Dynamics of Dangling Bonds of Water Molecules in pharaonis Halorhodopsin during Chloride Ion Transportation

2012 ◽  
Vol 3 (20) ◽  
pp. 2964-2969 ◽  
Author(s):  
Yuji Furutani ◽  
Kuniyo Fujiwara ◽  
Tetsunari Kimura ◽  
Takashi Kikukawa ◽  
Makoto Demura ◽  
...  
Keyword(s):  
Chloride Ion ◽  
Water Molecules ◽  
Dangling Bonds ◽  
Ion Transportation

Diffusion study of chloride and binding of water in concrete pore by molecular dynamics simulation using LAMMPS

2021 ◽  
Vol 12 (3) ◽  
pp. 88
Author(s):  
Md. Shafiqul Islam ◽  
Sayem Ahmeed ◽  
Sumon Kumar Ghosh
Keyword(s):  
Diffusion Coefficient ◽  
Chloride Ion ◽  
System Size ◽  
Dynamics Simulation ◽  
Chloride Diffusion ◽  
Water Molecules ◽  
Chloride Diffusion Coefficient ◽  
Average Value ◽  
Temperature And Pressure ◽  
Different Characteristics

As for the communication between concrete and the particles, the surface shows Cl− shock and Na adsorption. With expanded particle focus, the solid adsorption capacity for Cl− is upgraded as a result of a detailed overview of the dynamic molecular simulation studies examining the chloride diffusion coefficient. Different characteristics of the diffusion process, including molecular models, system-size effects, temperature, and pressure conditions, and the type of protection, are discussed. This paper focus on Molecular Dynamic Simulation to determine the diffusion coefficient of chloride ion and water molecules in concrete. The diffusion coefficient for NaCl salt obtained 6.60178x10-10m2/s and the diffusion coefficient for CaCl2 salt obtained 7.29305x10-10m2/s. So, the average chloride diffusion coefficient 6.9475x10-10m2/s. Diffusion coefficient obtained from graph 5.562x10-10m2/s. Diffusion coefficients for water molecules for NaCl solution are 6.125x10-10m2/s, 6.85x10-10m2/s, 1.044x10-10m2/s, 8.525x10-10m2/s, 6.25x10-10m2/s. diffusion coefficient of water molecules in CaCl2 solution are 4.5x10-10m2/s, 6.725x10-10m2/s, 1.254x10-10m2/s, 7.725x10-10m2/s, 1.3x10-10m2/s. Average value obtained for water molecule diffusion are 4.545x10-10m2/s, 7.4062x10-10m2/s and 1.149x10-10m2/s. This diffusion of chloride effects the binding of water in concrete pore.

A single crystal X-ray study of a sulphate-bearing buttgenbachite, Cu36Cl7.8(NO3)1.3(SO4)0.35(OH)62.2.5.2H2O, and a re-examination of the crystal chemistry of the buttgenbachite-connellite series

2003 ◽  
Vol 67 (1) ◽  
pp. 47-60 ◽  
Author(s):  
D. E. Hibbs ◽  
P. Leverett ◽  
P. A. Williams
Keyword(s):  
Single Crystal ◽  
Democratic Republic ◽  
Democratic Republic Of Congo ◽  
Chloride Ion ◽  
Chloride Ions ◽  
Water Molecules ◽  
Data Set ◽  
X Ray ◽  
Positional Disorder ◽  
Anion Substitution

AbstractThe single-crystal X-ray structure of a sulphate-bearing buttgenbachite, Cu36Cl7.8(NO3)1.3(SO4)0.35(OH)62.2.5.2H2O, from Likasi, Democratic Republic of Congo, has been determined at 100 and 288 K. The basic framework of the structure is the same as has been previously reported for buttgenbachite, except for the identification of a hydrogen-bonded chloride ion (occupancy 0.6) at the origin instead of a Cu ion with partial occupancy. The nature of nitrate positional disorder along channels in the c direction and how this relates to the presence of other species such as chloride ions and water molecules and, most importantly, sulphate ions has been elucidated. One nitrate ion, with an occupancy of 0.18, lies at 2/3,l/3,l/4 and shares the site with a chloride ion (occupancy 0.30) and also a sulphate ion (occupancy 0.09); a second nitrate, with an occupancy of 0.24, lies at 2/3,1/3,0.084 and shares the site with a water molecule (occupancy 0.06). As a result, a formula of Cu36Cl7.8(NO3)1.3(SO4)0.35(OH)62.2.5.2H2O is obtained. Re-refinement of deposited data for a supposed connellite crystal from the Toughnut mine,Tombstone, Arizona gives a related, but different, pattern of anion substitution. No sulphate could be detected in the structure and it is evident that this structure refers to buttgenbachite. A nitrate nitrogen atom and a chloride ion are disordered at 2/3,l/3,l/4, the overall site being fully occupied. A chloride ion with ∼0.5 occupancy is sited at the origin and the formula Cu36Cl7.9(NO3)1.1(OH)63.4H2O is indicated. Re-refinement of a deposited data set for another buttgenbachite crystal from the Likasi mine reveals a partially occupied nitrate centred at 2/3,l/3, z and a partially occupied chloride at 2/3,l/3,l/4. Either 0.5Cl–, OH–, H2O or H3O+ is located at the origin. If the latter is the case, the stoichiometry for this buttgenbachite is Cu36Cl6.5(NO3)1.5(OH)64.5.5H2O. The present study has highlighted the fact that a range of compositions for buttgenbachite exists, depending on the pH and relative activities of chloride, nitrate and sulphate ions in solutions from which the mineral crystallizes.

