Properties of the C−H···H Dihydrogen Bond: An ab Initio and Topological Analysis

The effect of adsorption and grafting on the acidity of [(HSO3)C3C1im]+[Cl]- on the surface of (SiO2)4O2H4 clusters

Both adsorption and graft of active components on the surface of the silica are paramount methods for preparing heterogeneous catalysts. In this paper, the acidity of [(HSO₃)C3C1im]⁺[Cl]^- adsorbed and grafted on the surface of silica clusters was calculated at the level of B3LYP-d3/6-311++g(d, p). The results showed that both methods can enhance the acidity of the ionic liquids (ILs). The hydroxyl group on the carrier surface can increase the acidity, and moreover the acidity increases with the number of hydroxyl group. Besides, geometric parameters, ESP, topology and NBO analysis proved that the ILs acidity on the hydroxyl-free surface was mainly influenced by the interaction between -SO₃ group and cluster surface. And yet the ILs acidity on the hydroxylated surface changes followed with the moderate strength hydrogen bond between the ILs and cluster surface.

Gas-phase electronic properties of tri-cationic imidazolium-based ionic liquids in comparison with mono- and di-cationic ionic liquids

The optimized geometries, electronic structures, and gas-phase properties of widely applicable non-linear trigeminal tri-cationic ILs (TT-X₃) were investigated using density functional theory (DFT) calculations and compared with mono- (M-X) and di-cationic (D-X₂) ionic liquids. The studied ILs are based on the imidazolium cation containing halide (X^‾) anions, where X^‾ = Cl^‾, Br^‾ and I^‾. Inter-molecular hydrogen bonds were studied by atoms in molecules (AIM) and natural bond orbital (NBO) analyses. Accordingly the most significant cation-anion charge transfer is related to C₁-H₁ … X (X = Cl, Br, I) interaction which strongly occurs in TT-X₃ ILs and especially in TT-Cl₃. Among ILs under investigation, TT-Cl₃ has the strongest cation-anion interaction. Also M - I IL has the largest and D-Cl₂ has the smallest electrical dipole moment.

Non-covalent interactions with inverted carbon: a carbo-hydrogen bond or a new type of hydrogen bond?

Crystal structure analysis and quantum chemical calculations enabled us to discover a new non-covalent interaction, coined as carbo-hydrogen bond (C_H-bond).

Xe⋯chalcogen aerogen bond. Effect of substituents and size of chalcogen atom

We have studied the effect of substituent and size of chalcogen atom on the aerogen bond between F₂XeO and R₁YR₂.

Theoretical studies on the noncovalent interaction of fructose and functionalized ionic liquids

As a new kind of solvent and catalyst, the functionalized ionic liquids (ILs) had been successfully used in the conversion of fructose to high value-added biofuels. In this work, a detailed density functional theory (DFT) calculation had been carried out to investigate the interactions of fructose-ILs system. To study the effect of different anions and cations on the interaction with fructose, 25 different kinds of functionalized imidazolium-based ILs were calculated by using M06-2X-D3/6-311 + G** level. It was found that the interaction energies of fructose-anions were higher than those of the fructose-cations. The interaction will become stronger for the fructose and ILs when the alkyl chain of imidazolium-based cations was replaced with a functional group (COOH, OH or HSO₃). However, when the length of the alkyl chain increased, it will result in a decrease in interaction energy due to the steric effect. In the anions (Y-SO₃), the greater electronegativity of SO₃ will lead to strong interaction with fructose. Also, this work simulates the interaction of fructose and ion pairs, with the results showing that hydrogen bonds (H-bonds) and π-stacking play an important role in the system. The present study provided basic aids to understand the structures and noncovalent interaction of fructose and functionalized ILs as well as the microscopic mechanism of fructose dissolution in the ILs.

The physical mechanism of electron excitation spectrum for photo redox device controlled by gate voltage, a first-principles study

This article uses quantum chemical methods and various wave function analysis methods to firstly analyze the optical absorption spectrum and electron migration mechanism of rhodamine 6G molecular complexes on graphene substrates during electron or hole injection. Secondly, since the light absorption properties are very important during photocatalysis, the intermolecular interaction and electronic structure in both cases were calculated and analyzed. Not only the experimental results of the previous photocatalytic devices were explained, but also the physical mechanism was promoted, and the guiding recommendations for the future catalytic device design.

