A comprehensive search of topologically distinct local minimum structures of protonated water octamer and the classification of O H topological types

Akase, Dai; Teramae, Hiroyuki; Aida, Misako

doi:10.1016/j.cplett.2014.10.071

Cited by 6 publications

(8 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Six of them are hydrogen-bonded O-H bonds. Four of them are free O-H bonds [43]. The free O-H bonds are explicitly represented by small vertices, each of which links to a larger vertex in the digraph representation in Fig.…”

Section: Classification Of O-h Bond In Pw Clustermentioning

confidence: 99%

“…It is not trivial to search full potential energy surface of PW octamer using a reliable level of calculation. Making use of different computational methods [41,42], 134 topologically distinct local minima of PW octamers were obtained [43] at the theoretical level of MP2/aug-cc-pVDZ. The lowest energy structure is TP1, which is Eigen type.…”

Section: Distribution Of Pw Octamermentioning

confidence: 99%

“…TP26 is the 26 th stable isomer, and the most stable isomer of the Zundel type. To gain insights into the thermodynamic stability of topologically distinct isomers, temperature-dependent populations of the optimized local minimum structures were estimated on the basis of the molecular partition functions [43] using the left method of Fig. 5.…”

Section: Distribution Of Pw Octamermentioning

confidence: 99%

“…15. The O-H vibrational frequencies spread from ~1200 cm −1 to ~3800 cm −1 : they can be classified according to the topological type of the O-H bond [43]. The vibrational frequency for free O-H of acceptor water molecule A is further classified into symmetric stretching A(s) and anti-symmetric stretching A(a) according to the vibration modes ( Fig.…”

Section: Vibrational Frequency Of O-h Topological Typementioning

confidence: 99%

“…The calculated harmonic IR spectra of the representative structures, TP1, TP26, TP33 and TP94 in the range of 2000-3800 cm −1 are given in [43]. The range of 3600-3800 cm −1 corresponds to the free O-H stretching modes of the topological types including A(s) (~3630 cm −1 ), D1A2 (~3670 cm −1 ), D1A1 (~3700 cm −1 ) and A(a) (~3750 cm −1 ).…”

Section: Calculated Ir Spectra and Assignment Of Coexisting Isomersmentioning

confidence: 99%

See 4 more Smart Citations

Hydrogen-bond pattern to characterize water network

Aida

Akase

2019

Pure and Applied Chemistry

Self Cite

View full text Add to dashboard Cite

Hydrogen-bond (HB) patterns correspond to topologically distinct isomers of water clusters, and can be expressed by digraphs. The HB pattern is used to divide the configuration space of water cluster at a finite temperature. The populations of the HB patterns are transformed into the relative Helmholtz energies. The method is based on the combination of molecular simulation with graph theory. At a finite temperature it can be observed that other isomers than local minimum structures on the potential energy surface are highly populated. The dipole moment of a constituent molecule in a water cluster is enhanced depending on the local HB network around the water molecule. Rooted digraph is used to represent topologically distinct isomers of protonated water (PW) clusters. O–H bonds of PW clusters are classified into 10 topological types based on the combination of the local HB types of the contributing water molecules to the O–H bond. If the topological type is the same, vibrational frequencies of those O–H bonds of PW clusters are similar even in different isomers; i.e. vibrational frequency of O–H bond is transferable, and can be used as a vibrational spectral signature of PW clusters.

show abstract

Section: Classification Of O-h Bond In Pw Clustermentioning

confidence: 99%

Section: Distribution Of Pw Octamermentioning

confidence: 99%

Section: Distribution Of Pw Octamermentioning

confidence: 99%

Section: Vibrational Frequency Of O-h Topological Typementioning

confidence: 99%

Section: Calculated Ir Spectra and Assignment Of Coexisting Isomersmentioning

confidence: 99%

See 3 more Smart Citations

Hydrogen-bond pattern to characterize water network

Aida

Akase

2019

Pure and Applied Chemistry

Self Cite

View full text Add to dashboard Cite

show abstract

Effect of NaOH on the preparation of two-dimensional flake-like zirconia nanostructures

Feng

Liu

et al. 2020

Chemical Physics Letters

View full text Add to dashboard Cite

Structure and Spectroscopy of Hydrated Sodium Ions at Different Temperatures and the Cluster Stability Rules

Fifen

Agmon

2016

J. Chem. Theory Comput.

View full text Add to dashboard Cite

The sodium cation plays an important role in several physiological processes. Understanding its solvation may help understanding ion selectivity in sodium channels that are pivotal for nerve impulses. This paper presents a thorough investigation of over 75 isomers of gas-phase Na(+)(H2O)(n=1-8) clusters, whose optimized structures, energies, and (harmonic) vibrational frequencies were computed quantum mechanically at the full MP2/6-31++G(d,p) level of theory. From these data, we have calculated the temperature effects on the cluster thermodynamic functions, and thus the equilibrium Boltzmann distribution for each n. For a selected number of isomers, we have corrected the calculations for basis set superposition error (BSSE) to obtain accurate clustering energies, in excellent agreement with experiment. The computed clusters are overwhelmingly 4-coordinated, as opposed to bulk liquid water, where sodium cations are believed to be mostly 5- or 6-coordinated. To explain this, we suggest the "cluster stability rules", a set of coordination-number-dependent hydrogen-bond (HB) strengths that can be obtained using a single BSSE correction. Assuming additivity and transferability, these reproduce the relative stability of most of our computed isomers. These rules enable us to elucidate the trends in HB strengths, outlining the major determinants of cluster stability. For n = 4 and 5, we have also performed anharmonic vibrational calculations (VPT2) to compare with available photodissociation infrared spectra of these gas-phase clusters. The comparison suggests that the experiments actually monitor a mixture of predominantly 3-coordinated isomers, which is quite remote from the computed Boltzmann distribution, particularly at low temperatures. Surprisingly, for these experiments, water evaporation pathways can rationalize the non-equilibrium isomer distribution. The equilibrium isomer distribution is, in turn, rationalized by the entropy of internal rotations of "dangling" water molecules.

show abstract

A comprehensive search of topologically distinct local minimum structures of protonated water octamer and the classification of O H topological types

Cited by 6 publications

References 40 publications

Hydrogen-bond pattern to characterize water network

Hydrogen-bond pattern to characterize water network

Effect of NaOH on the preparation of two-dimensional flake-like zirconia nanostructures

Structure and Spectroscopy of Hydrated Sodium Ions at Different Temperatures and the Cluster Stability Rules

Contact Info

Product

Resources

About