Intramolecular Natural Energy Decomposition Analysis: Applications to the Rational Design of Foldamers

We describe an intramolecular version of the natural energy decomposition analysis (NEDA), with the aim of evaluating interactions between molecular fragments across covalent bonds. The electronic energy in intramolecular natural energy decomposition analysis (INEDA) is divided into electrical, core, and charge transfer components. The INEDA method describes the fragments using the nonfragmented electronic density, and, therefore, there are no limitations in how to choose the boundary orbital. We used INEDA to evaluate the interaction energies that give origin to barriers of rotation around C_amide C_aromatic (C_am C_ar) and N_amide C_aromtaic (N_am C_ar) bonds in arylamide‐foldamer building blocks. We found that differences of barrier height between models with different ortho‐aryl substituents stem from charge transfer and core interactions. In three‐center hydrogen‐bond (H‐bond) models with an NH proton donor H‐bound to two electronegative ortho‐aryl substituents, the interaction energy of the three‐center system is larger than in either of the two‐center H‐bond subsystem alone, indicating an increase of overall rigidity. The combination of INEDA and NEDA allows the evaluation of intermolecular and intramolecular interactions using a consistent theoretical framework. © 2018 Wiley Periodicals, Inc.     

Comprehensive study of the interaction between hydrogen halides and methanol derivatives

The R? CH₂? HO…H? X (R = SCl, Cl, SH, NO₂, OMe, CHO, CN, C₂H₅, CH₃, H; X = F, Cl, Br) complexes are considered here as the interest sample for the consideration of different measures of H‐bond strength. The intermolecular interaction energies are predicted by using MP2/6‐31++G(d,p) and B3LYP/6‐31++G(d,p) methods with basis set superposition error and zero‐point energy corrections. The results showed that intermolecular hydrogen bonds for complexes with HF are stronger than such interactions in complexes with HCl and HBr. Quantum theory of “Atoms in Molecules” and natural bond orbitals method were applied to analyzed H‐bond interactions. The gas phase thermodynamic properties of complexes were predicted using quantum mechanical computations. The obtained results showed a strong influence of the R and X substituents on the thermodynamic properties of complexes. Numerous correlations between topological, geometrical, thermodynamic properties and energetic parameters were also found. © 2011 Wiley Periodicals, Inc.     

Theoretical study on intermolecular interactions in BrF/HnX adducts

Equilibrium geometries, interaction energies, and charge transfer for the intermolecular interactions between BrF and H_nX (HF, H₂O, and NH₃) were studied at the MP2/6-311++G(3d,3p) level. The halogen-bonded geometry and hydrogen-bonded geometry are observed in these interactions. The calculated interaction energies show that the halogen-bonded structures are more stable than the corresponding hydrogen-bonded structures. To study the nature of the intermolecular interactions, symmetry-adapted perturbation theory (SAPT) calculations were carried out and the results indicate that the halogen bonding interactions are dominantly inductive energy in nature, while electrostatic energy governs the hydrogen bonding interactions.     

Reaction paths of some open-shell reactive intermediates

The intermolecular interaction energy for reacting systems in singlet, triplet and doublet states was partitioned by the perturbation expansion method into the chemically meaningful five interaction terms: the Coulomb, exchange-repulsion, induction, dispersion, and charge-transfer energies. In the local ZDO approximation, these energy terms were evaluated for the dimerization of methylenes (^1,3CH₂), the additions of carbenes (^1,3CH₂ and^1,3CF₂) as well as amino radicals (²NH₂ and²NF₂) toward ethylene, and the hydrogen abstractions by methylenes (^1,3CH₂), nitrene (³NH), and hydroxyl radical (²OH) from methane. It has been found that the reaction path is much influenced by the spinmultiplicity, and that the charge-transfer and exchange-repulsion terms play a dominant role in determining the course of reactions.     

Theoretical study of molecular interactions of phosphorus ylide with HF, HCN, and HN3

The molecular interactions between phosphorous ylide (PY) and HX molecules (X?=?F, CN, and N₃) were investigated using the MP2 method at 6-311++G(2d,2p) basis set. Three different patterns including non-classical hydrogen bond H···C, X···P interaction and classical hydrogen bond H···X were found for complex formation between PY and HX molecules. From the predicted models, stability of the H···C type complexes are greater than other types. Quantum theories of atoms in molecules and natural bond orbitals methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies (SE), the second-order perturbation energy E ⁽²⁾, and the charge transfer qCT in the studied systems.     

