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.     

Theoretical study of molecular interactions of sulfur ylide with HSX (X = F, Cl, and Br) molecules

The molecular interactions between sulfur ylide (SY) and HSX molecules (X = F, Cl and Br) were investigated using the MP2 method with the 6-311++G (2d, 2p) basis set. The SY (CH₂=SH₂) have two reactive sites: CH₂ (denoted as C-interaction) and SH₂ (S-interaction) that both could interact with three atoms of HSX molecules. The results show that S···C, X···C, and H···C interactions (C-interactions) is preference over the X···S, H···S, and H···X interactions. 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, the second-order perturbation energies E⁽²⁾, and the charge transfer qCT in the studied systems.     

A computational study of 1:1 and 1:2 complexes of nitryl halides (O2NX) with HCN and HNC

Quantum calculations at the MP2/cc-pVTZ have been used to examine 1:1 and 1:2 complexes between O₂NX (X = Cl, Br) with HCN and HNC moieties. The interaction of the lone pair of the HCN(HNC) with the σ-hole and π-hole of O₂NX molecules and hydrogen bonding between lone pairs of X and O of O₂NX with H of HCN and HNC have been considered in 1:1 complexes. The 1:1 complexes can easily be differentiated using the stretching frequency of the N–X bond. Thus, those complexes with σ-hole and H···O₂NX interactions show a blue shift of the N-X bond stretching while a red shift is observed in the complexes along the π-hole and H···XNO₂ interactions. In the 1:2 complexes, the cooperative and diminutive energetic effects have been analyzed using the many-body interaction energies. The nature of the interactions has been characterized with the Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) methodologies. Stabilization energies of 1:1 and 1:2 complexes including the variation of the zero-point vibrational energy (ΔZPVE) are in the range 3–9 kJ mol^?1 and 21–40 kJ mol^?1, respectively.     

Can the substituent in the para position of anilide ion influence the N−···H–F → N–H···F− switching: a quantum chemical study

The effect of substituents in the para position of anilide ion (An) on the N^?···H–F → N–H···F^? switching in X–An–HF (X = H, Me, CHO, CN, NO, F, NO₂, OH and OMe) complexes was investigated by means of B3LYP and MP2 quantum chemical methods. To delve into the mechanistic details of the proton transfer process, potential energy curve and further geometrical parameters involved in H-bonding during the course of the proton transfer process were evaluated at the MP2/6-311++G(2d,2p) level of theory. The changes in H-bond strength because of variation of substituents were well accompanied by changes in formation energy of complexes, structural parameter, electron density, natural charge and charge transfer between subunits. For X = H, Me, CHO, CN, NO, F and NO₂ substituents, our results at MP2/6-311++G(2d,2p) level showed that the minimum energy structures correspond to the N···HF H-bonded complexes without proton transfer occurring. On the other hand, for electron-donating substituents OH and OMe, proton is transferred from HF to anilide ion and the minimum energy structures are HNH···F^? H-bonded complexes. The nature of HN^?···HF and HN–H···F^? interactions in complexes was characterized by means of atoms in molecules and natural bond orbital analyses.     

Revealing substituent effects on the concerted interaction of pnicogen, chalcogen, and halogen bonds in substituted s-triazine ring

Quantum chemical calculations have been performed to gauge the effect of substituents on concerted interactions of pnicogen, chalcogen, and halogen bonds in the X–TAZ···Y complexes (X = CN, F, Cl, Br, H, CH₃, OH, and NH₂, where TAZ and Y denote s-triazine ring and P, S, and Cl atoms, respectively) at the M06-2X/aug-cc-pVDZ level. The mutual interplay of these interactions is also investigated. The results indicate that diminutive effects are observed when the three kinds of noncovalent interactions pnicogen, chalcogen, and halogen bonds are coexisted in the complexes. These effects are studied in terms of energetic and geometric features of the complexes. In addition, Bader’s theory of “atoms in molecules” is used to analyze their strength of varying electron density at bond critical points. Natural bond orbital (NBO) theory is used to characterize the orbital interactions. The results indicate that the electron-withdrawing/donating substituents decrease/increase the magnitude of the binding energies compared to the unsubstituted X–TAZ···Y (X = H) complex. Good correlations among binding energies, Hammett constants, geometrical, atoms in molecular and NBO parameters are established in X–TAZ···Y complexes. By taking advantage of all the aforementioned computational methods, this study examines how these interactions mutually influence each other.     

