Calculation and analysis of the structure and vibrational spectra of uracil tautomers

Ten, G. N.; Нечаев, В. В.; Shcherbakov, R. S.; Баранов, В. И.

doi:10.1007/s10947-010-0005-3

Cited by 5 publications

(4 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…35,36 Numerous studies were devoted to the calculation of normal modes of uracil using purely empirical or semiempirical QM harmonic force fields 4,8,12,31 and scaled ab initio harmonic force fields (SQMFF). 9,15,21,22,[29][30][31]35,36,[38][39][40][41]47,51,53,56 Bandekar and Zundel 14 undertook a normal coordinate analysis on a unit cell of uracil. The problem of interpretation of spectra in the light of multiple Fermi resonances was first discussed in ref 24 and subsequently in refs 33, 52, and 54.…”

Section: Introductionmentioning

confidence: 99%

“…Due to high biological importance as one of the four RNA nucleobases, uracil (Figure ) has been extensively studied by various physical-chemical, nondestructive spectroscopic techniques for more than 50 years. − Because of its very low vapor pressure (75 mTorr at 210 °C), vibrational spectra and other molecular properties of uracil were mostly studied in various condensed states. Data for isolated molecules are relatively rare.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Section: Introductionmentioning

confidence: 99%

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

show abstract

“… We then turn to compare the Raman enhancement between P-GERTs and GERRTs. It is surprising to note that SERS signals of 4-NBT are completely overwhelmed by the SERS signals of fluorescent reporters at 536, 622, and 687 cm –1 (corresponding to N–H nonplanar vibration, CCN in-plane bending, and Si–O–Si symmetric stretching vibration) for GERRTs-775 and ones at 525, 559, and 1206 cm –1 (corresponding to phenyl out-of-plane substituent-sensitive vibration, phenyl in-plane deformation, and C–H in-plane deformation) for GERRTs-780, respectively. This can be explained by the fact that the Ag shell dramatically weakens the excitation efficiency and scattered photons of embedded 4-NBT but promotes the extraordinary SERRS effect of fluorescent reporters. , This can be further demonstrated by the result that GERRTs-780 show an increase in the Raman intensity of more than 2 orders of magnitude compared to that without Ag coating (see Figure S4).…”

Section: Resultsmentioning

confidence: 99%

Ag-Coated Au Nanopetals: Dual-Type Single-Nanoparticle Detection of Gap-Enhanced Resonance Raman Tags

2020

ACS Appl. Nano Mater.

View full text Add to dashboard Cite

Single-molecule (SM) detection in surface-enhanced Raman spectroscopy (SERS) demonstrates ultrahigh sensitivity and boosts wide applications. The bianalyte SERS (BiASERS) technique largely improves the accuracy and reliability of SM SERS detection over the monoanalyte approach by avoiding the use of ultralow-concentration samples and induced inaccuracy and very limited events. Herein, dual-type single-nanoparticle (SNP) SERS detection, an adapted version of the bianalyte SM technique, was developed for the first time with two types of ultrabright gap-enhanced resonance Raman tags (GERRTs) with embedded near-infrared resonant fluorescent molecules, showing concentration-and acquisition timedependent behaviors and the SNP sensitivity in both aqueous and dry states. Additionally, a correlative Raman imaging and scanning electron (RISE) microscopy confirms the SNP events of GERRTs on the substrate. Therefore, we expand the feasible application scenarios of the BiASERS technique from merely SM to SNP detection and more importantly demonstrate the effectiveness of the pure statistical model of BiASERS with the undoubted experimental examinations. Dual-type SNP detection of GERRTs may open new opportunities for development of ultrasensitive nanotags for reliable localized and quantitative detection in biological environments.

show abstract

“…The lower limit of this range corresponds to the van der Waals energies for intermolecular interactions of amino acids in proteins, and the upper one to the energy of covalent bond between CNTs and oxygen amino acid residues of an albumin. 31…”

Section: Interaction Of Carbon Nanotube Framework With Albuminmentioning

confidence: 99%

Laser structuring of carbon nanotubes in the albumin matrix for the creation of composite biostructures

et al. 2017

View full text Add to dashboard Cite

This paper presents the composite biostructures created by laser structuring of the single-walled carbon nanotubes (SWCNTs) in an albumin matrix. Under the exposure of femtosecond laser radiation, the heating of the albumin aqueous solution causes liquid water to evaporate. As a result, we obtained a solid-state composite in the bulk or film form. Using the molecular dynamic method, we showed the formation of a framework from SWCNTs by the example of splicing of the open end of one nanotube with the defect region of another nanotube under the action of the laser heating. Laser heating of SWCNTs up to a temperature of 80°C to 100°C causes the C ? C bond formation. Raman spectra measured for the composite biostructures allowed us to describe the binding of oxygen atoms of amino acid residues of the albumin with the carbon atoms of the SWCNTs. It is found that the interaction energy of the nanotube atoms and albumin atoms amounts up to 580 ?? kJ / mol . We used atomic force microscopy to investigate the surface of the composite biostructures. The pore size is in the range of 30 to 120 nm. It is proved that the proliferation of the fibroblasts occurred on the surface of the composite biostructures during 72 h of incubation.

show abstract

Calculation and analysis of the structure and vibrational spectra of uracil tautomers

Cited by 5 publications

References 9 publications

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

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

Ag-Coated Au Nanopetals: Dual-Type Single-Nanoparticle Detection of Gap-Enhanced Resonance Raman Tags

Laser structuring of carbon nanotubes in the albumin matrix for the creation of composite biostructures

Contact Info

Product

Resources

About