Force field in the methylamine molecule from ab initio MO calculation

Hamada, Yoshiaki; Tanaka, Naoki; Sugawara, Yoko; Hirakawa, Akiko Y.; Tsuboi, Masamichi; Kato, Shigekí; Morokuma, Keiji

doi:10.1016/0022-2852(82)90195-3

Cited by 68 publications

(23 citation statements)

References 18 publications

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“…The anharmonic vibrational frequencies of methylamine were calculated by combining ab initio harmonic frequencies with anharmonic DFT corrections as well as DFT large basis harmonic frequencies with DFT small basis anharmonic corrections. In both cases we obtained very good agreement with experimental results 12,15,17,22 at a relatively low computational cost. In addition, the power of these calculations for assignment and analysis of the dominant resonances in the methylamine isotopologues is demonstrated.…”

Section: Introductionsupporting

confidence: 82%

“…The more rigorous way consists of substituting the higher-level computed vibrational frequencies in the secondorder vibrational perturbation theory analysis for the lower-level anharmonic force field. The frequencies obtained by the different methods and basis sets were compared with the experimental results available for each molecule, 12,15,17,22 and the root mean square (RMS) error was calculated.…”

Section: Methodsmentioning

confidence: 99%

“…Because of these features, the methylamine molecule attracted much interest and has been extensively studied experimentally [12][13][14][15] and theoretically. [16][17][18][19][20][21] On these grounds, we thought it will be interesting to assess the performance of ab initio and DFT harmonic calculations combined with anharmonic corrections. For the latter, convergence in terms of integration grid was investigated, pointing to the dependence of the calculated fundamental frequencies on the employed grid.…”

Section: Introductionmentioning

confidence: 99%

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Fundamental vibrational frequencies and dominant resonances in methylamine isotopologues by ab initio and density functional theory methods

2007

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Ab initio and density functional theory (DFT) calculations were performed for obtaining fundamental vibrational frequencies of methylamine, CH3NH2, and its deuterated variants CH3ND2, CD3NH2, and CD3ND2. The calculations were carried out using the CCSD(T) coupled cluster approximation with cc-pVTZ and cc-pVQZ basis sets, and by the DFT method with the semiempirical hybrid functional B97-1 with polarization consistent pc-2 and pc-3 basis sets. Reasonable performance of the DFT harmonic and ab initio harmonic calculations was found, which improved considerably upon combination of the harmonic fundamental frequencies with anharmonic corrections from the smaller, pc-2, basis. The computed anharmonic fundamental frequencies of methylamine isotopologues agree very well with the experimental values and represent a useful tool for assignment and analysis of the dominant resonances.

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Section: Introductionsupporting

confidence: 82%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Fundamental vibrational frequencies and dominant resonances in methylamine isotopologues by ab initio and density functional theory methods

2007

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“…This weak M intensity in the M/bR difference spectra provides a means of focusing on the bR alterations, since the bR peaks appear relatively unaffected by the M difference spectra absorption. (14)(15)(16), the FTIR study on bR labeled with deuterated lysine (7), and recent observations of RR spectra of chromophores with a '3CE-labeled lysine chain (17) occurring between 1300 and 1400 cm-' (Fig. 3).…”

Section: Resultsmentioning

confidence: 75%

Participation of bacteriorhodopsin active-site lysine backbone in vibrations associated with retinal photochemistry.

Gat

Grossjean

Pinevsky

et al. 1992

Proc. Natl. Acad. Sci. U.S.A.