A theoretical investigation of electronic reorganizations accompanying core and valence ionization in simple hydrogen bonded systems

Non-empirical LCAO MO SCF calculations have been carried out on the ground state and core ionized states of some hydrogen bonded dimers, and in the particular case of H₂O the trimer has also been investigated. Comparison of absolute and relative binding energies and relaxation energies with respect to the corresponding monomers reveals that substantial changes occur in going to the associated species. The relaxation energies for a given core hole are shown to increase on going from monomer to dimer indicating that intermolecular contributions to relaxation energies are of the same sign irrespective of the sign for the shift in core binding energy. Creation of a core hole in the dimer species is shown to give rise to substantial changes in hydrogen bond energies compared with the neutral species. In the particular case of valence holes dominantly of 2s and 2p character it is shown that trends in shifts and relaxation energies parallel those for the core hole states.     

Fourth-order diagrammatic MB-RSPT calculations of the interaction energy between two helium atoms

The efficiency of the MB-RSPT in the calculations of the correlation contributions to the interaction energies was investigated, using He₂ as a model Van der Waals system. The attention has been focused on the convergency of the perturbation expansion in the calculations of the interaction energy and on the analysis of the fourth-order terms of MB-RSPT. The rôle of the renormalization term in the correct long-range behaviour of the interaction potential has been emphasized.     

Theoretical study of molecular interactions of sulfur ylide with HF, HCN, and HN3

The molecular interactions between sulfur ylide (SY) and HX molecules (X = F, CN, and N₃) were investigated using the MP2 method at 6-311++G(2d,2p) basis set. Three different patterns including non-classical hydrogen bond (HB) H···C and classical HB H···X were found for complex formation between SY and HX molecules. Stability of the H···C type complexes are greater than H···X complexes. Quantum theories of atoms in molecules, natural bond orbitals, and energy decomposition analysis methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies (SE), the second-order perturbation energy E ⁽²⁾ and the charge transfer qCT in the studied systems.     

Halogen Interactions in Halogenated Oxindoles: Crystallographic and Computational Investigations of Intermolecular Interactions

X-ray structural determinations and computational studies were used to investigate halogen interactions in two halogenated oxindoles. Comparative analyses of the interaction energy and the interaction properties were carried out for Br···Br, C-H···Br, C-H···O and N-H···O interactions. Employing Møller–Plesset second-order perturbation theory (MP2) and density functional theory (DFT), the basis set superposition error (BSSE) corrected interaction energy (E_int(BSSE)) was determined using a supramolecular approach. The E_int(BSSE) results were compared with interaction energies obtained by Quantum Theory of Atoms in Molecules (QTAIM)-based methods. Reduced Density Gradient (RDG), QTAIM and Natural bond orbital (NBO) calculations provided insight into possible pathways for the intermolecular interactions examined. Comparative analysis employing the electron density at the bond critical points (BCP) and molecular electrostatic potential (MEP) showed that the interaction energies and the relative orientations of the monomers in the dimers may in part be understood in light of charge redistribution in these two compounds.     

The role of π electrons in the formation of benzene-containing lithium-bonded complexes

The intermolecular interactions in C₆H₆???LiX (X=OH, NH₂, F, Cl, Br, NC, CN) complexes are investigated by using second‐order Møller–Plesset perturbation theory (MP2) calculations and quantum theory of “atoms in molecules” (QTAIM) studies, and the role of π electrons is studied in the formation of these benzene‐containing lithium‐bonded complexes. The molecular electrostatic potentials of benzene and LiX determine the geometries of the lithium‐bonded complexes. The electron densities at the lithium bond critical points in the πC₆H₆???LiX complexes are obviously stronger than those in the σC₆H₆???LiX complexes, which indicates that the intermolecular interactions in the C₆H₆???LiX complexes are mainly attributable to π‐type interaction. The topological and energy properties at the lithium bond critical points in both the C₆H₆???LiX and πC₆H₆???LiX complexes are linear with the interaction energies, thereby showing the crucial role of the π electrons in the formation of these complexes. Electron localization function (ELF) analysis indicates that the formation of the lithium bonds leads to the reduction of the ELF π‐electron density and volume, and the reduction of the π‐electron volume is linear with the interaction energies with the correction coefficient 0.9949.     

Nature of the water/aromatic parallel alignment interactions

The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its O? H bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to ΔE_{CCSD(T)(limit)} = ?2.45 kcal mol^?1 at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CH···O water/benzene interactions, but weaker than OH···π interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry‐adapted perturbation theory, and extended transition state‐natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV‐based analysis has shown that in structures with strong interaction energies charge transfer of the type π → σ*(O? H) between the monomers also exists. © 2014 Wiley Periodicals, Inc.     

