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

Relativistic compact effective potentials and efficient, shared-exponent basis sets for the third-, fourth-, and fifth-row atoms

1992 ◽  
Vol 70 (2) ◽  
pp. 612-630 ◽  
Author(s):  
Walter J. Stevens ◽  
Morris Krauss ◽  
Harold Basch ◽  
Paul G. Jasien
Keyword(s):  
Atomic Orbital ◽  
Basis Sets ◽  
Excitation Energies ◽  
Effective Potentials ◽  
Hartree Fock ◽  
The Third ◽  
Atomic Excitation ◽  
Core Electrons ◽  
Atomic Wavefunctions ◽  
Molecular Calculations

Relativistic compact effective potentials (RCEP), which replace the atomic core electrons in molecular calculations, have been derived from numerical Dirac–Fock atomic wavefunctions using shape-consistent valence pseudo-orbitals and an optimizing procedure based on an energy-overlap functional. Potentials are presented for the third-, fourth-, and fifth-row atoms of the Periodic Table (excluding the lanthanide series). The efficiency of molecular calculations is enhanced by using compact Gaussian expansions (no more than three terms) to represent the radial components of the potentials, and energy-optimized, shared-exponent, contracted-Gaussian atomic orbital basis sets. Transferability of the potentials has been tested by comparing calculated atomic excitation energies and ionization potentials with values obtained from numerical relativistic Hartree–Fock calculations. For the alkali and alkaline earth atoms, core polarization potentials (CPP) have been derived which may be added to the RCEP to make possible accurate molecular calculations without explicitly including core-valence correlating configurations in the wavefunction. Keywords: model potentials, effective core potentials, transition metals, relativistic calculations.

On the differential hydration of various forms of glycine in diluted aqueous solutions: a Monte Carlo study

2012 ◽  
Vol 31 (2) ◽  
pp. 295
Author(s):  
Biljana Bujaroska ◽  
Kiro Stojanoski ◽  
Ljupco Pejov
Keyword(s):  
Monte Carlo ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Water Molecules ◽  
Hydrogen Bonding Interaction ◽  
Liquid Environment ◽  
Zwitterionic Form ◽  
Solvent Water ◽  
Bonding Interaction ◽  
Solvent Molecules

Rigid-body Monte Carlo simulations were carried out to study the differential hydration of zwitterionic and neutral forms of glycine in water. To account for the solute polarization by the rather polar liquid environment, initial geometries were chosen as minima on the MP2/aug-cc-pVTZ potential energy surfaces of neutral and zwitterionic glycine continuously solvated by water, implementing the polarizable continuum model (PCM) within the integral equation formalism (IEFPCM). The dynamically changing hydrogen bonding network between the solute and solvent molecules was analyzed imposing distance, energy and angular distribution-based criteria. It was found that, on average, the zwitterionic form of glycine acts as an acceptor of 4.53 hydrogen bonds, while it plays the role of a proton donor in (on average) 2.73 hydrogen bonds with the solvent water molecules. In particular, we have found out that 2.73 solvent water molecules are involved in hydrogen bonding interaction with the ammonium group, acting as proton-acceptors. This is in excellent agreement with the recent experimental neutron diffraction studies, which have indicated that 3.0 water molecules reside in the vicinity of the NH3+ group of aqueous zwitterionic glycine. Neutral form of aqueous glycine, on the other hand, on average donates protons in 1.63 hydrogen bonds with the solvent water molecules, while at the same time it accepts 2.53 hydrogen bonds from the solvent molecules. The greater charge polarization in the zwitterionic form thus makes it much more exposed to hydrogen bonding interaction in polar medium such as water, which is certainly the main reason of the larger stability of this form of glycine in condensed media.

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.

The vibrational spectrum, barrier to internal rotation, and ab initio calculations of 2-chloropropane

1991 ◽  
Vol 69 (11) ◽  
pp. 1845-1856 ◽  
Author(s):  
J. F. Sullivan ◽  
Aiying Wang ◽  
Mei-Shiow Cheng ◽  
J. R. Durig
Keyword(s):  
Vibrational Spectrum ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Internal Rotation ◽  
Far Infrared ◽  
Basis Sets ◽  
Equilibrium Geometry ◽  
Coupling Term ◽  
Hartree Fock ◽  
Experimental Values

The Raman spectra (3200–50 cm−1) of gaseous, liquid, and solid 2-chloropropane-d3 (isopropyl-d3 chloride), CH3(CD3)CHCl, and the infrared spectra (3200–50 cm−1) of the gas and solid have been recorded. The torsional transitions observed in the far infrared spectrum of the gaseous sample recorded at a resolution of 0.10 cm−1 between 265 and 135 cm−1 were analyzed in terms of the semirigid rotor model. An effective barrier of 1378 ± 4 cm−1 (3.94 ± 0.01 kcal/mol), cosine–cosine coupling term of 166 ± 10 cm−1 (0.47 ± 0.03 kcal/mol), and sine–sine coupling term of −173 ± 1 cm−1 (−0.49 ± 0.01 kcal/mol) were determined by fitting ten observed frequencies arising from the CH3 and CD3 torsions. The assignment of the 27 fundamentals is given and discussed. A complete equilibrium geometry, barrier to internal rotation, and vibrational frequencies have been determined by ab initio Hartree–Fock gradient calculations employing either 3-21G* or 6-31G* basis sets for both the d0 and d3 species. These calculated results are compared to the experimental values as well as to the corresponding quantities for some similar molecules. Key words: 2-chloropropane, vibrational spectrum; ab initio calculations; barrier to internal rotation.

The simplified ab initio method calculation of linear polarizability

1973 ◽  
Vol 26 (5) ◽  
pp. 921 ◽  
Author(s):  
RD Brown ◽  
GR Williams
Keyword(s):  
Ab Initio ◽  
Small Molecules ◽  
Basis Set ◽  
Basis Sets ◽  
Orbital Method ◽  
Polarizability Anisotropy ◽  
Minimal Basis ◽  
Hartree Fock ◽  
Numerical Performance ◽  
Experimental Values

The simplified ab-initio molecular-orbital method described previously is particularly suited to the calculation of polarizabilities by the non-perturbative coupled Hartree-Fock technique. Trial calculations on CO and HF, for which comparison with corresponding ab-initio calculations is possible, show that the method gives an adequate numerical performance. Minimal basis set calculations in general tend to give values that are considerably too low because of inadequate flexibility of the basis and this is the origin of the large discrepancy between theory and experiment, especially for small molecules. ��� Results are also reported for N2O and O3. For these larger systems the SAI results with minimal basis sets are noticeably nearer experimental values. The polarizability anisotropy for N2O is particularly well reproduced by the SAI method. �

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