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Bacteriorhodopsin (bR) has been biosynthetically prepared with lysine deuterated at its a carbon (Ca-H). The labeled membranes containing bR were investigated by difference Fourier transform infrared (FTIR) spectroscopy. It has been derived from K/bR and M/bR difference spectra (K and M are photocycle intermediates) that several bands previously assigned to the retinal chromophore are coupled to the Ca-H. The vibrational modes that exhibit this coupling are principally associated with C15-H and N-H vibrations. [Ca-2H]Lysine-labeled bR was fragmented enzymatically, and bR structures were regenerated with the Ca-2H label either on lysine-216 and -172 or on the remaining five lysine residues of the protein. FTIR studies of the regenerated bR system, together with methylation of all lysines except the active-site lysine, reveal that the changes observed due to backbone labeling arise from the active-site lysine. The intensity of the C15-H out-of-plane wag is interpreted as a possible indication of a twist around the C15=N bond.Bacteriorhodopsin (bR), a 26-kDa pigment, acts as a lightdriven proton pump in the cell membrane of Halobacterium halobium (1). bR is composed of a chromophore (retinal) covalently linked to an amino acid polypeptide chain through the e-amino group of a lysine residue. The configuration of the chromophore of bR5a (light-adapted, proton-pumping active form) is an all-trans-retinal, and the linkage is through a protonated Schiff base (RSBH+) (2) (Fig. 1). Time-resolved absorption spectra on the light-adapted form reveals a photocycle that is kinetically coupled to proton transport (3,4). In this photocycle, spectroscopically distinct intermediates appear, which are designated J625, K630, L550, M412, N520, and Ow. Resonance Raman (RR) and Fourier transform infrared (FTIR) spectroscopy have been shown to be powerful tools for obtaining structural information on the light-induced structural alterations of the active-site retinal and various amino acids (5, 6). In all of these investigations, the possibility of structural alterations in the active-site lysine has not been addressed. McMaster and Lewis (7) have focused on the problem of lysine, and they showed that numerous bands in the previously investigated FTIR difference spectra associated with light absorption by the chromophore involved lysine. In this paper, we extend these measurements to include contributions to the FTIR spectra of the backbone of lysine. We prove that these contributions arise from the lysine that is complexed to the retinal chromophore, and we show that active-site lysine backbone vibrations are strongly coupled to modes that have been assigned previously to retinal. Furthermore, we observe that the nature of the coupling to the backbone is altered in going from bR to K.MATERIALS AND METHODS Lysine deuterated at the a carbon (Ca-H) was synthesized in a similar fashion to the method of Johns and Whelan (8). Incorporation into bR was carried out by growing halobacteria on a defined medium in which lysine was repl...

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“…The IR spectrum of methylamine at Ͼ2800 cm −1 is dominated by very strong C-H stretches at 2820 and 2961 cm −1 , along with another strong C-H stretching band at 2985 cm −1 . 13,14 By comparison, the symmetric and antisymmetric N-H stretching bands at 3361 and 3427 cm −1 are more than an order of magnitude weaker. We assign the band seen in Fig.…”

Section: Li"nh 2 Ch 3 …mentioning

confidence: 98%

Coordination structures of lithium-methylamine clusters from infrared spectroscopy and ab initio calculations

Salter

Ellis

2007

The Journal of Chemical Physics

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Spectra of clusters formed between lithium atoms and methylamine molecules are reported for the first time. Mass-selective infrared spectra of Li͑NH 2 CH 3 ͒ n have been recorded in both the N-H and C-H stretching fundamental regions. The infrared spectra are broadly in agreement with ab initio predictions, showing redshifted N-H stretching bands relative to free methylamine and a strong enhancement of the N-H stretching fundamentals relative to the C-H stretching fundamentals. The ab initio calculations suggest that, for n = 3, the methylamine molecules bunch together on one side of the lithium atom to minimize repulsive interactions with the unpaired electron density. The addition of a fourth methylamine molecule results in closure of the inner solvation shell and, thus, Li͑NH 2 CH 3 ͒ 5 is forced to adopt a two-shell coordination structure. This is consistent with neutron diffraction studies of concentrated lithium/methylamine solutions, which also suggest that the first solvation shell around the lithium atom can contain a maximum of four methylamine molecules.

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Force field in the methylamine molecule from ab initio MO calculation

Cited by 68 publications

References 18 publications

Fundamental vibrational frequencies and dominant resonances in methylamine isotopologues by ab initio and density functional theory methods

Fundamental vibrational frequencies and dominant resonances in methylamine isotopologues by ab initio and density functional theory methods

Participation of bacteriorhodopsin active-site lysine backbone in vibrations associated with retinal photochemistry.

Coordination structures of lithium-methylamine clusters from infrared spectroscopy and ab initio calculations

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