Hydrogen-bond pattern to characterize water network

2019 ◽  
Vol 91 (2) ◽  
pp. 301-316 ◽  
Author(s):  
Misako Aida ◽  
Dai Akase
Keyword(s):  
Hydrogen Bond ◽  
Finite Temperature ◽  
Water Cluster ◽  
Energy Surface ◽  
Water Clusters ◽  
Topological Type ◽  
Spectral Signature ◽  
Water Molecules ◽  
Water Network ◽  
Hydrogen Bond Pattern

Abstract 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.

scholarly journals Stabilization of Near Identical Hydrogen Bonded Octameric Water Clusters in Crystal Structures of Three Distinct Non-Charged Polyamide Macrocyclic Host Molecules

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2787
Author(s):  
Kajetan Dąbrowa ◽  
Magdalena Ceborska ◽  
Janusz Jurczak
Keyword(s):  
Hydrogen Bond ◽  
Water Cluster ◽  
Water Clusters ◽  
Membered Ring ◽  
Water Molecules ◽  
Aryl Substituent ◽  
Chemical Structures ◽  
Host Molecules ◽  
Solid State Structures ◽  
Suitable Environment

In this paper, we present a comparative analysis of the solid state structures of three well-resolved hydrates of macrocyclic host molecules 1a, 1b, and 2 containing an intrannular amide-aryl substituent (lariat arm) connected to a fixed 26-membered ring in a normal (-NHCOAr, hosts 1a and 1b) or reverse manner (-CONHAr, host 2). Despite different chemical structures, these hosts crystallize as isostructural tetrahydrates in the same P-1 space group. Moreover, their crystals exhibit identical hydrogen bond motifs resulting in a stabilization of an almost identical unusual octameric water cluster built from the cyclic tetramer core and four water molecules, attached sequentially in an “up-and-down” manner. Further analysis reveals that, among the series, the structure of host 2 provides the most suitable environment for the accommodation of this type of water cluster.

scholarly journals Towards complete assignment of the infrared spectrum of the protonated water cluster H+(H2O)21

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jinfeng Liu ◽  
Jinrong Yang ◽  
Xiao Cheng Zeng ◽  
Sotiris S. Xantheas ◽  
Kiyoshi Yagi ◽  
...  
Keyword(s):  
Water Clusters ◽  
Model Systems ◽  
Cluster Method ◽  
Spectral Signature ◽  
Water Molecules ◽  
Vibrational Resonance ◽  
Spectral Signatures ◽  
Phase Water ◽  
Coordinated Water ◽  
Degenerate Perturbation Theory

AbstractThe spectroscopic features of protonated water species in dilute acid solutions have been long sought after for understanding the microscopic behavior of the proton in water with gas-phase water clusters H+(H2O)n extensively studied as bottom-up model systems. We present a new protocol for the calculation of the infrared (IR) spectra of complex systems, which combines the fragment-based Coupled Cluster method and anharmonic vibrational quasi-degenerate perturbation theory, and demonstrate its accuracy towards the complete and accurate assignment of the IR spectrum of the H+(H2O)21 cluster. The site-specific IR spectral signatures reveal two distinct structures for the internal and surface four-coordinated water molecules, which are ice-like and liquid-like, respectively. The effect of inter-molecular interaction between water molecules is addressed, and the vibrational resonance is found between the O-H stretching fundamental and the bending overtone of the nearest neighboring water molecule. The revelation of the spectral signature of the excess proton offers deeper insight into the nature of charge accommodation in the extended hydrogen-bonding network underpinning this aqueous cluster.

scholarly journals Impact of a hydrophobic ion on the early stage of atmospheric aerosol formation

2019 ◽  
Vol 116 (45) ◽  
pp. 22540-22544 ◽  
Author(s):  
Linda Feketeová ◽  
Paul Bertier ◽  
Thibaud Salbaing ◽  
Toshiyuki Azuma ◽  
Florent Calvo ◽  
...  
Keyword(s):  
Atmospheric Aerosol ◽  
Water Cluster ◽  
Water Clusters ◽  
Early Stage ◽  
Cloud Formation ◽  
Water Molecules ◽  
Cluster Growth ◽  
Aerosol Formation ◽  
Early Stages ◽  
Pyridinium Ion

