Interpretation of vibrational IR spectrum of uracil using anharmonic calculation of frequencies and intensities in second-order perturbation theory

Ten, G. N.; Нечаев, В. В.; Krasnoshchekov, S. V.

doi:10.1134/s0030400x10010078

Cited by 11 publications

(27 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In Figure , the fully anharmonic IR spectra of the phenalenyl cation and anion, computed at the B3LYP/6–31 + G(d,p) level, are shown. For this level of theory, from the literature on this topic based on the comparison with experiment and state‐of‐the‐art calculations (see Refs ), a mean absolute error of 10–12 cm −1 and maximum discrepancies of 30 cm −1 are expected, which provide a reasonable guidance for astronomical detections, with possible improvements through hybrid schemes as discussed above. However, the phenalenyl cation and anion represent a complex case for VPT2 calculations.…”

Section: Challenges In Computational Chemistry Of Astrocomsmentioning

confidence: 98%

Computational challenges in Astrochemistry

Biczysko

Bloino

Puzzarini

2017

WIREs Comput Mol Sci

View full text Add to dashboard Cite

Cosmic evolution is the tale of progressive transition from simplicity to complexity. The newborn universe starts with the simplest atoms formed after the Big Bang and proceeds toward ‘astronomical complex organic molecules’ (astroCOMs). Understanding the chemical evolution of the universe is one of the main aims of Astrochemistry, with the starting point being the knowledge whether a molecule is present in the astronomical environment under consideration and, if so, its abundance. However, the interpretation of astronomical detections and the identification of molecules are not all straightforward. In particular, molecular species characterized by large amplitude motions represent a major challenge for molecular spectroscopy and, in particular, for computational spectroscopy. More in general, for flexible systems, the conformational equilibrium needs to be taken into account and accurately investigated. It is shown that crucial challenges in the computational spectroscopy of astroCOMs can be successfully overcome by combining state‐of‐the‐art quantum‐mechanical approaches with ad hoc treatments of the nuclear motion, thus demonstrating that the rotational and vibrational features can be predicted with the proper accuracy. The second key step in Astrochemistry is understanding how astroCOMs are formed and how they chemically evolve toward more complex species. The challenges in the computational chemistry of astroCOMs are related to the derivation of feasible formation routes in the typically harsh conditions (extremely low temperature and density) of the interstellar medium, as well as the understanding of the chemical evolution of small species toward macromolecules. Within the transition state theory, for instance, it is possible to obtain new astrochemical information by identifying the intermediate species and transition states connecting them in a plausible formation route. Depending on the sophistication of the model, different quantities may be needed. Nevertheless, accuracy can be critical, thus requiring state‐of‐the‐art computational approaches to derive geometries, energies, spectroscopic properties, and thermochemical data for each relevant structure along the reaction path. This article is categorized under: Theoretical and Physical Chemistry > Spectroscopy Electronic Structure Theory > Ab Initio Electronic Structure Methods Electronic Structure Theory > Density Functional Theory

show abstract

Section: Challenges In Computational Chemistry Of Astrocomsmentioning

confidence: 98%

Computational challenges in Astrochemistry

Biczysko

Bloino

Puzzarini

2017

WIREs Comput Mol Sci

View full text Add to dashboard Cite

show abstract

“…44,45,48,52,54,55,59 The most advanced analysis of vibrational spectra was carried out by Puzzarini et al 54 by comparison of experimental frequencies with the theoretical counterparts computed with the use of the best estimated CCSD(T)-based harmonic force field (see the section "The Method of Calculation" below for details) in combination with the B3LYP (in conjunction with the aug-N07D and aug-cc-pVTZ basis sets) anharmonic force constants (hybrid model). 54 Although abundant literature on modeling and interpretation of spectral features of uracil exists, none of the recent anharmonic theoretical studies 44,45,48,52,54,59 simultaneously analyzed available experimental IR and RS data, employed high-level theoretical methods [MP2 and CCSD(T)], used predicted IR and RS intensities for spectral interpretations, theoretically analyzed FR splittings and vibrational polyads, and employed systematic criteria for vibrational resonances. As recently noted by Katsyuba et al, 57 "there are still significant doubts on the interpretation of the IR spectrum of isolated uracil, the main problem being the large number of overtones and combination bands having intensities comparable to those of some fundamentals".…”

Section: Introductionmentioning

confidence: 99%

“…As it is very wellknown from the literature, Fermi (as well as Darling− Dennison) resonances play a major role in certain regions of uracil spectra. 24,33,52,54 An efficient theoretical approach, suited to most of the targets outlined above, is based on a solution of the vibrational Schrodinger equation using perturbation theory. Because the "zero-order" harmonic problem (Wilson GF-method 73 ) is amenable to an analytic solution, it is very convenient to consider a solution of a vibrational problem with a harmonic potential amended by cubic and quartic anharmonic terms as a perturbation of the zero-order problem.…”

Section: Introductionmentioning

confidence: 99%

Ab Initio Anharmonic Analysis of Vibrational Spectra of Uracil Using the Numerical-Analytic Implementation of Operator Van Vleck Perturbation Theory

