Amino-acid and water molecules adsorbed on water clusters in a beam

2005 ◽  
Vol 123 (7) ◽  
pp. 074301 ◽  
Author(s):  
Ramiro Moro ◽  
Roman Rabinovitch ◽  
Vitaly V. Kresin
Keyword(s):  
Amino Acid ◽  
Water Clusters ◽  
Water Molecules

Zwitterion formation in hydrated amino acid, dipole bound anions: How many water molecules are required?

2003 ◽  
Vol 119 (20) ◽  
pp. 10696-10701 ◽  
Author(s):  
Shoujun Xu ◽  
J. Michael Nilles ◽  
Kit H. Bowen
Keyword(s):  
Amino Acid ◽  
Water Molecules ◽  
Zwitterion Formation

scholarly journals Self-Organization of Water Molecules Over 11-Year Solar Cycle

2021 ◽  
Author(s):  
Igor Shevchenko
Keyword(s):  
Solar Activity ◽  
Water Clusters ◽  
The Self ◽  
Self Organization ◽  
Water Molecules ◽  
Annual Variations ◽  
The Earth ◽  
Rate Of Hydrolysis ◽  
Rotation Of The Earth ◽  
Northern And Southern Hemispheres

Abstract The variations of solar activity and distribution of solar energy due to the rotation of the Earth around its axis and around the Sun exert a strong influence on the self-organization of water molecules. As a result, the rate of hydrolytic processes with the participation of water clusters displays diurnal, very large annual variations, and is also modulated by the 11-year cycles of solar activity. It also depends on the geographic latitude and can be different at the same time in the Northern and Southern Hemispheres. This phenomenon is well accounted for by the influence of muons on the self-organization of water molecules. Muons are constantly generated in the upper atmosphere by the solar wind. They reach the surface of the Earth and can penetrate to some depth underground. Buildings also absorb muons. For this reason, the rate of hydrolysis outside and inside buildings, as well as underground, can differ significantly from each other.

scholarly journals Spectral, Thermal, Crystal Structure, Hirshfeld Surface Analyses and Biological Activities of New Hydrazinium Dipicolinato Copper(II) Tetrahydrate

2019 ◽  
Vol 31 (8) ◽  
pp. 1755-1761
Author(s):  
K. Naresh ◽  
B.N. Sivasankar
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Water Clusters ◽  
Hirshfeld Surface ◽  
Water Molecules ◽  
X Ray ◽  
Biological Studies ◽  
Calf Thymus ◽  
Hydrazinium Cation

A new copper complex of pyridine-2,6-dicarboxylate containing hydrazinium cation, formulated as (N2H5)2[Cu(PDC)2]·4H2O (PDC = pyridine-2,6-dicarboxylate) has been synthesized from copper(II) nitrate, hydrazine hydrate and pyridine-2,6-dicarboxylic acid as a single crystal and characterized by elemental analysis and spectroscopic (IR and UV-visible), thermal (TG/DTG), single crystal X-ray diffraction and biological studies. A six-coordinate complex with a distorted octahedral geometry around Cu(II) ion is proposed and confirmed by X-ray single crystal method. The structure reveals that two pyridine-2,6-dicarboxylate species acting as tridentate ligands and hydrazinium cation present as a counter ion along with non-coordinated four water molecules. The structural units of copper(II) is mutually held by the hydrogen bonds and π···π and C–O···π interactions. The copper(II) complex is connected to one another via O–H···O hydrogen bonds, forming water clusters, which plays an important role in the stabilization of the crystal structure. In the water clusters, the water molecules are trapped by the cooperative association of coordination interactions as well as hydrogen bonds. Both cation and anion interactions and crystal from various types of intermolecular contacts and their importance were explored using Hirshfeld surface analysis. This indicates that O···H/H···O interactions are the superior interactions conforming excessive H-bond in the molecular structure. The interaction of copper(II) complex with calf thymus DNA (CT-DNA) was investigated by electronic absorption spectroscopic technique. The electronic evidence strongly shows that the compound interacts with calf thymus through intercalation with a binding constant of Kb = 5.7 × 104 M–1.

scholarly journals Water inside β-cyclodextrin cavity: amount, stability and mechanism of binding

2019 ◽  
Vol 15 ◽  
pp. 1592-1600 ◽  
Author(s):  
Stiliyana Pereva ◽  
Valya Nikolova ◽  
Silvia Angelova ◽  
Tony Spassov ◽  
Todor Dudev
Keyword(s):  
Inclusion Complexes ◽  
Water Clusters ◽  
Bound Water ◽  
Thermodynamic Characteristics ◽  
Water Molecules ◽  
Native State ◽  
Hydrophobic Substances ◽  
Cyclodextrin Cavity ◽  
Stabilizing Factors ◽  
Native Host

Cyclodextrins (CDs) are native host systems with inherent ability to form inclusion complexes with various molecular entities, mostly hydrophobic substances. Host cyclodextrins are accommodative to water molecules as well and contain water in the native state. For β-cyclodextrin (β-CD), there is no consensus regarding the number of bound water molecules and the location of their coordination. A number of intriguing questions remain: (1) Which localities of the host’s macrocycle are the strongest attractors for the guest water molecules? (2) What are the stabilizing factors for the water clusters in the interior of β-CD and what type of interactions between water molecules and cavity walls or between the water molecules themselves are dominating the energetics of the β-CD hydration? (3) What is the maximum number of water molecules inside the cavity of β-CD? (4) How do the thermodynamic characteristics of β-CD hydration compare with those of its smaller α-cyclodextrin (α-CD) counterpart? In this study, we address these questions by employing a combination of experimental (DSC/TG) and theoretical (DFT) approaches.