A theoretical investigation on the complexes of B3O3H3 with acetylene and its substituted derivatives

The complexes of B₃O₃H₃ with acetylene and its substituted derivatives C₂HX (X=H, F, Cl, Br, CH₃, NH₂) are explored by theoretical calculations using MP2 and M06-2X methods with aug-cc-pVDZ as the basis set. The different molecular electrostatic potential features of B₃O₃H₃ with benzene (C₆H₆) and borazine (B₃N₃H₆) result in different stable structures of the complexes with C₂HX. The geometric analysis indicates that the global minimum is the parallel stacked (PS) structure with the linear C-C triple bond lies on the top of B₃O₃H₃, and this is much different from that of the B₃N₃H₆...C₂HX complex, in which the C-H bond directs towards the B₃N₃H₆ ring (T-shaped). The H-bonded structure where the C-H interacts with the O atom of B₃O₃H₃ is found to be a local minimum. Besides, there is an additional X…O halogen-bonded structures for the B₃O₃H₃…C₂HX (X=Cl, Br) complexes. As for the PS geometry, when one H atom in C₂H₂ is replaced by different X groups, the binding energies of the complexes increases in the order of F<H<Cl<Br<CH₃<NH₂, which is mainly determined by the strength of the π-hole bond. The nature of interaction in these complexes is further studied by the atoms-in-molecules (AIM) and noncovalent interaction (NCI) analysis. The natural bond orbital (NBO) analysis indicates that the main orbital interaction arises from LP_X→BD*_B‑O for B₃O₃H₃…C₂HX (X=Cl, Br, NH₂), and BD_C‑C→BD*_B‑O for B₃O₃H₃…C₂HX (X=H, CH₃) complexes. Complexes of B₃O₃H₃ with acetylene and its substituted derivatives.

Relationships between Interaction Energy and Electron Density Properties for Homo Halogen Bonds of the [(A)nY-X···X-Z(B)m] Type (X = Cl, Br, I)

Relationships between interaction energy (Eint) and electron density properties at the X···X bond critical point or the d(X···X) distance were established for the large set of structures [(A)nY-X···X-Z(B)m] bearing the halogen bonds Cl···Cl, Br···Br, and I···I (640 structures in total). The best estimator of Eint is the kinetic energy density (Gb), which reasonably approximates the whole set of the structures as -Eint = 0.128Gb2 - 0.82Gb + 1.66 (R2 = 0.91, mean absolute deviation 0.39 kcal/mol) and demonstrates low dispersion. The potential and kinetic energy densities, electron density, and the d(X···X) distance behave similarly as estimators of Eint for the individual series Cl···Cl, Br···Br, and I···I. A number of the Eint(property) correlations are recommended for the practical application in the express estimates of the strength of the homo-halogen bonds.

Coinage-Metal Bond between [1.1.1]Propellane and M2/MCl/MCH3 (M = Cu, Ag, and Au): Cooperativity and Substituents

A coinage-metal bond has been predicted and characterized in the complexes of [1.1.1]propellane (P) and M₂/MCl/MCH₃ (M = Cu, Ag, and Au). The interaction energy varies between −16 and −47 kcal/mol, indicating that the bridgehead carbon atom of P has a good affinity for the coinage atom. The coinage-metal bond becomes stronger in the Ag < Cu < Au sequence. Relative to M₂, both MCl and MCH₃ engage in a stronger coinage-metal bond, both -Cl and -CH₃ groups showing an electron-withdrawing property. The formation of coinage-metal bonding is mainly attributed to the donation orbital interactions from the occupied C-C orbital into the empty metal orbitals and a back-donation from the occupied d orbital of metal into the empty C-C anti-bonding orbital. In most complexes, the coinage-metal bond is dominated by electrostatic interaction, with moderate contribution of polarization. When P binds simultaneously with two coinage donors, negative cooperativity is found. Moreover, this cooperativity is prominent for the stronger coinage-metal bond.

Nature and Strength of M-H···S and M-H···Se (M = Mn, Fe, & Co) Hydrogen Bond

The significance of dispersion contribution in the formation of strong hydrogen bonds (H-bonds) can no more be ignored. It was illustrated that less electronegative and electropositive H-bond acceptors such as S, Se, and Te are also capable of forming strong N-H···Y H-bonds, mostly due to the high polarizabilities of H-bond acceptor atoms. Herein, for the first time, we report the evidence of formation of nonconventional M-H···Y H-bonds between metal hydrides (M-H, M = Mn, Fe, Co) and chalcogen H-bond acceptors (Y = O, S, or Se). The nature and the strength of unusual M-H···Y H-bonds were revealed by several quantum chemical calculations and H-bond descriptors. The structural parameters, electron density topology, donor-acceptor natural bond orbital (NBO) interaction energies, and spectroscopic observables such as M-H stretching frequencies and ¹H chemical shifts are well-correlated to manifest the existence and strength of M-H···Y H-bonding. The M-H···Y H-bonds are dispersive in nature, and the computed H-bond energies are found to be in the range from ∼5 to 30 kJ/mol, which can be compared to those of the conventional H-bonds such as O-H···O, N-H···O, and N-H···O═C H-bonds, etc.