(π)C—H···S, (allyl)C—H···C(π) and π···π intermolecular interactions: synthesis, characterization, and crystal structure of 2,2′-bipyridine bis(diallyldithiocarbamato)zinc(II)

A mixed-ligand Zn(II) complex formulated as [Zn(aldtc)₂(bipy)] (aldtc=diallyldithiocarbamate; bipy=2,2′-bipyridine) was synthesized and characterized by IR, ¹H and ¹³C NMR spectral measurements and X-ray crystallography. The crystal structure of this complex indicates that Zn has a distorted octahedral geometry. The Zn—N distances are invariant (2.168(2) Å), while those of the Zn—S are slightly different (2.5408(9) and 2.5440(9) Å). The N—Zn—N, S—Zn—S and N—Zn—S bond angles are in the range 75.35(13)–99.75(7)°, 70.48(3)–161.02(5)° and 95.26(7)–160.32(7)°, respectively. The crystal packing of the complex shows different motifs of supramolecularity resulting from both hydrophilic ((π)C—H···S) and hydrophobic ((allyl)C—H···C(π)) intermolecular interactions. These interactions result in a chain arrangement of molecules along crystallographic c axis and the chains are further connected via π···π stacking along with ((π)C—H···S along b axis leading to an overall crystal packing that can be regarded as layers of complexes along bc plane, which are held together through nonconventional hydrogen bonding and π···π stacking.     

Molecular structure and character of bonding of mono and divalent metal cations (Li+, Na+, K+, Mg2+, Ca2+, Zn2+, and Cu+) with guanosine: AIM and NBO analysis

The B3LYP/6-311++G (d,p) density functional approach was used to study the gas-phase metal affinities of Guanosine (ribonucleoside) for the Li⁺, Na⁺, K⁺, Mg²⁺, Ca²⁺, Zn²⁺, and Cu⁺ cations. In this study we determine coordination geometries, binding strength, absolute metal ion affinities, and free energies for the most stable products. We have also compared the results for Guanosine, with our previously reported results for 2′-Deoxyguanosine. Based on the results, it is obvious that MIA is strongly dependent on the charge-to-size ratio of the cation. Guanosine interacts more strongly with Zn²⁺ than do with Mg²⁺, Ca²⁺, and Cu⁺ and therefore stronger interactions lead to higher MIA. In both free molecules and their complexes, the Syn orientation of the base is stabilized by an intramolecular O5′–H···N3 hydrogen bond and the anti orientation of the base is stabilized by an intramolecular C–H···O hydrogen bond formed between the (C8-H8) and the O5′ atom of the sugar moiety. It is also interesting to mention that linear correlation between calculated MIA values and the atomic numbers (Z) of the metal ions of Li⁺, Na⁺, and K⁺ were found. Furthermore, the influences of metal cationization on the strength of the N-glycosidic bond, torsion angles, angle of pseudorotation (P), and intramolecular C–H···O and O–H···O hydrogen bonds have been studied. Natural bond orbital (NBO) analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules (QTAIM) was also applied to determine the nature of interactions.     

Theoretical study of substituents effects on characteristics of resonance-assisted hydrogen bond in (Z)-(thionitrosomethylene)hydrazine and its derivatives in ground and electronic excited state

The molecular geometry, intramolecular hydrogen bond strength, vibrational frequencies, ¹H NMR chemical shift, and nuclear quadrupole resonance parameters of ¹⁴N, ³⁵S and ²H atoms and several well-established indices of aromaticity in (Z)-(thionitrosomethylene)hydrazine molecule and its derivatives were studied by density functional theory method. The results of calculations were obtained at B3LYP/6-311++G** level of approximation on model species, with the resonance-assisted hydrogen bonds. A set of simple and mostly common substituents having different properties in resonance effect according to values of substituents constants were chosen to simulate the influence of substitution in R position of title molecule on the quasi-delocalization and H-bonding. The following substituents have been taken into consideration: F, Cl, NO₂, OCH₃, OCF₃, SCH₃, SH, and OH. The excited-state properties of intramolecular hydrogen bonding in substituted systems have been investigated theoretically using the time-dependent density functional theory method. Also, the possible charge transfer and the topological properties of investigated molecule and its derivatives were studied by means of natural bond orbital and atoms in molecules (AIM) theory. The energy of the N–H···S interactions studied here was found medium in strength ( \( E_{\text{HB}}^{*} \)  = ?36.5 to ?45.3 kJ mol^?1). The electron density (ρ), Laplacian (?² ρ) properties and the total electron energy density (HC), estimated by AIM calculations, indicate that H···S bond possesses low ρ, positive ?² ρ and HC < 0 which are in agreement with partially covalent character of HB.     

