Solvent Induced Shifts in the UV Spectrum of Amides

Abstract

Solvent effects on the electronic spectra of formamide and trans-N-methylacetamide are studied using four different levels of theory: singly excited configuration interaction (CIS), equations of motion coupled-cluster theory with singles and doubles (EOM-CCSD), completely renormalized coupled-cluster theory with singles and doubles with perturbative triple excitations (CR-EOM-CCSD(T)), and time-dependent density functional theory (TDDFT), employing small clusters of water molecules. The simulated electronic spectrum is obtained via molecular dynamics simulations with 100 waters modeled with the effective fragment potential method and exhibits a blue-shift and red-shift, respectively, for the n → π* and πnb → π* vertical excitation energies, in good agreement with the experimental electronic spectra of amides. Disciplines Chemistry CommentsReprinted (adapted) ABSTRACT: Solvent effects on the electronic spectra of formamide and trans-N-methylacetamide are studied using four different levels of theory: singly excited configuration interaction (CIS), equations of motion coupled-cluster theory with singles and doubles (EOM-CCSD), completely renormalized coupled-cluster theory with singles and doubles with perturbative triple excitations (CR-EOM-CCSD(T)), and time-dependent density functional theory (TDDFT), employing small clusters of water molecules. The simulated electronic spectrum is obtained via molecular dynamics simulations with 100 waters modeled with the effective fragment potential method and exhibits a blue-shift and red-shift, respectively, for the n → π* and π nb → π* vertical excitation energies, in good agreement with the experimental electronic spectra of amides.

Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework

“…Formamide represents the simplest model for the peptidic bond. The interest in the application of UV spectroscopy to the structural, dynamical, and electronic characterization of the peptidic linkage in proteins, has motivated a lot of experimental [27][28][29][30][31] and theoretical [32][33][34][35][36][37][38][39][40][41] research on the excitations and absorption of formamide, acetamide, and other related molecules. The UV spectrum of formamide is characterized by an intense band at 7.4 eV involving non-bonding and antibonding π orbitals (denoted π nb → π * ), 27,30 which experiences a red-shift of 0.5 eV in aqueous solution.…”

“…39 Very recently, Gordon et al have interpreted the observed solvatochromic shifts in terms of the solvent effect on the HOMO and LUMO energies. 41 In particular, they explored the finite temperature broadening of the spectral line shape both in vacuum and in solution, by performing molecular dynamics simulations with DFT and then computing the spectra at the TDDFT/PBE0 level for a set of configurations. The solvent environment was modelled in a QM-MM framework with the inclusion of 100 H 2 O molecules represented through the effective fragment potential EFP1.…”

“…The solvent environment was modelled in a QM-MM framework with the inclusion of 100 H 2 O molecules represented through the effective fragment potential EFP1. 41 Based on this approach, these authors reported absorption energies of 8.74 eV and 8.31 eV in the gas and in the aqueous phases, respectively.…”

A neural network protocol for electronic excitations of N -methylacetamide

“…The nπ* and ππ* excitations of NMA ( Fig. 1 A and B), regarded as a simplified model for the UV absorption of protein backbone, have been well studied by various electronic structure methods, including TDDFT and wavefunction-based electron correlation methods (16,17). Compared with expensive electron correlation methods such as coupled-cluster single and double excitation equation of motion approach (EOM-CCSD) and complete active space with second-order perturbation theory (CASPT2), TDDFT is able to obtain satisfactory electronic excitation energies of various types of molecules at a modest computation cost.…”

“…Compared with expensive electron correlation methods such as coupled-cluster single and double excitation equation of motion approach (EOM-CCSD) and complete active space with second-order perturbation theory (CASPT2), TDDFT is able to obtain satisfactory electronic excitation energies of various types of molecules at a modest computation cost. For NMA, Perdew-Burke-Ernzerhof hybrid functional (PBE0) functional has been employed in previous study by Gordon and coworkers (17). PBE0 has an error of about 0.3 eV in calculating transition energies of various molecules (18).…”