Structures and binding energies of benzene–methane and benzene–benzene complexes. An ab initio SCF/MP2 study

Sakaki, Shigeyoshi; Kato, Kenji; Miyazaki, T.; Musashi, Yasuo; Ohkubo, Katsutoshi; Ihara, Hirotaka; Hirayama, Chuichi

doi:10.1039/ft9938900659

Cited by 102 publications

(79 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In 1993, Sakai reported a computational study of the binding energies and structures of benzene-methane complexes and suggested that the dispersion force was the most important for C-H/π hydrogen bonding ( Figure 5) [159]. For the most stable methane-benzene complex 11, the orientation of the methane is above the plane with one hydrogen directed towards the center of the aromatic ring with an angle approaching 180°, thus although unimportant when considering the binding energy, electrostatics determine the geometry of C-H/π complexes.…”

Section: C-h/π Hydrogen Bondsmentioning

confidence: 99%

It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

Yunta¹

2017

AJMO

View full text Add to dashboard Cite

The effect of weak intermolecular interactions on the binding affinity between ligand-protein complexes plays an important role in stabilizing a ligand at the interface of a protein structure. In this review article, we will explore the different ways of taking into account these interactions, mainly intramolecular hydrogen bonds, in docking calculations. Their possible limitations and their suitable application domains are highlighted. Inspection of the outliers of this study probed very stimulating, as it provides opportunities and inspiration to medicinal chemists, being a reminder of the impact that minimal chemical modifications can have on biological activities.

show abstract

Section: C-h/π Hydrogen Bondsmentioning

confidence: 99%

It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

Yunta¹

2017

AJMO

View full text Add to dashboard Cite

show abstract

“…Our group had reported previously that carbonyl groups in Sil-ODA n are polarized to δ + (carbon) and δ -(oxygen). 48 Similarly in Sil-2, the carbonyl groups in the organic phase are polarized to δ + (carbon) and δ -(oxygen) and these polarized atoms can work as an electrostatic source of π-π interaction with π-electron containing guest molecules. As support of this, the selectivity between benzene-nitrobenzene was evaluated as it can be used as a criterion of the contribution of retention from π-interactions in the reversed phase system.…”

Section: Resultsmentioning

confidence: 99%

Synthesis, Characterization and Enhanced Selectivity in RP-HPLC of Polar Carbonyl Group Embedded Poly (Vinyl Octadecanoate) Grafted Stationary Phase by Simple Heterogeneous "Graft from" Technique

Rana

Karim

Takafuji³

2011

Bulletin of the Korean Chemical Society

View full text Add to dashboard Cite

A new high performance liquid chromatograpgy (HPLC) stationary phase that possesses an internal carbonyl functional group is synthesized by heterogeneous "graft from" method. Si CP/MAS NMR, elemental analysis and thermogravimetric analysis. Chromatographic properties of Sil-2 were evaluated under reversed phase condition by separating polycyclic aromatic hydrocarbons (PAHs) and comparing the chromatographic results with those on polymeric as well as monomeric octadecylated silica stationary phases.

show abstract

“…5,6) However, typical CH/p complexes such as benzene-methane [7][8][9] have been shown primarily of dispersion interactions based on high-level ab initio calculations. The interaction energies were also consistent with the experimental binding energy D o of benzene-X (Xϭmethane, 10) ethylene and acetylene, 26) and benzene 27,28) ) as CH/p complexes and benzene-XH 2 (XϭN 29) and O [30][31][32] ) as the T-shape form of hydrogen bonds.…”

Section: Results and Disscussion Relation Between Interaction Energy mentioning

confidence: 99%

“…4) In addition, they play a key role in determining the molecular orientation in molecular assemblies. The weak interaction between the C-H bond and the aromatic p system called the CH/p interaction, 5) has been determined to be a primary contributor to the electrostatic and charge-transfer terms 5,6) based on primary ab initio calculations using a small basis set. In recent years, high-level ab initio calculations of the typical CH/p complex have shown that dispersion is a major source of attraction.…”

mentioning

confidence: 99%

Properties of the Solute-Stationary Liquid Interactions in Gas Liquid Chromatography

Kawaki

2008

CHEMICAL & PHARMACEUTICAL BULLETIN

View full text Add to dashboard Cite

Noncovalent interactions are very important in molecular recognition of biochemistry, molecular crystals, [1][2][3] and hostguest complexes. 4) In addition, they play a key role in determining the molecular orientation in molecular assemblies. The weak interaction between the C-H bond and the aromatic p system called the CH/p interaction, 5) has been determined to be a primary contributor to the electrostatic and charge-transfer terms 5,6) based on primary ab initio calculations using a small basis set. In recent years, high-level ab initio calculations of the typical CH/p complex have shown that dispersion is a major source of attraction.7-9) MP2 interaction energy depends strongly on the basis set and small basis sets (6-31G*, 6-311G** and cc-pVDZ) greatly underestimate the attraction. Therefore, MP2/cc-pVXZ (XϭT or Q) or MP2/aug-cc-pVXZ (XϭD or T) level calculations are necessary for quantitative evaluation of the dispersion energy.10) The estimated CCSD(T) interaction energy for a methane-benzene complex as an example of a typical CH/p interaction at the basis set limit (D e ) was reported to be Ϫ1. 43 ). Furthermore, DEF calculations were discussed using BLYP, B3LYP, PW91 and PBE functions were determined to be in appropriate for the quantitative evaluation of the CH/p interaction energy.12-14) The calculated energy E CCSD(T)(limit) was determined to be appropriate for a quantitative evaluation of the CH/p interaction.In the solute-staitonary liquid interaction of gas liquid chromatography, the entropy changes DDS s o of dissolution were determined to be correlated to the descriptor s M in order to evaluate a physical adsorption using Eyring's model. 15,16) These findings supported the fact that van der Waals interactions were responsible for the formation CH/p complexes between C-H bond of squalane as the stationary liquid and the aromatic p system of the solute. Herein, we discuss the physical origin of the microscopic conditions under which the descriptor s M is correlated to the CH/p interaction energy introduced into the high-level ab initio calculations. ExperimentalRelative Retention Value log g g The log g defined by Eq. 1. Where t R (A) and t R (B) are the retention times of the reference and substituted benzenes, respectively. DH s o and DS s o denote the enthalpy and entropy of dissolution of A and B. All data for log g and the thermodynamic parameters were cited in references, [18][19][20] and the regression analyses were carried out using the statistical program. 21)Descriptors s s M and s s es for Regression Analysis The descriptor s M was derived from the Eyring's method: The activated translational entropy change DDS † ABC for Eyring's equation 15) is given by the following equation, when there is the interaction between the solutes (A and B are the reference and its derivatives) and the non-polar stationary liquid (where C is constant).Where R, k, T and h are the gas constant, Boltzmann's constant, absolute temperature and Plank's constant, respectively.When T is constant, Eq. 5 is given ...

show abstract

Structures and binding energies of benzene–methane and benzene–benzene complexes. An ab initio SCF/MP2 study

Cited by 102 publications

References 30 publications

It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

Synthesis, Characterization and Enhanced Selectivity in RP-HPLC of Polar Carbonyl Group Embedded Poly (Vinyl Octadecanoate) Grafted Stationary Phase by Simple Heterogeneous "Graft from" Technique

Properties of the Solute-Stationary Liquid Interactions in Gas Liquid Chromatography

Contact Info

Product

Resources

About