A theoretical study of the hydrogen bonding properties of H2BNH2: Some considerations on the basis set superposition error issue

2011 ◽  
Vol 967 (1) ◽  
pp. 147-151 ◽  
Author(s):  
Ibon Alkorta ◽  
Cristina Trujillo ◽  
Jose Elguero ◽  
Mohammad Solimannejad
Keyword(s):  
Hydrogen Bonding ◽  
Theoretical Study ◽  
Basis Set ◽  
Basis Set Superposition Error ◽  
Bonding Properties

Feasibility study of hydrogen-bonded nucleic acid base pairs in gas and water phases — A theoretical study

2011 ◽  
Vol 89 (11) ◽  
pp. 1403-1409 ◽  
Author(s):  
S. Arshadi ◽  
A.R. Bekhradnia ◽  
A. Ebrahimnejad
Keyword(s):  
Hydrogen Bonding ◽  
Nucleic Acid ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Biological Properties ◽  
Point Of View ◽  
Basis Set ◽  
Base Pairs ◽  
Bonding Properties ◽  
Energetic Point

To investigate the base pair binding probabilities for nucleic acid bases, numerous models were studied for contacts between adenine, thymine, guanine, cytosine, and uracil using density functional theory (DFT) in combination with the 6–311G* basis set. We obtained an assessment for the energy given by our calculations in gas and aqueous phases, which showed that it should be incorporated into hydrogen bonding and propeller rotational energies. The 42 complexes of base pairs (5 regular and 37 irregular base pairs) were proposed and their hydrogen-bonding (H-bonding) properties were verified. The hydrogen bonds in some irregular base pairs, including CC, UU, and TT (series 1), were stronger than in regular GC and AT base pairs. Also, the strength of the hydrogen bonds in the proposed base pairs, including CU, GG, GU, and TU (series 2), were similar to regular base pairs from an energetic point of view. The propeller rotations revealed a higher rotational barrier energy (6–7.5 kcal/mol; 1 cal = 4.184 J) for irregular base pairs (series 1 and 2) than regular GC and AT ones (1–3 kcal/mol). Nevertheless, the trend in these affinities of the complex contact probabilities and their biological properties were confirmed by our calculations.

A theoretical study on acetylene dimer, acetylene-s-tetrazine and acetylene-benzene associates

1988 ◽  
Vol 53 (11) ◽  
pp. 2495-2502 ◽  
Author(s):  
Helena Petrusová ◽  
Zdeněk Havlas ◽  
Pavel Hobza ◽  
Rudolf Zahradník
Keyword(s):  
Potential Energy ◽  
Interaction Energy ◽  
Theoretical Study ◽  
Van Der Waals ◽  
Basis Set ◽  
Dispersion Energy ◽  
Basis Set Superposition Error ◽  
Van Der Waals Molecules ◽  
Hartree Fock ◽  
Stabilization Energies

Stabilization energies for the title van der Waals molecules were calculated for various mutual orientations of the subsystems. The interaction energy was expressed as a sum of three contributions: the Hartree-Fock interaction energy, the basis set superposition error and the dispersion energy. The potential energy minima represent reasonably good estimates of the structures of the van der Waals molecules.

scholarly journals Spectroscopic and Theoretical Study of the Intramolecular π-Type Hydrogen Bonding and Conformations of 2-Cyclopenten-1-ol

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1106
Author(s):  
Esther J. Ocola ◽  
Jaan Laane
Keyword(s):  
Hydrogen Bonding ◽  
Internal Rotation ◽  
Energy Surface ◽  
Theoretical Study ◽  
Conformational Dynamics ◽  
The Other ◽  
Basis Set ◽  
Ring Puckering ◽  
High Level ◽  
Calculated Distance

The conformations of 2-cyclopenten-1-ol (2CPOL) have been investigated by high-level theoretical computations and infrared spectroscopy. The six conformational minima correspond to specific values of the ring-puckering and OH internal rotation coordinates. The conformation with the lowest energy possesses intramolecular π-type hydrogen bonding. A second conformer with weaker hydrogen bonding has somewhat higher energy. Ab initio coupled-cluster theory with single and double excitations (CCSD) was used with the cc-pVTZ (triple-ζ) basis set to calculate the two-dimensional potential energy surface (PES) governing the conformational dynamics along the ring-puckering and internal rotation coordinates. The two conformers with the hydrogen bonding lie about 300 cm−1 (0.8 kcal/mole) lower in energy than the other four conformers. The lowest energy conformation has a calculated distance of 2.68 Å from the hydrogen atom on the OH group to the middle of the C=C double bond. For the other conformers, this distance is at least 0.3 Å longer. The infrared spectrum in the O-H stretching region agrees well with the predicted frequency differences between the conformers and shows the conformers with the hydrogen bonding to have the lowest values. The infrared spectra in other regions arise mostly from the two hydrogen-bonded species.