Theoretical Studies on the Electronic Structure Parameters and Reactive Activity of Neu5Gc and Neu5Ac under Food Processing Solvent Environment

The animal product hazard factor N-glycolylneuraminic (Neu5Gc) and brain nutrient substance N-acetylneuraminic acid (Neu5Ac) were studied at the M062X/6-311 + G(d,p) geometry optimization level. We considered the electronic structure parameters with different solvents: (benzene ε = 2.27, acetic acid ε = 6.25, ethanol ε = 24.85, lactic acid ε = 22.00, formic acid ε = 51.1, water ε = 78.35). The maximum molecular surface electrostatic potentials, which were 62.77 for Neu5Gc and 60.90 kcal/mol for Neu5Ac, are both located on the carboxyl group hydrogen. The orbital analysis showed that the amide group and carboxyl group confer the sites with susceptibility to nucleophilic and electrophilic attack, respectively. The solvent effect showed that polar solvents, such as formic acid and water, can enhance the two molecules’ nucleophilic activity. To better understand the roles of the hydroxyl group in the two molecules, the independent gradient model theory confirmed the four intramolecular hydrogen bonds of Neu5Gc at gas phase, whereas Neu5Ac only has two. The lowest bond dissociation energy in solvent occurs at O7-H, which is 104.03 kcal/mol in water for Neu5Gc and 104.57 kcal/mol in lactic acid for Neu5Ac. The lowest proton affinity value for Neu5Gc (20.34 kcal/mol) and Neu5Ac (20.76 kcal/mol) was both occur at the carboxyl group O6-H under ethanol. The antioxidant mechanisms of the two sialic acid are prone to sequential proton-loss electron transfer under polar or non-polar solvents.

Non-covalent loading of ionic liquid-functionalized nanoparticles for bovine serum albumin: experiments and theoretical analysis

Biomacromolecule-based nanomaterials have attracted much attention due to their excellent function in sensing, catalysis, medicine, biology and recognition. In this work, a silane-coupling ionic liquid, 1-(3-trimethoxysilylpropyl)-3-methylimidazolium chloride ([TMIM]Cl), was synthesized and applied to prepare ionic liquid-functionalized nanoparticles (SiO₂@IL) using surface grafting technology. By employing multiple non-covalent interactions, including electrostatic interactions, hydrogen bonding and π–π stacking, the obtained functional nanoparticles were able to bind bovine serum albumin (BSA) with strong binding affinity, which has been illustrated through experiments and theoretical calculations. Moreover, the stability of SiO₂@IL further demonstrated that it is promising in applications for biomacromolecule immobilization.

Non-covalent binding between nanosilica and bovine serum albumin has been illustrated by experiments and theoretical calculations.

Computer-Aided Design of Molecularly Imprinted Polymers for Simultaneous Detection of Clenbuterol and Its Metabolites

Molecular imprinting technology (MIT) offers an effective technique for efficient separation and enrichment of specific analytes from complicated matrices and has been used for illicit veterinary drug detectionin recent years due to its high selectivity, good chemical stability, and simple preparation. The development of in silico-based approaches has enabled the simulation of molecularly imprinted polymers (MIPs) to facilitate the selection of imprinting conditions such as template, functional monomer, and the best suitable solvent. In this work, using density functional theory (DFT), the molecularly imprinted polymers of clenbuterol and its metabolites were designed by computer-aided at B3LYP/6-31 + G (d, p) level. Screening molecular imprinting components such as functional monomers, cross-linkers, and solvents has been achieved in the computational simulation considerations. The simulation results showed that methacrylic acid (MAA) is the best functional monomer; the optimal imprinting ratio for both clenbuterol (CLB) and its dummy template molecule of phenylephrine (PE) to functional monomer is 1:3, while the optimal imprinting ratio for the two dummy template molecules of CLB's metabolites is 1:5. Choosin gethyleneglycol dimethacrylate (EDGMA) as a crosslinker and aprotic solvents could increase the selectivity of the molecularly imprinted system. Atoms in Molecules (AIM) topology analysis was applied to investigate the template-monomer complexes bonding situation and helped to explain the nature of the reaction in the imprinting process. These theoretical predictions were also verified by the experimental results and found to be in good agreement with the computational results. The computer-simulated imprinting process compensates for the lack of clarity in the mechanism of the molecular imprinting process, and provides an important reference and direction for developing better recognition pattern towards CLB and its metabolite analytes in swine urine samples at the same time.

