Intermolecular interactions in group 14 hydrides: Beyond CH···HC contacts

In line with previous work in which we established the factors that enhance attractive C?H···H?C dihydrogen interactions in alkanes, an extended theoretical analysis of noncovalent intermolecular interactions in group 14 hydrides is presented here. Remarkably, these weak interactions may play a major role in determining the crystal structures adopted by several families of molecules. A combined structural and computational analysis at the MP2 level allowed us to identify and characterize different interactions of the type E?H···H?E and E···H?E (E = Si, Ge, Sn, and Pb), and to find also the most suitable scenario for the establishment of each particular type. The nature of the interactions has been analyzed in terms of natural charges of the atoms involved and a topological analysis of the electron density of several dimers confirms the existence of H···H and H···E attractive contacts. We have observed that the interaction strength increases when descending down the periodic group and that silicon has a marked tendency to establish Si···H?Si interactions. A size‐dependent backbone effect that reinforces H···H dihydrogen interactions in polyhedral systems has also been found.     

Rapid evaluation of the binding energies between peptide amide and DNA base

The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 20 hydrogen‐bonded amide–base dimers are evaluated from the analytic potential energy function established in our laboratory recently. The analytic potential energy function is used to calculate the N? H···N, N? H···O?C, C? H···N, and C? H···O?C dipole–dipole attractive interaction energies and C?O···O?C, N? H···H? N, and N? H···H? C dipole–dipole repulsive interaction energies in the 20 dimers composed of DNA bases adenine, guanine, cytosine, or thymine and peptide amide. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6‐311+G** calculations by including the basis set superposition error (BSSE) correction. For all the 20 dimers, the analytic potential energy function yields the binding energies of the MP2/6‐311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 19 dimers, only one difference is larger than 0.50 kcal/mol and the difference is only 0.61 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6‐311+G** with BSSE correction within the error limits of 0.030 Å for all the 20 dimers. The analytic potential energy function is further applied to four more complicated DNA base‐peptide amide systems involving amino acid side chain and β‐sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen‐bonded peptide amide–DNA base dimers quickly and accurately. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

复合物HNO···H2O2内N-H···O蓝移氢键的理论研究

A theoretical study on the blue-shifted H-bond N-H…O and red-shifted H-bond O-H…O in the complexHNO…H_2O_2 was conducted by employment of both standard and counterpoise-corrected methods to calculate thegeometric structures and vibrational frequencies at the MP2/6-31G(d),MP2/6-31 G(d,p),MP2/6-311 q G(d,p),B3LYP/6-31G(d),B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels.In the H-bond N-H…O,the calcu-lated blue shift of N-H stretching frequency is in the vicinity of 120 cm~(-1) and this is indeed the largest theoreticalestimate of a blue shift in the X-H…Y H-bond ever reported in the literature.From the natural bond orbital analy-sis,the red-shifted H-bond O-H…O can be explained on the basis of the dominant role of the hyperconjugation.For the blue-shifted H-bond N-H…O,the hyperconjugation was inhibited due to the existence of significant elec-tron density redistribution effect,and the large blue shift of the N-H stretching frequency was prominently due tothe rehybridization of sp~n N-H hybrid orbital.     

An insight into CH···N hydrogen bond and stability of the complexes formed by trihalomethanes with ammonia and its monohalogenated derivatives

A theoretical study of the C?H···N hydrogen bond in the interactions of trihalomethanes CHX₃ (X = F, Cl, Br) with ammonia and its halogen derivatives NH₂Y (Y = F, Cl, Br) has been carried out thoroughly. The complexes are quite stable, and their stability increases in going from CHF₃ to CHCl₃ then to CHBr₃ when Y keeps unchanged. With the same CHX₃ proton donor, enhancement of the gas phase basicity of NH₂Y strengthens stability of the CHX₃···NH₂Y complex. The C?H···N hydrogen bond strength is directly proportional to the increase of proton affinity (PA) at N site of NH₂Y and the decrease of deprotonation enthalpy (DPE) of C?H bond in CHX₃. The CHF₃ primarily appears to favor blue shift while the red‐shift is referred to the CHBr₃. The blue‐ or red‐shift of CHCl₃ strongly depends on PA at N site of NH₂Y. We suggest the ratio of DPE/PA as a factor to predict which type of hydrogen bond is observed upon complexation. The SAPT2+ results show that all C?H···N interactions in the complexes are electrostatically driven regardless of the type of hydrogen bond, between 48% and 61% of the total attractive energy, and partly contributed by both induction and dispersion energies.     

