A theoretical study on the intermolecular interaction of energetic system-Nitromethane dimer

Three optimized geometries of nitromethane dimer have been obtained at the HF/6-31G level.Dimer binding energies have been corrected for the basis set superposition error (BSSE) and the zero point energy.Computed results indicate that the cyclic structure of (CH3NO2)2 is the most stable of three optimized geometries,whose corrected binding energyis 17.29 kJ mol-1 at the MP4SDTQ/6-31G//HF/6-31G level.In the optimized structures of nitromethane dimer,the inter-molecular hydrogen bond has not been found; and the charge-transfer interaction between CH3NO2 subsystems is weak; and the correlation interaction energy makes a little contribution to the intermolecular interaction energy of the dimer.     

Concept of Ir-catalyzed CH bond activation/borylation by noncovalent interaction

Noncovalent interactions play a fundamental role in molecular biology, crystal engineering, supramolecular chemistry, drug design, sensing applications, and many other research fields in the chemical sciences. Because of this importance, thorough research efforts have been focused on the interpreting and quantifying these interactions, which include H-bonding, electrostatic effects, ππ interaction, cation-π interaction, hydrophobic-hydrophobic interaction, van der Waals forces, and other such type of interactions. However, on the synthetic standpoint, use of these noncovalent interactions are rare, although might be beneficial for the site-selective CH bond activation and functionalization by transition metal catalysis. In this context, iridium-catalyzed CH borylation has gained immense popularity due to the versatility conferred to the CB bonds. Very recently, researchers have started employing these interactions as a governing factor for attaining regioselectivity in arene CH borylation. In this perspective, we will focus on the advancements made so far by the use of various noncovalent interactions in Ir-catalyzed borylations.     

Theoretical study on intermolecular interaction of epoxyethane dimer

Ab initio calculations at Hartree–Fock and fourth‐order Mø ller–Plesset (MP4) correlation correction levels with 6‐31G* basis set have been performed on the epoxyethane dimer. Dimer binding energies have been corrected for the basis set superposition error (BSSE) and the zero‐point energy. The greatest corrected dimer binding energy is −8.36 kJ/mol at the MP4/6‐31G*//HF/6‐31G* level. The natural bond orbital analysis has been performed to trace the origin of the weak interactions that stabilize dimer. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 94–98, 2000     

基于两分子和三分子相互作用的流体界面张力研究

提出了一个改进的密度泛函理论模型.该模型同时考虑了流体中两分子和三分子相互作用对体系Helm hlotz自由能的贡献,对Ar,N2,CH4,CO2等四种流体的气液界面张力进行了预测,结果与实验值均吻合良好.通过与仅考虑两分子作用的理论计算值和分子模拟值进行比较,表明流体中的三分子相互作用对描述非均相流体的结构与性质有重要影响.     

硝酸乙酯分子间相互作用的ab initio研究

在abinitio-HF/6-31G水平上求得硝酸乙酯二聚体势能面上的四种优化构型和电子结构。经MP2电子相关校正和基组叠加误差(BSSE)以及零点能(ZPE)校正，求得二聚体的最大结合能为11.46kJ.mol^-^1，还进行HF/6-311G和HF/6-311++G水平的总能量比较计算，发现6-31G基组对计算结合能比较适合，二子体系间的电荷转移很少，对优化构型进行振动分析，并基于统计热力学求得从单体形成二聚体的热力学性质变化。     

The intermolecular interaction in the charge-transfer complexes between amines and halogens: A theoretical characterization of the trends in halogen bonding

The trends in the properties of prereactive or charge-transfer complexes formed between the simple amines NH₃, CH₃NH₂, (CH₃)₂NH, and (CH₃)₃N and the halogens F₂, ClF, Cl₂, BrF, BrCl, and Br₂ were investigated by the ab initio restricted Hartree–Fock approach, the Møller–Plesset second-order method, and with several density functional theory variants using extended polarized basis sets. The most important structural parameters, the stabilization energies, the dipole moments, and other quantities characterizing the intermolecular halogen bond in these complexes are monitored, discussed, and compared. A wide range of interaction strengths is spanned in these series. Successive methyl substitution of the amine as well as increasing polarities and polarizabilities of the halogen molecules both systematically enhance the signature of charge-transfer interaction. These trends in halogen bonds of varying strength, in many aspects, parallel the features of hydrogen bonding.     