Fourth-order diagrammatic MB–RSPT calculations of the correlation energy: N2, CO,F2 and the reaction energy of the process ½F2 + ½H2 = HF

The correlation energies obtained by the fourth-order diagrammatic perturbation theory were analyzed for three diatomic molecules: N₂, CO, and F₂. The results were compared with correlation energies obtained previously for the ten-electron hydrides HF, H₂O, and NH₃. The relative importance of contributions which arise from the double excitations, from the quadruple excitations, as well as from the renormalization term was investigated. It is shown that for the diatomic molecules under study these contributions are considerably larger than for the ten-electron hydrides not only in absolute value but also in percentage: they represent about 3, 3, and 5%, respectively, of the valence shell correlation energy obtained by the perturbation theory up to the fourth order. A careful analysis of the fourth-order correlation effects is also presented for the reaction energy of the process ½H₂ + ½F₂ = HF.     

高能体系分子间相互作用研究: 含NNO~2和NH~2混合物

以abinitioHF/6-31G^*计算求得NH~3+NH~2NO~2的两种优化构型,经MP4电子相关能校正和Boys-Bernardi方案校正基组叠加误差求得精确的分子间相互作用能。还用PM3方法计算研究TATB(均三氨基三硝基苯)分别与HMX(奥克托金)和RDX(黑索金)的混合体系,经色散能校正电子相关近似地求得分子间相互作用能。结果表明,NH~3与NH~2NO~2之间的最大结合能为-38.32kJ/mol;分子间相互作用增强了N-NO~2键强度;TATB与HMX,RDX的结合能远大于石墨与HMX或RDX的结合能,表明TATB对HMX和RDX的润湿和钝感作用较石墨更强。     

Theoretical study on the interactions of halogen‐bonds and pnicogen‐bonds in phosphine derivatives with Br2, BrCl,and BrF

The MP2 ab initio quantum chemistry methods were utilized to study the halogen‐bond and pnicogen‐bond system formed between PH₂X (X = Br, CH₃, OH, CN, NO₂, CF₃) and BrY (Y = Br, Cl, F). Calculated results show that all substituent can form halogen‐bond complexes while part substituent can form pnicogen‐bond complexes. Traditional, chlorine‐shared and ion‐pair halogen‐bonds complexes have been found with the different substituent X and Y. The halogen‐bonds are stronger than the related pnicogen‐bonds. For halogen‐bonds, strongly electronegative substituents which are connected to the Lewis acid can strengthen the bonds and significantly influenced the structures and properties of the compounds. In contrast, the substituents which connected to the Lewis bases can produce opposite effects. The interaction energies of halogen‐bonds are 2.56 to 32.06 kcal·mol^?1; The strongest halogen‐bond was found in the complex of PH₂OH???BrF. The interaction energies of pnicogen‐bonds are in the range 1.20 to 2.28 kcal·mol^?1; the strongest pnicogen‐bond was found in PH₂Br???Br₂ complex. The charge transfer of lp(P) ? σ*(Br? Y), lp(F) ? σ*(Br? P), and lp(Br) ? σ*(X? P) play important roles in the formation of the halogen‐bonds and pnicogen‐bonds, which lead to polarization of the monomers. The polarization caused by the halogen‐bond is more obvious than that by the pnicogen‐bond, resulting in that some halogen‐bonds having little covalent character. The symmetry adapted perturbation theory (SAPT) energy decomposition analysis showes that the halogen‐bond and pnicogen‐bond interactions are predominantly electrostatic and dispersion, respectively.     

Nature of weak inter- and intramolecular interactions in crystals. 1. The F...O and F...H contacts in the crystal of 2-trifluoroacetyl-5-trifluoromethylpyrrole

The topological analysis of the electron density distribution in the crystal of 2-trifluoroacetyl-5-trifluoromethylpyrrole revealed that the F...H and F...O intermolecular contacts correspond to attractive interactions. The energies of these interactions were estimated from the experimental data and it was shown that these contacts are similar to the C—H...O contacts. Analysis of the deformation electron density revealed that the F...O contacts correspond to transfer of the lone electron pair of a fluorine atom to the antibonding -orbital of the C=O bond.     

Density Functional Theory Studies on Intermolecular Interactions of 4‐Amino‐3,5‐dinitropyrazole with NH3 and H2O

Density functional theory (DFT) method with 6‐311++G** basis set was applied to study intermolecular interactions of 4‐amino‐3,5‐dinitropyrazole (LLM‐116)/NH₃ and LLM‐116/H₂O supermolecules. Four optimized stable supermolecules were found on the potential energy surface. The intermolecular interaction energy was calculated with basis set superposition error (BSSE) correction and zero point energy (ZPE) correction. The greatest corrected intermolecular interaction energies of LLM‐116/NH₃ and LLM‐116/H₂O supermolecules are –42.75 and –19.09 kJ×mol^‐1 respectively, indicating that the intensity of interaction between LLM‐116 and NH₃ is stronger than that of LLM‐116/H₂O. The intermolecular interaction is an exothermic process accompanied by a decrease in the probability of supermolecules formation, and the interactions become weak as temperature increase. Natural bond orbital (NBO) analysis was performed to reveal the origin of interaction. The IR spectra were obtained and assigned by vibrational analysis. Based on vibrational analysis, the changes of thermodynamic properties from LLM‐116 to supermolecules with temperature ranging from 200.0 to 400.0 K were obtained using statistical thermodynamic method.     