Studies of two different types of intramolecular C–H···F–C interactions from polyfluorinated diiodometal(II) diimine complexes

The X‐ray crystal structures of the polyfluorinated complexes [5,5′‐bis(HCF₂CF₂CF₂CF₂CH₂OCH₂)‐2,2′‐bpy]MI₂ ( 55‐8F‐PtI ₂ and 55‐8F‐PdI ₂ where M = Pt and Pd, respectively) were obtained. These two structures are found to show not only two different types of intramolecular, six‐membered cyclic C–H···F–C interactions (F₂C–H···F–C and HC–H···F–C) as important structural features but also alternating fluorinated and non‐fluorinated layers. The F₂C–H···F–C interactions, which are close to the metal core, are much better structurally characterized in this type of complexes with fluorous ponytails at the 5,5′ positions than those previously reported at the 4,4′ positions. The molecular planes of (bpy)MI₂ are extended by self‐matching, using two C–H···I hydrogen bonds and one C–H···F–C blue‐shifting hydrogen bond. The F₂C–H···F–C hydrogen bonds interact at the supramolecular level such that one polyfluorinated ponytail of the title compounds is transoid without an intramolecular C–H···F–C interaction, while the other polyfluorinated ponytail is cisoid with an intramolecular C–H···F–C interaction. Why one ponytail is cisoidal while the other is transoidal will be explained. Furthermore, the second type of C–H···F–C interactions involving the methylene H atom has been identified for the first time. In addition, these two metal structures are studied by density functional theory (DFT).     

Van Der Waals heterogeneous layer‐layer carbon nanostructures involving π···H‐C‐C‐H···π···H‐C‐C‐H stacking based on graphene and graphane sheets

Noncovalent interactions involving aromatic rings, such as π···π stacking, CH···π are very essential for supramolecular carbon nanostructures. Graphite is a typical homogenous carbon matter based on π···π stacking of graphene sheets. Even in systems not involving aromatic groups, the stability of diamondoid dimer and layer‐layer graphane dimer originates from C − H···H − C noncovalent interaction. In this article, the structures and properties of novel heterogeneous layer‐layer carbon‐nanostructures involving π···H‐C‐C‐H···π···H‐C‐C‐H stacking based on [n ]‐graphane and [n ]‐graphene and their derivatives are theoretically investigated for n = 16–54 using dispersion corrected density functional theory B3LYP‐D3 method. Energy decomposition analysis shows that dispersion interaction is the most important for the stabilization of both double‐ and multi‐layer‐layer [n ]‐graphane@graphene. Binding energy between graphane and graphene sheets shows that there is a distinct additive nature of CH···π interaction. For comparison and simplicity, the concept of H‐H bond energy equivalent number of carbon atoms (noted as NHEQ), is used to describe the strength of these noncovalent interactions. The NHEQ of the graphene dimers, graphane dimers, and double‐layered graphane@graphene are 103, 143, and 110, indicating that the strength of C‐H···π interaction is close to that of π···π and much stronger than that of C‐H···H‐C in large size systems. Additionally, frontier molecular orbital, electron density difference and visualized noncovalent interaction regions are discussed for deeply understanding the nature of the C‐H···π stacking interaction in construction of heterogeneous layer‐layer graphane@graphene structures. We hope that the present study would be helpful for creations of new functional supramolecular materials based on graphane and graphene carbon nano‐structures. © 2017 Wiley Periodicals, Inc.     

