The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding

Abstract

The vibrational spectra of protonated water clusters: A benchmark for selfconsistent-charge density-functional tight binding AbstractProton transfers are involved in many chemical processes in solution and in biological systems. Although water molecules have been known to transiently facilitate proton transfers, the possibility that water molecules may serve as the "storage site" for proton in biological systems has only been raised in recent years. To characterize the structural and possibly the dynamic nature of these protonated water clusters, it is important to use effective computational techniques to properly interpret experimental spectroscopic measurements of condensed phase systems. Bearing this goal in mind, we systematically benchmark the self-consistent-charge density-functional tight-binding �SCC-DFTB� method for the description of vibrational spectra of protonated water clusters in the gas phase, which became available only recently with infrared multiphoton photodissociation and infrared predissociation spectroscopic experiments. It is found that SCC-DFTB qualitatively reproduces the important features in the vibrational spectra of protonated water clusters, especially concerning the characteristic signatures of clusters of various sizes. In agreement with recent ab initio molecular dynamics studies, it is found that dynamical effects play an important role in determining the vibrational properties of these water clusters. Considering computational efficiency, these benchmark calculations suggest that the SCC-DFTB/molecular mechanical approach can be an effective tool for probing the structural and dynamic features of protonated water molecules in biomolecular systems. The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding Proton transfers are involved in many chemical processes in solution and in biological systems. Although water molecules have been known to transiently facilitate proton transfers, the possibility that water molecules may serve as the "storage site" for proton in biological systems has only been raised in recent years. To characterize the structural and possibly the dynamic nature of these protonated water clusters, it is important to use effective computational techniques to properly interpret experimental spectroscopic measurements of condensed phase systems. Bearing this goal in mind, we systematically benchmark the self-consistent-charge density-functional tight-binding ͑SCC-DFTB͒ method for the description of vibrational spectra of protonated water clusters in the gas phase, which became available only recently with infrared multiphoton photodissociation and infrared predissociation spectroscopic experiments. It is found that SCC-DFTB qualitatively reproduces the important features in the vibrational spectra of protonated water clusters, especially concerning the characteristic signatures of clusters of various sizes. In agreement with recent ab initio molecular dynamics studies, it is found that dynamic...

Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin

“…Various applications have shown that SCC-DFTB is able to reproduce DFT results with sufficient accuracy in many systems (34,35). For the present study, the ability of SCC-DFTB to reproduce strongly hydrogen bonded structures and proton affinities as well as the qualitative spectral features of various water clusters have been shown in recent studies (36,37) (also see SI for additional benchmarks).…”

“…The IR spectrum for the QM region is computed by the Fourier transform of the dipole autocorrelation function collected from SCC-DFTB/MM molecular dynamics trajectories; multiple independent simulations are carried out for statistical significance. The nuclear quantum effect on the computed IR spectra is approximated with a harmonic quantum correction factor as done in the recent study of water clusters (37). See SI for additional technical details and discussions.…”

Toward molecular models of proton pumping: Challenges, methods and relevant applications

“…The "intermolecular proton bond" explains the short distance between the two Glu sidechains as observed in several crystal structures. Importantly, this Glu-pair model qualitatively captures the continuum feature in the IR spectra near 18002000 cm 1 (Figure 3(c)); similar to the case of protonated water cluster [82], MD simulations are essential for capturing the proper continuum feature. Moreover, the connection between the proton de-localization and the continuum band was shown explicitly by a simulation in which only one of the Glu sidechains was treated as QM, thus abolishing both delocalization of the stored proton and the continuum band.…”

Исследование Индукционно-Резонансного Взаимодействия Кластеров Воды В Минералах Фторапатита Методами Поляризационной ИК И Кр-Спектроскопии

“…полос в рамках кластерной схемы строения воды (Н 2 О) n в соответствии с литературными данными [33,34]. Особенность спектров КР в диапазоне 4000−3000 сm −1 заключалась в значительном различии интенсивностей (I) полос для компонент излучения, рассеянного в ортогональных направлениях (I z z и I z y ) и (I y y и I y z ) соответственно вдоль и поперек c-каналов об-разца (рис.…”

“…Полосы в области 4000−3750 cm −1 относятся к антисимметричным колебаниям свободных гидроксилов [34,35]. Диффузная полоса 2960−2900 сm [37][38][39][40].…”