scholarly journals Ground-State Structures of Hydrated Calcium Ion Clusters From Comprehensive Genetic Algorithm Search

2021 ◽  
Vol 9 ◽  
Author(s):  
Ruili Shi ◽  
Zhi Zhao ◽  
Xiaoming Huang ◽  
Pengju Wang ◽  
Yan Su ◽  
...  
Keyword(s):  
Genetic Algorithm ◽  
Calcium Ion ◽  
Cluster Size ◽  
Lone Pair ◽  
Water Molecules ◽  
Ion Clusters ◽  
Adjacent Water ◽  
Leading Role ◽  
Ground State Structures ◽  
Hydrated Calcium

We searched the lowest-energy structures of hydrated calcium ion clusters Ca2+(H2O)n (n = 10–18) in the whole potential energy surface by the comprehensive genetic algorithm (CGA). The lowest-energy structures of Ca2+(H2O)10–12 clusters show that Ca2+ is always surrounded by six H2O molecules in the first shell. The number of first-shell water molecules changes from six to eight at n = 12. In the range of n = 12–18, the number of first-shell water molecules fluctuates between seven and eight, meaning that the cluster could pack the water molecules in the outer shell even though the inner shell is not full. Meanwhile, the number of water molecules in the second shell and the total hydrogen bonds increase with an increase in the cluster size. The distance between Ca2+ and the adjacent water molecules increases, while the average adjacent O-O distance decreases as the cluster size increases, indicating that the interaction between Ca2+ and the adjacent water molecules becomes weaker and the interaction between water molecules becomes stronger. The interaction energy and natural bond orbital results show that the interaction between Ca2+ and the water molecules is mainly derived from the interaction between Ca2+ and the adjacent water molecules. The charge transfer from the lone pair electron orbital of adjacent oxygen atoms to the empty orbital of Ca2+ plays a leading role in the interaction between Ca2+ and water molecules.

FIRST-PRINCIPLES STUDY OF STRUCTURES AND ELECTRONIC PROPERTIES FOR NITRIDE-DOPED ALUMINUM CLUSTERS

2005 ◽  
Vol 19 (15n17) ◽  
pp. 2380-2385 ◽  
Author(s):  
BAOLIN WANG ◽  
DALING SHI ◽  
XIAOSHUANG CHEN ◽  
GUANGHOU WANG ◽  
JIJUN ZHAO
Keyword(s):  
Genetic Algorithm ◽  
Electronic Properties ◽  
Atomic Structure ◽  
Ground State ◽  
First Principles ◽  
Cluster Size ◽  
Aluminum Clusters ◽  
Structural And Electronic Properties ◽  
Ground State Structures ◽  
Homo Lumo

By using Gaussian98 package at BPW91 6-31g(d,p) level combined a genetic algorithm (GA) simulation, we have studied the lowest energy structural and electronic properties of the Al n N ( n =2-13) clusters. The ground-state structures, the charge transfers from Al to N site, HOMO-LUMO gap and the covalent, ionic and metallic nature with cluster size and atomic structure are investigated. Al 7 N , Al 9 N and Al 12 N cluster is found particularly stable among the Al n N clusters.

Protein environment affects the water–tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants

2018 ◽  
Vol 20 (18) ◽  
pp. 12664-12677 ◽  
Author(s):  
Nad'a Špačková ◽  
Zuzana Trošanová ◽  
Filip Šebesta ◽  
Séverine Jansen ◽  
Jaroslav V. Burda ◽  
...  
Keyword(s):  
Amino Acids ◽  
Lone Pair ◽  
Binding Mode ◽  
The Other ◽  
Water Molecules ◽  
Interaction Type ◽  
Nmr Studies ◽  
Engrailed Homeodomain ◽  
The One ◽  
Protein Environment

Water molecules can interact with the π-face of tryptophan either forming an O–H⋯π hydrogen bond or by a lone-pair⋯π interaction. Surrounding amino acids can favor the one or the other interaction type.

