Electrostatic DFT map for the complete vibrational amide band of NMA.

نویسندگان

  • Tomoyuki Hayashi
  • Wei Zhuang
  • Shaul Mukamel
چکیده

An anharmonic vibrational Hamiltonian for the amide I, II, III, and A modes of N-methyl acetamide (NMA), recast in terms of the 19 components of an external electric field and its first and second derivative tensors (electrostatic DFT map), is calculated at the DFT(BPW91/6-31G(d,p)) level. Strong correlations are found between NMA geometry and the amide frequency fluctuations calculated using this Hamiltonian together with the fluctuating solvent electric field obtained from the MD simulations in TIP3 water. The amide I and A frequencies are strongly positively correlated with the C=O and N-H bond lengths. The C=O and C-N amide bond lengths are negatively correlated, suggesting the solvent-induced fluctuations of the contribution of zwitterionic resonance form. Sampling the global electric field in the entire region of the transition charge densities (TCDs) is required for accurate infrared line shape simulations. Collective electrostatic solvent coordinates which represent the fluctuations of the 10 lowest amide fundamental and overtone states are reported. Normal-mode analysis of an NMA-3H(2)O cluster shows that the 660 cm(-1) to 1100 cm(-1) oscillation found in the frequency autocorrelation functions of the amide modes may be ascribed to the two bending vibrations of intermolecular hydrogen bonds with the amide oxygen of NMA.

منابع مشابه

The Effect of Aluminum, Gallium, Indium- Doping on the Zigzag (5, 0) Boron-Nitride Nanotubes: DFT, NMR, Vibrational, Thermodynamic Parameters and Electrostatic Potential Map with Electrophilicity Studies

Influence of Aluminum, Gallium, Indium- Doping on the Boron-Nitride Nanotubes (BNNTs) investigated with density functional theory (DFT) and Hartreefock (HF) methods. For this purpose, the chemical shift of difference atomic nucleus was studied using the gauge included atomic orbital (GIAO) approch. In the following, structural parameter values, electrostatic potential, thermodynamic parameters,...

متن کامل

Simulation protocols for coherent femtosecond vibrational spectra of peptides.

Two algorithms for simulating the response of peptides to sequences of IR pulses are developed and applied to N-methyl acetamide (NMA) and a 17 residue alpha-helical peptide (YKKKH17) in D(2)O. A fluctuating vibrational-exciton Hamiltonian for the amide I mode is constructed from molecular dynamics trajectories. Coupling with the environment is described using a density functional theory electr...

متن کامل

Two-Dimensional Vibrational Lineshapes of Amide III, II, I and A Bands in a Helical Peptide.

An effective exciton Hamiltonian for all amide bands is used to calculate the linear absorption and photon echo spectra of a 17 residue helical peptide (YKKKH17). The cross peak bandshapes are sensitive to the inter-band couplings. Fluctuations of the local amide frequencies of the all amide fundamental and their overtone and combination states are calculated using the multipole electric field ...

متن کامل

Dependence of amide vibrations on hydrogen bonding.

The effect of hydrogen bonding on the amide group vibrational spectra has traditionally been rationalized by invoking a resonance model where hydrogen bonding impacts the amide functional group by stabilizing its [(-)O-C=NH (+)] structure over the [O=C-NH] structure. However, Triggs and Valentini's UV-Raman study of solvation and hydrogen bonding effects on epsilon-caprolactum, N, N-dimethylace...

متن کامل

Modeling the amide I bands of small peptides.

In this paper different floating oscillator models for describing the amide I band of peptides and proteins are compared with density functional theory (DFT) calculations. Models for the variation of the frequency shifts of the oscillators and the nearest-neighbor coupling between them with respect to conformation are constructed from DFT normal mode calculations on N-acetyl-glycine-N(')-methyl...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

متن کامل
عنوان ژورنال:
  • The journal of physical chemistry. A

دوره 109 43  شماره 

صفحات  -

تاریخ انتشار 2005