Does the molecular structure of CaH2 affect the dihydrogen bonding in CaH2 … HY (Y = CH3, C2H3, C2H, CN, and NC) complexes? A quantum chemistry study using MP2 and B3LYP methods

Second-order M ller-Plesset(MP2) and density functional theory(DFT) calculations have been carried out in order to investigate the structures and properties of dihydrogen-bonded CaH 2 HY(Y = CH 3,C 2 H 3,C 2 H,CN,and NC) complexes.Our calculations revealed two possible structures for CaH 2 in CaH 2 HY complexes:linear(I) and bent(II).The bond lengths,interaction energies,and strengths for H H interactions obtained by both MP2 and B3LYP methods are quite close to each other.It was found that the interaction energy decreases with increasing electron density at the Ca-H bond critical point.Atom-in-molecule(AIM) results show that for all of Ca-H H-Y interactions considered here,the Laplacian of the electron density at the H H bond critical point is positive,indicating the electrostatic nature of these Ca-H H-Y dihydrogen bonded systems.     

Rapid Evaluation of Individual Hydrogen Bonding Energies in Linear Water Chains

A model is proposed to rapidly evaluate the individual hydrogen bonding energies in linear water chains. We regarded the two O--H bonds of a water molecule as two dipoles. The magnitude of the O--H bond dipole mo- ment can be varied due to the other water molecules＇ presence. An analytic potential energy function, which explicitly contains the permanent dipole-dipole interactions, the polarization interactions, the van der Waals interactions and the covalent interactions, was therefore established. The individual hydrogen bonding energies in a series of linear water chains were evaluated via the analytic potential energy function and compared with those obtained from the CP-corrected MP2/aug-cc-pVTZ calculations. The results show that the analytic potential energy function not only can produce the individual hydrogen bonding energies as accurately as the CP-corrected MP2/aug-cc-pVTZ method, but is very efficient as well, demonstrating the model proposed is reasonable and useful. Based on the individual hy- drogen bonding energies obtained, the hydrogen bonding cooperativity in the linear water chains was explored and the natures of the hydrogen bonding in these water chains were discussed.     

Theoretical Investigation on the Geometries and Properties of Guanine-BX3 （X = F, Cl） Complex

Geometries and binding energies were predicted at the B3LYP/6-311+G* level for the guanine-BX3 (X = F, Cl) systems and four isomers with no imaginary frequencies have been obtained for both guanine-BF3 and guanine-BCl3, respectively. Single energy calculations using much larger basis sets (6-311+G(2df,p) and aug-cc-pVDZ were carried out as well. It was found that the most stable isomer of guanine-BF3 is BF3 connected to N3 of guanine with the stabilization energy of –19.93 kcal/mol (BSSE corrected), while that of guanine-BCl3 is BCl3 connected to O10 of guanine having stabilization energy of –15.02 kcal/mol at the same level. The analyses for the combining interaction between BX3 and guanine with the atom-in-molecules theory (AIM) and natural bond orbital (NBO) methods have been performed. The results indicated that all the isomers are formed with σ-p type interactions between guanine and BX3, in which pyridine-type nitrogen or carbonyl oxygen or nitrogen atom of amino group offers its lone pair electrons to the empty p orbital of boron atom and the concomitance of charge transfer from guanine to BX3 has occurred. Still, one or two hydrogen bonds exist in some isomers of guanine-BX3 system and contribute to the stability of complex systems. Frequency analysis suggested that the stretching vibration of BX3 undergoes a red shift in complexes. Guanine-BF3 complex is more stable than guanine-BCl3 although the B–Y (Y=N, O) bond distance in the latter is shorter.     