The crystal-structure determination and redefinition of eztlite, Pb22+ Fe33+(Te4+O3)3(SO4)O2Cl

2018 ◽  
Vol 82 (6) ◽  
pp. 1355-1367 ◽  
Author(s):  
Owen P. Missen ◽  
Stuart J. Mills ◽  
John Spratt ◽  
Mark D. Welch ◽  
William D. Birch ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mixed Valence ◽  
Lone Pair ◽  
Water Molecules ◽  
Monoclinic Space Group ◽  
Charge Balance ◽  
X Ray Diffraction ◽  
International Mineralogical Association ◽  
Bond Valence Analysis

ABSTRACTThe crystal structure of eztlite has been determined using single-crystal synchrotron X-ray diffraction and supported using electron microprobe analysis and powder diffraction. Eztlite, a secondary tellurium mineral from the Moctezuma mine, Mexico, is monoclinic, space group Cm, with a = 11.466(2) Å, b = 19.775(4) Å, c = 10.497(2) Å, β = 102.62(3)° and V = 2322.6(9) Å3. The chemical formula of eztlite has been revised to ${\rm Pb}_{\rm 2}^{2 +} {\rm Fe}_3^{3 +} $(Te4+O3)3(SO4)O2Cl from that stated previously as ${\rm Fe}_6^{3 +} {\rm Pb}_{\rm 2}^{2 +} $(Te4+O3)3(Te6+O6)(OH)10·nH2O. This change has been accepted by the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association, Proposal 18-A. Eztlite was reported originally to be a mixed-valence Te oxysalt; however the crystal structure, bond-valence analysis and charge balance considerations clearly show that all Te is tetravalent. Eztlite contains a unique combination of elements and is only the second Te oxysalt to contain both sulfate and chloride. The crystal structure of eztlite contains mitridatite-like layers, with a repeating triangular nonameric [${\rm Fe}_9^{3 +} $O36]45– arrangement formed by nine edge-sharing Fe3+O6 octahedra, decorated by four trigonal pyramidal Te4+O3 groups, compared to PO4 or AsO4 tetrahedra in mitridatite-type minerals. In eztlite, all four tellurite groups associated with one nonamer are orientated with the lone pair of the Te atoms pointing in the same direction, whereas in mitridatite the central tetrahedron is orientated in the opposite direction to the others. In mitridatite-type structures, interlayer connections are formed exclusively via Ca2+ and water molecules, whereas the eztlite interlayer contains Pb2+, sulfate tetrahedra and Cl–. Interlayer connectivity in eztlite is achieved primarily by connections via the long bonds of Pbφ8 and Pbφ9 groups to sulfate tetrahedra and to Cl–. Secondary connectivity is via Te–O and Te–Cl bonds.

scholarly journals A Computational Study of the Relative Aromaticity of Pyrrole, Furan, Thiophene and Selenophene, and Their Diels-Alder Stereoselectivity

2020 ◽  
Author(s):  
Veejendra Yadav
Keyword(s):  
Computational Study ◽  
Lone Pair ◽  
Alder Reaction ◽  
Diels Alder ◽  
Size Mismatch ◽  
Aromatic Character ◽  
Diels Alder Reaction ◽  
Ground State Structures ◽  
Better Than

The collinearity of terminal <i>p</i> orbitals of a diene with that of a dienophile is required for an effective overlap to result in s bond formation during the Diels-Alder reaction. The ease of the DA reaction of a cyclic diene with a given dienophile, therefore, must also depend on the distance between the termini of the diene. A distance larger than the unsaturated bond of the dienophile is expected to raise the energy of activation. This scenario has been amply demonstrated from the study of reactions of several dienes, some designed to serve the purpose, with different dienophiles. The five-ring heterocycles pyrrole, furan, thiophene and selenophene possess varying aromatic character for the varied resonance participation of the heteroatom lone pair with ring p bonds. The aromaticity decreases in the same order due to: (a) the increasing s<sub>C-X</sub> (X = heteroatom) bond length lifts the bond uniformity required for ring current, hence aromaticity, such as in benzene and (b) size-mismatch of the interacting lone pair orbital and the ring <i>p</i> orbitals, especially in thiophene and selenophene, both allowing poor overlap in the ground state structures. It is demonstrated that increase alone in the activation energies of the DA reactions of pyrrole, furan, thiophene and selenophene cannot be considered a measure of relative aromaticity as often done and even theoretically attempted in many ways to prove just that. The separation of the termini of the diene has a much larger role in the determination of activation energy, especially in thiophene and selenophene, than their aromaticity profile. There cannot be a measure better than the relative intensity of heteroatom lone pair overlap with ring p bonds, giving rise to a six-electron like system in following Hückel’s 4n+2 rule, to assess the relative aromaticity.

