scholarly journals Ab Initio Study of Proton Transfer and Hydration in Phosphorylated Nata de Coco

2017 ◽  
Vol 17 (3) ◽  
pp. 523 ◽  
Author(s):  
Sitti Rahmawati ◽  
Cynthia Linaya Radiman ◽  
Muhamad Abdulkadir Martoprawiro
Keyword(s):  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Ab Initio ◽  
Minimum Energy ◽  
Ring Structure ◽  
Energy Structure ◽  
Water Molecules ◽  
Pyranose Ring ◽  
Positive Interaction ◽  
Negative Change

This research aims to calculate energetics parameters, hydrogen bonding, characteristics local hydration, and proton transfer in phosphorylated nata de coco (NDCF) membrane using ab initio method. The minimum energy structure of NDCF membranes and the addition of n water molecules (n = 1-10) determined at the B3LYP/6-311G** level indicates that proton dissociation requires a minimum of four water molecules. Dissociated protons stabilize with the formation of (hydronium, Zundel, Eigen) ions. Calculation of the interaction energy with n water molecules indicates an increasingly negative change in energy (ΔE) and enthalpy (ΔH), and hence an increasingly positive interaction with water molecules. This interaction facilitates the transfer of protons in the membrane matrix. Calculation of the rotational energy at the center of C-O indicates that the pyranose ring structure, with a maximum barrier energies of ~ 12.5 J/mol, is much more flexible than the aromatic backbones of sulfonated poly(phenylene) sulfone (sPSO2) and the polytetrafluoroethylene (PTFE) backbones in perfluorosulfonic acid ionomers (PFSA). These energy calculations provide the basis that the flexibility of the pyranose ring and the hydrogen bonding between water molecules and phosphonate groups influence the transfer of protons in the membrane of NDCF.

scholarly journals QM AND AB INITIO INVESTIGATION ON THE HYDROGEN BONDING, NMR CHEMICAL SHIFTS AND SOLVENT EFFECTS ON THE DPPE

2010 ◽  
Vol 7 (3) ◽  
pp. 260-272
Author(s):  
M. Monajjemi ◽  
A. Nouri ◽  
H. Monajemi
Keyword(s):  
Hydrogen Bonding ◽  
Ab Initio ◽  
Atomic Orbital ◽  
Theoretical Data ◽  
Basis Sets ◽  
Stable Complex ◽  
Head Group ◽  
Water Molecules ◽  
Hartree Fock ◽  
Zwitterionic Form

The hydrogen bonding effects that were produced from interaction of membrane lipid dipalmitoylphosphatidyl-ethanolamine (DPPE) with 1-5 water molecules, has been theoretically  investigated through the quantum mechanical calculations at the Hartree-Fock level of theory and the 3-21G, 6-31G and 6-31G* basis sets with the computational package of Gaussian 98. According to the obtained results of the structural optimization of the isolated DPPE in the gas phase, we can see the evidences of interactions in the head group of this macromolecule (from the molecular point of view we have a proton transfer from the ammonium group to the phosphate oxygen of zwitterionic form. As we know that the hydrogen bonding of DPPE with water molecules which have surrounded its head group plays an important role in the permeability of DPPE. So, in order to understand the microscopic physico-chemical nature of this subject we have analyzed bond and torsion angles of DPPE before and after added water molecules.  In this paper we have theoretically studied the complexes DPPE with water molecules which have surrounded its head group. As mentioned before, this theoretically study has been done through Hartree-Fock level of theory by using simple basis sets. Theoretical data shows that the interaction of head group of DPPE with water molecules causes some changes in the geometry of DPPE which were explained by the contribution of zwitterionic form of DPPE macromolecule, and finally hydrated DPPE becomes stable complex. Comparison between theoretical and experimental geometry data of DPPE macromolecule shows that the calculation at the HF/3-21 level of theory produces results which they are in better agreement with the experimental data. Moreover the hydrogen bonding effects on the NMR shielding tensor of selected atoms in the hydrated complexes of DPPE were reported. The ";Gauge Including Atomic Orbitals"; (GIAO) approaches within the SCF-Hartree-Fock approximation have been used in order to investigate the influence of hydrogen bonding of DPPE-water complex on the shielding tensors. Finally, the solvent affects on the stability of DPPE macromolecule, dipole moment and atomic charge of some selected atoms of DPPE molecule was discussed using Onsager model and Merz-Singh-Kolman schema.   Keywords  : Gauge Including Atomic Orbital, DPPE, hydrogen bonding, solvation, quantum mechanics, ab initio

scholarly journals Crystal structure and hydrogen bonding in the water-stabilized proton-transfer salt brucinium 4-aminophenylarsonate tetrahydrate

2016 ◽  
Vol 72 (5) ◽  
pp. 751-755 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Network Structure ◽  
Three Dimensional ◽  
Water Molecules ◽  
Arsanilic Acid ◽  
Dimensional Network

In the structure of the brucinium salt of 4-aminophenylarsonic acid (p-arsanilic acid), systematically 2,3-dimethoxy-10-oxostrychnidinium 4-aminophenylarsonate tetrahydrate, (C23H27N2O4)[As(C6H7N)O2(OH)]·4H2O, the brucinium cations form the characteristic undulating and overlapping head-to-tail layered brucine substructures packed along [010]. The arsanilate anions and the water molecules of solvation are accommodated between the layers and are linked to them through a primary cation N—H...O(anion) hydrogen bond, as well as through water O—H...O hydrogen bonds to brucinium and arsanilate ions as well as bridging water O-atom acceptors, giving an overall three-dimensional network structure.

