Intermolecular π/π and H/π interactions in dimers researched by different computational methods

2014 ◽  
Vol 13 (07) ◽  
pp. 1450057
Author(s):  
Cuihong Wang ◽  
Yue Jiang ◽  
Ruiqin Zhang ◽  
Zijing Lin
Keyword(s):  
High Efficiency ◽  
Dipole Moments ◽  
Binding Energies ◽  
Basis Set ◽  
Theoretical Research ◽  
Basis Sets ◽  
Π Interactions ◽  
Π Stacking ◽  
Structures And Properties ◽  
Satisfactory Precision

The analysis of π/π and H /π interactions in complexes are a challenging aspect of theoretical research. Due to the different approximations of different levels of theory, results tend to be inconsistent. We compared the reliabilities of HF, SVWN, M06L, PW91, BLYP, B3LYP, BHandHLYP, B97D, MP2, and DFTB-D approaches in researching π/π and H /π interactions by calculating the binding energies of five benzene-containing dimers. The effects of 6-31+G**, 6-311++G** and 6-311++G(2df,2p) basis sets on the results were analyzed too. We found that the DFTB-D and B97D methods combined with the 6-311++G** basis set perform well for dimers that contain π/π and H /π interactions. With high efficiency and satisfactory precision, DFTB-D is helpful for the calculation of complexes containing π/π and H /π stacking. We further calculated the structures and properties of phenylalanine-containing dimers using the DFTB-D and B97D methods. The properties of low energy conformers such as rotational constants, dipole moments and molecular orbitals were also analyzed. These data should be helpful for research into systems that contain π/π and H /π stacking.

A COMPARATIVE STUDY ON INTERMOLECULAR HYDROGEN BOND INTERACTIONS IN MOLECULAR DIMERS USING DIFFERENT LEVELS OF COMPUTATIONAL METHODS

2012 ◽  
Vol 11 (06) ◽  
pp. 1237-1259 ◽  
Author(s):  
CUIHONG WANG ◽  
RUIQIN ZHANG ◽  
ZIJING LIN
Keyword(s):  
Hydrogen Bond ◽  
High Efficiency ◽  
Intermolecular Hydrogen Bond ◽  
Good Choice ◽  
Binding Energies ◽  
Basis Set ◽  
Basis Sets ◽  
Bond Lengths ◽  
Hydrogen Bond Interactions ◽  
Theoretical Approaches

Hydrogen bond interactions in biological systems are important scientific issues but are challenging for their theoretical determinations at quantum-mechanical level of theory. Due to the different approximations, the available theoretical approaches often predict diverse hydrogen bond lengths and strengths. In this work, we evaluated the reliabilities of a number of widely used theoretical approaches including HF, SVWN, BLYP, PW91, B3LYP, BH and HLYP, B97D, M06L, MP2, and DFTB-D in studying hydrogen bonding, by calculating the hydrogen bond lengths and binding energies of 23 dimers formed by HCOOH , NH3 and Glycine. We also compared the effects of STO-3G, 6-31+G**, 6-311++G** and 6-311++G(2df,2p) basis sets on the results. Our result shows that, M06L, B3LYP and BHandHLYP methods can predict accurate dimer structures with a moderate basis set. Moreover, DFTB-D also gives reasonably reliable results with high efficiency and satisfactory precision, being a good choice for studying complex structures which contain hydrogen bonds.

scholarly journals Stable Occupancy of Hydrogen Molecules in Clathrate Hydrates and + THF Clathrate Hydrates Determined by Ab Initio Calculations

2010 ◽  
Vol 2010 ◽  
pp. 1-6 ◽  
Author(s):  
Prasad Yedlapalli ◽  
Sangyong Lee ◽  
Jae W. Lee
Keyword(s):  
Ab Initio ◽  
Binding Energies ◽  
Clathrate Hydrates ◽  
Basis Set ◽  
Large Cavity ◽  
Basis Sets ◽  
Pure Hydrogen ◽  
Point Energy ◽  
Small Cavity ◽  
Hydrogen Molecules