ELECTRON TOPOLOGICAL AND ENERGETIC STUDY OF THE INTERMOLECULAR HALOGEN BONDING INTERACTIONS IN COMPLEXES H2O ⋯ M (M = F2, ClF, ANDCF4)

2009 ◽  
Vol 08 (04) ◽  
pp. 615-629 ◽  
Author(s):  
HAI-BEI LI ◽  
YU BIN BAI ◽  
SHAN XI TIAN ◽  
JINLONG YANG
Keyword(s):  
Hydrogen Bonding ◽  
Interaction Strength ◽  
Halogen Bonding ◽  
Basis Set ◽  
Basis Set Superposition Error ◽  
Error Corrections ◽  
Bond Stretching ◽  
High Level ◽  
Induction Energy ◽  
Good Agreement

The halogen bonding complexes H 2 O ⋯ M ( M = F 2, ClF , and CF 4) in comparison with the hydrogen bonding H 2 O ⋯ HF complex are studied by high-level ab initio calculations and electron topological atoms-in-molecules (AIM) analyses. The basis set superposition error corrections are important to predict if the structures are in good agreement with the experimental results. Both the CCSD(T)/aug-cc-pVTZ calculations and the AIM analyses indicate a interaction strength order: H 2 O ⋯ HF > H 2 O ⋯ ClF ⋯ H 2 O ⋯ F 2 ⋯ H 2 O ⋯ CF 4, with the interaction energies –7.91, –4.16, –1.11, and –1.05 kcal/mol, respectively. The symmetry-adapted perturbation theory analyses have been carried out towards understanding of the nature of the halogen bonding interactions in the complexes H 2 O ⋯ M ( M = F 2, ClF , and CF 4), where the exchange energies are the predominant repulsive components. For the complexes involving polar monomers, the hydrogen bonding H 2 O ⋯ HF and the halogen bonding H 2 O ⋯ ClF , the largest attractive contributions are the electrostatic energies. However, in H 2 O ⋯ F 2 and H 2 O ⋯ CF 4, the attractive dispersion energies become more important, and the induction energy in the former complex is a little higher than that in the latter. In contrary to the red-shifts of H – F , Cl – F , and F – F bond stretching vibrational frequencies in the complexes H 2 O ⋯ M ( M = HF , ClF , and F 2), the blue-shifts are predicted for C – F bonds neighboring water in H 2 O ⋯ CF 4.

DFT computations on the hydrogen bonding interactions between methacrylic acid-trimethylolpropane trimethacrylate copolymers and letrozole as drug delivery systems

2016 ◽  
Vol 15 (02) ◽  
pp. 1650015 ◽  
Author(s):  
Saeedeh Kazemi ◽  
Aliasghar Sarabi Daryani ◽  
Majid Abdouss ◽  
Zahra Shariatinia
Keyword(s):  
Drug Delivery ◽  
Hydrogen Bonding ◽  
Methacrylic Acid ◽  
Density Functional ◽  
Drug Delivery Systems ◽  
Delivery Systems ◽  
Basis Set ◽  
Basis Set Superposition Error ◽  
Hydrogen Bonding Interactions ◽  
Spontaneous Interaction

The hydrogen bonding interactions between letrozole (Let) anticancer drug and three copolymers of methacrylic acid-trimethylolpropane trimethacrylate (M1–M3 as molecular imprinted polymers) were studied using density functional theory (DFT) at both B3LYP and B3PW91 levels. The binding energies were corrected for the basis set superposition error (BSSE) and zero-point vibrational energies (ZPVE) so that the most negative [Formula: see text] were measured for compounds 7 and 8 formed between M1 copolymer and endocyclic N1 and N2 atoms of drug, respectively. Also, among complexes 13–15 in which two copolymers were contributed in the formation of O–H[Formula: see text]N bonds with the drug, compound 13 (containing two M1 copolymers) showed the highest [Formula: see text] value. The interactions of all copolymers with drug were exergonic (spontaneous interaction) and exothermic. The QTAIM data supported the covalent character of the C–N, C–H, N–N, C–O, O–H and O–H[Formula: see text]N bonds, the intermediate nature of C[Formula: see text]N and C[Formula: see text]O bonds while the electrostatic character of C–H[Formula: see text]O, HC[Formula: see text]HC and CH[Formula: see text]N interactions. According to the [Formula: see text], [Formula: see text] and [Formula: see text] values, it was suggested that t complexes 7 and 8 (among two particles systems) as well as complex 13 (among three particles systems) can be the most promising drug delivery systems.

Theoretical study of intramolecular hydrogen bonding and molecular geometry of 2-trifluoromethylphenol

10.1002/jcc.2 ◽  
1996 ◽  
Vol 17 (16) ◽  
pp. 1804-1819 ◽  
Author(s):  
Attila Kov�cs ◽  
Istv�n Kolossv�ry ◽  
G�bor I. Csonka ◽  
Istv�n Hargittai
Keyword(s):  
Hydrogen Bonding ◽  
Theoretical Study ◽  
Molecular Geometry ◽  
Intramolecular Hydrogen Bonding ◽  
Intramolecular Hydrogen
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