A CSOV study of the difference between HF and DFT intermolecular interaction energy values: the importance of the charge transfer contribution

Intermolecular interaction energy decompositions using the Constrained Space Orbital Variation (CSOV) method are carried out at the Hartree-Fock level on the one hand and using DFT with usual GGA functionals on the other for a number of model complexes to analyze the role of electron correlation in the intermolecular stabilization energy. In addition to the overall stabilization, the results provide information on the variation, with respect to the computational level, of the different contributions to the interaction energy. The complexes studied are the water linear dimer, the N-methylformamide dimer, the nucleic acid base pairs, the benzene-methane and benzene-N2 van der Waals complexes, [Cu+ -(ImH)3]2, where "ImH" stands for the Imidazole ligand, and ImH-Zn++. The variation of the frozen core energy (the sum of the intermolecular electrostatic energy and the Pauli repulsion energy) calculated from the unperturbed orbitals of the interacting entities indicates that the intramolecular correlation contributions can be stabilizing as well as destabilizing, and that general trends can be derived from the results obtained using usual density functionals. The most important difference between the values obtained from HF and DFT computations concerns the charge transfer contribution, which, in most cases, undergoes the largest increase. The physical meaning of these results is discussed. The present work gives reference calculations that might be used to parametrize new correlated molecular mechanics potentials.     

Comparison of basis set superposition error corrected perturbation theories for calculating intermolecular interaction energies

Recently, two different but conceptually similar basis set superposition error (BSSE) free second‐order perturbation theoretical schemes were developed by us that are being based on the chemical Hamiltonian approach (CHA). Using these CHA‐MP2 and CHA‐PT2 methods, a comparison is made between the a posteriori and a priori BSSE correction schemes at the correlated level. Sample calculations are presented for four hydrogen bonded complexes (HFH₃N, HFH₂O, H₂SHF, and H₂OHCl) in nine different basis sets (from 6–31G to TZV**++). The results show that the BSSE content is very significant in the interaction energy if electron correlation is accounted for, so removing the BSSE is very important. The differences of the two perturbational theories discussed are connected solely with the different one electron orbital sets used for building up the unperturbed single determinant wave function. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 274–283, 1999     

The effect of basis set superposition error on the convergence of intermolecular interaction energies for deprotonated complexes

The intermolecular interaction energies of the deprotonated hydrogen-bonded complexes F(-)(HF), F(-)(H(2)O), F(-)(NH(3)), Cl(-)(HF), SH(-)(HF), H(2)P(-)(HF), OH(-)(H(2)O), OH(-)(H(2)O)(2), OH(-)(NH(3)), Cl(-)(H(2)O), SH(-)(H(2)O), H(2)P(-)(H(2)O), Cl(-)(NH(3)), SH(-)(NH(3)), H(2)P(-)(NH(3)), Cl(-)(HCl), Cl(-)(H(2)S), Cl(-)(PH(3)), SH(-)(H(2)S), SH(-)(PH(3)), and H(2)P(-)(PH(3)) were calculated with correlation consistent basis sets at the MP2, MP4, QCISD(T), and CCSD(T) levels. When the basis set is smaller, the counterpoise-uncorrected intermolecular interaction energies are closer to the complete basis set limit than the counterpoise-corrected intermolecular interaction energies. The counterpoise-uncorrected intermolecular interaction energies obtained at the MP2/aug-cc-pVDZ level of theory are close to the interaction energies obtained at the extrapolated complete basis set limit in most of the complexes. Also, we investigate the accuracy of the other levels.     