Existence of aromatic sp~2 C-H…O = C intramolecular interaction similar to hydrogen bond

A 'H NMR signal shifted drastically to down field (δ - 10.0) at the bay area and in dose proximity to C = O group for H-1 was observed through complete assignments of 1H NMR spectra for pyridino- and benzobenzanthrones. It is concluded that this phenomenon is due not only to the anisotropy effect of C=O plus aromatic ring current effect, but also to the electrostatic attraction of C-H (δ+)…O(δ-)=C interaction. The evidence for the sp2C-H…O = C intramolecular interaction similar to hydrogen bond has also been given by EI-MS and MS/MS (CID) spectroscopy and IR spectroscopy, as well as MNDO-PM3 calculations. This new kind of interaction might be called 'quasi-hydrogen bond'.     

Theory Studies on the Intermolecular Interactions of Urea Nitrate with RDX

Six fully optimized geometries of urea nitrate cation and RDX complexes have been obtained with DFT-B3LYP and MP2 methods at the 6-311++G** level. The intermolecular interaction energies have been calculated with basis set superposition error (BSSE) and zero point energy (ZPE) correction. The nature of intermolecular interaction has been revealed by the analysis of AIM and NBO. The results indicate that the greatest binding energy of urea nitrate with RDX is –82.47kJ/mol. The O–H…O and N–H…O hydrogen bonds are important intermolecular interactions of urea nitrate cation with RDX, and the origin of hydrogen bonds is the oxygen atom offering its lone-pair electrons to the σ(O-H)* or σ(O-H)* antibonding orbital. The intermolecular interactions strengthen the N–NO2 bond, leading to the reduced sensitivity of urea nitrate and RDX mixture explosive.     

Theoretical Investigations on the Interaction Nature of Br2 with HF, H2O and NH3

The interactions of HF, H2O and NH3 with Br2 are investigated at the MP2(full)/ aug-cc-pVDZ level. It is found that two kinds of stable complexes, halogen-bonded and hydrogen- bonded complexes, exist between Br2 and HF and between Br2 and H2O. The interaction energy analysis and natural population analysis (NPA) are conducted to these two kinds of complexes, indicating the halogen-bonded complexes are more stable than the corresponding hydrogen-bonded ones, and the binding energies of the former increase in the order HFH2O for the latter.     

Computational studies of σ-type weak interactions between NCO/NCS radicals and XY(X = H,Cl;Y = F,Cl,and Br)

The triatomic radicals NCO and NCS are of interest in atmospheric chemistry,and both the ends of these radicals can potentially serve as electron donors during the formation of σ-type hydrogen/halogen bonds with electron acceptors XY(X = H,Cl;Y = F,Cl,and Br).The geometries of the weakly bonded systems NCO/NCS···XY were determined at the MP2/aug-cc-pVDZ level of calculation.The results obtained indicate that the geometries in which the hydrogen/halogen atom is bonded at the N atom are more stable than those where it is bonded at the O/S atom,and that it is the molecular electrostatic potential(MEP)-not the electronegativity-that determines the stability of the hydrogen/halogen bond.For the same electron donor(N or O/S) in the triatomic radical and the same X atom in XY,the bond strength decreases in the order Y = F > Cl > Br.In the hydrogen/halogen bond formation process for all of the complexes studied in this work,transfer of spin electron density from the electron donor to the electron acceptor is negligible,but spin density rearranges within the triatomic radicals,being transferred to the terminal atom not interacting with XY.     

Substituent Effects on the Hydrogen Bonding between 4-Substituted Phenols and HF, H2O, NH3

Density function theory UB3LYP/6-31 g(d) calculations were performed to study the hydrogen bonds between para-substituted phenols and HF, H2O, or NH3. It revealed that many properties of the non-covalent complexes, such as the interaction energies, donor-acceptor distances, bond lengths and vibration frequencies, showed well-defined substituent effects. Therefore, from the substituent effects not only the mechanism of a certain non-covalent interaction can be better understood, but also the interaction energies and structures of a certain non-covalent complex, which otherwise might be very hard or resource-consuming to estimate, can be easily predicted.     

