Topological Analysis Of The Electron Density In Weak Bonds (Hydrogen Bonds, Halogen Bonds, And Lithium Bonds)

Intermolecular interactions are of vital importance in the existence of the liquid phase (especially in the water phase), also in the structures and properties of biomacromolecules such as DNA, RNA, and proteins. Intermolecular interactions also play a key role in the molecular-recognition process, one of the most important processes in our life. Recently, the applications of intermolecular interactions are of especially interest within the fields of supramolecular chemistry, molecular biology, crystal engineering, and material science. Intermolecular interactions have been the popular topics of theoretical and experimental investigations.In this work, the nature and characteristics of weak bonds—hydrogen bonds, halogen bonds, and lithium bonds were studied systematically. The appropriate calculation model were established, the program of topological analysis of electron density were compiled to characterize intermolecular interactions. Theoretical studies of typical n-type,Ï€-type and pseudo-Ï€-type systems containing weak interactions were performed by means of the ab initio calculations and topological analysis of the electron density. The present work reports a detailed examination of electrostatic potential, equilibrium geometries, interaction energies, the interactions of donor and acceptor orbitals, topological properties of electron density, and the properties of atom basin integration. The main researches are as follows:1. Topological program of electron density was improved and new revision GTA-2010 was put forward. The model ofσandÏ€electron density separation and the idea of molecule formation density difference were established and the corresponding program were compiled and added to the topological program of electron density GTA, which was developed by us and registered at QCPE (register number QCPE-661). TheÏ€electron density can be separated from the total electron density, and the contour of the Laplacian ofÏ€electron density can be plotted using our modified program. The idea of molecule formation density difference (MFDD) is introduced to study of the weak interaction between molecule A and B, which is combined to a super molecule A-B mode. The MFDD graph shows clearly the formation processes of weak bonds.2. The effect of molecular electrostatic potential was investigated. The electrostatic potential on the molecular surface of electron-donor (sulfide, cyanide, ethene, cyclopropane, furan etc.) and electron-acceptor (dihalogen molecules, hydrogen halides, lithium halides) were studied, the position and values of the most negative potentials (VS, min) and the most positive potentials (VS, max) determined the geometries of the complexes. VS, max on the surface of dihalogen molecules become more positive as the series of Cl*–Br, Cl₂, Br₂, Br*–Cl, Cl*–F, Br*–F (the reactive halogen atom is marked with *). VS,min becomes more negative as the series of FCN < ClCN < BrCN < CH≡CCN < CH₂=CHCN < CH₃CN < C₂H₅CN. The magnitudes of VS, max and VS, min correlated with interaction energies, geometrical parameters, and topological properties of electron density, indicating that the electrostatic interaction plays an important role in these intermolecular interactions.3. The nature and characteristics of halogen bond were studied. Several typical halogen bonding systems (CH₂)₂O···XY, (CH₂)₂S···XY(XY = Cl₂, Br₂, ClF, BrF, BrCl ),B···XY(B= H₂S, H₂CS, (CH₂)2S; XY= Cl₂, Br₂, ClF, BrF, BrCl),and RCN···XY (R = F, Cl, Br, C≡CH, CH=CH₂, CH₃, C₂H₅; XY= BrF, BrCl, Br₂) were investigated systematically. Electrostatic potentials, bond lengths, vibrational frequencies, dipole moment, interaction energies, electron transfer, electron density properties, energy density properties, and their relationship were discussed. It was found that most of these halogen bonding interactions belong to weak interactions with an electrostatic nature. The electrostatic interaction plays an important role in these halogen bonds. The topological properties of electron density at the bond critical points correlate well with binding energies, the electrostatic potential, geometrical parameters, and NBO electron transfer,. For the same electron donor, the interaction energies follows the B···BrF > B···ClF > B···BrCl > B···Br₂ > B···Cl₂ > B···ClBr (B= H₂S, H₂CS, (CH₂)₂S) order. Examination of the electrostatic potentials of substituted cyanide monomers has indicated that the inductive effect of substituents has a large influence on the most negative electrostatic potential on the surface of the interacting nitrogen and thus modulates these halogen-bonding interactions. The stronger the electron-releasing the substitution on cyano group is, the stronger is the halogen bond to which it gives rise. For the same electron-acceptor, the interaction energies are follow the FCN···BrY < ClCN···BrY < BrCN···BrY < CH≡CCN···BrY < CH₂=CHCN···BrY < CH₃CN···BrY < C₂H₅CN···BrY (Y=F, Cl, Br) order.4. Comparison study on the nature of halogen bonds and hydrogen bonds was perform. The nature and properties of n-type B···XY/HY(B = H₂O, H₂CO, (CH₂)₂O; X, Y = F, Cl, Br),Ï€-type and pseudo-Ï€-type B···XY/HY(B = C₂H₂, C₂H₄, C₃H₆; X = Cl, Br; Y = F, Cl, Br) halogen/hydrogen-bonded complexes were discussed. The geometries, binding energies, and topological characteristics of halogen-bonded systems were compared with those of hydrogen-bonded systems. In general, many properties of the halogen bond are analogous to those of the hydrogen bond. The studied halogen bonding and hydrogen bonding belong to "closed-shell" weak