scholarly journals Infrared Spectrum for the New Exobiological Nanomolecules Asi, Csi, Tsi and Gsi

2021 ◽  
pp. 25-31
Author(s):  
Ricardo Gobato ◽  
Alireza Heidari ◽  
Lauro Figueroa Valverde ◽  
Abhijit Mitra
Keyword(s):  
Infrared Spectrum ◽  
Quantum Chemistry ◽  
Ab Initio ◽  
Basis Sets ◽  
Minimal Basis ◽  
Hartree Fock ◽  
Standard Bases ◽  
Quantum Chemistry Calculations ◽  
Computational Calculations ◽  
Correlation Consistent

The core of the work is based on the replacement of carbon atoms by silicon atoms, on the basis of four standard bases of DNA: A, C, G and T (adenine, cytosine, guanine, thymine). Determining with minimum computational methods via ab initio Hartree-Fock methods, infrared spectrum and their peak absorbance frequencies. The option for simple replacement of carbon by silicon is due to the peculiar characteristics between both. Atomic interactions under non-carbon conditions were studied, with only the Hydrogen, Silicon, Nitrogen and Oxygen atoms, in CNTP, for the four standard bases of DNA, A, C, G and T, thus obtaining by quantum chemistry four new compounds, named here as: ASi, CSi, GSi and TSi. Computational calculations admit the possibility of the formation of such molecules, their existence being possible via quantum chemistry. Calculations obtained in the ab initio Unrestricted and Restrict Hartree-Fock method, (UHF and RHF) in the set of basis used Effective core potential (ECP) minimal basis, UHF CEP-31G (ECP split valance) and UHF CEP-121G (ECP triple-split basis), CC-pVTZ (Correlation-consistent valence-only basis sets triple-zeta) and 6-311G**(3df, 3pd) (Gaussian functions quadruple-zeta basis sets).

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. �

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

Theoretical investigation of [Ru(tpy)2]2+, [Ru(tpy)(bpy)(H2O)]2+ and [Ru(tpy)(bpy)(Cl)]+ complexes in acetone revisited: Inclusion of strong spin–orbit couplings to quantum chemistry calculations

2016 ◽  
Vol 15 (01) ◽  
pp. 1650001
Author(s):  
Kenji Mishima ◽  
Takumi Kinoshita ◽  
Michitoshi Hayashi ◽  
Ryota Jono ◽  
Hiroshi Segawa ◽  
...  
Keyword(s):  
Experimental Data ◽  
Quantum Chemistry ◽  
Absorption Spectra ◽  
Density Functional ◽  
Order Perturbation ◽  
Basis Sets ◽  
Spin Orbit ◽  
First Order ◽  
Quantum Chemistry Calculations ◽  
First Order Perturbation

In the present paper, we theoretically reinvestigate structural properties, and photo-physical and chemical characteristics and electronic absorption spectra of three kinds of ruthenium polypyridyl complexes [Ru(tpy)[Formula: see text], [Ru(tpy)(bpy)(H2O)][Formula: see text], and [Ru(tpy)(bpy)(Cl)][Formula: see text] complexes in acetone (tpy[Formula: see text]2,2[Formula: see text],2[Formula: see text]-terpyridine and bpy[Formula: see text]2,2[Formula: see text]-bipyridine). In particular, the experimental absorption spectra of these complexes are revisited theoretically in detail and are simulated using the first-order perturbation theory based on time-dependent density functional theory (TD-DFT) where the first-order perturbation term is the spin–orbit (SO) coupling Hamiltonian, and quantum chemistry calculations based on various functionals and basis sets. It was found that in general the theory including SO coupling can reproduce experimental data better than the simple quantum chemistry calculation neglecting SO coupling, which indicates that SO coupling is very important to understand the optical features of these complexes and that therefore the mixing between singlet and triplet states is strong due to the large SO coupling constant of Ru atom involved in these complexes. This suggests the fact that the disagreement between the experimental and calculated absorption spectra was found in TDB3LYP/(SDD with triple-[Formula: see text] for Ru and 6-31G* for others) [Jakubikova EJ et al., Inorg Chem 48:10720, 2009] can be tracked down to the neglect of SO couplings. It was also found that the choice of the DFT functionals and basis sets is crucial for a good theoretical reproduction of experimental data.

scholarly journals Ab initio study of the mechanism of the reaction ClO + O --> Cl + O2

2021 ◽  
Vol 66 (1) ◽  
Author(s):  
S. Naskar ◽  
G. Nandi ◽  
T. K. Ghosh
Keyword(s):  
Reaction Mechanism ◽  
Ab Initio ◽  
Minimum Energy ◽  
Transition States ◽  
Basis Set ◽  
Heat Of Reaction ◽  
Minimal Basis ◽  
Dissociation Energies ◽  
Correlation Consistent ◽  
Equilibrium Geometries

Abstract. Ab initio investigation on the reaction mechanism of ClO + O --> Cl + O2 reaction has been performed using correlation consistent triple zeta basis set. The geometry and frequency of the reactants, products, minimum energy geometries and transition states are obtained using MP2 method and energetics are obtained at the QCISD(T)//MP2 level of theory. Primarily, a possible reaction mechanism is obtained on the basis on IRC calculations using MP2 level of theory. To obtain true picture of the reaction path, we performed IRC calculations using CASSCF method with a minimal basis set 6-31G**. Some new equilibrium geometries and transition states have been identified at the CASSCF level. Energetics are also obtained at the QCISD(T)//CASSCF method. Possible reaction paths have been discussed, which are new in literature. Heat of reaction is found to be consistent with the experimental data. Bond dissociation energies to various dissociation paths are also reported.

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.

Comparison of ab initio quantum chemistry calculations on matrix isolated molecules with Mössbauer effect studies

1988 ◽  
Vol 40 (1-4) ◽  
pp. 111-122 ◽  
Author(s):  
E. Bominaar ◽  
J. Guillin ◽  
V. R. Marathe ◽  
A. Sawaryn ◽  
A. X. Trautwein
Keyword(s):  
Quantum Chemistry ◽  
Ab Initio ◽  
Mössbauer Effect ◽  
Mossbauer Effect ◽  
Quantum Chemistry Calculations ◽  
Isolated Molecules
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