Staged Development of Modified Silicon Dioxide Films

The hydrolytic generation of SiO₂ films from chlorosilanes or alkoxysilanes is interrupted by incorporating labile organic groups which stop SiO₂ formation at a processable prepolymer stage. The monomers for the prepolymer have electron withdrawing substituents in the -position. The organic groups are removed from the prepolymer at low temperature, extruding ethylene. The formation of SiO₂ proceeds by intramolecular condensation of the electronegative substituents which are now in a hydrolytically unstable bond with silicon and hydroxyl groups or ambient moisture. Films of the prepolymer spun onto silicon wafers are converted into uniform SiO₂-rich films at temperatures between 150–400°C.     

Theoretical study on intermolecular interactions between furan and dihalogen molecules XY(X,Y=F,Cl,Br)

Equilibrium geometries, interaction energies, atomic charge, and charge transfer for the intermolecular interactions between furan and dihalogen molecules XY(X; Y=F,Cl,Br) were studied at the MP2aug-cc-pVDZ level. Three types of geometry are observed in these interactions: the pi-type geometry (I), in which the XY lies above the furan ring and almost perpendicularly to the C4-C5 bond of furan; the sigma-type geometry (II), where the X atom is pointed toward the nonbonding electron pair (n pair) of oxygen atom in furan; and the chi-type geometry (III), describing a blueshift hydrogen bond formed between the hydrogen atom of furan and dihalogen molecules XY. The calculated interaction energies show that the pi-type structures are more stable than the corresponding sigma-type and chi-type structures. To study the nature of the intermolecular interactions, an energy decomposition analysis was carried out and the results indicate that both the pi-type and sigma-type interactions are dominantly inductive energy in nature, while dispersion energy governs the chi-type interactions.     

Structures,vibrational frequencies,topologies, and energies of hydrogen bonds in cysteine‐formaldehyde complexes

The hydrogen bonding interactions between cysteine (Cys) and formaldehyde (FA) were studied with density functional theory regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules and natural bond orbital analyses were employed to elucidate the interaction characteristics in the Cys‐FA complexes. The intramolecular hydrogen bonds (H‐bonds) formed between the hydroxyl and the N atom of cysteine moiety in some Cys‐FA complexes were strengthened because of the cooperativity. Most of intermolecular H‐bonds involve the O atom of cysteine/FA moiety as proton acceptors, while the strongest H‐bond involves the O atom of FA moiety as proton acceptor, which indicates that FA would rather accept proton than providing one. The H‐bonds formed between the CH group of FA and the S atom of cysteine in some complexes are so weak that no hydrogen bonding interactions exist among them. In most of complexes, the orbital interaction of H‐bond is predominant during the formation of complex. The electron density (ρ_b) and its Laplace (?²ρ_b) at the bond critical point significantly correlate with the H‐bond parameter δR, while a linearly relationship between the second‐perturbation energy E(2) and ρ_b has been found as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Balancing Donor-Acceptor and Dispersion Effects in Heavy Main Group Element π Interactions: Effect of Substituents on the Pnictogen⋅⋅⋅π Arene Interaction

High-level ab initio calculations using the DLPNO-CCSD(T) method in conjunction with the local energy decomposition (LED) were performed to investigate the nature of the intermolecular interaction in bismuth trichloride adducts with π arene systems. Special emphasis was put on the effect of substituents in the aromatic ring. For this purpose, benzene derivatives with one or three substituents (R=NO₂, CF₃, OCHO, OH, and NH₂) were chosen and their influence on donor-acceptor interaction as well as on the overall interaction strength was examined. Local energy decomposition was performed to gain deeper insight into the composition of the interaction. Additionally, the study was extended to the intermolecular adducts of arsenic and antimony trichloride with benzene derivatives having one substituent (R=NO₂ and NH₂) in order to rationalize trends in the periodic table. The analysis of natural charges and frontier molecular orbitals shows that donor-acceptor interactions are of π→σ* type and that their strength correlates with charge transfer and orbital energy differences. An analysis of different bonding motifs (Bi⋅⋅⋅π arene, Bi⋅⋅⋅R, and Cl⋅⋅⋅π arene) shows that if dispersion and donor-acceptor interaction coincide as the donor highest occupied molecular orbital (HOMO) of the arene is delocalized over the π system, the M⋅⋅⋅π arene motif is preferred. If the donor HOMO is localized on the substituent, R⋅⋅⋅π arene bonding motifs are preferred. The Cl⋅⋅⋅π arene bonding motif is the least favorable with the lowest overall interaction energy.