Comparison of aromatic NH···π, OH···π, and CH···π interactions of alanine using MP2, CCSD, and DFT methods

A comparison of the performance of various density functional methods including long‐range corrected and dispersion corrected methods [MPW1PW91, B3LYP, B3PW91, B97‐D, B1B95, MPWB1K, M06‐2X, SVWN5, ωB97XD, long‐range correction (LC)‐ωPBE, and CAM‐B3LYP using 6‐31+G(d,p) basis set] in the study of CH···π, OH···π, and NH···π interactions were done using weak complexes of neutral (A) and cationic (A⁺) forms of alanine with benzene by taking the Møller–Plesset (MP2)/6‐31+G(d,p) results as the reference. Further, the binding energies of the neutral alanine–benzene complexes were assessed at coupled cluster (CCSD)/6‐31G(d,p) method. Analysis of the molecular geometries and interaction energies at density functional theory (DFT), MP2, CCSD methods and CCSD(T) single point level reveal that MP2 is the best overall performer for noncovalent interactions giving accuracy close to CCSD method. MPWB1K fared better in interaction energy calculations than other DFT methods. In the case of M06‐2X, SVWN5, and the dispersion corrected B97‐D, the interaction energies are significantly overrated for neutral systems compared to other methods. However, for cationic systems, B97‐D yields structures and interaction energies similar to MP2 and MPWB1K methods. Among the long‐range corrected methods, LC‐ωPBE and CAM‐B3LYP methods show close agreement with MP2 values while ωB97XD energies are notably higher than MP2 values. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010     

Rapid and accurate evaluation of the binding energies and the individual N-H···O=C, N-H···N, C-H···O=C, and C-H···N interaction energies for hydrogen-bonded peptide-base complexes

The binding energies of thirty-six hydrogen-bonded peptide-base complexes, including the peptide backbone-ase complexes and amino acid side chain-base complexes, are evaluated using the analytic potential energy function established in our lab recently and compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparison indicates that the analytic potential energy function yields the binding energies for these complexes as reasonable as MP2 does, much better than the force fields do. The individual N H…O=C, N H…N, C H…O=C, and C H…N attractive interaction energies and C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interaction energies, which cannot be easily obtained from ab initio calculations, are calculated using the dipole-dipole interaction term of the analytic potential energy function. The individual N H…O=C, C H…O=C, C H…N attractive interactions are about 5.3±1.8, 1.2±0.4, and 0.8 kcal/mol, respectively, the individual N H … N could be as strong as about 8.1 kcal/mol or as weak as 1.0 kcal/mol, while the individual C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interactions are about 1.8±1.1, 1.7±0.6, 0.6±0.3, and 0.35±0.15 kcal/mol. These data are helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies.     

S···X halogen bonds and H···X hydrogen bonds in H2CS-XY (XY = FF, ClF, ClCl, BrF, BrCl, and BrBr) complexes: cooperativity and solvent effect

Using ab initio calculations, we have studied the structures, properties, and nature of halogen bonds in H(2)CS-XY (XY = FF, ClF, ClCl, BrF, BrCl, and BrBr) complexes. The results show that the ring-shaped complexes are formed by a halogen bond (S···X) and a secondary hydrogen bond (H···X). We also analyzed the H(2)CS-ClF-ClF and FCl-H(2)CS-ClF complexes to investigate the cooperative and diminutive halogen bonding. The cooperative effect of halogen bonding is found in the former, while the diminutive effect is present in the latter. We finally considered the solvent effect on the halogen bond in H(2)CS-BrCl complex and found that the solvent has a prominent enhancing effect on it. The complexes have also been analyzed with natural bond orbital, atoms in molecules, and symmetry adapted perturbation theory method.     