Theoretical Study on the Structures and Properties of Hydrogen Bonding Complexes between Diazines and Water

Density functional theory B3LYP method and second-order Moller-Plesset perturbation theory MP2 method were employed to obtain the optimized geometries of the ground state and interaction energy for diazines and water complexes. The results show that the ground state complexes have strong hydrogen bonding interaction with -20.99, -16.73 and -15.31 kJ/mol after basis set superposition error and zero-point vibration energy correction for pyridazine-water, pyrimidine-water and pyrazine-water, respectively, and large red-shift for the symmetric H-O stretching vibration frequencies due to the formation of N…H-O hydrogen bond in the diazine-water complexes. The NBO analysis indicates that intermolecular charge transfer are 0.0316, 0.0255 and 0.0265 e respectively. In addition, the first singlet （n,n＊） vertical excitation energy of the monomer and the hydrogen bonding complexes between diazines and water was investigated by time-dependent density functional theory.     

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.     

Theoretical Study of Hydrated Cd~（2＋） Interactions with Guanine

Theoretical study was performed to investigate how the hydration of cadmium ca-tion influences the structure and properties of guanine.The aqueous environment was simulated by both explicit solvent(1-5 water molecules) model and implicit solvent model.For complexes in which Cd2+ attached to the N(7) and O(6) sites of guanine,energy analysis together with the Natural Bonding Orbital(NBO) analysis were performed to elucidate the bonding characteristics in detail.The most stable structures are penta-coordinate complexes without aqua ligand located at the guanine site.Higher number of water ligands corresponds to higher stabilization energies.Average bonding energies of G-Cd increase with the number of water molecules.Bonding energies of water ligands depend on its position in the complexes.The charge distribution of guanine changed with increasing the number of water ligands,which may also influence the base-pairing pattern of guanine.There is positive charge transfer from guanine to aqua ligand as the number of the hydration waters increases.IEFPCM optimization has results comparable to the [CdG(H2O)5]2+ structure 5a.     

Theoretical study of the N—H···O red-shifted andblue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO···HNO, HCOOH···HNO, HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F. The geomet- ric structures and vibrational frequencies of these six complexes at the MP2/6-31 G(d,p), MP2/6-311 G(d,p), B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO···HNO and HCOOH···HNO the N—H bond is strongly contracted and N—H···O blue-shifted hydrogen bonds are observed. While in complexes HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F, the N—H bond is elongated and N—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 redistribu- tion, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X—H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO···HNO and HCOOH···HNO, the shortening effects dominate which lead to the blue shift of the N—H stretching frequencies. In complexes HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F where elongating effects are dominant, the N—H···O hydrogen bonds are red-shifted.     

Synthesis, Crystal Structure and Electrochemistry Properties of a (N,N'-Ethylene-bis(salicylaldiminato)) Nickel(Ⅱ) Complex, [Ni2(salen)2]·NCS-NH4

A new Ni(Ⅱ) complex [Ni2(salen)2]·(NCS)·NH4 (salen = N,N'-bis(salicylidenea-mino)ethanato) has been prepared and structurally characterized by elemental analysis, IR spectra and single crystal X-ray diffraction. It crystallizes in the orthorhombic system, space group Pbca with a = 16.8725(13), b = 19.0046(15), c = 20.0583(16) (A), Z = 8, V = 6431.8(9) (A)3, C33H32N6Ni2O4S1, Mr= 726.13, Dc = 1.500 g/cm3, F(000) = 3008, μ = 1.284 mm-1, the final R = 0.0394 and wR = 0.0767 for 4449 observed reflections with Ⅰ＞2σ(Ⅰ). The complex involves a N,N'-ethylene-bis(salicylaldiminato) Schiff base, an isothiocyanato anion and an ammonium cation. The nickle(Ⅱ) ion adopts a distorted square coordination geometry with N2O2 set of Schiff base ligand. The complexes are linked into a dimmer via intermolecular hydrogen bonds and the [Ni(salen)] moieties are connected together to form a 2-D layer structure by intermolecular N-H…O hydrogen bonds and π-π stacking. Cyclic-voltammetry method was used to characterize electrochemically the complex.     