GIAO,DFT, AIM and NBO analysis of the N?H···O intramolecular hydrogen‐bond influence on the 1J(N,H) coupling constant in push–pull diaminoenones

In the series of diaminoenones, large high‐frequency shifts of the ¹H NMR of the N? H group in the cis‐position relative to the carbonyl group suggests strong N? H···O intramolecular hydrogen bonding comprising a six‐membered chelate ring. The N? H···O hydrogen bond causes an increase of the ¹J(N,H) coupling constant by 2–4 Hz and high‐frequency shift of the ¹⁵N signal by 9–10 ppm despite of the lengthening of the relevant N? H bond. These experimental trends are substantiated by gauge‐independent atomic orbital and density functional theory calculations of the shielding and coupling constants in the 3,3‐bis(isopropylamino)‐1‐(aryl)prop‐2‐en‐1‐one (12) for conformations with the Z‐ and E‐orientations of the carbonyl group relative to the N? H group. The effects of the N? H···O hydrogen‐bond on the NMR parameters are analyzed with the atoms‐in‐molecules (AIM) and natural bond orbital (NBO) methods. The AIM method indicates a weakening of the N? H···O hydrogen bond as compared with that of 1,1‐di(pyrrol‐2‐yl)‐2‐formylethene (13) where N? H···O hydrogen bridge establishes a seven‐membered chelate ring, and the corresponding ¹J(N,H) coupling constant decreases. The NBO method reveals that the LP(O) →σ*_{N? H} hyperconjugative interaction is weakened on going from the six‐membered chelate ring to the seven‐membered one due to a more bent hydrogen bond in the former case. A dominating effect of the N? H bond rehybridization, owing to an electrostatic term in the hydrogen bonding, seems to provide an increase of the ¹J(N,H) value as a consequence of the N? H···O hydrogen bonding in the studied diaminoenones. Copyright © 2010 John Wiley & Sons, Ltd.     

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.     

Hydrogen‐bonded complexes of nicotine with simple alcohols

Ab initio and density functional theory studies have been performed on the hydrogen‐bonded complexes of neutral and protonated nicotine with ethanol, methanol, and trifluromethanol to explore their relative stability in a systematic way. Among all the hydrogen‐bonded nicotine complexes considered here, protonated forms in nicotine–ethanol and nicotine–methanol, and neutral form in nicotine–trifluromethanol complexes have been found to be the most stable. In the former two complexes, the proton attached to the pyrrolidine nitrogen acts as a strong hydrogen bond donor, whereas the pyrrolidine nitrogen atom acts as a hydrogen bond acceptor in the latter case. Neutral complex of nicotine with trifluromethanol has been found to possess a very short hydrogen bond (1.57 Å) and basis set superposition error corrected hydrogen bond energy value of 19 kcal/mol. The nature of the various hydrogen bonds formed has been investigated through topological aspects using Bader's atoms in molecules theory. From the calculated topological results, excellent linear correlation is shown to exist among the hydrogen bond length, electron density, and its Laplacian at the bond critical points for all the complexes considered. The natural bond orbital analysis has been carried out to investigate the charge transfer in the nicotine alcohol complexes. In contrast to the blue shifting behavior that is generally exhibited by other C? H···O hydrogen bonds involving sp³ carbon atom, the C? H···O hydrogen bond in the protonated nicotine–ethanol and methanol complexes has been found to be proper with red shifting in nature. © 2011 Wiley Periodicals, Inc.     