Substituent effects on CL···N, S···N, and P···N noncovalent bonds

Cl, S, and P atoms have previously been shown as capable of engaging in a noncovalent bond with the N atom on another molecule. The effects of substituents B on the former atoms on the strength of this bond are examined, and it is found that the binding energy climbs in the order B = CH(3) < NH(2) < CF(3) < OH < Cl < NO(2) < F. However, there is some variability in this pattern, particularly for the NO(2) group. The A···N bonds (A = Cl, S, P) can be quite strong, amounting to as much as 10 kcal/mol. The binding energy arises from approximately equal contributions from its induction and electrostatic components, although the former becomes more dominant for the stronger bonds. The induction energy is due in large measure to the transfer of charge from the N lone pair to a B-A σ* antibonding orbital of the electron-acceptor molecule containing Cl, S, or P. These A···N bonds typically represent the lowest-energy structure on each potential energy surface, stronger than H-bonds such as NH···F, CH···N, or SH···N.     

Structural organization and dimensionality at the hands of weak intermolecular Au···Au, Au···X and X···X (X = Cl, Br, I) interactions

The salts K[AuCl(2)(CN)(2)]·H(2)O (1), K[AuBr(2)(CN)(2)]·2H(2)O (2) and K[AuI(2)(CN)(2)]·?H(2)O (3) were synthesized and structurally characterized. Compound 1 crystallizes as a network of square planar [AuCl(2)(CN)(2)](-) anions separated by K(+) cations. However, 2 and 3 feature 2-D sheets built by the aggregation of [AuX(2)(CN)(2)](-) anions via weak, intermolecular X···X interactions. The mixed anion double salts K(3)[Au(CN)(2)](2)[AuBr(2)(CN)(2)]·H(2)O (4) and K(5)[Au(CN)(2)](4)[AuI(2)(CN)(2)]·2H(2)O (5) were also synthesized by cocrystallization of K[Au(CN)(2)] and the respective K[AuX(2)(CN)(2)] salts. Similarly to 2 and 3, the [Au(CN)(2)](-) and [AuX(2)(CN)(2)](-) anions form 2-D sheets via weak, intermolecular Au(I)···X and Au(I)···Au(I) interactions. In the case of 5, a rare unsupported Au(I)···Au(III) interaction of 3.5796(5) ? is also seen between the two anionic units. Despite the presence of Au(I) aurophilic interactions of 3.24-3.45 ?, neither 4 nor 5 exhibit any detectable emission at room temperature, suggesting that the presence of Au(I)···X or Au(I)···Au(III) interactions may affect the emissive properties.     

Cooperativity between S···π and Rg···π in the OCS···C6H6···Rg (Rg = He, Ne, Ar, and Kr) van der Waals complexes

The complexes OCS···C(6)H(6), C(6)H(6)···Rg, and OCS···C(6)H(6)···Rg (Rg = He, Ne, Ar, and Kr) have been studied by means of MP2 calculations and QTAIM analyses. The optimized geometries of the title complexes have C(6v) symmetry. The intermolecular interactions in the OCS···C(6)H(6)···Rg complexes are comparatively stronger than that in the OCS···C(6)H(6) complex, which prove that the He, Ne, Ar, and Kr atoms have the ability to form weak bonds with the benzene molecule. In QTAIM studies, the π-electron density of benzene was separated from the total electron density. The molecular graphs and topological parameters of the OCS···πC(6)H(6), πC(6)H(6)···Rg, and OCS···πC(6)H(6)···Rg complexes indicate that the interactions are mainly attributed to the electron density provided by the π-bonding electrons of benzene and the top regions of the S and Rg atoms. Charge transfer is observed from the benzene molecule to SCO/Rg in the formation of the OCS···C(6)H(6), C(6)H(6)···Rg, and OCS···C(6)H(6)···Rg complexes. Molecular electrostatic potential (MEP) analyses suggest that the electrostatic energy plays a pivotal role in these intermolecular interactions.     

