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.

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 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.

The Distal Effect of N-Electron-withdrawing Groups on the Stability of Peptide Carbon Radicals

2011 ◽  
Vol 64 (4) ◽  
pp. 403 ◽  
Author(s):  
Junming Ho ◽  
Michelle L. Coote ◽  
Christopher J. Easton
Keyword(s):  
Hydrogen Bonding ◽  
Ab Initio ◽  
Radical Formation ◽  
Ab Initio Methods ◽  
Amide Nitrogen ◽  
Amide Carbonyl ◽  
Carbon Radicals ◽  
The Stability ◽  
High Level ◽  
Calculated Activation

The effect of electron-withdrawing substituents, hydrogen bonding and protonation at amide nitrogen on the stability of radicals formed by loss of either a distal C–H adjacent to the amide carbonyl or one proximal to the amide nitrogen for a series of acetamides and diketopiperazines has been studied via high-level ab initio methods. These studies show that the effect is to destabilize the radicals formed by abstraction of the proximal hydrogens, typically by 10–20 kJ mol–1, and stabilize the distal radicals typically by 5–10 kJ mol–1, but only if the distal radicals are polarized by another dative substituent. The different radical stabilities are not directly mirrored in calculated activation energies or experimental rates of radical formation in bromination reactions, because there is significant charge development in these reaction transition states.

PEMANFAATAN GLISERIN DARI RESIDU GLISERIN SEBAGAI PLASTICIZER UNTUK PEMBUATAN BIOPLASTIK DENGAN BAHAN BAKU PATI BONGGOL PISANG KEPOK

2017 ◽  
Vol 5 (4) ◽  
pp. 26-32 ◽  
Author(s):  
Azaria Robiana ◽  
M. Yashin Nahar ◽  
Hamidah Harahap
Keyword(s):  
Tensile Strength ◽  
Hydrogen Bonding ◽  
Fatty Acid ◽  
Maximum Yield ◽  
Sem Analysis ◽  
Water Molecules ◽  
Banana Weevil ◽  
Gelatinization Temperature ◽  
Recharge Area ◽  
Maximum Quantity

Glycerin residue is waste oleochemical industry that still contain glycerin. To produce quality and maximum quantity of glycerin, then research the effect of pH acidification using phosphoric acid. Glycerin analysis includes the analysis of pH, Fatty Acid and Ester (FAE), and analysis of the levels of glycerin. The maximum yield obtained at pH acidification 2 is grading 91,60% glycerin and Fatty Acid and Ester (FAE) 3,63 meq/100 g. Glycerin obtained is used as a plasticizer in the manufacture of bioplastics. Manufacture of bioplastics using the method of pouring a solution with varying concentrations of starch banana weevil (5% w/v and 7% w/v), variations of the addition of glycerin (1 ml, 3 ml, 5 ml and 7 ml), and a variety of gelatinization temperature (60°C, 70°C, and 80°C). Analysis of bioplastics include FTIR testing, tensile strength that is supported by SEM analysis. The results obtained in the analysis of FTIR does not form a new cluster on bioplastics starch banana weevil, but only a shift in the recharge area only, it is due to the addition of O-H groups originating from water molecules that enter the polysaccharide through a mechanism gelatinitation that generates interaction hydrogen bonding strengthened. The maximum tensile strength of bioplastics produced at a concentration of starch 7% w/v, 1 ml glycerine and gelatinization temperature of 80°C is 3,430 MPa. While the tensile strength bioplastic decreased with increasing glycerin which can be shown from the results of SEM where there is a crack, indentations and lumps of starch insoluble.

Configurational Assignment and Conformational Study of Methylglyoxal Bisdimethylhydrazones Derived from the 2-Ethoxypropenal Precursor

2006 ◽  
Vol 59 (3) ◽  
pp. 211 ◽  
Author(s):  
Leonid B. Krivdin ◽  
Lyudmila I. Larina ◽  
Kirill A. Chernyshev ◽  
Natalia A. Keiko
Keyword(s):  
Ab Initio Calculations ◽  
Ab Initio ◽  
Experimental Measurements ◽  
Conformational Study ◽  
Lone Pairs ◽  
Configurational Assignment ◽  
Out Of Plane ◽  
High Level

A configurational assignment of the isomeric methylglyoxal bisdimethylhydrazones derived from the 2-ethoxypropenal precursor has been performed based on experimental measurements and high-level ab initio calculations of 1J(C,C) and 1J(C,H) couplings. The results reveal the marked stereochemical dependence upon the orientation of the lone pairs of both nitrogen atoms in different isomers. Methylglyoxal bisdimethylhydrazone is shown to exist in a mixture of the EE and ZE isomers (ca. 75:25), both of which adopt predominant s-trans conformations with minor (up to 8°) out-of-plane deviations.

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