A two-dimensional hydrogen-bonded water layer in the structure of a cobalt(III) cubane complex

2014 ◽  
Vol 70 (2) ◽  
pp. 198-201 ◽  
Author(s):  
Ji Qi ◽  
Xiang-Sheng Zhai ◽  
Hong-Lin Zhu ◽  
Jian-Li Lin
Keyword(s):  
Water Clusters ◽  
Three Dimensional ◽  
Water Layer ◽  
Water Molecules ◽  
Supramolecular Network ◽  
Two Dimensional ◽  
Solvent Water ◽  
Water Layers ◽  
Hydrogen Bonded

A tetranuclear CoIIIoxide complex with cubane topology, tetrakis(2,2′-bipyridine-κ2N,N′)di-μ2-carbonato-κ4O:O′-tetra-μ3-oxido-tetracobalt(III) pentadecahydrate, [Co4(CO3)2O4(C10H8N2)4]·15H2O, with an unbounded hydrogen-bonded water layer, has been synthesized by reaction of CoCO3and 2,2′-bipyridine. The solvent water molecules form a hydrogen-bonded net with tetrameric and pentameric water clusters as subunits. The Co4O4cubane-like cores are sandwiched between the water layers, which are further stacked into a three-dimensional metallo-supramolecular network.

HYDRATION AND DISSOCIATION OF CALCIUM HYDROXIDE IN WATER CLUSTERS: A QUANTUM CHEMICAL STUDY

2007 ◽  
Vol 06 (03) ◽  
pp. 595-609 ◽  
Author(s):  
CLARA JIAYUN MEN ◽  
FU-MING TAO
Keyword(s):  
Calcium Hydroxide ◽  
Quantum Chemical ◽  
Density Functional ◽  
Water Clusters ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Structure Stability ◽  
Water Molecules ◽  
Aerosol Formation ◽  
Hydrated Clusters

The structure, stability, and properties of the hydrated clusters of calcium hydroxide, Ca ( OH )2( H 2 O )n, n = 1–6, were investigated using density functional and ab initio quantum chemical methods. The results show that six water molecules are needed to result in the complete dissociation of Ca ( OH )2. The stable and ionic conformer of Ca ( OH )2( H 2 O )6 has C 3 symmetry. Its surprising stability and high IR activity render hydrated clusters of Ca ( OH )2 potentially significant in the nucleation of noctilucent clouds in the mesosphere. Trends in the interaction energies (ΔEe) of the complexes show that water molecules in the first shell of Ca 2+ are highly stable, further alluding to the role of hydrated Ca ( OH )2 in aerosol formation.

AB Initio Simulation on Grotthuss Mechanism

2005 ◽  
Author(s):  
Jiahua Han ◽  
Hongtan Liu
Keyword(s):  
Ab Initio ◽  
Water Clusters ◽  
Dominant Role ◽  
High Mobility ◽  
Weight Fraction ◽  
Solvation Shell ◽  
Water Molecules ◽  
Proton Diffusion ◽  
Ab Initio Simulations ◽  
Grotthuss Mechanism

Ab initio simulations on Grotthuss mechanism have been carried out. Using the simulation results together with the existing experimental data, all the popular propositions for Grotthuss mechanism, including the one recently proposed by Noam [1], have been checked. Combining with the charge distribution calculation and the movement of the positive charge center inside the protonated water cluster during the proton diffusion process, only one mechanism is shown probable, while all the other proposed mechanisms are excluded. According to this probable mechanism, the high mobility of proton inside water is caused by the high diffusion rate of H5O2+, while the diffusion of H5O2+ is mainly induced by the thermal movement of water molecules at the second solvation shell of H5O2+ cation and the Zundel polarization inside the cation ion. Furthermore, the external field and thermo-dynamic effects play important roles during the transport process by affecting the reorientation of water molecules at the neighborhood of the second solvation shell of H5O2+ to induce the Zundel polarization and by providing the energy for the cleavage of the hydrogen bond between a newly formed water molecule and H5O2+. Because the weight (fraction) of H5O2+ among protonated water clusters decreases as temperature increases, this proposed mechanism is considered to play the dominant role only when temperature is below 572 K, above which, protons transport by other mechanisms become dominant.

scholarly journals Entropy-Enthalpy Compensations Fold Proteins in Precise Ways

2021 ◽  
Vol 22 (17) ◽  
pp. 9653
Author(s):  
Jiacheng Li ◽  
Chengyu Hou ◽  
Xiaoliang Ma ◽  
Shuai Guo ◽  
Hongchi Zhang ◽  
...  
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Amino Acid ◽  
Gibbs Free Energy ◽  
Energy Equation ◽  
Protein Structures ◽  
Water Molecules ◽  
Side Chains ◽  
Hydrophobic Collapse ◽  
Polypeptide Chains

Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.

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