scholarly journals Influence of Pore Size and Fatigue Loading on NaCl Transport Properties in C-S-H Nanopores: A Molecular Dynamics Simulation

Materials ◽  
2020 ◽  
Vol 13 (3) ◽  
pp. 700 ◽  
Author(s):  
Qingyu Cao ◽  
Yidong Xu ◽  
Jianke Fang ◽  
Yufeng Song ◽  
Yao Wang ◽  
...  
Keyword(s):  
Diffusion Coefficient ◽  
Pore Size ◽  
Transport Properties ◽  
Diffusion Rate ◽  
Chloride Ion ◽  
Fatigue Loading ◽  
Chloride Ions ◽  
Water Molecules ◽  
Ion Diffusion ◽  
Chloride Ion Diffusion

The transport properties of chloride ions in cement-based materials are one of the major deterioration mechanisms for reinforced concrete (RC) structures. This paper investigates the influence of pore size and fatigue loading on the transport properties of NaCl in C-S-H nanopores using molecular dynamics (MD) simulations. Molecular models of C-S-H, NaCl solution, and C-S-H nanopores with different pore diameters are established on a microscopic scale. The distribution of the chloride ion diffusion rate and the diffusion coefficient of each particle are obtained by statistically calculating the variation of atomic displacement with time. The results indicate that the chloride ion diffusion rate perpendicular to C-S-H nanopores under fatigue loading is 4 times faster than that without fatigue loading. Moreover, the diffusion coefficient of water molecules and chloride ions in C-S-H nanopores increases under fatigue loading compared with those without fatigue loading. The diffusion coefficient of water molecules in C-S-H nanopores with a pore size of 3 nm obtained from the MD simulation is 1.794 × 10−9 m2/s, which is slightly lower than that obtained from the experiment.

1-Carboxymethyl-3-methyl-1H-imidazol-3-ium chloride 2-(3-methyl-1H-imidazol-3-ium-1-yl)acetate monohydrate: a crystal stabilized by imidazolium zwitterions

2013 ◽  
Vol 69 (10) ◽  
pp. 1173-1176 ◽  
Author(s):  
Heng Zhang ◽  
Liangliang Chang ◽  
Na Wang ◽  
Xiaopeng Xuan
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Chloride Ion ◽  
Water Molecules ◽  
Dimensional Chain ◽  
Acetate Monohydrate ◽  
One Dimensional ◽  
Compound C ◽  
Methylene Groups

The title compound, C6H9N2O2+·Cl−·C6H8N2O2·H2O, contains one 2-(3-methyl-1H-imidazol-3-ium-1-yl)acetate inner salt molecule, one 1-carboxymethyl-3-methyl-1H-imidazol-3-ium cation, one chloride ion and one water molecule. In the extended structure, chloride anions and water molecules are linkedviaO—H...Cl hydrogen bonds, forming an infinite one-dimensional chain. The chloride anions are also linked by two weak C—H...Cl interactions to neighbouring methylene groups and imidazole rings. Two imidazolium moieties form a homoconjugated cation through a strong and asymmetric O—H...O hydrogen bond of 2.472 (2) Å. The IR spectrum shows a continuous D-type absorption in the region below 1300 cm−1and is different to that of 1-carboxymethyl-3-methylimidazolium chloride [Xuan, Wang & Xue (2012).Spectrochim. Acta Part A,96, 436–443].

scholarly journals Crystal structure ofcis-aquachlorido(rac-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ4N)chromium(III) tetrachloridozincate trihydrate from synchrotron data