On the Correlation between the Blue Shift of Hydrogen Bonding and the Proton Donor-Proton Acceptor Distance

It is demonstrated that in all types of hydrogen bonds (X—H…Y) there is a balance between the long-range attractive orbital interactions and short-range Pauli/nucleus repulsions. When the proton acceptor approaches the proton donor from distance, the hydrogen bonding energy becomes more negative at relatively large distance, goes through a minimum, and then starts to become less negative when the short-range repulsive forces come into effect.Meanwhile, the X--H bond length increases at relatively large distances, goes through a maximum and starts to shorten when the short-range repulsive forces come into effect. Whether the hydrogen bond is red or blue shifted is dictated by the energy minimum position. If at the energy minimum position the X—H bond length is shorter than that for the free monomer, the hydrogen bond is blue shifted and vice versa. Further studies demonstrate that the recent report about the correlation of C—H bond lengths with proton donor-acceptor distance in F3C—H…OH2 and F3C—H…Cl^- is not fully correct because the authors conducted an inappropriate comparison. Furthermore, it is shown for the first time that the Pauli/nucleus repulsion theory is applicable to the blue-shifted hydrogen bonds in the X—H…π complexes and the blue-shifted lithium bonds in the X—Li…Y complexes.     

Ein lamellarer Schichtverband auf der Grundlage von Wasserstoffbrücken und π‐Stapelung: Kristallstruktur des Lithiumkomplexes [Li{C6H4(SO2)2N}(H2O)3] und ein Vergleich mit anderen Metall(I)‐benzol‐1, 2‐di(sulfonyl)amiden

The title complex, obtained by treating ortho‐benzenedisulfonimide (HZ) with LiOH in aqueous solution, has been characterized by low‐temperature X‐ray diffraction (triclinic, space group P&1macr;, Z' = 1). The lithium cation is bonded to one sulfonyl oxygen atom and three water molecules in a distorted tetrahedral configuration [Li‐O 189.3(3)‐201.2(3) pm, O‐Li‐O 98.5(2)‐123.2(2)?]. The zero‐dimensional [Li(Z)(H₂O)₃] complexes, which display an intramolecular O(W)‐H···O hydrogen bond, are cross‐linked via five O(W)‐H···O/N/O(W) interactions and a remarkably short C‐H···O bond (H···O 217 pm, C‐H···O 170?) to form a two‐dimensional assembly comprising an internal polar lamella of metal cations, (SO₂)₂N groups and water molecules, and hydrophobic peripheral regions consisting of protruding benzo groups. In the packing, alternate carbocycles drawn from adjacent layers set up a π‐stacking array of parallel aromatic rings (intercentroid distances 349 and 369 pm, cycle spacings 331 and 336 pm). In a short survey, the currently known crystal packings of seven M^IZ · n H₂O (n ≥ 0) complexes are examined and compared.     

Synthesis and crystal structure of 2-{5-[2-(2,6-dichlorophenylamino)benzyl]-4-p-tolyl-4H-1,2,4-triazol-3-ylthio}acetate

The compound 2-{5-[2-(2,6-dichlorophenylamino)benzyl]-4-p-tolyl-4H-1,2,4-triazol-3-ylthio}acetate has been prepared and characterized by IR, ¹H NMR, ¹³C NMR and mass spectra. The crystal and molecular structure were further confirmed using single crystal X-ray diffraction. The crystal structure has been found to be stabilized by intermolecular C–H···O interaction generating bifurcated hydrogen bonds whereas the C–H···N interactions generate chain of molecules. The intramolecular N–H···N hydrogen bond forms a ring with S(7) graph-set motif.     