Experimental and theoretical NMR studies of interaction between phenylalanine derivative and egg yolk lecithin

The interaction of phenylalanine diamide (Ac‐Phe‐NHMe) with egg yolk lecithin (EYL) in chloroform was studied by ¹H and ¹³C NMR. Six complexes EYL–Ac‐Phe‐NHMe, stabilized by N–H···O or/and C–H···O hydrogen bonds, were optimized at M06‐2X/6‐31G(d,p) level. The assignment of EYL and Ac‐Phe‐NHMe NMR signals was supported using GIAO (gauge including atomic orbital) NMR calculations at VSXC and B3LYP level of theory combined with STO‐3G_mag basis set. Results of our study indicate that the interaction of peptides with lecithin occurs mainly in the polar ‘head’ of the lecithin. Additionally, the most probable lecithin site of H‐bond interaction with Ac‐Phe‐NHMe is the negatively charged oxygen in phosphate group that acts as proton acceptor. Copyright © 2014 John Wiley & Sons, Ltd.     

Correlated intermolecular interaction components from asymptotically corrected Kohn-Sham orbitals

In these years there was considerable interest inunderstanding of intermolecular forces in energetic(explosive) systems[1—3]. The supermolecular approach(SM) is widely adopted for calculating ab initio in-termolecular interactions. Nevertheless, it is unable toprovide physically meaningful interaction contribu-tions such as electrostatic, induction, repulsion anddispersion energies. In contrast, the symmetry-adaptedperturbation theory (SAPT)[4—8] has the ability to de-rive these correlated…     

Prediction of drug-target interaction by integrating diverse heterogeneous information source with multiple kernel learning and clustering methods

BackgroundIdentification of potential drug-target interaction pairs is very important for pharmaceutical innovation and drug discovery. Numerous machine learning-based and network-based algorithms have been developed for predicting drug-target interactions. However, large-scale pharmacological, genomic and chemical datum emerged recently provide new opportunity for further heightening the accuracy of drug-target interactions prediction.ResultsIn this work, based on the assumption that similar drugs tend to interact with similar proteins and vice versa, we developed a novel computational method (namely MKLC-BiRW) to predict new drug-target interactions. MKLC-BiRW integrates diverse drug-related and target-related heterogeneous information source by using the multiple kernel learning and clustering methods to generate the drug and target similarity matrices, in which the low similarity elements are set to zero to build the drug and target similarity correction networks. By incorporating these drug and target similarity correction networks with known drug-target interaction bipartite graph, MKLC-BiRW constructs the heterogeneous network on which Bi-random walk algorithm is adopted to infer the potential drug-target interactions.ConclusionsCompared with other existing state-of-the-art methods, MKLC-BiRW achieves the best performance in terms of AUC and AUPR. MKLC-BiRW can effectively predict the potential drug-target interactions.     

Investigation of the interactions between ginsenosides and amino acids by mass spectrometry and theoretical chemistry

In order to evaluate the essence of the interactions of ginsenosides and proteins which are composed by α-amino acids, electrospray ionization mass spectrometry was employed to study the noncovalent interactions between ginsenosides (Rb₂, Rb₃, Re, Rg₁ and Rh₁) and 18 kinds of α-amino acids (Asp, Glu, Asn, Phe, Gln, Thr, Ser, Met, Trp, Val, Gly, Ile, Ala, Leu, Pro, His, Lys and Arg). The 1:1 and 2:1 noncovalent complexes of ginsenosides and amino acids were observed in the mass spectra. The dissociation constants for the noncovalent complexes were directly calculated based on peak intensities of ginsenosides and the noncovalent complexes in the mass spectra. Based on the dissociation constants, it can be concluded that the acidic and the basic amino acids, Asp, Glu, Lys and Arg, bound to ginsenosides more strongly than other amino acids. The experimental results were verified by theoretical calculations of parameters of noncovalent interaction between ginsenoside Re and Arg which served as a representative example. Two kinds of binding forms, “head–tail” (“H–T”) and “head–head” (“H–H”), were proposed to explain the interaction between ginsenosides and amino acids. And the interaction in “H–T” form was stronger than that in “H–H” form.     

