Łukasz Boda

Theoretical model for a tetrad of hydrogen bonds and its application to interpretation of infrared spectra of salicylic acid

Theoretical model of vibrational interactions in hydrogen-bonded salicylic acid dimer is presented which takes into account the adiabatic couplings between high- and low-frequency O-H and O...O stretching vibrations, resonance interactions between both intermolecular hydrogen bonds and between inter- and intramolecular hydrogen bonds, and Fermi resonance between the O-H stretching fundamental and the first overtone of the O-H in-plane bending vibrations. The model is used for theoretical simulation of the nu(s) stretching bands of salicylic acid and its OD derivative at 300 K. The effect of deuteration is successfully reproduced by our model. Infrared, far infrared, Raman, and low-frequency Raman spectra of the polycrystalline salicylic acid and its deuterated derivative have been measured. The geometry and experimental frequencies are compared with the results of density-functional theory calculations performed at the B3LYP6-31 ++ G**, B3LYP/cc-pVTZ, B3PW916-31 ++ G**, and B3PW91/cc-pVTZ levels. O-H, O-D, and O...O stretching frequencies are used in theoretical simulation of the nu(s) stretching bands.

Theoretical model of infrared spectra of hydrogen bonds in molecular crystals and its application to interpretation of infrared spectra of 1-methylthymine

A theoretical model for vibrational interactions in the hydrogen bonds in molecular crystals with four molecules forming two centrosymmetric dimers in the unit cell is presented. The model takes into account anharmonic-type couplings between the high-frequency N-H(D) and the low-frequency N...O stretching vibrations in each hydrogen bond, resonance interactions (Davydov coupling) between equivalent hydrogen bonds in each dimer, resonance interdimer interactions within a unit cell, and Fermi resonance between the N-H(D) stretching fundamental and the first overtone of the N-H(D) in-plane bending vibrations. The vibrational Hamiltonian, selection rules, and expressions for the integral properties of an absorption spectrum are derived. The model is used for theoretical simulation of the NH stretching bands of 1-methylthymine and its ND derivative at 300 K. The effect of deuteration is successfully reproduced by our model. Infrared, far-infrared, Raman, and low-frequency Raman spectra of 1-methylthymine and its deuterated derivative have been measured. Experimental geometry and frequencies are compared with the results of density functional theory calculations performed at the B3LYP6-311++G**, B3LYP/cc-pVTZ, B3PW916-311++G**, and B3PW91/cc-pVTZ levels.

Theoretical modeling of the O–H stretching IR bands of hydrogen-bonded dimers of benzoic acid in S0 and S1 electronic states

Theoretical model for vibrational interactions in the hydrogen-bonded dimer of benzoic acid is presented. The model takes into account anharmonic-type couplings between the high-frequency O-H and the low-frequency O[cdots, three dots, centered]O stretching vibrations in two hydrogen bonds, resonance interactions (Davydov coupling) between two hydrogen bonds in the dimer, and Fermi resonance between the O-H stretching fundamental and the first overtone of the O-H in-plane bending vibrations. The vibrational Hamiltonians and selection rules for the C(2h) geometry in the S(0) state and for the C(s) in-plane bent geometry in the S(1) state of the dimer are derived. The model is used for theoretical simulation of the O-H stretching IR absorption bands of benzoic acid dimers in the gas phase in the electronic ground and first excited singlet states. Ab initio CIS and CIS(D)6-311++G(d,p) calculations have been performed to determine geometry, frequencies, and excited state energies of benzoic acid dimer in the S(1) state.

Theoretical study of proton tunneling in the excited state of tropolone

Ab initio CIS/6-311++G(d,p) calculations of geometry and vibrational frequencies have been carried out in the A state of tropolone. The grids of potential energy surfaces along the coordinates of high frequency tunneling vibration and the low-frequency coupled vibration have been calculated. Two-dimensional model potentials, formed from symmetric mode coupling potential and squeezed double well potential, have been fitted to the calculated potential energy surfaces and used to analyze proton dynamics. The tunneling splittings for different vibrationally excited states have been calculated and compared with the available experimental data. The model potential energy surfaces, based on the CIS/6-311++G(d,p) calculations, give good estimation of the tunneling energy splittings in the vibrationally ground and excited states of tropolone and explain monotonic decrease in tunneling splittings with the excitation of low-frequency out-of-plane modes and increase in the tunneling splittings with the excitation of low-frequency planar modes.

Molecular Dynamics Simulations of Vibrational Spectra of Hydrogen-Bonded Systems

In this chapter, we present current studies on molecular dynamics (MD) simulations of hydrogen-bonded systems with emphasis on vibrational spectra analysis. One of the most informative experimental data are spectroscopic data (infrared and Raman spectroscopy), which give information important in diverse fields, e.g. protein folding, drug design, sensors, nanotechnology, separations, etc. Spectroscopic data are very sensitive on inter- and intramolecular interactions. The processes of melting, boiling, unfolding and strand separation involve disruption of molecular interactions, that engage attractive or repulsive forces between molecules. In this chapter, we focus on calculations of IR spectra of hydrogen-bonded complexes based on linear response theory, in which the spectral density is the Fourier transform of the autocorrelation function of the dipole moment operator involved in the IR transitions. Recently, Born–Oppenheimer molecular dynamics (BOMD), Car–Parrinello molecular dynamics (CPMD), path integral molecular dynamics (PIMD), hybrid molecular dynamics (QM/MM) and other methods which use trajectories from molecular dynamics have been employed to simulate IR spectra of hydrogen-bonded systems. Each of these methods has some advantages and disadvantages which will be discussed in this chapter presenting also recent applications of these methods.

Quantum-mechanical study of energies, structures, and vibrational spectra of the H(D)Cl complexed with dimethyl ether

Interaction energies, molecular structure and vibrational frequencies of the binary complex formed between H(D)Cl and dimethyl ether have been obtained using quantum-chemical methods. Equilibrium and vibrationally averaged structures, harmonic and anharmonic wavenumbers of the complex and its deuterated isotopomer were calculated using harmonic and anharmonic second-order perturbation theory procedures with Density Functional Theory B3LYP and B2PLYP-D and ab initio Møller-Plesset second-order methods, and a 6-311++G(3d,3p) basis set. A phenomenological model describing anharmonic-type vibrational couplings within hydrogen bonds was developed to explain the unique broadening and fine structure, as well as the isotope effect of the Cl-H and Cl-D stretching IR absorption bands in the gaseous complexes with dimethyl ether, as an effect of hydrogen bond formation. Simulations of the rovibrational structure of the Cl-H and Cl-D stretching bands were performed and the results were compared with experimental spectra.

Theoretical Studies of Dynamic Interactions in Excited States of Hydrogen-Bonded Systems

Theoretical model for vibrational interactions in the hydrogen-bonded benzoic acid dimer is presented. The model takes into account anharmonic-type couplings between the high-frequency O–H and the low-frequency O⋯O stretching vibrations in two hydrogen bonds, resonance interactions between two hydrogen bonds in the dimer, and Fermi resonance between the O–H stretching fundamental and the first overtone of the O–H in-plane bending vibrations. The model is used for theoretical simulation of the O–H stretching IR absorption bands of benzoic acid dimers in the gas phase in the first excited singlet state. Ab initio CIS and CIS(D)/CIS/6-311