Infrared and ab initio studies of hydrogen bonding and proton transfer in the complexes formed by pyrazoles

2003 ◽  
Vol 660 (1-3) ◽  
pp. 25-40 ◽  
Author(s):  
J.P. Castaneda ◽  
G.S. Denisov ◽  
S.Yu. Kucherov ◽  
V.M. Schreiber ◽  
A.V. Shurukhina
Keyword(s):  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Ab Initio

A Comparative Study of the BJH- and MCYL-Type Potentials Applied to the Gaseous Water Dimer

1991 ◽  
Vol 46 (5) ◽  
pp. 426-432
Author(s):  
Zdenek Slanina
Keyword(s):  
Gas Phase ◽  
Minimum Energy ◽  
Water Dimer ◽  
Energy Structure ◽  
Water Molecules ◽  
Constant Matrix ◽  
Force Constant Matrix ◽  
Molecular Force ◽  
Phase Water ◽  
Derivatives Of

AbstractVarious refined potentials describing the intra- and inter-molecular force fields of water molecules arc used to calculate the properties of the gas-phase water dimer. The intra-molecular parts have been taken from spectroscopic or quantum-chemical sources. The minimum energy structure was found iteratively using the first derivatives of the potential; the force-constant matrix was constructed by numerical difierentation. A quite close agreement between the Bopp-Jancso-Heinzinger and the Matsuoka-Clementi-Yoshimine-Lie potentials is found. The treatment is applied to seven observed water-dimer isotopomeric isomerizations

Ab initio study of the minimum-energy structure of trans-azobenzene

2002 ◽  
Vol 360 (3-4) ◽  
pp. 349-354 ◽  
Author(s):  
Noriyuki Kurita ◽  
Tsutomu Ikegami ◽  
Yasuyuki Ishikawa
Keyword(s):  
Ab Initio ◽  
Minimum Energy ◽  
Energy Structure ◽  
Ab Initio Study ◽  
Trans Azobenzene

scholarly journals Photophysical properties of pyrrolocytosine, a cytosine fluorescent base analogue

2016 ◽  
Vol 18 (30) ◽  
pp. 20189-20198 ◽  
Author(s):  
Quynh L. Nguyen ◽  
Vincent A. Spata ◽  
Spiridoula Matsika
Keyword(s):  
Hydrogen Bonding ◽  
Ab Initio ◽  
Photophysical Properties ◽  
Fluorescence Properties ◽  
Water Molecules ◽  
Pi Stacking ◽  
High Level

The fluorescence properties of pyrrolocytosine, a cytosine analogue, are investigated using high level ab initio methods, and they are found to be affected by hydrogen bonding to water molecules, as well as by pi-stacking with guanine.

AN AB INITIO STUDY OF PROTON-TRANSFER REACTION IN Be2+(H2O)n AND THE SPATIAL CHANGING FEATURE IN THE FORMATION PROCESS OF HYDROXIDE

2006 ◽  
Vol 05 (01) ◽  
pp. 75-85 ◽  
Author(s):  
XIN LI ◽  
ZHONG-ZHI YANG
Keyword(s):  
Proton Transfer ◽  
Ab Initio ◽  
Formation Process ◽  
Turning Point ◽  
Transfer Reaction ◽  
Proton Transfer Reaction ◽  
Water Molecules ◽  
Formation Processes ◽  
Classical Turning Point ◽  
Intrinsic Characteristic

The proton-transfer reaction in Be 2+( H 2 O )n is investigated by an ab initio calculation. With an increasing number of water molecules, there are different formation processes of hydroxide, and the reaction barrier is dependent on the cluster size n. By MELD ab initio program and own-coding programs, we have calculated the potential acting on an electron within a molecule, and have investigated the changing of spatial appearance for the formation process of hydroxide, by the molecular intrinsic characteristic contour defined in terms of the classical turning point of electron movement.

Ab-Initio Study of Neutral Indium Diffusion in Uniaxially- and Biaxially-Strained Silicon

2008 ◽  
Vol 8 (9) ◽  
pp. 4565-4568
Author(s):  
Young-Kyu Kim ◽  
Bum-Goo Cho ◽  
Soon-Yeol Park ◽  
Taeyoung Won
Keyword(s):  
Ab Initio ◽  
Minimum Energy ◽  
Silicon Layer ◽  
Strained Silicon ◽  
Energy Structure ◽  
Migration Energy ◽  
Elastic Band ◽  
Tetrahedral Position ◽  
Substitutional Site ◽  
Indium Diffusion

In this paper, we present our ab-initio study on energy configurations, minimum energy path (MEP), and migration energy for neutral indium diffusion in a uniaxial and biaxial tensile strained {100} silicon layer. Our ab-initio calculation of the electronic structure allowed us to figure out transient atomistic configurations during the indium diffusion in strained silicon. We found that the lowest-energy structure (Ins – SiiTd) consists of indium sitting on a substitutional site while stabilizing a silicon self-interstitial in a nearby tetrahedral position. Our ab-initio calculation implied that the next lowest energy structure is IniTd, the interstitial indium at the tetrahedral position. We employed the nudged elastic band (NEB) method for estimating the MEP between the two structures. The NEB method allowed us to find that that diffusion pathway of neutral indium is kept unchanged in strained silicon while the migration energy of indium fluctuates in strained silicon.

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