Minimal basis sets in calculations of intermolecular interaction energies

Several minimal (7, 3/3) Gaussian basis sets have been used to calculate the energies and some other properties of CH₄ and H₂O. Improved basis sets developed for these molecules have been extended to NH₃ and HF and employed to H₂CO and CH₃OH. Interaction energies between XH_n molecules have been calculated using the old and the new minimal basis sets. The results obtained with the new basis sets are comparable in accuracy to those calculated with significantly more extended basis sets involving polarization functions. Binding energies calculated using the counterpoise method are not much different for the new and the old minimal basis sets, and are likely to be more accurate than the results of much more extended calculations.     

Optimized domain size and enlarged D/A interface by tuning intermolecular interaction in all‐polymer ternary solar cells

The selection of sensitizer and its existence in the blend films are important to the performance of all‐polymer ternary solar cells. Herein, all‐polymer ternary solar cell devices, which used poly[4,8‐bis(5‐(2‐ethylhexyl)thiophen‐2‐yl)benzo[1,2‐b:4,5‐b′] dithiophene‐alt‐3‐fluorothieno[3,4‐b]thiophene‐2‐carboxy‐late] (PTB7‐Th) as donor, poly[[N,N‐bis(2‐octyldodecyl)‐napthalene‐1,4,5,8‐bis(dicarboximide)?2,6‐diyl]‐alt‐5, 5′‐(2,2′‐bithiophene)] (N2200) as acceptor and poly[N?900‐hepta‐decanyl‐2,7‐carbazole‐alt‐5,5‐(40,70‐di‐2‐thienyl‐20,10,30‐benzothiadiazole) (PCDTBT) as sensitizer, are successfully demonstrated. The intermolecular interaction between donor PTB7‐Th and sensitizer PCDTBT may lead to aggregation of PTB7‐Th which decreases domain sizes and enlarges D/A effective interface area. In addition, the PCDTBT molecules also extend light absorption and cascaded energy levels of the ternary blend system. As a result, with 15% PCDTBT we get a power conversion efficiency of 5.11%, almost 20% higher than control device due to more favored exciton dissociation and higher charge transport efficiency. This study reveals a promising way to achieve high efficiency all‐polymer solar cells using a low‐band gap polymer PCDTBT. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1811–1819     

Understanding the role of noncovalent interactions on the rate of some Diels-Alder reactions in different solvents

In this article, the role of noncovalent interactions (NCI) on four types of cycloaddition reactions in different solvents was investigated by employing quantum chemistry calculations. For this purpose, explicit and implicit solvation models were applied in the experimental conditions of temperature and pressure. NCI analysis indicates that van der Waals (vdW) interactions, as a part of NCI, change the stability and Gibbs energy of the transition states (TSs), which in turn affects the rate of the reaction. On the basis of NCI analysis, a partial covalent nature of the forming C C bonds at the TSs was confirmed. Energy analysis confirms that vdW interactions can be considered as the main part of the solute-solvent interactions in the cycloaddition reactions. Moreover, cycloaddition reactions of the polar reactants are faster in polar solvents, while nonpolar solvents induce a contrast effect on the rate of these reactions.     