Structure II clathrate hydrates of pure hydrogen and binary hydrates of are studied using ab initio calculations to determine the stable occupancies of small cavities. Ab initio calculations are carried out for a double cavity consisting of one dodecahedron (small cavity) and one hexakaidecahedron (large cavity). These two cavities are attached to each other as in sII hydrates to form a double cavity. One or two molecules are placed in the small cavity and one THF (or 4 molecules) molecule is placed in the large cavity. We have determined the binding energies of the double cavities at the MP2 level using various basis sets (3-21G, 3-21G(2p), 3-21 G(2p), 6-31G, 6-31G(2p), and 6-31 G(2p)). Different basis sets yield different stable occupancies of the small cavity. The results from the highest basis set (6-31 G(2p) with zero point energy corrections) indicate that the single occupancy is slightly more favorable than the double occupancy in both the cases of pure hydrates and THF + double hydrates.

Standardized Medium-Size Basis Sets for Calculations of Molecular Electric Properties: Group IIIA

2003 ◽  
Vol 68 (2) ◽  
pp. 211-239 ◽  
Author(s):  
Ivan Černušák ◽  
Vladimir Kellö ◽  
Andrzej J. Sadlej
Keyword(s):  
Reference Data ◽  
Dipole Moments ◽  
Relativistic Effects ◽  
Basis Set ◽  
Basis Sets ◽  
Medium Size ◽  
Polarized Basis Sets ◽  
First Order ◽  
Atomic Dipole ◽  
High Level

The idea of what is called the basis set polarization method is reviewed and the available polarized basis sets are surveyed. Following the basis set polarization approach and certain empirical rules developed earlier, the first-order polarized basis sets for the Group IIIA elements are generated. These basis sets have been developed for both nonrelativistic and spin-averaged Douglas-Kroll relativistic calculations. Their performance is tested in calculations of atomic dipole polarizabilities and in high-level-correlated calculations of the dipole moments of GaF, InF, and TlF. The relativistic effects have been found to significantly affect the calculated molecular dipole moments of the studied fluorides. The results are in satisfactory agreement with reference data. The present study completes the library of the first-order polarized basis sets for all atoms of the main groups of the Periodic Table.

Pseudopotentials for second row atoms. Abinitio molecular calculations on PH3, H2S, and HCl

1985 ◽  
Vol 63 (7) ◽  
pp. 1922-1924 ◽  
Author(s):  
Rezső Gáspár ◽  
Rezső Gáspár Jr.
Keyword(s):  
Dipole Moments ◽  
Substantial Reduction ◽  
Binding Energies ◽  
Force Constants ◽  
Ionization Potentials ◽  
Basis Set ◽  
Pseudopotential Method ◽  
Bond Angles ◽  
Bond Lengths ◽  
Molecular Calculations

Gaussian nonlocal pseudopotentials are introduced for the simplification of the description of second row elements. Pseudopotential parameters for P, S, and Cl are presented. The pseudopotential method is applied to HCl, H2S, and PH3. Substantial reduction in the dimension of the orbital basis set is achieved. Results on total valence energies, binding energies, ionization potentials, force constants, equilibrium bond angles, bond lengths, and dipole moments are presented and compared to experiment as well as to the results of calculations with other methods.

scholarly journals Selection the Drug Efficacy of Oroidin Derivatives as Hsp90 Inhibitors by Computer Aided Drug Design Method

2020 ◽  
pp. 630-651
Author(s):  
Subhajit Sarkar ◽  
Rajesh Kumar Das
Keyword(s):  
Chemical Potential ◽  
Design Method ◽  
Molecular Descriptor ◽  
Dipole Moments ◽  
Binding Energies ◽  
Basis Set ◽  
Toxicity Tests ◽  
In Vitro Test ◽  
In Silico Studies