Computational Study on the Unconventional Hydrogen‐Bonded F–H···C Systems

The F–H···YZ₂ (Y = C, Si, BH, A1H;Z = H, PH₃) systems were examined using density functional theory calculations. The main focus of this work is to demonstrate that the chemistry of Y(PH₃)₂ exhibits a novel feature which is a central Y atom with unexpected high basicity. Further, the hydrogen bond strength can be adjusted by the substitution of H atoms of YH₂ by PH₃ groups. The FH···C(PH₃)₂ system has the strongest hydrogen bond interaction, which is larger than a conventional hydrogen bond. In addition to electrostatic interaction, donor‐acceptor interaction also plays an important role in determining the hydrogen bond strength. Therefore, a carbon atom can not only be the hydrogen bond acceptor but also can create an unusual stabilized hydrogen bond complex. Also, X₃B–YZ₂ (X = H, F; Y = C, Si, BH, A1H;Z = PH₃, NH₃) systems were examined, and it was found that the bond strength is controlled predominately by the HOMO‐LUMO gap (ΔIP). The smaller the ΔIP, the larger the bond dissociation energy of the B–Y bond. In addition, NH₃ is a better electron‐donating group than PH₃, and thus forms the strongest donor‐acceptor interaction between X₃B and Y(NH₃)₂.     

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.     

Theoretical investigations on the weak nonbonded CS···CH2 interactions: Chalcogen‐bonded complexes with singlet carbene as an electron donor

In this article, we explored the noncovalent bonding interactions between O?C?S, S?C?S, F₂C?S, Cl₂C?S, and singlet carbene. Six chalcogen‐bonded complexes were obtained. It is found that all the vibrational frequencies of C?S bond presented a red shift character. Interaction energy, topology property of the electron density and its Laplacian, and the donor–acceptor interaction have been investigated. All these results show that there exists a weak nonbonded interaction between the chalcogen bond donor and CH₂. An energy decomposition analysis was performed to disclose that the electrostatic interaction is the main stabilized factor in these nonbonded complexes. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Blue‐shifted H‐bond in aromatic sulfines: An ab initio calculation

The intramolecular C? H···O?S H‐bond in the aromatic sulfines, HRC?S?O, was analyzed by NBO and QTAIM methods. The results of QTAIM analysis at the MP2/aug‐cc‐pVDZ level of theory show that the C? H···O?S H‐bond meets all the characteristics of an improper, blue shift hydrogen bond. NBO analysis at the MP2/6–31++G(d,p)//MP2/aug‐cc‐pVDZ level predicts a normal relationship between change of bond length and C? H rehybridization. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

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     

C?H···N and C?H···O intramolecular hydrogen bonding effects in the 1H, 13C and 15 N NMR spectra of the configurational isomers of 1‐vinylpyrrole‐2‐carbaldehyde oxime substantiated by DFT calculations

According to the ¹H, ¹³C and ¹⁵N NMR spectroscopic data and DFT calculations, the E‐isomer of 1‐vinylpyrrole‐2‐carbaldehyde adopts preferable conformation with the anti‐orientation of the vinyl group relative to the carbaldehyde oxime group and with the syn‐arrangement of the carbaldehyde oxime group with reference to the pyrrole ring. This conformation is stabilized by the C? H···N intramolecular hydrogen bond between the α‐hydrogen of the vinyl group and the oxime group nitrogen, which causes a pronounced high‐frequency shift of the α‐hydrogen signal in ¹H NMR (～0.5 ppm) and an increase in the corresponding one‐bond ¹³C–¹H coupling constant (ca 4 Hz). In the Z‐isomer, the carbaldehyde oxime group turns to the anti‐position with respect to the pyrrole ring. The C? H···O intramolecular hydrogen bond between the H‐3 hydrogen of the pyrrole ring and the oxime group oxygen is realized in this case. Due to such hydrogen bonding, the H‐3 hydrogen resonance is shifted to a higher frequency by about 1 ppm and the one‐bond ¹³C–¹H coupling constant for this proton increases by ～5 Hz. Copyright © 2008 John Wiley & Sons, Ltd.     

C—H···X (X = N,O, S) intramolecular interaction in 1‐vinyl‐2‐(2′‐heteroaryl)pyrroles as monitored by 1H and 13C NMR spectroscopy

¹H and ¹³C NMR spectroscopy of a series of 1‐vinyl‐2‐(2′‐heteroaryl)‐pyrroles were employed for the analysis of their electronic and spatial structure. The C—H···N intramolecular interaction between the α‐hydrogen of the vinyl group and the pyridine nitrogen, a kind of hydrogen bonding, was detected in 1‐vinyl‐2‐(2′‐pyridyl)pyrrole, which disappeared in its iodide methyl derivative. It was shown that this interaction is stronger than the C—H···O and C—H···S interactions in 1‐vinyl‐2‐(2′‐furyl)‐ and ‐2‐(2′‐thienyl)‐pyrroles. Copyright © 2001 John Wiley & Sons, Ltd.     