Electronic Absorption Spectroscopy of H2X （X=O,Te, Po）： Theoretical Treatment of Spin-Orbit Effects

The electronic spectroscopy of H2X （X=O, Te, Po） was investigated by means of spinorbit configuration interaction （EPCISO） and restricted active space state interaction （SORASSI）. The transition energies to the low-lying singlet and triplet states of H2O, in which the SO interaction is zero, compare rather well with the experimental data as well as to other theoretical values. The theoretical electronic absorption spectrum is characterized by three allowed transitions A^1B1 （2px（O）→σ^＊g/3s（O））, B^1A1（σg→σ^＊g/3s（O）） and A^1S2（σg→σ^＊u） calculated at 7.68, 9.94, and 11.72 eV, respectively. The theoretical absorption spectra of H2X （X=Te, Po） are shifted to the red with the A^1B1 （npx（X）→σ^＊g） states calculated at 5.06 eV （H2Te） and 4.40 eV （H2Po） and the A^1B2 （σg→σ^＊u） states calculated at 7.89 eV （H2Te） and 7.77 eV （H2Po）. The largest SO splitting amounts to 0.34 eV and is found for the lowest a^3A1 of H2Po. In H2Te the SO effects are still negligible with a maximum splitting of 0.04 eV for the lowest a^3B2. The two methods lead to comparable results but the EPCISO approach depends strongly on the reference wavefunction.     

Cocrystal Assembled by 1,2-Diiodotetrafluorobenzene and Acridine via C-I…N Halogen Bond and Tr-hole…F Bonds

The concepts on o-hole and ~-hole bonds are suggested. A cocrystal with repeated 8-F-atom unit as basic struc- tural motif is assembled based on bifurcated C-I…N…I-C halogen/σ-hole bond and antiparallel double π-hole… F bonds by 1,2-diiodotetrafluorobenzene and acridine and characterized well by XRD, powder XRD and solid 19F NMR, etc. Also the calculated interaction energies are -26.8 and -31.5 kJ/mol for bifurcated C-I…N sp……2 halogen bonds, and -14.3 kJ/mol for a pair of n-hole…F bonds. In this system C-I…N halogen bond has stronger competitive ability to C-I…π halogen bond due to stronger basicity of N than π-system in acridine. The combination of the halogen/σ-hole and π-hole bonds or together with other weak interactions could play a key role in assembling function materials, molecular recognition and design of drugs and so on.     

Mechanistic Study on the Monofunctional Binding of Hydrolysis Products of Non-planar Heterocyclic Complexes Trans-[PtCl_2NH_3（piperidine）] and Trans-[PtCl_2（piperidine）_2] to DNA Purine Bases

The monofunctional substitution reactions between trans-[PtCl(H2O)(NH3)(pip)]+,trans-[Pt(H2O)2(NH3)(pip)]2+,trans-[PtCl(H2O)(pip)2]+,trans-[Pt(H2O)2(pip)2]2+ (pip = piperidine) and adenine/guanine nucleotides are explored by using B3LYP hybrid functional and IEF-PCM salvation models. For the trans-[Pt(H2O)2(NH3)(pip)]2+ and trans-[PtCl(H2O)(NH3)(pip)]+ complexes,the computed barrier heights in aqueous solution are 13.5/13.5 and 11.6/11.6 kcal/mol from trans-Pt-chloroaqua complex to trans/cis-monoadduct for adenine and guanine,and the corresponding values are 20.7/20.7 and 18.8/18.8 kcal/mol from trans-Pt-diaqua complex to trans/cis-monoadduct for adenine and guanine,respectively. For trans-[PtCl(H2O)(pip)2]+ and trans-[Pt(H2O)2(pip)2]2+,the corresponding values are 21.5/21.3 and 19.4/19.4 kcal/mol,and 26.0/26.0 and 20.7/20.8 kal/mol for adenine and guanine,respectively. Our calculations demonstrate that the barrier heights of chloroaqua are lower than the corresponding values of diaqua for adenine and guanine. In addition,the free energies of activation for guanine in aqueous solution are all smaller than that for adenine,which predicts a preference of 1.9 kcal/mol when trans-[PtCl(H2O)(NH3)(pip)]+ and trans-[Pt(H2O)2(NH3)(pip)]2+ are the active agents and ～1.9 and ～ 5.3 kcal/mol when trans-[PtCl(H2O)(pip)2]+ and trans-[Pt(H2O)2(pip)2]2+ are the active agents,respectively. For the reaction of trans-Pt-chloroaqua (or diaqua) to cis-monoadduct,we obtain the same transition-state structure as from the reaction of trans-Pt-chloroaqua (or diaqua) to trans-monoadduct,which seems that the trans-Pt-chloroaqua (or diaqua) complex can generate trans-or cis-monoadduct via the same transition-state.     