Heat shock protein 90 (Hsp90) is a conserved molecular chaperone associated with regulation of hundreds of client proteins that are key drivers, regulators and promoters of numerous refractory diseases including cancer. Consequently, Hsp90 is a significant target for the development of harmless anticancer therapies. Marine organisms are the rich source of pharmacological important compounds, especially oroidin. Oroidin, a pyrrole-2-aminoimidazole alkaloid, isolated from the marine sponge Agelas oroides, binds ATP pocket of Hsp90 and suppresses the ATPase activity of the protein. Natural product oroidin was selected as potent inhibitor of Hsp90 and its drug candidature was accordingly improved by substituting various functional groups. Virtual screenings were done through in silico studies, carried out on thirty nine derivatives of oroidin. DFT study was performed with Gaussian16, UB3LYP/6-311G++ (d, p) basis set to investigate the quantum mechanical parameters such as HOMO-LUMO energies, dipole moments. Derived parameters like ionization potential, electron affinity, softness-hardness, chemical potential and electrophilicity index were also calculated. Using AutoDock 4.0 programme, we studied docking of the thirty-nine designed derivatives with macromolecule Hsp90 and recorded the binding energy values of the best conformation out of nine in each docked compound. ADME predictions, molecular descriptor properties, and theoretical toxicity tests were evaluated using preADMET, molinspiration, and OSIRIS property explorer web tools respectively. We found twenty eight derived compounds, each docked at the same region of Hsp90, possessing higher binding energies compare to the precursor oroidin. Seven of them qualified all the rules of drug candidature and could be safe in using as effective drugs for cancer treatment. This study suggests that these compounds could be synthesized for in vitro test and may leads to a novel anticancer therapeutics.

Basis set convergence of binding energy with and without CP-correction utilizing PBE0 method: A benchmark study of X2 (X=Ge, As, Se, Sc, Ti, V, Cr, Mn, Co, Cu, Zn)

2019 ◽  
Vol 18 (08) ◽  
pp. 1950034
Author(s):  
S. Akbudak ◽  
G. Uğur ◽  
Ş. Uğur ◽  
H. Y. Ocak
Keyword(s):  
Binding Energy ◽  
Binding Energies ◽  
Basis Set ◽  
Basis Sets ◽  
Set Convergence ◽  
Hartree Fock ◽  
Counterpoise Correction ◽  
Benchmark Study ◽  
Complete Basis Set ◽  
Speed Up

A DFT study of homonuclear X2 ([Formula: see text], As, Se, Sc, Ti, V, Cr, Mn, Fe, Co, Cu, Zn) is presented using PBEO exchange (xc) functional which is a mixing of Perdew–Burke–Ernzerhof (PBE) and Hartree Fock (HF) exchange energy. However, we used cc-pVXZ and aug-cc-pVXZ basis sets where X is maximum angular momentum number in basis set. Convergence pattern of binding energy with respect to basis set was observed. Two-point extrapolations to complete basis set (CBS) limit were applied to speed up convergence and decrease the basis set incompleteness error (BSIE). Counterpoise correction (CP) method was utilized to alleviate basis set superposition errors (BSSE). Both CP-corrected and uncorrected binding energies were obtained and compared with the experimental and theoretical binding energy values in literature.

Benchmark study of the linear and nonlinear optical polarizabilities in proto-type NLO molecule of para-nitroaniline

2019 ◽  
Vol 18 (06) ◽  
pp. 1950030 ◽  
Author(s):  
Shabbir Muhammad ◽  
Rao Aqil Shehzad ◽  
Javed Iqbal ◽  
Abdullah G. Al-Sehemi ◽  
M. Saravanabhavan ◽  
...  
Keyword(s):  
Nonlinear Optical ◽  
Dipole Moments ◽  
Basis Set ◽  
Basis Sets ◽  
Frontier Molecular Orbital ◽  
Structure Property ◽  
Electronic Communications ◽  
Nlo Properties ◽  
Nlo Materials ◽  
Linear And Nonlinear

