Electron localization function and electron localizability indicator applied to study the bonding in the peroxynitrous acid HOONO

The ground‐state electronic structure of peroxynitrous acid (HOONO) and its singlet biradicaloid form (HO ··· ONO) have been studied using topological analysis of the electron localization function (ELF), together with the electron localizability indicator (ELI‐D), at the DFT (B3LYP, M05, M052X, and M06), CCSD, and CASSCF levels. Three isomers of HOONO (cis‐cis, cis‐perp, and trans‐perp) have been considered. The results show that from all functionals applied, only B3LYP yields the correct geometrical structure. The ELF and ELI‐D‐topology of the O? O and central N? O bonds strongly depends on the wave function used for analysis. Calculations carried out at CAS (14,12)/aug‐cc‐pVTZ//CCSD(T)/aug‐cc‐pVTZ level reveal two bonds of the charge‐shift type: a protocovalent N? O bond with a basin population of 0.82–1.08e, and a more electron depleted O? O bond with a population of 0.66–0.71e. The most favorable dissociation channel (HOONO → HO + ONO) corresponds to breaking of the most electron‐deficient bond (O? O). In the case of cis‐ and trans‐HO ··· ONO, the ELF, ELI‐D, and electron density fields results demonstrate a closed‐shell O ··· O interaction. The α‐spin electrons are found mainly (0.64e) in the lone pairs of oxygen V_{i = 1,2} (O) from the OH group. The β‐spin electrons are delocalized over the ONO group, with the largest concentration (0.34e) on the lone pair of nitrogen V(N). © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Nature of the ring-closure process along the rearrangement of octa-1,3,5,7-tetraene to cycloocta-1,3,5-triene from the perspective of the electron localization function and catastrophe theory

We analyze the behavior of the energy profile of the ring‐closure process for the transformation of (3Z,5Z)‐octa‐1,3,5,7‐tetraene 5 to (1Z,3Z,5Z)‐cycloocta‐1,3,5‐triene 6 through a combination of electron localization function (ELF) and catastrophe theory (CT). From this analysis, concepts such as bond breaking/forming processes, formation/annihilation of lone pairs, and other electron pair rearrangements arise naturally through the reaction progress simply in terms of the different ways of pairing up the electrons. A relationship between the topology and the nature of the bond breaking/forming processes along this rearrangement is reported. The different domains of structural stability of the ELF occurring along the intrinsic reaction path have been identified. The reaction mechanism consists of six steps separated by fold and cusp catastrophes. The transition structure is observed in the third step, d(C1? C8) = 2.342 Å, where all bonds have topological signature of single bonds (C? C). The “new” C1? C8 single bond is not formed in transition state and respective catastrophe of the ELF field (cusp) is localized in the last step, d(C1? C8) ≈ 1.97 Å, where the two monosynaptic nonbonding basins V(C1) and V(C8) are joined into single disynaptic bonding basin V(C1,C8). The V(C1,C8) basin corresponds to classical picture of the C1? C8 bond in the Lewis formula. In cycloocta‐1,3,5‐triene 6 the single C1? C8 bond is characterized by relatively small basin population 1.72e, which is much smaller than other single bonds with 2.03 and 2.26e. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Internucleotide J-couplings and chemical shifts of the N-H···N hydrogen-bonds in the radiation-damaged guanine-cytosine base pairs