Cooperative and diminutive unusual weak bonding in F3CX···HMgH···Y and F3CX···Y···HMgH trimers (X = Cl, Br; Y = HCN, and HNC)

MP2 calculations with cc-pVTZ basis set were used to analyze intermolecular interactions in F(3)CX···HMgH···Y and F(3)CX···Y···HMgH triads (X = Cl, Br; Y = HCN, and HNC) which are connecting with three kinds of unusual weak interactions, namely halogen-hydride, dihydrogen, and σ-hole. To understand the properties of the systems better, the corresponding dyads are also studied. Molecular geometries, binding energies, and infrared spectra of monomers, dyads, and triads were investigated at the MP2/cc-pVTZ computational level. Particular attention is given to parameters such as cooperative energies, cooperative dipole moments, and many-body interaction energies. Those complexes with simultaneous presence of a σ-hole bond and a dihydrogen bond show cooperativity energy ranging between -1.02 and -2.31 kJ mol(-1), whereas those with a halogen-hydride bond and a dihydrogen bond are diminutive, with this energetic effect between 0.1 and 0.63 kJ mol(-1). The electronic properties of the complexes have been analyzed using the molecular electrostatic potential (MEP), the electron density shift maps, and the parameters derived from the atoms in molecules (AIM) methodology.     

Morpholine adducts of Co, Ni, and Mn benzoylacetonates: isostructurality and C–H···O hydrogen bonding

Morpholine adducts of nickel(II), cobalt(II), and manganese(II) benzoylacetonates, as well as a morpholine solvate of manganese(II) benzoylacetonate, were prepared and characterized by X-ray diffraction and thermal analysis. All four compounds crystallize in the P2₁/c space group with two complex molecules per unit cell. The morpholine solvate, along with the two adduct molecules, also contains four solvent morpholine molecules in the unit cell. The non-solvate compounds are isostructural, with crystal structures comprising 2D networks formed by C–H···O hydrogen bonding between phenyl rings and morpholine oxygen atoms. The topology of these networks can be described as intersecting C₂²(24) chains forming R₄⁴(48) rings. Networks with the same topology are also present in the solvate, but they are heavily distorted due to the presence of solvent morpholine molecules. Thermogravimetric analysis shows similar behavior of the non-solvate compounds upon thermal decomposition, with three degradation steps which can be related to gradual loss of morpholine molecules and subsequent overall decomposition. Decomposition of the solvate also proceeds in several steps, the first of which can be related to loss of solvent morpholine molecules and the further steps are analogous to those in the non-solvate compounds.     

Calcium and strontium,and zinc (phenazine)−· species

Calcium and strontium react with phenazine in tetrahydrofuran (THF) at ca 20 ° C to yield red solutions containing paramagnetic species based on (phenazine)⁻· (ESR characterization). Zinc reacts in THF in the presence of zinc chloride or bromide, or without metal halide in pyridine, to yield green or red ESR-active solutions also based on (phenazine)⁻·, and then, for the reaction in pyridine, a brown paramagnetic solid of composition Zn(phenazine)(pyridine)₂.     

On the properties of X···N noncovalent interactions for first-, second-, and third-row X atoms

In addition to a structure with a PH···N H-bond, a second complex of greater stability is formed when the PH(3) is rotated such that its P-H bond is pointing away from the approaching N lone pair of NH(3). Quantum calculations are applied to examine whether such a complex is characteristic only of P, or may occur as well for other atoms of the first, second, or third rows of the periodic table. The molecules PH(3), H(2)S, HCl, AsH(3), and NH(3) are all paired with NH(3) as electron donor. While NH(3) will not engage in an N···N attraction, all the others do form a X···N complex. The energetics, geometries, and other properties of these complexes are relatively insensitive to the nature of the X atom. This uniformity contrasts sharply with the H-bonded XH···N complexes where a strong sensitivity to X is observed. The three-dimensional nature of the electrostatic potential, in conjunction with the striving for a linear H-X···N orientation that maximizes charge transfer, serves as an excellent tool in understanding both the shape of the potential energy surface and the proclivity to engage in a X···N interaction.     