interactions. For the same electron acceptor H or X atom, the properties such as bond distance, binding energy, electron density decrease in the sequence of B···HF > B···HCl > B···HBr, B···ClF > B···Cl₂, B···BrF > B···BrCl > B···Br₂ (B = H₂O, H₂CO, (CH₂)₂O, C₂H₂, C₂H₄, C₃H₆). The quantitative relationship of binding energy and O···X/O···H distances d(O···X)/d(O···H), the variation of X–Y/H–Y bond lengthδd(X–Y)/δd(H–Y), frequency△ν(X–Y)/△ν(H–Y), the electron density at the O···X/O···H bond critical pointsρc(O···X)/ρc(O···H) for n-type complexes were discussed. It was found that d(O···X),δd(X–Y),△ν(X–Y),ρc(O···X),â–³²Ïc(O···X) may be applied as the measures of the halogen bond strength for heterogeneous samples. d(O···H),△ν(H–Y) andρc(O···H) may be applied as the measures of the hydrogen-bond strength. In the study of typicalÏ€-type and pseudo-Ï€-type halogen/hydrogen-bonded complexes B···XY/HY (B = C₂H₄, C₂H₂, C₃H₆; X = Cl, Br; Y = F, Cl, Br), theÏ€electron density was separated from the total electron density, and the distribution ofÏ€electron density was discussed. It was found that the lengths of the weak bond d(X···π)/d(H···π), the frequencies of the weak bondν(X···π)/ν(H···π), the frequency shifts△ν(X–Y)/△ν(H–Y), the electron densities at the BCP of the weak bondsρc(X···π)/ρc(H···π), and the electron density changes△ρ_c(X–Y)/△ρc(H–Y) could be utilized as measures of the strengths of typicalÏ€-type and pseudo-Ï€-type halogen/hydrogen bonds.5. The structure and properties of lithium bonds and hydrogen bonds were studied and compared. The comparison study on the nature of n-type andÏ€-type hydrogen/lithium-bonded complexes RCN···LiY/HY (R = F, Cl, Br, C₂H, C2H₃, CH₃, C₂H₅; Y= Cl, Br), furan···LiY/HY, thiophene···LiY/HY(Y = F, Cl, Br) were performed. The geometries, frequencies, energies and topological characteristics, and the properties of atom basin integration of lithium-bonded systems have been compared with those of hydrogen-bonded systems. These studied interactions belong to "closed-shell" weak interactions. There are some similarities in two types of interactions. The study on the RCN···LiY/HY (R = F, Cl, Br, C2H, C2H3, CH3, C2H5; Y= Cl, Br) shows that the strength of interactions connected with the influence of substitution on cyano group, N···Li/N···H distance, topological properties of electron density at the N···Li/N···H bond critical points. For furan···LiY/HY and thiophene···LiY/HY(Y = F, Cl, Br) systems, the topological properties at the bond critical points (the electron densityρc, its Laplacianâ–³²Ïc and the eigenvalueλ3 of the Hessian matrix), as well as the energy properties (Gc and Vc) of lithium bond and hydrogen bond were exponentially dependent on intermolecular distance d(H-bond) and d(Li-bond), which enables interpretation of the strength of these interactions in terms of thoseρ(r) properties. The differences between lithium and hydrogen bonds are as follows: The interaction energies of the studied lithium-bonded complexes are larger than the corresponding hydrogen-bonded complexes representing a basic difference between these interactions. For the same electron donors, The bond strength of lithium bonds increases according to the sequence Y = F < Cl < Br, while the bond strength of hydrogen bonds decreases in the sequence Y = F > Cl > Br. Electron transfer plays more important role in the formation of hydrogen bond than that in the lithium bond, the electrostatic interaction of lithium bond are more dominant than that of hydrogen bond. Integral basin properties are different: Upon complex formation, the X atom is the main electron acceptor during the charge transferring from B to HX, and the Li atom is the main electron acceptor from B to LiX. The energies of the hydrogen atoms increase while those of the lithium atoms decrease.The innovations of this work include:1. The ideas ofσandÏ€electron density separation and the molecule formation density difference were introduced in the topological program of electron density GTA, which was developed by us and registered at QCPE (register number QCPE-661). New revision GTA-2010 program was put forward.2. The separation ofσandÏ€electron density and topological analysis ofÏ€electron density were investigated in intermolecular interaction systems for the first time.3. The idea of molecule formation density difference (MFDD) was applied to study the intermolecular interaction successfully for the first time. The MFDD graph shows electron transfer clearly in the formation of the lithium and hydrogen bond.4. The relationships between the electrostatic potential and equilibrium geometries, binding energies, and topological properties of electron density were discussed quantitatively for the first time. From the perspective of electrostatic potential, the cause of bothσ-type andÏ€-type interactions in furan···HY/LiY, but onlyÏ€-type interaction in thiophene···HY/LiY were revealed.5. n-Type andÏ€-type hydrogen bonds, halogen bonds, and lithium bonds were studied systematically. The similarities and differences of these weak bonds were compared. The characteristic and topological measures of the weak bonding strength were summarized. Both the Laplacianâ–³²Ïb and the energy density Hb at the weak bond critical points could be used as criteria to characterize weak bonding. In this thesis, the topological properties at the bond critical points (the electron densityρ_c, its Laplacianâ–³²Ïc and the eigenvalueλ₃ of the Hessian matrix), as well as the energy properties (G_c and V_c) correlate well with bond lengths and binding energies and might each be applied as measures of the strengths of weak bonding.