results concerned linear dichroic effects, H/D isotopic and temperature effects, observed in the spectra of the hydrogen and of the deuterium bonds in cinnamic acid crystals, at the frequency ranges of the ν O–H and the ν O–D bands. The basic crystal spectral properties could be satisfactorily interpreted in a quantitative way for a centrosymmetric cyclic hydrogen bond dimer model. Such a model explains not only a two-branch structure of the ν O–H and ν O–D bands in crystalline spectra, but also some essential linear dichroic effects in the band frequency ranges, measured for isotopically diluted crystals. Model calculations, performed within the limits of the ‘strong-coupling’ model, allowed for quantitative interpretation and for understanding of the basic properties of the hydrogen bond IR spectra of cinnamic acid crystals, H/D isotopic, temperature and dichroic effects included. In the scope of our studies the mechanism of H/D isotopic ‘self-organization’ processes, taking place in the crystal hydrogen bond lattices, was also recognized. It was proved that for isotopically diluted crystalline samples of cinnamic acid, a non-random distribution of protons and deuterons occurs exclusively in the hydrogen bond dimers. Nevertheless, these co-operative interactions between the hydrogen bonds do not involve the adjacent hydrogen bond dimers in each unit cell. The two-branch fine structure pattern of the ν O–H and ν O–D bands was ascribed to the vibronic mechanism of vibrational dipole selection rule breaking in centrosymmetric hydrogen bond dimers. The observed in the spectra very high intensity of the forbidden transition sub-band in the analyzed ν O–H and ν O–D bands is a manifestation of an extremely effective symmetry rule breaking mechanism. It correlates with a relatively large excess electron charge on the cinnamic aid dimer carboxyl groups. This effect is a result of a partial withdrawal of the electron charge, from the conjugated π-bond systems of the styryl substituents, by the carboxyl groups. This statement has been supported by ab initio calculations.
- Published
- 2004
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