N?H···S and S?H···N intramolecular hydrogen bond in β‐thioaminoacrolein: A quantum chemical study

The conformational study of β‐thioaminoacrolein was performed at various theoretical levels, HF, B3LYP, and MP2 with 6‐311++G(d,p) basis set, and the equilibrium conformations were determined. To have more reliable energies, the total energies of all conformers were recomputed at high‐level ab initio methods, G2MP2, G3, and CBS‐QB3. According to these calculations, the intramolecular hydrogen bond is accepted as the origin of conformational preference in thialamine (TAA) and thiolimine groups. The hydrogen bond strength in various resonance‐assisted hydrogen bond systems was evaluated by HB energy, geometrical parameters, topological parameters, and charge transfers corresponding to orbital interactions. Furthermore, our results reveal that the TAA tautomer has extra stability with respect to the other tautomers. The population analyses of the possible conformations by NBO predict that the origin of this preference is mainly due to the π‐electron delocalization in framework of TAA forms, especially usual π_C?C → π*_C?S and Lp (N) → π*_C?C charge transfers. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Characterization of the N?H···ON and N?H···NO H‐bonds in nitrosamine dimers

Ab initio molecular orbital and DFT calculations have been carried out for three most stable dimers of parent nitrosamine (NA) in order to elucidate the structures and energetics of the dimers. The structures were optimized using HF, B3LYP, and MP2 methods with 6‐311+G(d,p) and 6‐311++G(2d,2p) basis sets. At the optimized geometries obtained at MP2/6‐311++G(2d,2p) level of theory, the energies were evaluated at QCISD/aug‐cc‐pVDZ and CCSD/aug‐cc‐pVDZ levels. The most stable dimer has two N? H···O?N hydrogen bonds and the least stable dimer has two N? H···N?O hydrogen bonds. The natural bond orbital analysis showed that the lpO(N) → BD*(N? N) and lpO(N) → BD*(N? H_b) interactions play a decisive role in the stabilization of the NH···O(N) hydrogen bonds in dimers. The atoms in molecules results reveal that the intermolecular N? H···O(N) H‐bonds in dimers have electrostatic character. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

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.     

A new unconventional halogen bond C?X···H?M between HCCX (X = Cl and Br) and HMH (M = Be and Mg): An ab initio study

In this article, a new type of halogen‐bonded complex YCCX···HMY (X = Cl, Br; M = Be, Mg; Y = H, F, CH₃) has been predicted and characterized at the MP2/aug‐cc‐pVTZ level. We named it as halogen‐hydride halogen bonding. In each YCCX···HMY complex, a halogen bond is formed between the positively charged X atom and the negatively charged H atom. This new kind of halogen bond has similar characteristics to the conventional halogen bond, such as the elongation of the C? X bond and the red shift of the C? X stretch frequency upon complexation. The interaction strength of this type of halogen bond is in a range of 3.34–10.52 kJ/mol, which is smaller than that of dihydrogen bond and conventional halogen bond. The nature of the electrostatic interaction in this type of halogen bond has also been unveiled by means of the natural bond orbital, atoms in molecules, and energy decomposition analyses. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Investigation on the individual contributions of N?H···OC and C?H···OC interactions to the binding energies of β‐sheet models

In this article, the binding energies of 16 antiparallel and parallel β‐sheet models are estimated using the analytic potential energy function we proposed recently and the results are compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparisons indicate that the analytic potential energy function can produce reasonable binding energies for β‐sheet models. Further comparisons suggest that the binding energy of the β‐sheet models might come mainly from dipole–dipole attractive and repulsive interactions and VDW interactions between the two strands. The dipole–dipole attractive and repulsive interactions are further obtained in this article. The total of N? H···H? N and C?O···O?C dipole–dipole repulsive interaction (the secondary electrostatic repulsive interaction) in the small ring of the antiparallel β‐sheet models is estimated to be about 6.0 kcal/mol. The individual N? H···O?C dipole–dipole attractive interaction is predicted to be ?6.2 ± 0.2 kcal/mol in the antiparallel β‐sheet models and ?5.2 ± 0.6 kcal/mol in the parallel β‐sheet models. The individual C^α? H···O?C attractive interaction is ?1.2 ± 0.2 kcal/mol in the antiparallel β‐sheet models and ?1.5 ± 0.2 kcal/mol in the parallel β‐sheet models. These values are important in understanding the interactions at protein–protein interfaces and developing a more accurate force field for peptides and proteins. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Synthesis,Crystal Structure and Vibrational Spectroscopy of NH4[Co(NH3)5(H2O)][B4O5(OH)4]2·6H2O