Internucleotide ^2hJ_NN spin‐spin couplings and chemical shifts (δ(¹H) and Δδ(¹⁵N)) of N? H···N H‐bond units in the natural and radiation‐damaged G‐C base pairs were predicted using the appropriate density functional theory calculations with a large basis set. Four possible series of the damaged G‐C pairs (viz., dehydrogenated and deprotonated G‐C pairs, GC^?? and GC^?+ radicals) were discussed carefully in this work. Computational NMR results show that radicalization and anionization of the base pairs can yield strong effect on their ^2hJ_NN spin scalar coupling constants and the corresponding chemical shifts. Thus, variations of the NMR parameters associated with the N? H···N H‐bonds may be taken as an important criterion for prejudging whether the natural G‐C pair is radiation‐damaged or not. Analysis shows that ^2hJ_NN couplings are strongly interrelated with the energy gaps (ΔE_LP→σ*) and the second‐order interaction energies (E(2)) between the donor N lone‐pair (LP_N) and the acceptor σ^*_{N? H} localized NBO orbitals, and also are sensitive to the electron density distributions over the σ*(N? H) orbital, indicating that ^2hJ_NN couplings across the N? H···N H‐bonds are charge‐transfer‐controlled. This is well supported by variation of the electrostatic potential surfaces and corresponding charge transfer amount between G and C moieties. It should be noted that although the NMR spectra for the damaged G‐C pair radicals are unavailable now and the states of the radicals are usually detected by the electron spin resonance, this study provides a correlation of the properties of the damaged DNA species with some of the electronic parameters associated with the NMR spectra for the understanding of the different state character of the damaged DNA bases. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.     

A five‐coordinate iron(III) porphyrin complex including a neutral axial pyridine N‐oxide ligand

While six‐coordinate iron(III) porphyrin complexes with pyridine N‐oxides as axial ligands have been studied as they exhibit rare spin‐crossover behavior, studies of five‐coordinate iron(III) porphyrin complexes including neutral axial ligands are rare. A five‐coordinate pyridine N‐oxide–5,10,15,20‐tetraphenylporphyrinate–iron(III) complex, namely (pyridine N‐oxide‐κO)(5,10,15,20‐tetraphenylporphinato‐κ⁴N,N′,N′′,N′′′)iron(III) hexafluoroantimonate(V) dichloromethane disolvate, [Fe(C₄₄H₂₈N₄)(C₅H₅NO)][SbF₆]·2CH₂Cl₂, was isolated and its crystal structure determined in the space group P. The porphyrin core is moderately saddled and the Fe—O—N bond angle is 122.08 (13)°. The average Fe—N bond length is 2.03 Å and the Fe—ONC₅H₅ bond length is 1.9500 (14) Å. This complex provides a rare example of a five‐coordinate iron(III) porphyrin complex that is coordinated to a neutral organic ligand through an O‐monodentate binding mode.     

Investigation of substituent effects in aerogen‐bonding interaction between ZO3 (Z=Kr,Xe) and nitrogen bases

The substituent effects in aerogen bond interactions between ZO₃ (Z = Kr, Xe) and different nitrogen bases are studied at the MP2/aug‐cc‐pVTZ level of theory. The nitrogen bases include the sp bases NCH, NCF, NCCl, NCBr, NCCN, NCOH, NCCH₃ and the sp³ bases NH₃, NH₂F, NH₂Cl, NH₂Br, NH₂CN, NH₂OH, and NH₂CH₃. The nature of aerogen bonds in these complexes is analyzed by means of molecular electrostatic potential, electron localization function, quantum theory atoms in molecules, noncovalent interaction index, and natural bond orbital analyses. The interaction energy (E_int) ranges from ?4.59 to ?9.65 kcal/mol in the O₃Z···NCX complexes and from ?5.30 to ?13.57 kcal/mol in the O₃Z···NH₂X ones. The dominant charge‐transfer interaction in these complexes occurs across the aerogen bond from the nitrogen lone‐pair (n_N) of the Lewis base to the σ*_Z‐O antibonding orbital of the ZO₃. Besides, the formation of aerogen bond tends to decrease the ⁸³Kr or ¹³¹Xe chemical shielding values in these complexes. © 2016 Wiley Periodicals, Inc.     