Theoretical study of the N-H…O red-shifted and blue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO…HNO, HCOOH…HNO, HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F. The geometric structures and vibrational frequencies of these six complexes at the MP2/6-31 G(d,p), MP2/6-311 G(d,p), B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO…HNO and HCOOH…HNO the N-H bond is strongly contracted and N-H…O blue-shifted hydrogen bonds are observed. While in complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F, the N-H bond is elongated and N-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, and the other three factors belong to the bond shortening effects. In complexes HCHO…HNO and HCOOH…HNO, the shortening effects dominate which lead to the blue shift of the N-H stretching frequencies. In complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F where elongating effects are dominant, the N-H…O hydrogen bonds are red-shifted.     

Theoretical Studies on Structures and Properties of Endohedral Fullerenes Complexes： XHn@C32（X=F,O, N,C; n=l-4）

Theoretical studies on structures and properties of endohedral fullerene complexes formed by encapsulating small molecules of HF, H20, NH3, and CH4 in a C32 fullerene cage, were carried out by ab initio method. Current calculations reveal that these processes to encase them in fullerene are energetically unfavorable because of the small cavity size of C32. The red shift in the F-H stretching frequency indicates the potential existence of hydrogen bonding between the HF molecule and the carbon cage.     

Theoretical Study on the Structures and Stability of Isomers and Complex of[Si,C,O,O] Sytem

A detailed singlet potential energy surface(PES) of [Si,C,O,O] system including a van der Waals (vdW) comples SiO……CO2,eight isomers,and twelve transiton states is investigated by MP2 and QCISD(T) (single-point)methods.At the final QCISD(T)/6-311 G(2df)//MP2/6-311G(d) level with zero-point energy included,the complex SiO……CO is found to be thermodynamically and kinetically the most stable species.Although eight ismoers are located as local energy minima,they are rather unstable toward isomerization to the dissociation fragments or comples.For the reaction of silocon atoms with carbon dioxide,two competitive reaction channels are found,and the primary pathway,which leads to the products of SiO and CO fragments,is the direct oxygen-abstraction process from carbon dioxide by silicon atom with a41.16 kJ/mol reaction barrier height.Our predications are in good agreement with previous experimental and theoretical studies.     

N-H…X (X = F, Cl, Br, and I) hydrogen bonding in aromatic amide derivatives in crystal structures

Intramolecular N H···X (X=F, Cl, Br, and Ⅰ) hydrogen bonding patterns of aromatic amides in the solid state are summarized. It is revealed that the key for the formation of this kind of weak intramolecular hydrogen bonding in X-ray crystal structures is to suppress the competition of strong intermolecular N H···O C hydrogen bonding of the amide unit. For amides with identical backbones, the bonding capacity of halogen atoms as hydrogen bonding acceptors is in the order of F>Cl>Br>I, which is in accordance with their electronegativity strength. Generally, the five-membered hydrogen bonding is easier to form than the six-membered one.