Factors determining the enzyme catalytic power caused by noncovalent interactions: Charge alterations in enzyme active sites

Understanding the origin of the enormous catalytic power of enzymes is very important. Electrostatic interactions and desolvation are the phenomena that are most proposed to explain the catalysis of enzymes; however, they also decelerate enzymatic reactions. How enzymes catalyze reactions through noncovalent interactions is still not well-understood. In this study, we explored how enzyme-substrate noncovalent interactions affect the free energy barriers (ΔG³s) of reactions by using a theoretical derivation approach. We found that enzymes reduce ΔG³s of reactions by decreasing positive charges and/or increasing negative charges in the electron-donating centers and by decreasing negative charges and/or increasing positive charges in the electron-accepting centers of reactions. Enzyme-substrate noncovalent interactions are essential approaches through which the charge alterations lead to ΔG³ reductions. Validations with reported experimental data demonstrated that this charge alteration mechanism can explain the catalyses caused by diverse types of noncovalent interactions. Electrostatic interactions and desolvation are the most observed noncovalent interactions essential for ΔG³ reductions. This mechanism does not contradict any specific enzymatic catalysis and overcomes the shortages of the electrostatic interaction and desolvation mechanisms. This study can provide useful guidance in exploring enzymatic catalysis and designing catalyst.     

Typical aromatic noncovalent interactions in proteins: A theoretical study using phenylalanine

A systematic study of CH ··· π, OH ··· π, NH ··· π, and cation ··· π interactions has been done using complexes of phenylalanine in its cationic, anionic, neutral, and zwitterionic forms with CH₄, H₂O, NH₃, and NH at B3LYP, MP2, MPWB1K, and M06‐2X levels of theory. All noncovalent interactions are identified by the presence of bond critical points (bcps) of electron density (ρ( r )) and the values of ρ( r ) showed linear relationship to the binding energies (E_total). The estimated E_total from supermolecule, fragmentation, and ρ( r ) approaches suggest that cation ··· π interactions are in the range of 36 to 46 kcal/mol, whereas OH ··· π, and NH ··· π interactions have comparable strengths of 6 to 27 kcal/mol and CH ··· π interactions are the weakest (0.62–2.55 kcal/mol). Among different forms of phenylalanine, cationic form generally showed the highest noncovalent interactions at all levels of theory. Cooperativity of multiple interactions is analyzed on the basis of ρ( r ) at bcps which suggests that OH ··· π and NH ··· π interactions show positive, whereas CH ··· π and cation ··· π interactions exhibit negative cooperativity with respect to the side chain hydrogen bond interactions. In general, side chain interactions are strengthened as a result of aromatic interaction. Solvation has no significant effect on the overall geometry of the complex though slight weakening of noncovalent interactions by 1–2 kcal/mol is observed. An assessment of the four levels of theory studied herein suggests that both MPWB1K and M06‐2X give better performance for noncovalent interactions. The results also support the fact that B3LYP is inadequate for the study of weak interactions. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

A characteristic ribbon-like supramolecular structure and intermolecular D–A interactions in the crystals of triptycenequinones, triptycene-TCNQs and their clathrates as studied by X-ray investigations

A common ribbon-like structure was found in the crystals of triptycenequinones (TPQs), triptycene-TCNQs (TP-TCNQs) and their clathrates. The characteristic structure can be regarded as a supramolecular unit the formation of which is aided by weak intermolecular D–A interactions. This view is supported by the host–guest D–A interactions appeared in the crystals of the clathrates of 5,8-dimethyl-TPQ and 5,8-dimethoxy-TP-TCNQ. Intermolecular C–HO hydrogen bonds seem to be present in TPQ derivatives.     

Vibrational spectra and noncovalent interactions of carbohydrates molecules

The differences between the vibrational spectra of carbohydrates of the same chemical structure caused by the noncovalent intra- and intermolecular interactions have been systematized. In the general case, these differences show up as the following specific features of changes in the bond intensities: change in the intensity ratio of closely spaced bands (IR and Raman spectra); selective change (increase, decrease) in intensities of individual bands (IR and Raman spectra); change (increase, decrease) in intensities of practically all bands (IR and Raman spectra); appearance of strong bands in the region of low frequencies from 50 to 200 cm⁻¹ (Raman spectra); appearance of strong diffuse bands in the low-frequency range with a simultaneous great reduction in the other bands (practical disappearance of the majority of bands) (Raman Spectra). The causes of such a kind of changes in the band intensities in the vibrational spectra of carbohydrates are discussed.