SH···N and SH···P blue-shifting H-bonds and N···P interactions in complexes pairing HSN with amines and phosphines

Quantum calculations at the MP2/aug-cc-pVDZ level examine complexes pairing HSN with aliphatic amines and phosphines. Complexes are cyclic and contain two attractive interactions. The first is a SH···N/P H-bond in which the S-H covalent bond contracts and shifts its stretching frequency to the blue, more so for amines than for phosphines. The second interaction is different for the amines and phosphines. The amines engage in a NH···N H-bond comparable in strength to the aforementioned SH···N interaction. In contrast, the second interaction in the phosphine complexes is a direct N···P attraction without an intervening H. This interaction is due in part to opposite partial charges on the N and P atoms, as well as covalent forces generated by charge transfer effects.     

C-X···π halogen and C-H···π hydrogen bonding: interactions of CF3X (X = Cl, Br, I or H) with ethene and propene

Using FTIR and Raman spectroscopy, the formation of halogen bonded complexes of the trifluorohalomethanes CF(3)Cl, CF(3)Br and CF(3)I with ethene and propene dissolved in liquid argon has been investigated. For CF(3)Br and CF(3)I, evidence was found for the formation of C-X···π halogen bonded 1:1 complexes. At a higher ratio of CF(3)I/propene, weak absorptions due to a 2:1 complex were also observed. Using spectra recorded at different temperatures, the complexation enthalpies for the complexes were determined to be -5.3(2) kJ mol(-1) for CF(3)Br·ethene, -7.5(2) kJ mol(-1) for CF(3)I·ethene, -5.6(1) kJ mol(-1) for CF(3)Br·propene, -8.8(1) kJ mol(-1) for CF(3)I·propene and -16.5(6) kJ mol(-1) for (CF(3)I·)(2)propene. The complexation enthalpies of the hydrogen bonded counterparts, with CF(3)H as the Lewis acid, were determined to be -4.6(4) kJ mol(-1) for CF(3)H·ethene and -5.1(2) kJ mol(-1) for CF(3)H·propene. For both hydrogen bonded complexes, a blue shift, by +4.8 and +4.0 cm(-1), respectively, was observed for the C-H stretching mode. The results from the cryospectroscopic study are compared with ab initio calculations at the MP2/aug-cc-pVDZ(-PP) level.     

Layered structures constructed by second-sphere coordination via N–H ··· Cl and C–H ··· Cl hydrogen bonding: synthesis and crystal structures of tribenzylamine and [MCl6] (M = Sn,Re, and Te)

A series of second-sphere coordination complexes of tribenzylamine (L ¹ ) and [MCl₆] (M = Sn, Re, Te) have been synthesized and characterized by spectroscopic techniques (IR, NMR) and single-crystal X-ray diffraction. The main driving force for the encapsulation of [MCl₆] and recognition with L ¹ is the second-sphere coordination of metal halides by the amide protons of the ligand via hydrogen bonding (N–H ··· Cl–M and C–H ··· Cl–M); new layered structures are described. Thermal stability and irreversible behavior of second-sphere coordination complexes [L ² ] · 0.5[TeCl₆]^2? · HCl · (H₃O)⁺ · 0.5H₂O (L ² = N,N,N′,N′-tetrabenzyl-ethylenediamine) in contact with water vapor are also described.     

Interaction in the ternary complexes of HNO3···HCl···H2O: a theoretical study on energetics, structure, and spectroscopy

Ternary complexes of HNO(3)···HCl···H(2)O were investigated by ab initio calculations with aug-cc-pVDZ and aug-cc-pVTZ basis sets. The results are analyzed in terms of structures, energetics, and infrared vibrational frequencies. In all minima, neither HNO(3) nor HCl becomes ionized. The contribution of the nonadditivity effect, which is significant for hydrogen-bonded clusters, is bigger for the cyclic structures in which HNO(3) acts as a proton donor to HCl, although the global minimum contains HNO(3) donating its proton to a H(2)O molecule.     