Synthesis and Characterization of Iron(III) Complexes of 5‐(8‐Carboxy‐1‐naphthyl)‐10, 15, 20‐tritolyl Porphyrin

5‐(8‐Carboxy‐1‐naphthyl)‐10, 5, 20‐tritolyl porphyrin (H₃CNTTP) and its iron(III) complexes, [Fe(CNTTP)]₂ and [Fe(CNTTP)(N‐MeIm)₂], were synthesized and characterized. X‐ray crystallography revealed that the carboxylate group is “hanging” over the porphyrin plane. The rigid framework makes the distance between the carboxylate oxygen and iron in the same porphyrin too long to form a coordination bond. On the other hand, the carboxylate group is not bulky enough to block the axial binding site. In the presence of OH^–, the carboxylate oxygen is coordinated to iron in the symmetry‐related unit, which led to the dimeric structure, [Fe(CNTTP)]₂. In the presence of excess N‐methylimidazole, a six‐coordinate species, [Fe(CNTTP)(N‐MeIm)₂], was obtained. In such a structure, CH ··· O interactions between the carboxylate group and imidazole probably play an important role to determine the orientation of imidazole plane. Two imidazole planes have relative parallel orientation. For [Fe(CNTTP)(N‐MeIm)₂], ¹H NMR shows pyrrole protons at the region –10 to –25 ppm. EPR shows rhombic spectrum. Those suggest [Fe(CNTTP)(N‐MeIm)₂] is a type II low‐spin iron(III) porphyrinate.     

Multiple Bonding Between Group 3 Metals and Fe(CO)3−

Heteronuclear Group 3 metal/iron carbonyl anion complexes ScFe(CO)₃⁻, YFe(CO)₃⁻, and LaFe(CO)₃⁻ are prepared in the gas phase and studied by mass-selective infrared (IR) photodissociation spectroscopy as well as quantum-chemical calculations. All three anion complexes are characterized to have a metal–metal-bonded C_3v equilibrium geometry with all three carbonyl ligands bonded to the iron center and a closed-shell singlet electronic ground state. Bonding analyses reveal that there are multiple bonding interactions between the bare group-3 elements and the Fe(CO)₃⁻ fragment. Besides one covalent electron-sharing metal–metal σ bond and two dative π bonds from Fe to the Group 3 metal, there is additional multicenter covalent bonding with the Group 3 atom bonded to Fe and the carbon atoms.     

Multiple Bonding Between Group 3 Metals and Fe(CO)3−

Heteronuclear Group 3 metal/iron carbonyl anion complexes ScFe(CO)₃^?, YFe(CO)₃^?, and LaFe(CO)₃^? are prepared in the gas phase and studied by mass‐selective infrared (IR) photodissociation spectroscopy as well as quantum‐chemical calculations. All three anion complexes are characterized to have a metal–metal‐bonded C_3v equilibrium geometry with all three carbonyl ligands bonded to the iron center and a closed‐shell singlet electronic ground state. Bonding analyses reveal that there are multiple bonding interactions between the bare group‐3 elements and the Fe(CO)₃^? fragment. Besides one covalent electron‐sharing metal–metal σ bond and two dative π bonds from Fe to the Group 3 metal, there is additional multicenter covalent bonding with the Group 3 atom bonded to Fe and the carbon atoms.     

Nature of the interaction between ammonia derivatives and carbon disulfide. A theoretical investigation

The interactions between NH₃, its methylated and chlorinated derivatives and CS₂ are investigated by ab initio CCSD(T) and density functional BLYP‐D3 methods. The CCSD(T)/aug‐cc‐pVTZ calculated interaction energies of complexes characterized by the S···N chalcogen bonds range between ?1.71 and ?2.78 kcal mol^?1. The S···N bonds are studied by atoms in molecules, natural bond orbital, and noncovalent interaction methods. The lack of correlation between the interaction energies of methylated amines complexes and the electrostatic potential results from the lone pair effect in aliphatic amines. Different structures of CS₂ complexed with ammonia derivatives, stabilized by other than the S···N chalcogen bonds, are also predicted. These structures are characterized by interaction energies ranging between 1.15 and 3.46 kcal mol^?1. The results show that the complexing ability of CS₂ is not very high but this molecule is able to attack the electrophilic or nucleophilic sites of a guest molecule.     