scholarly journals Prevention of Secondary Caries Using Resin-Based Pit and Fissure Sealants Containing Hydrated Calcium Silicate

Polymers ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1200
Author(s):  
Song-Yi Yang ◽  
Ji-Won Choi ◽  
Kwang-Mahn Kim ◽  
Jae-Sung Kwon
Keyword(s):  
Flexural Strength ◽  
Calcium Ion ◽  
Water Sorption ◽  
Distilled Water ◽  
Acid Neutralization ◽  
Fissure Sealants ◽  
Ion Release ◽  
Hydrated Calcium Silicate ◽  
Pit And Fissure Sealants ◽  
Hydrated Calcium

The objective of this study was to investigate the effects of hydrated calcium silicate filler (hCS) on resin-based pit and fissure sealants’ acid neutralization, calcium ion release, and mechanical and physical properties. To produce the hCS filler, Portland cement (CS) was mixed with distilled water and ground into fine particles. The particles were then mixed with silanized glass filler and added to a photo-activated resin matrix. To evaluate the acid neutralization and calcium ion release properties, the specimens were immersed in a pH 4.0 lactic acid solution and distilled water for 28 days. Also, the flexural strength, depth of cure, water sorption, and solubility were tested. All of the groups containing hCS and CS required less than one minute to increase the pH from 4.0 to 5.5. With 50% hCS, the calcium ion release was higher than 50% CS in the distilled water at the initial time. The flexural strength and depth of cure decreased according to the increasing proportion of hCS added. The water sorption and solubility had an increasing trend as increasing proportions of hCS were added. These findings showed that pit and fissure sealant containing hCS exhibit superior acid neutralization and calcium release properties, and may be promising for caries-inhibiting dental material.

ABEEMσπ FLUCTUATING CHARGE FORCE FIELD APPLIED TO ALANINE DIPEPTIDE AND ALANINE DIPEPTIDE–WATER SYSTEMS

2010 ◽  
Vol 09 (supp01) ◽  
pp. 77-97 ◽  
Author(s):  
CUI LIU ◽  
DONG-XIA ZHAO ◽  
ZHONG-ZHI YANG
Keyword(s):  
Force Fields ◽  
Lone Pair ◽  
Water Systems ◽  
Water Molecules ◽  
Hydration Water ◽  
Electronegativity Equalization Method ◽  
Lone Pair Electrons ◽  
Alanine Dipeptide ◽  
Packing Effects ◽  
Atom Bond

Atom-bond electronegativity equalization method at σπ level fused into molecular mechanics (ABEEMσπ/MM) divides the bond regions into σ and π bond regions on the basis of previous ABEEM/MM. It may suitably reflect intramolecular and intermolecular interaction and polarization. The fitting function k H-bond in the hydrogen bond (HB) interaction region increases the capability of ABEEMσπ/MM to simulate the hydration. Hydration of alanine dipeptide (AD) in aqueous solution is determined by the intramolecular and intermolecular HBs and the competition among the molecular packing effects. The acceptor molecule in HB complex contains at least one pair of lone pair electrons, sometimes contains π bonds, whose orientations directly effect the orientation of HBs. Therefore, ABEEMσπ/MM has obviously predominance to discuss the AD and AD–water systems, which contain many lone pair electrons, π bonds, and abundant HB nets. Properties of six AD conformers, clusters AD +( H2O )1–4 obtained from ABEEMσπ/MM agree well with the results of experiments, ab initio and other force fields. Structural and dynamical properties of the hydration water molecules have just embodied that the ABEEMσπ/MM gives correct hydration description relative to other force fields.

Sign in / Sign up

Export Citation Format

Share Document