Synthesis, characterization and thermal properties of trimetallic N3-Cr[quadruple bond]Cr···M-N3 azide complexes with M = Cr, Mn, Fe, and Co

We report here two novel synthetic pathways toward the preparation of a family of trimetallic diazide compounds of the type Cr(2)M(dpa)(4)(N(3))(2), with M = Cr (10), Mn (4), Fe (5), and Co (11). Reaction of either Cr(2)M(dpa)(4)(OTf)(2) (for M = Mn and Fe) or [Cr(2)M(dpa)(4)(MeCN)(2)](PF(6))(2) (for M = Cr and Co) with sodium azide in methanol leads to the formation of the corresponding diazide compounds, and single crystal X-ray diffraction measurements confirm the predicted structures. Compounds 4, 5, and 10 are all high-spin compounds, but 11 is a spin-crossover compound exhibiting low-spin behavior at low temperatures (~100 K). Thermolytic characterization by DSC and TGA reveals an exothermic reaction corresponding to the loss of two dinitrogen molecules from compounds 5, 10, and 11. Further characterization by solution NMR measurements and cyclic voltammetry are also presented.     

Discrete, solvent-free alkaline-earth metal cations: metal···fluorine interactions and ROP catalytic activity

Efficient protocols for the syntheses of well-defined, solvent-free cations of the large alkaline-earth (Ae) metals (Ca, Sr, Ba) and their smaller Zn and Mg analogues have been designed. The reaction of 2,4-di-tert-butyl-6-(morpholinomethyl)phenol ({LO(1)}H), 2-{[bis(2-methoxyethyl)amino]methyl}-4,6-di-tert-butylphenol ({LO(2)}H), 2-[(1,4,7,10-tetraoxa-13-azacyclopentadecan-13-yl)methyl]-4,6-di-tert-butylphenol ({LO(3)}H), and 2-[(1,4,7,10-tetraoxa-13-azacyclo-pentadecan-13-yl)methyl]-1,1,1,3,3,3-hexafluoropropan-2-ol ({RO(3)}H) with [H(OEt(2))(2)](+)[H(2)N{B(C(6)F(5))(3)}(2)](-) readily afforded the doubly acidic pro-ligands [{LO(1)}HH](+)[X](-) (1), [{LO(2)}HH](+)[X](-) (2), [{LO(3)}HH](+)[X](-) (3), and [{RO(3)}HH](+)[X](-) (4) ([X](-) = [H(2)N{B(C(6)F(5))(3)}(2)](-)). The addition of 2 to Ca[N(SiMe(3))(2)](2)(THF)(2) and Sr[N(SiMe(3))(2)](2)(THF)(2) yielded [{LO(2)}Ca(THF)(0.5)](+)[X](-) (5) and [{LO(2)}Sr(THF)](+)[X](-) (6), respectively. Alternatively, 5 could also be prepared upon treatment of {LO(2)}CaN(SiMe(3))(2) (7) with [H(OEt(2))(2)](+)[X](-). Complexes [{LO(3)}M](+)[X](-) (M = Zn, 8; Mg, 9; Ca, 10; Sr, 11; Ba, 12) and [{RO(3)}M](+)[X](-) (M = Zn, 13; Mg, 14; Ca, 15; Sr, 16; Ba, 17) were synthesized in high yields (70-90%) by reaction of 3 or 4 with the neutral precursors M[N(SiMe(3))(2)](2)(THF)(x) (M = Zn, Mg, x = 0; M = Ca, Sr, Ba, x = 2). All compounds were fully characterized by spectroscopic methods, and the solid-sate structures of compounds 1, 3, 7, 8, 13, 14, {15}(4)·3CD(2)Cl(2), {16}(4)·3CD(2)Cl(2), and {{17}(4)·EtOH}·3CD(2)Cl(2) were determined by X-ray diffraction crystallography. Whereas the complexes are monomeric in the case of Zn and Mg, they form bimetallic cations in the case of Ca, Sr and Ba; there is no contact between the metal and the weakly coordinating anion. In all metal complexes, the multidentate ligand is κ(6)-coordinated to the metal. Strong intramolecular M···F secondary interactions between the metal and F atoms from the ancillary ligands are observed in the structures of {15}(4)·3CD(2)Cl(2), {16}(4)·3CD(2)Cl(2), and {{17}(4)·EtOH}·3CD(2)Cl(2). VT (19)F{(1)H} NMR provided no direct evidence that these interactions are maintained in solution; nevertheless, significant Ae···F energies of stabilization of 25-26 (Ca, Ba) and 40 kcal·mol(-1) (Sr) were calculated by NBO analysis on DFT-optimized structures. The identity and integrity of the cationic complexes are preserved in solution in the presence of an excess of alcohol (BnOH, (i)PrOH) or L-lactide (L-LA). Efficient binary catalytic systems for the immortal ring-opening polymerization of L-LA (up to 3,000 equiv) are produced upon addition of an excess (5-50 equiv) of external protic nucleophilic agents (BnOH, (i)PrOH) to 8-12 or 13-17. PLLAs with M(n) up to 35,000 g·mol(-1) were produced in a very controlled fashion (M(w)/M(n) ≈ 1.10-1.20) and without epimerization. In each series of catalysts, the following order of catalytic activity was established: Mg ? Zn < Ca < Sr ≈ Ba; also, Ae complexes supported by the aryloxide ligand are more active than their parents supported by the fluorinated alkoxide ancillary, possibly owing to the presence of Ae···F interactions in the latter case. The rate law -d[L-LA]/dt = k(p)·[L-LA](1.0)·[16](1.0)·[BnOH](1.0) was established by NMR kinetic investigations, with the corresponding activation parameters ΔH(++) = 14.8(5) kcal·mol(-1) and ΔS(++) = -7.6(2.0) cal·K(-1)·mol(-1). DFT calculations indicated that the observed order of catalytic activity matches an increase of the L-LA coordination energy onto the cationic metal centers with parallel decrease of the positive metal charge.     