Atmospheric aerosols are one of the major factors affecting planetary climate, and the addition of anthropogenic molecules into the atmosphere is known to strongly affect cloud formation. The broad variety of compounds present in such dilute media and their specific underlying thermalization processes at the nanoscale make a complete quantitative description of atmospheric aerosol formation certainly challenging. In particular, it requires fundamental knowledge about the role of impurities in water cluster growth, a crucial step in the early stage of aerosol and cloud formation. Here, we show how a hydrophobic pyridinium ion within a water cluster drastically changes the thermalization properties, which will in turn change the corresponding propensity for water cluster growth. The combination of velocity map imaging with a recently developed mass spectrometry technique allows the direct measurement of the velocity distribution of the water molecules evaporated from excited clusters. In contrast to previous results on pure water clusters, the low-velocity part of the distributions for pyridinium-doped water clusters is composed of 2 distinct Maxwell–Boltzmann distributions, indicating out-of-equilibrium evaporation. More generally, the evaporation of water molecules from excited clusters is found to be much slower when the cluster is doped with a pyridinium ion. Therefore, the presence of a contaminant molecule in the nascent cluster changes the energy storage and disposal in the early stages of gas-to-particle conversion, thereby leading to an increased rate of formation of water clusters and consequently facilitating homogeneous nucleation at the early stages of atmospheric aerosol formation.

Interesting fluorine anion water clusters [F−·(H2O)n] in metal complex crystals

CrystEngComm ◽  
2018 ◽  
Vol 20 (27) ◽  
pp. 3849-3857 ◽  
Author(s):  
Fang Fang Jian ◽  
E. Liu ◽  
Jun Ying Ma
Keyword(s):  
Metal Complex ◽  
Water Cluster ◽  
Water Clusters ◽  
Fluoride Anion ◽  
Water Molecules ◽  
Hybrid Cluster ◽  
Complex Crystals ◽  
Fluorine Anion

Three crystalline complexes containing fluorine anion water cluster were reported. The fluoride anions and water molecules are H-bonded to each other in an alternating fashion within the fluoride–water hybrid cluster, where a fluoride anion plays the important role.

Analysis of hydrogen bond energies and hydrogen bonded networks in water clusters (H2O)20 and (H2O)25 using the charge-transfer and dispersion terms

2014 ◽  
Vol 16 (23) ◽  
pp. 11310-11317 ◽  
Author(s):  
Suehiro Iwata
Keyword(s):  
Hydrogen Bond ◽  
Charge Transfer ◽  
Water Clusters ◽  
Water Molecules ◽  
Bond Energies ◽  
Dispersion Terms ◽  
Relationship Of ◽  
The Relationship ◽  
Hydrogen Bond Energies ◽  
Hydrogen Bonded

The relationship of the charge-transfer and dispersion terms with the O–O length for every pair of hydrogen bonded water molecules in the isomers of (H2O)17–(H2O)21.

Ab Initio Study of Water Clusters Adsorption on Graphite Surface

2010 ◽  
Vol 105-106 ◽  
pp. 499-501
Author(s):  
Bing Bing Fan ◽  
Hai Long Wang ◽  
Li Guan ◽  
De Liang Chen ◽  
Rui Zhang
Keyword(s):  
Hydrogen Bond ◽  
Density Functional ◽  
Water Clusters ◽  
Density Functional Theory Method ◽  
Graphite Surface ◽  
Water Molecules ◽  
Geometrical Structures ◽  
Graphite Sheet ◽  
The Density Functional Theory ◽  
Formed Hydrogen

Using the density functional theory method, we have characterized the geometrical structures and adsorption energy of water clusters adsorption on graphite surface. When one water molecule inter- acts with graphite surface, one of the H-O bonds formed hydrogen-bond with carbon atom in graphite sheet; in the two water molecules structure, the linear dimmer nearly parallel to the graphite surface, and also formed the hydrogen-bond; when the number of water molecules increased to six, all the H-O bond that point to the graphite surface has formed Hydrogen-bond with it. The binding energy of the water clusters with a graphite surface depends only on the number of water molecules that form hydrogen bond.

A Density Functional Theory Study on the Water Aggregation Behaviour of Fatty-Acid Based Anionic Surface Active Ionic Liquids

2021 ◽  
Author(s):  
Suresh Sampathkumar ◽  
Subramaniam Vijayakumar
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Ionic Liquids ◽  
Fatty Acid ◽  
Water Cluster ◽  
Density Functional ◽  
Water Molecules ◽  
Hydrogen Bond Interaction ◽  
Functional Theory ◽  
Aggregation Behaviour

Abstract The hydrogen bond interactions between methyl-imidazolium cation (MIM+) and fatty-acid anions (CmHnCOO–, where m=1–6; n-3–13) of ionic liquids are studied in both gas phase and water phase using density functional theory. The structural properties show that the presence of N–H···O and C–H···O hydrogen bonds between [MIM]+ and [CmHnCOO]– (m=1–6;n-3–13) ionic liquids. From the vibrational frequency analysis it was found that the hydrogen bond interaction between [MIM]+ and [CmHnCOO]– (m=1–6;n-3–13) ionic liquids are red-shifted in frequency. The natural bond orbital analysis show that the N–H···O hydrogen bond associated with the large charge transfer which has the higher stabilization energy (i.e. E(2) ~ 38 kcal/mol). Further, the cation/anion–water cluster (H2O)1-3 interactions show that the water molecules are preferred to interact with anions. In the case of ionic liquids–water cluster interaction, the water molecules occupies the interstitial space between cation and anion of ionic liquids which results in weakening the cation-anion interaction.