2015

View full text Add to dashboard Cite

The numerical-analytic implementation of the operator version of the canonical Van Vleck second-order vibrational perturbation theory (CVPT2) is employed for a purely ab initio prediction and interpretation of the infrared (IR) and Raman anharmonic spectra of a medium-size molecule of the diketo tautomer of uracil (2,4(1H,3H)-pyrimidinedione), which has high biological importance as one of the four RNA nucleobases. A nonempirical, semidiagonal quartic potential energy surface (PES) expressed in normal coordinates was evaluated at the MP2/cc-pVTZ level of theory. The quality of the PES was improved by replacing the harmonic frequencies with the "best" estimated CCSD(T)-based values taken from the literature. The theoretical method is enhanced by an accurate treatment of multiple Fermi and Darling-Dennison resonances with evaluation of the corresponding resonance constants W and K (CVPT2+WK method). A prediction of the anharmonic frequencies as well as IR and Raman intensities was used for a detailed interpretation of the experimental spectra of uracil. Very good agreement between predicted and observed vibrational frequencies has been achieved (RMSD ∼4.5 cm(-1)). The model employed gave a theoretically robust treatment of the multiple resonances in the 1680-1790 cm(-1) region. Our new analysis gives the most reliable reassignments of IR and Raman spectra of uracil available to date.

show abstract

“…There are slight modifications detected in region of the -OH group stretching for the αCD/5FU, αCD/U, HPαCD/5FU and HP αCD/U systems. However, the band around 3300 cm -1 is shifted and broadened much more in case of HPβCD/5FU, HPβCD/U, βCD/U and βCD/5FU systems which for the encapsulation of the ligand is accomplished by involving a large number of hydrogen bonds [21].…”

Section: Resultsmentioning

confidence: 97%

“…In 5FU spectrum, the bands at 3120 cm -1 , 3064 cm -1 , 2929 cm -1 and 2826 Table 1 WEIGHT PERCENT (%) OF THE COMPLEXES RESULTED FROM DEHYDRATION AND GUEST LOSS PROCESSES cm -1 show both aromatic and aliphatic C-H stretching vibrations, a band at 1719 cm -1 is attributed to the imide group stretching of heterocyclic ring, the band at 1644 cm -1 is due to the -C=C-group stretching vibration, at 1428 cm -1 the band is due to N-H bending vibration, a band at 1243 cm -1 shows ring stretching vibrations and C-F stretching vibration was observed at 1222 cm -1 and 803 cm -1 respectively [18][19][20]. In the FTIR spectrum of U the principal absorption peaks are at 3088 cm -1 (N-H stretching band), 2985 cm -1 , 2933 cm -1 and 2821 cm -1 respectively, which could be due to both aromatic and aliphatic C-H stretching vibrations, 1712 cm -1 (C-N stretch vibrations), 1642 cm -1 (carbonyl stretching vibration), 1417 cm -1 (N-H in plane bending vibration), 1233 cm -1 and 821 cm -1 due to C-H stretching vibrations [21,22]. The pure CDs spectra show a characteristic large band with the absorption maximum at 3288 cm -1 for αCD, at 3314 cm -1 for βCD, 3302 cm -1 for HPαCD and 3330 cm -1 for HPβCD.…”

Section: Resultsmentioning

confidence: 99%

Characterization and Comparison of the Solid State Inclusion Compounds of alfa-, beta-Cyclodextrins and its 2-Hydroxypropyl Derivatives with Uracil and 5-fluorouracil

Neacsu¹,

Pincu²,

Munteanu³

et al. 2018

Rev. Chim.

View full text Add to dashboard Cite

The objective of the present work was to obtain and evaluate the solid inclusion complexes of a-, b-cyclodextrins and hydroxypropyl-a-, hydroxypropyl-b-cyclodextrins derivatives with uracil (U) and anti-cancer agent 5-fluorouracil (5FU). The thermogravimetry (TG), differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy in attenuated total reflectance mode (FTIR-ATR) and scanning electron microscopy (SEM) were used to characterize these inclusion compounds. New information on the physicochemical behavior of these solid state complexes synthesized by melting in solution was obtained. Corelating the experimental data we found that the complexation occurs for each host:guest system thus, the preparation method exhibited a real efficiency to interaction achievements. The inclusion capability and the thermal stability of the studied complexes were due to both the flexibility and the size of the cyclodextrin ring as well the stereoelectronic effect of the U or 5FU molecule. We appreciated that the complexes between U or 5FU with 2-hydroxypropyl derivatives of a- and b- CD have the largest content of guest and are the most stable. The obtained results could be useful in formulation of the pharmaceutical products and also in drug delivery.

show abstract

Interpretation of vibrational IR spectrum of uracil using anharmonic calculation of frequencies and intensities in second-order perturbation theory

Cited by 11 publications

References 19 publications

Computational challenges in Astrochemistry

Computational challenges in Astrochemistry

Ab Initio Anharmonic Analysis of Vibrational Spectra of Uracil Using the Numerical-Analytic Implementation of Operator Van Vleck Perturbation Theory

Characterization and Comparison of the Solid State Inclusion Compounds of alfa-, beta-Cyclodextrins and its 2-Hydroxypropyl Derivatives with Uracil and 5-fluorouracil

Contact Info

Product

Resources

About