Influence of insertion of a noble gas atom on halogen bonding in H2O···XCCNgF and H3N···XCCNgF (X = Cl and Br; Ng = Ar, Kr, and Xe) complexes

The H₂O···XCCNgF and H₃N···XCCNgF (X = Cl and Br; Ng = Ar, Kr, and Xe) complexes have been studied with quantum chemical calculations at the MP2/aug-cc-pVTZ level. The results show that the inserted noble gas atom has an enhancing effect on the strength of halogen bond, and this enhancement is weakened with the increase of noble gas atomic number. The methyl and Li substituents in the electron donor strengthen the halogen bond. The interaction energy increases from ?3.75 kcal/mol in H₃N–BrCCF complex to ?9.66 kcal/mol in H₂LiN–BrCCArF complex. These complexes have been analyzed with atoms in molecules, natural bond orbital, molecular electrostatic potentials, and energy decomposition calculations.     

OH···X (X = O, S) hydrogen bonding in thetrahydrofuran and tetrahydrothiophene

In this article, hydrogen bonding interaction between p-cresol (p-CR) and cyclic ether, tetrahydrofuran (THF) and thioether, tetrahydrothiophene (THT) has been investigated. Two-color resonantly enhanced two-photon ionization in conjunction with the fluorescence detected IR (FDIR) spectroscopy was used to record the changes in the OH stretching frequency in these complexes. The FDIR spectra showed existence of a single conformer of the p-CR·THF and two conformers of the p-CR·THT complex. With the help of computed IR spectra and atoms-in-molecules analysis, the two conformers of p-CR·THT were assigned as the complex of p-CR with THT (C(2))/THT (C(S)). The redshift of OH stretching frequency for the p-CR·THF complex was greater compared to those for the conformers of the p-CR·THT complex. The binding energies of the p-CR·THF and p-CR·THT complexes were computed to be 7.42 and 6.15 kcal/mole. These were of the same order as those for the acyclic analogs, diethylether (DEE), and diethylsulfide (DES), of the solvent molecules under investigation. Although the DEE and THF consist of same number of carbon atoms, the dispersion energy contribution was much higher (43%) for DEE than that for THF (30%). In the case of sulfur analogs, however, it was similar (~50%) in the case of both DES well as THT complexes. All the computed H-bond indicators for these two complexes nicely correlate with the observed redshift of the O-H stretch.