EVOLUTIONARY DISCOVERY OF TRANSITION STATES IN WATER CLUSTERS

2012 ◽  
Vol 11 (05) ◽  
pp. 965-995 ◽  
Author(s):  
MOSTAFA M. H. ELLABAAN ◽  
YEW SOON ONG ◽  
Q. C. NGUYEN ◽  
JER-LAI KUO
Keyword(s):  
Hydrogen Bond ◽  
Transition State ◽  
Water Clusters ◽  
Minimum Energy ◽  
Transition States ◽  
Deep Understanding ◽  
Computational Effort ◽  
Water Evaporation ◽  
Water Molecules ◽  
Search Performance

As a basic Aristotle element, water is the most abundant and more importantly crucial substance on earth. Without water, there would not be any form of life as we know. Understanding many phenomena in water such as water evaporation and ice melting and formation requires a deep understanding of hydrogen bond breaking and formation. In particular transition states play a key role in the understanding of such hydrogen bond behavior. Transition states, unlike other metastable states, are energy maxima along the minimum energy path connecting two isomers of molecular clusters. Geometry optimization of transition state structures, however, is a difficult task, and becomes even more arduous, especially when dealing with complex biochemical systems using first-principles calculations. In this paper, a novel molecular memetic algorithm (MOL-MA) composing of specially designed molecular-based water evolutionary operators coupled with a transition-state-local search solver and valley adaptive clearing scheme for the discovery of multiple precise transition states structures is proposed. The transition states of water clusters up to four water molecules uncovered using MOL-MA are reported. MOL-MA is shown not only to reproduce previously found transition states in water clusters, but also established newly discovered transition states for sizes 2–4 water molecules. The search performance of MOL-MA is also shown to outperform its compeers when pitted against those reported in the literature for finding transition states as well as recent advances in niching algorithms in terms of solution precision, computational effort, and number of transition states uncovered.

Interaction of Gold Atom with Clusters of Water: Few Computational Mise-En-Scènes with Hydrogen Bonding Motif

2008 ◽  
Vol 73 (11) ◽  
pp. 1457-1474 ◽  
Author(s):  
Eugene S. Kryachko
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Computational Model ◽  
Photoelectron Spectroscopy ◽  
Water Clusters ◽  
Gold Atom ◽  
Proton Acceptor ◽  
Anion Photoelectron Spectroscopy ◽  
Relationship Of ◽  
First Time

The present work outlines the fair relationship of the computational model with the experiments on anion photoelectron spectroscopy for the gold-water complexes [Au(H2O)1≤n≤2]- that is established between the auride anion Au- and water monomer and dimer thanks to the nonconventional hydrogen bond where Au- casts as the nonconventional proton acceptor. This work also extends the computational model to the larger complexes [Au(H2O)3≤n≤5]- where gold considerably thwarts the shape of water clusters and even particularly breaks their conventional hydrogen bonding patterns. The fascinating phenomenon of the lavish proton acceptor character of Au- to form at least six hydrogen bonds with molecules of water is computationally unveiled in the present work for the first time.

High proton conductivity in a nickel(ii) complex and its hybrid membrane

2019 ◽  
Vol 48 (6) ◽  
pp. 2190-2196 ◽  
Author(s):  
Shuai-Liang Yang ◽  
Yue-Ying Yuan ◽  
Fei Ren ◽  
Chen-Xi Zhang ◽  
Qing-Lun Wang
Keyword(s):  
Hydrogen Bond ◽  
Proton Conductivity ◽  
Hybrid Membrane ◽  
Water Molecules ◽  
Hybrid Membranes ◽  
High Proton Conductivity ◽  
High Proton ◽  
Hydrogen Bond Networks

A novel 2D nickel(ii) complex (1) has been successfully synthesized using a 2,2′-bipyridyl, polycarboxylsulfonate ligand H4SBTC and Ni2+ ions. Owing to the presence of abundant water molecules, hydrogen bond networks and other protons, 1 and its hybrid membranes demonstrate high proton conductivity.

Sign in / Sign up

Export Citation Format

Share Document