In the present investigation, for the first time, we have performed a thorough study about different functionals and basis sets for linear and nonlinear optical (NLO) properties of para-nitroaniline ([Formula: see text]-NA), which is considered as proto-type NLO molecule, among organic NLO materials. There is a dire need of such data base for [Formula: see text]-NA because many investigators are using such values of [Formula: see text]-NA for comparative analysis. A range of different functionals including HF, BLYP, PW91, PBE, B3LYP, M06, M06-2X, PBE0, BHandHLYP, CAM-B3LYP, LC-BLYP, and B3LYP-D3 are applied in conjugation with several commonly basis sets such as 6-31G*, 6-311G*, 6-311G**, 6-311+G**, cc-pVDZ, and cc-pVTZ. A variety of functional and basis sets combinations are calculated and graphically compared with each other. The calculated total dipole moment for the [Formula: see text]-NA is found to be 6.79[Formula: see text]D which is quite closer to experimentally determined value. The lowest calculated value for linear isotropic polarizability at HF/6-31G* level of theory is [Formula: see text] esu while higher values observed with remaining all methods especially 14% polarizability increases in presence of basis set with diffuse functions and similar trend of variation is also observed in linear anisotropic polarizability. Similarly, the calculated value of frequency dependent second-order polarizability is found to be [Formula: see text] esu at PBE0/6-311+G** level of theory which is quite closer to experimental value of [Formula: see text] esu. A comparison between the calculated and experimental results shows good agreement among geometries, dipole moments and NLO polarizabilities for [Formula: see text]-NA. Moreover, the frontier molecular orbital (FMO) and electron density difference map (EDDM) analysis along with density of state (DOS) plots are also presented to get more physical intuitions into the structure–property relationship and electronic communications between terminal accepter and donor groups through [Formula: see text]-conjugation. The present investigation provides benchmark data including various commonly used functionals and basis sets for the calculation of NLO properties of [Formula: see text]-NA. Thus, the present investigation will put straight several future studies when it comes to comparative NLO study of organic materials.

Medium-size polarized basis sets for high-level correlated calculations of molecular electric properties

1988 ◽  
Vol 53 (9) ◽  
pp. 1995-2016 ◽  
Author(s):  
Andrzej J. Sadlej
Keyword(s):  
Intermolecular Interactions ◽  
Dipole Moments ◽  
Electric Properties ◽  
Basis Set ◽  
Basis Sets ◽  
Medium Size ◽  
Molecular Dipole ◽  
Large Molecules ◽  
Polarized Basis Sets ◽  
High Level

The basis set polarization approach is applied to the generation of medium-size polarized GTO/CGTO basis sets for accurate calculations of molecular dipole moments and polarizabilities. The polarized basis sets determined in this paper for H and C through F are employed in SCF HF and MBPT calculations of dipole moments and polarizabilities of FH, H2O, NH3, and CH4. The excellent results obtained at both the SCF HF and MBPT(4) levels of approximation indicate that the present basis sets can be employed for the accurate high-level correlated studies of relatively large molecules The use of those basis sets in calculations of intermolecular interactions is also discussed.

STACKING INTERACTION IN PYRAZINE DIMER

2006 ◽  
Vol 05 (03) ◽  
pp. 609-619 ◽  
Author(s):  
BRIJESH KUMAR MISHRA ◽  
N. SATHYAMURTHY
Keyword(s):  
Center Of Mass ◽  
Binding Energies ◽  
Mass Separation ◽  
Basis Set ◽  
Basis Sets ◽  
Mutual Orientation ◽  
Coupled Cluster ◽  
Basis Set Superposition Error ◽  
Moller Plesset ◽  
Plesset Perturbation Theory

The structure and stability of pyrazine dimer in different orientations have been investigated using second- and fourth-order Møller–Plesset perturbation theory (MP2, MP4) and coupled-cluster singles and doubles with non-iterative perturbative triples method [CCSD(T)] with various basis sets (6-31G*, 6-311G**, 6-311++G**, cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ). With the largest basis set (aug-cc-pVTZ) at the MP2 level of theory, the calculated binding energies (basis set superposition error corrected) for the sandwich, N–N axial-displaced, lateral-displaced, cross-displaced, T-shaped ( T N-ring and T H-ring ), and wedge-shaped ( W N–C and W C–C ) geometries are found to be 3.01, 4.18, 4.63, 5.92, 4.54, 2.78, 2.89, and 3.23 kcal/mol, respectively. Although MP2 calculations predict the cross-displaced geometry to be the most stable one, MP4 and CCSD(T) calculations show the most stable geometry to be T-shaped ( T N-ring ), with a center-of-mass separation of 4.2 Å. Dispersion interaction seems to be the major source of attraction in all the geometries considered, while the nature of electrostatic interaction depends on the mutual orientation of the two rings.

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