Hydrogen bonding characterization of XH2NH2···HNO(X = B,Al, Ga) complexes: A theoretical investigation

The complexes of XH₂NH₂···HNO(X = B, Al, Ga) are characterized as head to tail with hydrogen bonding interactions. The structural characteristics can be confirmed by atoms in molecules (AIM) analysis, which also provide comparisons of hydrogen bonds strengths. The calculated interaction energies at G2MP2 level show that stability of complexes decrease as BH₂NH₂···HNO > AlH₂NH₂···HNO > GaH₂NH₂···HNO. On the basis of the vibrational frequencies calculations, there are red‐shifts for ν(X1? H) and blue‐shifts for ν(N? H) in the complexes on dihydrogen bonding formations (X1? H···H? N). On hydrogen bonding formations (N? H···O), there are red‐shifts for ν(N? H) compared to the monomers. Natural bond orbital (NBO) analysis is used to discuss the reasons for the ν(X1? H) and ν(N? H) stretching vibrational shifts by hyperconjugation, electron density redistribution, and rehybridization. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Characterization of <Emphasis Type="Italic">σ</Emphasis>-hole interactions in 1:1 and 1:2 complexes of YOF<Subscript>2</Subscript>X (X = F,Cl, Br,I; Y = P,As) with ammonia: competition between halogen and pnicogen bonds

Ab initio calculations at the MP2/aug-cc-pVTZ level of theory are performed to examine 1:1 and 1:2 complexes of YOF₂X (X = F, Cl, Br, I; Y = P, As) with ammonia. The YOF₂X:NH₃ complexes are formed through the interaction of the lone pair of the ammonia with the σ-hole region associated with the X or Y atom of YOF₂X molecule. The calculated interaction energies of halogen-bonded complexes are between ?1.06 kcal/mol in the POF₃···NH₃ and ?6.21 kcal/mol in the AsOF₂I···NH₃ one. For a given Y atom, the largest pnicogen bond interaction energy is found for the YOF₃, while the smallest for the YOF₂I one. Almost a strong linear relationship is evident between the interaction energies and the magnitudes of the positive electrostatic potentials on the X and Y atoms. The results indicate that the interaction energies of halogen and pnicogen bonds in the ternary H₃N:YOF₂X:NH₃ systems are less negative relative to the respective binary systems. The interaction energy of Y···N bond is decreased by 1–22 %, whereas that of X···N bond by about 5–61 %. That is, both Y···N and X···N interactions exhibit anticooperativity or diminutive effects in the ternary complexes.     

A theoretical evidence for mutual influence between S···N(C) and hydrogen/lithium/halogen bonds: competition and interplay between π-hole and σ-hole interactions

Ab initio calculations were performed to investigate the cooperativity between the S···N(C) bond and the hydrogen/lithium/halogen bond interactions in O₂S···NCX···NCH and O₂S···CNX···CNH triads (X=H, Li, Cl, and Br). To understand the properties of the systems better, the corresponding dyads are also studied. It is evident that the lithium bond has a bigger influence on the chalcogen bond than vice versa. The results indicate that the enhanced interaction energies of the S···N(C) and X···N(C) interactions in the triad increase in the order NCCl < NCBr < NCH < NCLi and CNCl < CNBr < CNH < CNLi. This is the order of the increasing positive electrostatic potential V _S,max on the X atom. The nature of S···N(C) and X···N(C) interactions of the complexes is unveiled by energy decomposition analysis and natural bond orbital (NBO) theory. The cooperativity between both types of interaction is chiefly caused by the electrostatic effects.     

Global and local interactions in the structure of crystalline 7-(diethylamino)-2-(2-oxo-2<Emphasis Type="Italic">H</Emphasis>-chromen-3-yl)chromenium perchlorate

Computational methods were used to calculate the crystal lattice energy reflecting global interactions, predominantly long-range electrostatic interactions between ions, as well as the energy of selected specific local C–H···O, C–H···π and π···π interactions found in synthesized 7-(diethylamino)-2-(2-oxo-2H-chromen-3-yl)chromenium perchlorate, the structure of which was determined by X-ray crystallography. Local interactions occurring between specific sites of molecules, amounting to a few tens of kJ mol^?1, most likely account for the mutual arrangement of molecular ions, whereas global ones, exceeding half-a-thousand kJ mol^?1, are responsible for the thermodynamic stability of the compound investigated in the crystalline solid phase, whose potential applications are briefly outlined.     