Theoretical and experimental research on self-assembly system of molecularly imprinted polymers formed via chloramphenicol and methacrylic acid

Chloramphenicol was chosen as the imprinting molecule and the methacrylic acid was chosen as the functional monomer to prepare molecularly imprinted polymers. Ethylene glycol dimethacrylate, pentaerythritol triacrylate, and trimethylolpropane trimethylacrylate were used as the cross-linking agents, respectively. The interaction processes between chloramphenicol and methacrylic acid were simulated by using the ωB97XD/6-31G (d,p) method. The self-assembled configuration, bonding sites, binding number, binding energy, and interaction principle of stable complex formed by chloramphenicol and methacrylic acid with different molar ratios have been studied. The selectivity of the most stable complex formed from chloramphenicol and methacrylic acid was discussed with the thiamphenicol and florfenicol as the analogues of chloramphenicol. The results showed that chloramphenicol and methacrylic acid were interacted through the hydrogen bonds. When the molar ratio was 1:10 and pentaerythritol triacrylate as the cross-linking agent, the ordered complex formed by chloramphenicol and methacrylic acid has the largest amount of hydrogen bonds and the lowest binding energy. Scatchard analysis showed that the maximum apparent adsorption capacity was 173.3 mg/g (0.536 mol/g), and the selection factor of florfenicol was the largest. This study provides a reliable theoretical and experimental basis for the design, preparation, and characterization of chloramphenicol molecularly imprinted polymers.

Krypton-methanol spectroscopic study: Assessment of the complexation dynamics and the role of the van der Waals interaction

The Kr-CH₃OH (Krypton-Methanol) system has several technological applications, such as the determination of diffusivity coefficients, their use in the development of detectors and combustion techniques among others. We report an extensive theoretical study concerning the stability of such complex. A mix between molecular dynamics, electronic structure calculations and solution of the nuclear Schrodinger equation lead to investigation of spectroscopic constants, lifetime of the complex and its Quantum Theory Atom in Molecules (QTAIM) properties. The study of the Potential Energy Curves (PEC) suggested three configurations to be stable as their potential well were able to harbor 9 vibrational levels. Properties from the curves also allowed us to obtain the lifetime of the complex, whose values were >1 ps regardless of the conformation. Furthermore, topological investigations of the charge density profile of the complex, in the scope of QTAIM properties, show that van der Waals type interactions takes place between the noble gas and the methanol molecule. These features are in consonance to the experimental fact that this complex is stable.

Weak interactions in furan dimers

Dimers of furan, 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran were investigated with the use of theoretical methods to determine the interactions that keep the molecules together. The QTAIM and NCI methods confirmed that for furan dimers the C-H⋯O hydrogen bond and stacking interactions can form the dimers with similar energy. For 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran, the decisive mechanism of dimer formation is the stacking interaction between the furan rings.

Theoretical studies on glycolysis of poly(ethylene terephthalate) in ionic liquids

Ionic liquids (ILs) present superior catalytic performance in the glycolysis of ethylene terephthalate (PET). To investigate the microscopic degradation mechanism of PET, density functional theory (DFT) calculations have been carried out for the interaction between ILs and dimer, which is considered to symbolize PET. We found that hydrogen bonds (H-bonds) play a critical role in the glycolysis process. In this study, 24 kinds of imidazolium-based and tertiary ammonium-based ILs were used to study the effect of different anions and cations on the interaction with PET. Natural bond orbital (NBO) analysis, atoms in molecules (AIM) and reduced density gradient (RDG) approaches were employed to make in-depth study of the nature of the interactions. It is concluded that the interaction of cations with dimer is weaker than that of anions and when the alkyl chain in the cations is replaced by an unsaturated hydrocarbon, the interaction will become stronger. Furthermore, anions play more important roles than cations in the actual interactions with dimer. When the hydrogen of methyl is replaced by hydroxyl or carboxyl, the interaction becomes weak for the amino acid anions and dimer. This work also investigates the interaction between dimer and ion pairs, with the results showing that anions play a key role in forming H-bonds, while cations mainly attack the oxygen of carbonyl and have a π-stacking interaction with dimer. The comprehensive mechanistic study will help researchers in the future to design an efficient ionic liquid catalyst and offer a better understanding of the mechanism of the degradation of PET.