A novel hydrated cobalt tetraborate complex NH₄[Co(NH₃)₅(H₂O)][B₄O₅(OH)₄]₂·6H₂O, was synthesized by the reaction of NH₄‐borate aqueous with CoCl₂ and its structure was determined by single crystal X‐ray diffraction. The crystal system of this complex is orthorhombic, the space group is Pnma, and the unit cell parameters are a=1.2901(2) nm, b=1.6817(3) nm, c=1.1368(2) nm, α=β=γ=90°, V=2.4742(8) nm³, and Z=4. This compound contains infinite borate layers constructed from [B₄O₅(OH)₄]^2? units via hydrogen bonds. The adjacent polyborate anion layers are further linked together with the octahedral [Co(NH₃)₅(H₂O)]³⁺ groups through hydrogen bonds to form 3D framework. The groups and guest water molecules are deposited in the empty space of this framework and interact with the layers by extensive hydrogen bonds. Infrared and Raman spectra (4000–400 cm^?1) of NH₄[Co(NH₃)₅(H₂O)][B₄O₅(OH)₄]₂·6H₂O were recorded at room temperature and analyzed. Fundamental vibrational modes were identified and band assignments were made. The middle band observed at 575 cm^?1 in Raman spectrum is the pulse vibration of [B₄O₅(OH)₄]^2?.     

Solvothermal Synthesis and Crystal Structure of a Layered Thioantimonate(Ⅲ) [C4H9NH3]2Sb4S7

An inorganic-organic hybrid thioantimonate(Ⅲ) [CH3(CH2)3NH3]2Sb4S7 1 with layered structure was synthesized by solvothermal method.1 crystallizes in the triclinic system, space group P with a = 7.0124(11), b = 11.919(2), c = 14.879(3) (A), α = 108.791(3), β = 102.441(3), γ = 92.846(2)o, V = 1140.1(3) (A)3, Mr = 859.71, Z = 2, Dc = 2.504 g/cm3, μ= 5.324 mm-1, F(000) = 804, S = 1.013, the final R = 0.0297 and wR = 0.0618 for 3534 observed reflections with I＞2σ(I). 1 consists of [C4H9NH3] cations and two-dimensional [Sb4S7]n2n-anion which is composed of three SbS3 trigonal pyramids and one SbS4 unit joined by sharing common corners. The anionic layers are stacked perpendicularly to the c axis of the unit cell forming two-dimensional channels between the layers. The [C4H9NH3] cations interdigitate in a bilayer and reside in the 2D channels leading to a sandwich-like arrangement of the anion and cations.     

Complexes with Dative Bonds between d‐ and s‐Block Metals: Synthesis and Structure of [(Cy3P)2Pt?Be(Cl)X] (X=Cl,Me)

A platinum–beryllium adduct (see structure) was prepared by the reaction of [Pt(PCy₃)₂] and BeCl₂. Treatment with methyllithium resulted in ligand substitution at the beryllium center. Both complexes were structurally characterized and display unprecedented two‐center two‐electron bonds between a transition metal and beryllium.

     

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     

A novel single‐electron sodium bond system of H3C···Na?Y (YH,OH, F,CCH, CN,and NC)

A novel single‐electron sodium bond system of H₃C···Na? H (I), H₃C···Na? OH(II), H₃C···Na? F(III), H₃C···Na‐CCH(IV), H₃C···Na? CN (V) and H₃C···Na? NC (VI) complexes has been studied by using MP2/6‐311++G** and MP2/aug‐cc‐pVTZ methods for the first time. We demonstrated that the single‐electron sodium bond H₃C···Na? Y formed between H₃C and Na? Y (Y?H, OH, F, CCH, CN, and NC) could induce the Na? Y increased and stretching frequencies of I–IV and VI are red‐shifted, including the Na? N bond in complex V is blue‐shifted abnormally. The interaction energies are calculated at two levels of theory [MP2, CCSD(T)] with different basis. The results shows that the strength of binding bond in group 2 (IV–VI) with π electrons are stronger than that of group 1 (I–III) without π electrons. For all complexes, the main orbital interactions between moieties H₃C and Na? Y are LP₁(C)→LP*₁(Na). By comparisons with some related systems, it is concluded that the strength of single‐electron bond is increased in the order: hydrogen bond < bromine bond < sodium bond < lithium bond. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Synthesis and Crystal Structure of Tetraamminelithium-Rubidiumtriselenide, Li(NH3)4RbSe3, and Pentaamminesodium-Rubidiumtriselenide-Ammonia(1/3), Na(NH3)5RbSe3 · 3NH3

Summary. The ammoniates Li(NH₃)₄RbSe₃ and Na(NH₃)₅RbSe₃·3NH₃ were prepared by the reduction of Rb₂Se₅ with lithium or sodium in liquid ammonia. Single crystals were isolated and characterized by X-ray structure analysis using low temperature techniques. Both compounds contain triselenide anions Se₃^2–, which coordinate to rubidium cations forming ¹[RbSe₃]^– or ¹[Rb(NH₃)₂Se₃]^– chains. The chains are separated in the crystal structures by the homoleptic ammine complexes Li(NH₃)₄⁺ and Na(NH₃)₅⁺.     