Quantum chemical topology: The electronic structure of the alkaline nitrites MONO (M = Li,Na, K) studied by means of topological analysis of the electron localization function

In the search of the protocovalent bonding, previously recognized in the nitrous acid (HONO), a nature of the chemical bonds in the alkaline nitrites MONO (M = Li, Na, K) has been studied by means of the topological analysis of the Electron Localization Function (ELF) and Electron Localizability Indicator (ELI‐D). Calculations carried out with the B3LYP and MP2(full) methods, in conjunction with the aug‐cc‐pVTZ and 6‐311++G(3df,3pd) basis sets, revealed the cis (C_2v, more stable) and trans (C_s) isomers as minima on PES. Alkaline nitrites consist of the alkali metal cation M^δ+ interacting, mainly via electrostatic forces, with the nitrite anion [ONO]^δ− (δ ≈ 1e). The covalent N O bonds are characterized by disynaptic basins V(N,O) with the basin populations: 1.58÷1.62e for cis‐M^δ+[ONO]^δ− but 1.39÷1.49e for single N O bond and 1.81÷1.87e for formally double NO bond in trans M^δ+[O NO]^δ−. The protocovalent nitrogen–oxygen bond has not been observed. The N O bonds are slightly polarized towards the nitrogen atom with the polarity index p_NO ≤ 0.12. Two different sets of the hybrid (Lewis) structures are compared leading to different pictures of the bonding. According to NBO data there is a delocalization between the single N O and double NO type bonds, meanwhile results of the ELF analysis emphasize an electron delocalization between the single N O and ionic O⁻N⁺ hybrids. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Assessment of intermolecular interactions at three sites of the arylalkyne in phenylacetylene‐containing lithium‐bonded complexes: Ab initio and QTAIM studies

The intermolecular interactions existing at three different sites between phenylacetylene and LiX (X = OH, NH₂, F, Cl, Br, CN, NC) have been investigated by means of second‐order Møller?Plesset perturbation theory (MP2) calculations and quantum theory of “atoms in molecules” (QTAIM) studies. At each site, the lithium‐bonding interactions with electron‐withdrawing groups (? F, ? Cl, ? Br, ? CN, ? NC) were found to be stronger than those with electron‐donating groups (? OH and ? NH₂). Molecular graphs of C₆H₅C?CH···LiF and πC₆H₅C?CH···LiF show the same connectional positions, and the electron densities at the lithium bond critical points (BCPs) of the πC₆H₅C?CH···LiF complexes are distinctly higher than those of the σC₆H₅C?CH···LiF complexes, indicating that the intermolecular interactions in the C₆H₅C?CH···LiX complexes can be mainly attributed to the π‐type interaction. QTAIM studies have shown that these lithium‐bond interactions display the characteristics of “closed‐shell” noncovalent interactions, and the molecular formation density difference indicates that electron transfer plays an important role in the formation of the lithium bond. For each site, linear relationships have been found between the topological properties at the BCP (the electron density ρ_b, its Laplacian ?²ρ_b, and the eigenvalue λ₃ of the Hessian matrix) and the lithium bond length d(Li‐bond). The shorter the lithium bond length d(Li‐bond), the larger ρ_b, and the stronger the π···Li bond. The shorter d(Li‐bond), the larger ?²ρ_b, and the greater the electrostatic character of the π···Li bond. © 2012 Wiley Periodicals, Inc.     