Co-interaction lead to glycolysis of ethylene terephthalate (PET) in ionic liquids (ILs): H-bonds and π-stacking.

The borazine dimer: the case of a dihydrogen bond competing with a classical hydrogen bond

Dimers of borazine were studied using matrix isolation infrared spectroscopy and ab initio quantum chemical calculations. Computations were performed at the MP2 and M06-2X levels of theory using the 6-311++G(d,p) and aug-cc-pVDZ basis sets for the various homodimers. At both levels of theory, an aligned stacked structure was found to be the global minimum, which was nearly isoenergetic to a parallel displaced structure. A T-shaped structure, where the N-H of one borazine pointed towards the N of the second borazine, was found to be a local minimum. In addition to these structures, a dihydrogen bonded structure, where the hydrogen attached to the nitrogen of borazine interacted with the hydrogen attached to the boron atom of another borazine, was also indicated. Experimentally, we observed the T-shaped dimer and the dihydrogen bonded dimer. This is one of the rare examples of experimental evidence for a dihydrogen bond, in a system other than in a metal hydride. These results for the borazine dimer were clearly different from the benzene dimer where the parallel displaced structure was found to be the global minimum followed by the T-shaped structure at the MP2/aug-cc-pVDZ level of theory. AIM, EDA and NBO analyses were carried out for all the structures to explore the nature of interactions.

Why does β-cyclodextrin prefer to bind nucleotides with an adenine base rather than other 2'-deoxyribonucleoside 5'-monophosphates?

β-Cyclodextrin (β-CD), which resides in the α-hemolysin (αHL) protein pore, can act as a molecular adapter in single-molecule exonuclease DNA sequencing approaches, where the different nucleotide binding behavior of β-CD is crucial for base discrimination. In the present contribution, the inclusion modes of β-CD towards four 2'-deoxyribonucleoside 5'-monophosphates (dNMPs) were investigated using quantum mechanics (QM) calculations. The calculated binding energy suggests that the binding affinity of dAMP to β-CD are highest among all the dNMPs in solution, in agreement with experimental results. Geometry analysis shows that β-CD in the dAMP complex undergoes a small conformational change, and weak interaction analysis indicates that there are small steric repulsion regions in β-CD. These results suggest that β-CD has lower geometric deformation energy in complexation with dAMP. Furthermore, topological analysis and weak interaction analysis suggest that the number and strength of intermolecular hydrogen bonds and van der Waals interactions are critical to dAMP binding, and they both make favorable contributions to the lower interaction energy. This work reveals the reason why β-CD prefers to bind dAMP rather than other dNMPs, while opening exciting perspectives for the design of novel β-CD-based molecular adapters in the single-molecule exonuclease method of sequencing DNA. Graphical Abstract The binding affinity of β-cyclodextrin towards four 2'-deoxyribonucleoside 5'-monophosphates was investigated using quantum mechanics calculations.

Intermolecular interactions boost aggregation induced emission in carbazole Schiff base derivatives

The structure–property relationship was discussed and we found that the C–H⋯π interactions and H⋯H interactions played a significant role in AIE performance.

Modulating the strength of tetrel bonding through beryllium bonding

Quantum chemical calculations were performed to investigate the stability of the ternary complexes BeH2···XMH3···NH3 (X = F, Cl, and Br; M = C, Si, and Ge) and the corresponding binary complexes at the atomic level. Our results reveal that the stability of the XMH3···BeH2 complexes is mainly due to both a strong beryllium bond and a weak tetrel-hydride interaction, while the XMH3···NH3 complexes are stabilized by a tetrel bond. The beryllium bond with a halogen atom as the electron donor has many features in common with a beryllium bond with an O or N atom as the electron donor, although they do exhibit some different characteristics. The stability of the XMH3···NH3 complex is dominated by the electrostatic interaction, while the orbital interaction also makes an important contribution. Interestingly, as the identities of the X and M atoms are varied, the strength of the tetrel bond fluctuates in an irregular manner, which can explained by changes in electrostatic potentials and orbital interactions. In the ternary systems, both the beryllium bond and the tetrel bond are enhanced, which is mainly ascribed to increased electrostatic potentials on the corresponding atoms and charge transfer. In particular, when compared to the strengths of the tetrel and beryllium bonds in the binary systems, in the ternary systems the tetrel bond is enhanced to a greater degree than the beryllium bond. Graphical Abstract A tetrel bond can be strengthened greatly by a beryllium bond.