Hydration of highly charged ions

Hofer, Thomas S.; Weiss, Alexander K. H.; Randolf, Bernhard R.; Rode, Bernd M.

doi:10.1016/j.cplett.2011.05.060

Cited by 50 publications

(54 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study the ab initio quantum mechanical charge-field molecular dynamics (QMCF-MD) approach [2,3] has been used as it had already yielded accurate insight into the hydration properties of a wide range of cations [4][5][6] and anions [7], as well as complexes [8][9][10]. In particular, a number of trivalent cations of the lanthanoide [11][12][13][14][15] and actinoide series [16] have already been successfully investigated, the results being in very good agreement with experimental data where available.…”

Section: Computational Methodologysupporting

confidence: 55%

“…Beyond their second hydration layers no influence of the ions were found, which is in contrast to the trivalent main group ion aluminum(III) [46] and tetravalent ions studied via the QMCF-MD approach [16,47]. While trivalent ions of main group and transition metal elements such as aluminum, iron, vanadium and iridium have very stable first hydration shells [4], MRT values in the picosecond range are specific characteristics for trivalent lanthanoide ions.…”

Section: Resultsmentioning

confidence: 96%

“…For both ions the radius of the QM core zone was chosen as 3.3Å and the QM layer radius as 5.7Å, including a smoothing region of 0.2Å at the outer boundary. This setup includes the ions' first and second hydration layers in the QM treatment, which ensures an adequate description of H-bonding between the two shells, being of great importance for highly charged ions [4]. Successfully applied in other studies on various aqueous solutions, the well-tested Dunning double-polarization basis sets [19] were employed for the hydrogen and oxygen atoms.…”

Section: Computational Methodologymentioning

confidence: 99%

See 2 more Smart Citations

The hydration properties of Gd(III) and Tb(III): An ab initio quantum mechanical molecular dynamics study

Canaval

Passler

Rode

2015

Chemical Physics Letters

Self Cite

View full text Add to dashboard Cite

Section: Computational Methodologysupporting

confidence: 55%

Section: Resultsmentioning

confidence: 96%

Section: Computational Methodologymentioning

confidence: 99%

See 1 more Smart Citation

The hydration properties of Gd(III) and Tb(III): An ab initio quantum mechanical molecular dynamics study

Canaval

Passler

Rode

2015

Chemical Physics Letters

Self Cite

View full text Add to dashboard Cite

“…QM/MM-MD [1,4,5,14,15,29,37,43,44] simulations are of ever-growing interest for the investigation of metalion complexes [19,28,30,38,41] and biomolecules [36], such as proteins and ribonucleic acids, because of their methodological flexibility, the capacity to investigate subpicosecond events as well as the possibility to predict interor intramolecular interactions and even chemical reactions. Besides the higher accuracy, the main advantage of hybrid QM/MM-MD to classical MM-MD simulations that 47 Page 2 of 7 computations were performed, utilizing a triple-zeta basis set [12,45].…”

Section: Introductionmentioning

confidence: 99%

Optimizing link atom parameters for DNA QM/MM simulations

et al. 2016

Self Cite

View full text Add to dashboard Cite

utilize popular force fields like AMBER [9], CHARMM [8], OPLS [23] or GROMOS [35] is the ability to describe effects stemming from the intra-or intermolecular shifts of electron density for any desired chemical system. Due to this, phenomena such as charge transfers, the cleavage or formation of covalent bonds and polarization effects can be studied in-depth. Additionally, the influence of different spin states, Jahn Teller distortion and even electronic excitations can be investigated without having to resort to specifically tailored force fields.One of the major challenges for that kind of investigation is a proper description of the interface between the QM and the MM region, especially if covalent bonds are reaching through the boundary between the two regions [27]. There exist a variety of approaches to describe that frontier bond, for example capping potentials [22,26], generalized hybrid orbitals [16] or localized self-consisted field [3,33,40], but the simplest, yet very accurate [2] and therefore also highly popular [27,36] method is hydrogen capping [39].A big question regarding hydrogen-capping approaches is the proper placement of the inserted atom, so that its influence on the behavior of the surrounding atoms is minimized as much as possible. In a previous work [18], this was discussed in detail for amino acids, with the recommendation to use separate parameters for each type of sidechain to considerably improve the description of the link bond. In this work, the focus lies on the QM/MM separation of DNA nucleosides, with the C-N bond between the deoxyribose and the nucleobase acting as the link bond. Abstract This work optimizes the link bond description of the quantum mechanical/molecular mechanical separation of deoxynucleosides. The nucleosides are separated at the C-N bond between the nucleobase and the deoxyribose, with the former acting as the quantum mechanically described species. By using a flexible link atom-ansatz plus a harmonic potential to correct the energy deviation from a full quantum mechanical description, the potential energy well of the bond's stretching motion is mimicked with very high accuracy.

show abstract

“…So far, an amount of simulations covering classical molecular mechanical (MM) MD, quantum mechanical (QM) and plane-wave type Car-Parrinello MD (CPMD) [16] and hybrid QM/MM MD have been reported on the hydrated Ln(III) ions [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34]. A notable merit of CPMD is that it can directly handle electronic properties [17,18,23,29] at sizable computational costs.…”

Section: Introductionmentioning

confidence: 99%