Reinvestigation of intramolecular hydrogen bond in malonaldehyde derivatives: An ab initio,AIM and NBO study

The RAHB systems in malonaldehyde and its derivatives at MP2/ 6‐311++G(d,p) level of theory were studied and their intramolecular hydrogen bond energies by using the related rotamers method was obtained. The topological properties of electron density distribution in O? H···O intramolecular hydrogen bond have been analyzed in term of quantum theory of atoms in molecules (QTAIM). Correlations between the H‐bond strength and topological parameters are probed. The results of QTAIM clearly showed that the linear correlation between the electron density distribution at HB critical point and RAHB ring critical point with the corresponding hydrogen bond energies was obtained. Moreover, it was found a linear correlation between the electronic potential energy density, V(r_cp), and hydrogen bond energy which can be used as a simple equation for evaluation of HB energy in complex RAHB systems. Finally, the similar linear treatment between the geometrical parameters, such as O···O or O? H distance, and Lp(O)→σ*_OH charge transfer energy with the intramolecular hydrogen bond energy is observed. © 2010 Wiley Periodicals, Inc., Int J Quantum Chem, 2011     

Nature of MoH···I bonds in Cp2Mo(L)H···I‐C≡C‐R Complexes (L=H,CN, PPh2, C(CH3)3; R=NO2, Cl,Br, H,OH, CH3, NH2)

The nature of the MoH···I bond in Cp₂Mo(L)H···I‐C≡C‐R (L= H, CN, PPh₂, C(CH₃)₃; R=NO₂, Cl, Br, H, OH, CH₃, NH₂) was investigated using electrostatic potential analysis, topological analysis of the electron density, energy decomposition analysis and natural bond orbital analysis. The calculated results show that MoH···I interactions in the title complexes belong to halogen‐hydride bond, which is similar to halogen bonds, not hydrogen bonds. Different to the classical halogen bonds, the directionality of MoH···I bond is low; Although electrostatic interaction is dorminant, the orbital interactions also play important roles in this kind of halogen bond, and steric interactions are weak; the strength of H···I bond can tuned by the most positive electrostatic potential of the I atom. As the electron‐withdrawing ability of the R substituent in the alkyne increases, the electrostatic potential maximum of the I atom increases, which enhances the strength of the H···I halogen bond, as well as the electron transfer.     

Synthesis and crystal structure of methyl 2-(2,4-dichloro-5-fluorobenzoyl)-3-(pyrimidin-2-ylamino)acrylate

Methyl 2-(2,4-dichloro-5-fluorobenzoyl)-3-(pyrimidin-2-ylamino)acrylate has been prepared. Its crystal structure is discussed. The compound crystallizes in the triclinic space group P-1 with a = 11.6259 (7) Å, b = 11.8789 (7) Å, c = 13.9206 (5) Å, α = 68.0250 (10)°, β = 77.5660 (10)°, γ = 62.4950 (10)°, V = 1579.18 (14) ų, Z = 4. There are two independent but chemically identical molecules in the asymmetric unit. The molecules are packed in the crystal structure by weak intermolecular C–H···O and C–H···F interactions.     

A comparative study of some lithium and hydrogen‐bonded complexes: Ab initio and QTAIM studies

The nature of the interactions of cyanide with lithium and hydrogen halides was investigated using ab initio calculations and topological analysis of electron density. The computed properties of the lithium‐bonded complexes RCN···LiX (R = H, F, Cl, Br, C?CH, CH?CH₂, CH₃, C₂H₅; X = Cl, Br) were compared with those of corresponding hydrogen‐bonded complexes RCN···HX. The results show that both types of intermolecular interactions are “closed‐shell” noncovalent interactions. The effect of substitution on the interaction energy and electron density at the bond critical points of the lithium and hydrogen bonding interactions is similar. In comparison, the interaction energies of lithium‐bonded complexes are more negative than those of hydrogen‐bonded counterparts. The electrostatic interaction plays a more important role in the lithium bond than in the hydrogen bond. On complex formation, the net charge and energy of the Li atom decrease and the atomic volume increases, while the net charge and energy of the H atom increase and the atomic volume decreases. © 2013 Wiley Periodicals, Inc.     

A theoretical study on the structure and hygroscopicity of ammonium dinitramide

Density functional theory (DFT) and the dispersion corrected DFT have been used to investigate the hygroscopicity of ammonium dinitramide (ADN). Calculation results show that the gaseous ADN has a strong hydrogen bond. But the ionic pair structure NH₄ ⁺ · N(NO₂)^? is stabilized upon the addition of water molecules. Natural bond orbital calculations suggest that the intra- and intermolecular orbital interactions LP(O) → σ*(N–H) or LP(O) → σ*(O–H) make the system stabilized as a whole. En energy decomposition analysis reveals that the interactions between ADN and H₂O are dominated by the electrostatic and orbital interactions. The formation reactions become more spontaneous with the increasing number of water molecules but can be weakened by the growing temperature from 200 to 400 K. Moreover, the molecular dynamic method is applied to explore a more realistic cluster model to study the interactions between ADN and H₂O.