Theoretical study of the S?H···O blue‐shifted hydrogen bond

Theoretical calculations were performed to study the nature of the hydrogen bonds in the complexes HCHO···HSO, HCOOH···HSO, HCHO···HOO, and HCOOH···HOO. The geometric structures and vibrational frequencies of these four complexes at the MP2/6‐31G(d,p) and MP2/6‐311+G(d,p) levels are calculated by standard and counterpoise‐corrected methods, respectively. The results indicate that in the complexes HCHO···HSO and HCOOH···HSO the S? H bond is strongly contracted. In the S? H···O hydrogen bonds, the calculated blue shifts for the S? H stretching frequencies are in the vicinity of 50 cm^?1. While in the complexes HCHO···HOO and HCOOH···HOO, the O? H bond is elongated and O? H···O red‐shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X? H bond length in the X? H···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization, and structural reorganization. Among them hyperconjugation has the effect of elongating the X? H bond. Electron density redistribution and rehybridization belong to the bond shortening effects, while structural reorganization has an uncertain influence on the X? H bond length. In the complexes HCHO···HSO and HCOOH···HSO, the shortening effects dominate which lead to the blue shift of the S? H stretching frequencies. In the complexes HCHO···HOO and HCOOH···HOO where elongating effects are dominant, the O? H···O hydrogen bonds are red‐shifted. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Cooperative enhancement of water binding to antiparallel β‐sheet models: Analysis by ab initio calculations

The cooperative enhancement of water binding to the antiparallel β‐sheet models has been studied by quantum chemical calculations at the MP2/6‐311++G**//MP2/6‐31G* level. The binding energies of the two antiparallel β‐sheet models consisting of two strands of diglypeptide are calculated by supermolecular approach. Then water molecules are gradually bonded to the diglypeptide by N? H···OH₂ and C?O···HOH hydrogen bonds. Our calculation results indicated that the hydrogen bond length and the atom charge distribution are affected by the addition of H₂O molecules. The binding energy of antiparallel diglypeptide β‐sheet models has a great improvement by the increasing of the hydrogen bond cooperativity and the more H₂O molecules added the more cooperativity enhancement can be found. The orbital interactions are calculated by natural bond orbital analysis, and the results indicate that the cooperative enhancement is closely related to the orbital interaction. © 2012 Wiley Periodicals, Inc.     

Hydrogen Bonding Interaction of Formic Acid-, Formaldehyde-, Formylfluoride-Nitrosyl Hydride： Theoretical Study on the Geometries, Interaction Energies and Blue- or Red-Shifted Hydrogen Bonds

The hydrogen bonding interaction of formic acid-, formaldehyde-, formylfluoride-nitrosyl hydride complexes was investigated by the density functional theory （DFT） and ab inito method in conjunction with 6-311＋＋G（2d,2p） basis set. The geometries, vibrational frequencies and interaction energies of the complexes were calculated by both standard and CP-corrected methods respectively. Moreover, G3B3 method was employed to estimate the interaction energies. There are C--H…O, N--H…O, N--H…F blue-shifted H-bonds and red-shifted O----H…O H-bond in the complexes. Electron density redistribution and rehybridization contribute to the N--H and C--H blue shifts. All geometric reorganizations contribute to the N--H blue shifts and partial geometric reorganizations contribute to the C--H blue shifts. The geometric reorganizations of the complex C except ZH（5）-O（4）-C（1） contribute to the O----H red shift. For the N--H blue shifts, the effect of r（N--O） variation on the N--H blue shifts is larger than that of ZH-N-O variation. Rehybridization plays a dominant role in the degree of N--H blue shifts, whereas the electron density redistribution contributes more to the degree of C--H blue shifts than the other effects do.