Synthesis and Crystal Structure of Copper(I) Chloride π-Complexes with N-Allyl- and N,N'-Diallylpiperazinium Dichlorides: [C3H5NH(CH2)4NH2]Cu2Cl4and [C3H5NH(CH2)4NHC3H5]0.5CuCl2

The crystals of copper(I) π-complexes with N-allyl piperazine derivatives, [C₃H₅NH(CH₂)₄NH₂]Cu₂Cl₄(I) and [C₃H₅NH(CH₂)₄NHC₃H₅]_0.5CuCl₂(II), were prepared by alternating-current electrochemical synthesis. X-ray diffraction study showed that compounds Iand IIcrystallize in the monoclinic system: for I, space group P2₁/a, a= 10.254(4) Å, b= 12.306(4) Å, c= 10.656(4) Å, γ = 98.83(3)°, V= 1329(2) ų, Z= 4, R= 0.0457 for 1334 independent reflections; for II, space group P2₁/n, a= 10.187(2) Å, b= 7.283(2) Å, c= 10.480(3) Å, γ = 100.72(2)°, V= 764.0(6) ų, Z= 4, R= 0.0371 for 1025 independent reflections. The structure of Iis composed of {Cu₂Cl₄(C₇H₁₆N₂)}₂dimers linked by fairly strong (N)H···Cl hydrogen bonds (2.35(4) Å). The structure of IIconsists of centrosymmetrical dimeric Cu₂Cl₄ ^2–anions, whose copper atoms coordinate the allyl groups of different centrosymmetrical organic cations. The dimer–ligand chains are stretched along the [ $ {11} $ 0] direction and are joined by hydrogen contacts (N)H···Cl (2.62(4) Å).     

Synthesis and Crystal Structure of MnSm_4(SiO_4)_3O

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On the reactivity of metal and organometallic halides toward R3Sn?O?SnR3 systems

Interaction of metallic salts (M = Hg, Sb, and Te) with bis(triorganotin)oxide, (R₃Sn)₂O, where (R = C₆H₅, p‐CH₃C₆H₄, and cyclo‐C₆H₁₁) at room temperature proceeded with the simultaneous cleavage of the Sn C and Sn O bonds, invariably yielding R₂SnO along with other products. Thus the treatment of HgX₂ (X = Cl, CN, SCN) with (R₃Sn)₂O resulted in the formation of polymeric diorganotin oxide R₂SnO along with R₃SnX and RHgX derivatives. The reaction of SbCl₃ with (R₃Sn)₂O was found to give R₂SnO, R₃SnCl, and RSbCl₂, whereas interaction with SbCl₅ provided R₂SnO, R₂SnCl₂, and R₂SbCl₃. Treatment of TeCl₄ with (R₃Sn)₂O provided R₂SnO, R₃SnCl, and RTeCl₃ at room temperature. At reflux temperature, reaction of PhTeCl₃ with (R₃Sn)₂O yielded R₂SnO, R₃SnCl, and mixed diorganotellurium dichloride, RPhTeCl₂. The course of reaction indicated the instability of Sn O Sn system proceeding via a four‐centered mechanism, providing organometallic compounds in profitable yield. © 2009 Wiley Periodicals, Inc. Heteroatom Chem 20:278–283, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20547     

Synthesis and Crystal Structure of 2,4-Diiodo-6-[(2-morpholin-4-yl-ethylimino)-methyl]-phenol-copper(Ⅱ)

2,4-Diiodo-6-[(2-morpholin-4-yl-ethylimino)-methyl]-phenol-copper(Ⅱ) has been designed and synthesized.The structure was determined by UV,IR and single-crystal X-ray study.The title complex crystallizes in the triclinic system,space group P1 with a=6.6090(13),b=10.377(2),c=12.550(3),α=113.29(3),β=93.84(3),γ=98.31(3)°,V=774.9(3)3,Dc=2.215g/cm3,C26H30CuO4N4I4,Mr=1033.68,F(000)=487,μ=4.726 mm-1,Z=1,the final R=0.0563 and wR=0.1475 for 2101 observed reflections(I2σ(I)).The central copper(Ⅱ) is four-coordinated by two nitrogen atoms and two oxygen atoms from two 3,5-diiodosalicylaldehyde-2-morpholinoethylamine Schiff bases.The complex is linked into a column by π-π stacking interaction.The complex was assayed for antibacterial activities against three Gram positive bacterial strains(B.subtilis,S.aureus and S.faecalis) and three Gram negative bacterial strains(E.coli,P.aeruginosa and E.cloacae) by MTT method.Fortunately,the title complex shows potent antibacterial activity against these six bacterial strains.     