A comparative study of O2, CO,and NO binding to iron–porphyrin

Minimum-energy structures of O₂, CO, and NO iron–porphyrin (FeP) complexes, computed with the Car–Parrinello molecular dynamics, agree well with the available experimental data for synthetic heme models. The diatomic molecule induces a 0.3–0.4 Å displacement of the Fe atom out of the porphyrin nitrogen (N_p) plane and a doming of the overall porphyrin ring. The energy of the iron–diatomic bond increases in the order Fe(SINGLE BOND)O₂ (9 kcal/mol) < Fe(SINGLE BOND)CO (26 kcal/mol) < Fe(SINGLE BOND)NO (35 kcal/mol). The presence of an imidazole axial ligand increases the strength of the Fe(SINGLE BOND)O₂ and Fe(SINGLE BOND)CO bonds (15 and 35 kcal/mol, respectively), with few structural changes with respect to the FeP(CO) and FeP(O₂) complexes. In contrast, the imidazole ligand does not affect the energy of the Fe(SINGLE BOND)NO bond, but induces significant structural changes with respect to the FeP(NO) complex. Similar variations in the iron–imidazole bond with respect to the addition of CO, O₂, and NO are also discussed. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 69: 31–35, 1998     

Density functional investigation and bonding analysis of pentacoordinated iron complexes with mixed cyano and carbonyl ligands

The equilibrium structures and vibrational frequencies of the iron complexes [Fe⁰(CN)_n(CO)_5?n]^n? and [Fe^II(CN)_n(CO)_5?n]^2?n (n = 0–5) have been calculated at the BP86 level of theory. The Fe⁰ complexes adopt trigonal bipyramidal structures with the cyano ligands occupying the axial positions, whereas corresponding Fe²⁺ complexes adopt square pyramidal structures with the cyano ligands in the equatorial positions. The calculated geometries and vibrational frequencies of the mixed iron Fe⁰ carbonyl cyanide complexes are in a very good agreement with the available experimental data. The nature of the Fe? CN and Fe? CO bonds has been analyzed with both charge decomposition and energy partitioning analysis. The results of energy partitioning analysis of the Fe? CO bonds shows that the binding interactions in Fe⁰ complexes have 50–55% electrostatic and 45–50% covalent character, whereas in Fe²⁺ 45–50% electrostatic and 50–55% covalent character. There is a significant contribution of the π‐ orbital interaction to the Fe? CO covalent bonding which increases as the number of the cyano groups increases, and the complexes become more negatively charged. This contribution decreases in going from Fe⁰ to Fe²⁺ complexes. Also, this contribution correlates very well with the C? O stretching frequencies. The Fe? CN bonds have much less π‐character (12–30%) than the Fe? CO bonds. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Metal complexes of a phenol-tailed porphyrin with different hydrogen bonds

Hydrogen bonds are very common and important interactions in biological systems, they are used to control the microenvironment around metal centers. It is a challenge to develop appropriate models for studying hydrogen bonds. We have synthesized two metal complexes of the phenol-tailed porphyrin, [Zn(HL)] and [Fe(HL)(C₆H₄(OH)(O))]. X-ray crystallography reveals that the porphyrin functions as a dianion HL^2? and the phenol OH is involved in hydrogen bonds in both structures. In [Zn(HL)], an intramolecular hydrogen bond is formed between the carbonyl oxygen and OH. In [Fe(HL)(C₆H₄(OH)(O))], the unligated O(5) of the ligand is involved in two hydrogen bonds, as a hydrogen bond donor and a hydrogen bond acceptor. The overall electronic effect on the ligand could be very small, with negligible impact on the structure and the spin state of iron(III). The structural differences caused by the hydrogen bonds are also discussed.     

Stereoelectronic Aspects of the Anomeric Effect in Fluoromethylamine

High-level ab initio calculations have been made for fluoromethylamine to study structural and energetic effects of the relative orientation of the N lone pair to the C? F bond. The anti-conformer (N lone pair anti-planar to the C? F bond) corresponds to the global energy minimum. It has the longest C? F distance, the shortest C? N distance, and is 7.5 kcal·mol^?1 more stable than the related perpendicular conformation (lone pair perpendicular to the C? F bond). The syn-conformation also shows hallmarks of the anomeric effect: long C? F bond, short C? N bond, and energetic stability when allowance is made for the two pairs of eclipsed hydrogens. The transition state for N inversion is close to the syn-structure; rotation about the C? N bond is strongly coupled with this inversion process. Small bond distance changes of ca. 0.02 Å between parallel and perpendicular conformations are associated with dissociation energy differences of ca. 30 kcal·mol^?1. Various criteria for assessing the strength of the anomeric effect are discussed.     