2015 ◽  
Vol 71 (9) ◽  
pp. 1054-1057
Author(s):  
Dohyun Moon ◽  
Jong-Ha Choi
Keyword(s):  
Crystal Packing ◽  
Complex Cation ◽  
Macrocyclic Ligand ◽  
Three Dimensional ◽  
Chloride Ion ◽  
Water Molecules ◽  
Bond Lengths ◽  
Dimensional Network ◽  
Distorted Octahedral ◽  
Additional Water

The structure of the title compound,cis-[CrCl(cycb)(H2O)][ZnCl4]·3H2O (cycbisrac-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane; C16H36N4), has been determined from synchrotron data. In the complex cation, the CrIIIion is bound by four N atoms from the tetradentate cycbligand, a chloride ion and one water molecule in acisarrangement, displaying a distorted octahedral coordination geometry. The distorted tetrahedral [ZnCl4]2−anion and three additional water molecules remain outside the coordination sphere. The Cr—N(cycb) bond lengths are in the range of 2.0837 (14) to 2.1399 (12) Å while the Cr—Cl and Cr—(OH2) bond lengths are 2.2940 (8) and 2.0082 (13) Å, respectively. The crystal packing is stabilized by hydrogen-bonding interactions between the N—H groups of the macrocyclic ligand, the O—H groups of the water molecules and the Cl atoms of the tetrachloridozincate anion, leading to the formation of a three-dimensional network.

scholarly journals Crystal structure of chlorido(2-{[2-(phenylcarbamothioyl)hydrazin-1-ylidene](pyridin-2-yl)methyl}pyridin-1-ium)gold(I) chloride sesquihydrate

2015 ◽  
Vol 71 (9) ◽  
pp. 1070-1072 ◽  
Author(s):  
Claudia C. Gatto ◽  
Iariane J. Lima
Keyword(s):  
Metal Ion ◽  
Positive Charge ◽  
Rotation Axis ◽  
Chloride Ion ◽  
Gold Complex ◽  
Water Molecules ◽  
Thiosemicarbazone Ligand ◽  
Structural Assembly ◽  
Cl Atom ◽  
Linear Geometry

The title complex, [AuCl(C18H16N5S)]Cl·1.5H2O, may be considered as a gold(I) compound with the corresponding metal site coordinated by a thiosemicarbazone ligand through the S atom. The ligand adopts anEconformation and the gold(I) atom displays the expected linear geometry with a Cl atom also bonded to the metal ion [Cl—Au—S = 174.23 (5)°]. One of the pyridyl rings is protonated, giving the gold complex an overall positive charge. Two solvent water molecules, one of which is located on a twofold rotation axis, and a non-coordinating chloride ion complete the structural assembly. The molecular structure is stabilized by intramolecular and intermolecular N—H...Cl, N—H...N, O—H...Cl and O—H...O hydrogen bonding.

X-Ray Diffraction Studies on Ternary MgCl2-KCI-H2O and MgCI2-CsCl-H2O Solutions Saturated with the Corresponding Double Salts

1991 ◽  
Vol 46 (4) ◽  
pp. 307-312 ◽  
Author(s):  
Kenji Waizumi ◽  
Yusuke Tamura ◽  
Hideki Masuda ◽  
Hitoshi Ohtaki
Keyword(s):  
Hydration Number ◽  
Chloride Ion ◽  
Chloride Ions ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
Coordination Numbers ◽  
X Ray Scattering ◽  
Double Salts ◽  
Scattering Measurements

Abstract X-ray scattering measurements have been done on aqueous MgCl2-KCl and MgCl2 CsCl solutions saturated with their double salts of MgCl2• KCl • 6 H2O and MgCl2 • KCl • 6 H2O respectively, at 293 K. The Mg2+ ion was found to be coordinated with six water molecules at an Mg-O distance of 209 and 208 pm, respectively, whereas K+ and Cs+ ions were surrounded by both water molecules and chloride ions in the first coordination sphere. The interatomic distance between the alkali cation and the chloride ion was 320 pm and 339 pm for K+ and Cs+ , respectively, and the coordination numbers of K+ and Cs+ with respect to CP were 2.4 and 2.0, respectively. The alkali metal H20 distance and the hydration number of the cation were 277 pm and 3.7, respectively, for K+ and 315 pm and 4.7, respectively, for Cs+ . The structures of the solutions are discussed in connection with the nucleation processes of the salts from the aqueous solutions

Striking example of a contact chloride ion pair with bridging water molecules in the solid state

1992 ◽  
Vol 114 (12) ◽  
pp. 4945-4946 ◽  
Author(s):  
Edward F. Kleinman ◽  
Jon Bordner ◽  
Bradley J. Newhouse ◽  
Kurtis MacFerrin
Keyword(s):  
Solid State ◽  
Chloride Ion ◽  
Ion Pair ◽  
Water Molecules
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