Cooperative influence of water binding to peptides by N?H···OH2 and CO···HOH hydrogen bonds: Study by Ab Initio calculations

In this article, the geometry structures of hydrogen bond chains of formamide and N‐methylacetamide and their hydrogen‐bonded complexes with water were optimized at the MP2/6‐31G* level. Then, we performed Møller–Plesset perturbation method with 6‐311++g**, aug‐cc‐pvtz basis sets to study the cooperative influence to the total hydrogen bond energy by the N? H ··· OH₂ and C?O ··· HOH hydrogen bonds. On the basis of our results, we found that the cooperativity of the hydrogen‐bonded complexes become weaker as N? H ··· OH₂ and C?O ··· HOH hydrogen bonds replacing N? H ··· O?C hydrogen bonds in protein and peptide. It means that the N? H and C?O bonds in peptide prefer to form N? H ··· O?C hydrogen bond rather than to form C?O ··· HOH and N? H ··· OH₂. It is significant for understanding the structures and properties of the helical or sheet structures of protein and peptide in biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Effect of Al?H···H?O dihydrogen bond on the reaction between diphenylmethanol and pyrazolate‐bridged dialuminum complex. An ONIOM DFT/AM1 study

To elucidate the nature of the Al? H···H? O dihydrogen bond and its effect on the reaction between diphenylmethanol and pyrazolate‐bridged dialuminum complex, a theoretical study was carried out using the ONIOM(B3LYP/6‐31+G(d,p):AM1) method. Calculations indicate that this reaction is a two‐step process. The first step is nucleophilic addition and the resulting intermediate is stabilized by an Al? H···H? O dihydrogen bond. Topology analyses based on the “atoms‐in‐molecules” theory show that the Al? H···H? O dihydrogen bond in dialuminum intermediate is stronger than normal hydrogen bond. This step is not barrierless, which is contrary to the result predicted by using simplified model. The second step, eliminating a molecule of dihydrogen, requires an activation free energy of 9.9 kcal/mol in gas phase, which implies the simplified model underestimates the energy barrier of this elimination step. ONIOM calculations also show that, using the simplified model without zero‐point energy correction, the dihydrogen bonding strength has been underestimated and unreliable results have been obtained. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

High‐Resolution Crystal Structure of a Silver(I)–RNA Hybrid Duplex Containing Watson–Crick‐like C?Silver(I)?C Metallo‐Base Pairs

Metallo‐base pairs have been extensively studied for applications in nucleic acid‐based nanodevices and genetic code expansion. Metallo‐base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo‐base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T Hg^II T base pairs. Herein, we have determined a high‐resolution crystal structure of the second natural metallo‐base pair between pyrimidine bases C Ag^I C formed in an RNA duplex. One Ag^I occupies the center between two cytosines and forms a C Ag^I C base pair through N3 Ag^I N3 linear coordination. The C Ag^I C base pair formation does not disturb the standard A‐form conformation of RNA. Since the C Ag^I C base pair is structurally similar to the canonical Watson–Crick base pairs, it can be a useful building block for structure‐based design and fabrication of nucleic acid‐based nanodevices.     

Concerted Interaction between Pnicogen and Halogen Bonds in XCl?FH2P?NH3 (X=F,OH, CN,NC, and FCC)

We analyze the interplay between pnicogen‐bonding and halogen‐bonding interactions in the XCl? FH₂P? NH₃ (X=F, OH, CN, NC, and FCC) complex at the MP2/aug‐cc‐pVTZ level. Synergetic effects are observed when pnicogen and halogen bonds coexist in the same complex. These effects are studied in terms of geometric and energetic features of the complexes. Natural bond orbital theory and Bader’s theory of “atoms in molecules” are used to characterize the interactions and analyze their enhancement with varying electron density at critical points and orbital interactions. The physical nature of the interactions and the mechanism of the synergetic effects are studied using symmetry‐adapted perturbation theory. By taking advantage of all the aforementioned computational methods, the present study examines how both interactions mutually influence each other.