Tripodal Ligands: Design of Distorted Coordination Polyhedra in Biomimetic Metal Complexes. Crystal structures of [Zn(SCN)(ntb)](SCN) · iPrpOH and [Fe(acac)(ntb)](ClO4)2 · 2CH2Cl2 · iPrpOH,ntb = N-tris(2-benzimidazolylmethyl)amine

The tripodal ligand N-tris(2-benzimidazolylmethyl)-amine (ntb) was used for the preparation of zinc(II) and iron(III) complexes, [Zn(SCN)(ntb)](SCN) · ⁱPrpOH ( 1 ) and [Fe(acac)(ntb)](ClO₄)₂ · 2CH₂Cl₂ · ⁱPrpOH ( 2 ). 1 has a highly distorted trigonal-bipyramidal ZnN₅ coordination geometry. The donor atoms are nitrogens of one amine, three benzimidazoles and one SCN^?. A striking feature of the complex is the length of the Zn? N_amine bond of 2.539(6)Å. The octahedral N₄O₂ coordination sphere of the iron in 2 is less distorted than that of the zinc in 1 . The metal is surrounded by an amine and three benzimidazole nitrogens of the ligand and two oxygens of the bidentate acetylacetonate co-ligand. The Fe? O bond lengths differ by about 0.1 Å. As for the unusual long Zn? N bond in 1 this is a result of a trans effect. 1 crystallizes in the space group P1 with: a = 9.530(1)Å, b = 13.402(1)Å, c = 13.578(2)Å, α = 98.83(1), β = 95.19(1), γ = 101.21(1)°, Z = 2; 2 is also triclinic, space group P1 , with: a = 9.875(6)Å, b = 12.929(10)Å, c = 18.635(15)Å, α = 94.95(8)°, β = 101.01(6)°, γ = 111.09(4)°, Z = 2.     

Polysulfonylamine. CLXXVIII Onium‐Salze des Benzol‐1,2‐di(sulfonyl)amins (HZ): Eine zweite Kristallform des Ammonium‐Salzes NH4Z·H2O und Kristallstruktur des Bis(triphenylphosphoranyliden)ammonium‐Salzes [Ph3PNPPh3]Z

Polysulfonylamines. CLXXVIII. Onium Salts of Benzene‐1,2‐di(sulfonyl)amine (HZ): A Second Crystal Form of the Ammonium Salt NH₄Z·H₂O and Crystal Structure of the Bis(triphenylphosphoranylidene)ammonium Salt [Ph₃PNPPh₃]Z A dimorphic form of NH₄Z·H₂O, where Z^? is N‐deprotonated ortho‐benzenedisulfonimide, has been obtained and structurally characterized (previously known form 1A : monoclinic, P2₁/c, Z′ = 1; new polymorph 1B : monoclinic, P2₁/n, Z′ = 1). Both structures are dominated by an abundance of classical hydrogen bonds N⁺–H/O–H···O=S/OH₂, whereby the anionic N^? function does not act as an acceptor. The major difference between the dimorphs arises from the topology of the hydrogen bond network, which is two‐dimensional in 1A , leading to a packing of discrete lamellar layers, but three‐dimensional in 1B . Moreover, the latter network is reinforced by a set of weak C–H··O/N hydrogen bonds, whereas the layered structure of 1A displays only one independent C–H···O bond, providing a link between adjacent layers. The compound [Ph₃PNPPh₃]Z ( 2 , monoclinic, P2₁/c, Z′ = 1) is the first structurally authenticated example of an ionic Z^? derivative in which the cation contains neither metal bonding sites nor strong hydrogen bond donors. This structure exhibits columns of anions, surrounded by four parallel columns of cations, giving a square array. The large cations are associated into a three‐dimensional framework via weak C–H···C(π) interactions and an offset face‐to‐face phenyl interaction, while the anions occupy tunnels in this framework and are extensively bonded to the surrounding cations by C–H···O/N^? hydrogen bonds and C–H···C(π) interactions.     

Drum-shaped mono-organooxotin assembly through solvothermal synthesis with 2,3,4,5-tetrafluorobenzoic acid: crystal structure,hydrogen bonding and π–π stacking interactions

A drum-shaped organooxotin (IV) complex with 2,3,4,5-tetrafluorobenzoic acid of the type {[SnR₂(2,3,4,5-F₄C₆HCO₂)]O}₆ (R?=?m-Cl-PhCH₂) has been solvothermally synthesized and structurally characterized by elemental, IR, ¹H, ¹³C, ¹¹⁹Sn NMR spectra and X-ray crystallography diffraction analysis. This complex exhibits a new structural environment appearing as a “drum” arrangement with hexa-coordinated tin atoms in a four-membered stannoxane ring, (–Sn–O–)₂, as a common structural feature. Each tin(IV) displays a distorted octahedral geometry. Weak, but significant, intramolecular C–H?···?F hydrogen bonds and π–π stacking interactions are shown. These contacts lead to aggregation and supramolecular self-assembly. Cleavage of Sn–C bond occurred in complexes under the influence of strong acid.     

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     

Complexes of the Triolide from (R)-3-Hydroxybutanoic Acid with Sodium,Potassium, and Barium Salts: Crystal Structures,Ester Chelates and Ester Crowns,Crystal Packing,Bonding, and Electron-Localization Functions

The triolide of (R)-3-hydroxybutanoic acid ((R,R,R,))-3,7,11-trimethyl-2,6,10-trioxadodecane-1,5,9-trione; ( 1 ), readily available from the corresponding biopolymer P(3-HB) in one step, forms crystalline complexes with alkali and alkaline earth salts. The X-ray crystal structures of three such complexes, (3 NaSCN)·4 1 ( 2 ), (2 KSCN)·2 1 · H₂O ( 3 ), and (2) Ba(SCN)₂ · 2 1 · 2 H₂O · THF ( 4 ), have been determined and are compared. The triolide is found in these structures (i) as a free molecule, making no contacts with a cation (clathrate-type inclusion), (ii) as a monodentate ligand coordinated to a single ion with one carbonyl O-atom only, (iii) as a chelator, forming an eight-membered ring, with two carbonyl O-atoms attached to the same ion, (iv) as a linker, using two carbonyl O-atoms to bind to the two metals of an ion-X-ion unit (ten-membered ring), and (v), in a crown-ester complex, in which an ion is sitting on the three unidirectional C?O groups of a triolide molecule (Figs. 1–3). The crystal packing is such that there are columns along certain axes in the centers of which the cations are surrounded by counterions and triolide molecules, with the non-polar parts of 1 on the outside (Fig. 4). In the complexes 2–4 , the triolide assumes conformations which are slightly distorted, with the carbonyl O-atoms moved closer together, as compared to the ‘free’ triolide 1 (Fig. 5). These observed features are compatible with the view that oligo (3-HB) may be involved in the formation of Ca polyphosphate ion channels through cell membranes. A comparison is also made between the triolide structure in 1–4 and in enterobactin, a super Fe chelator (Fig. 5). To better understand the binding between the Na ion and the triolide carbonyl O-atoms in the crown-ester complex, we have applied electron-localization function (ELF) calculations with the data set of structure 2 , and we have produced ELF representations of ethane, ethene, and methyl acetate (Figs. 6–9). It turns out that this theoretical method leads to electron-localization patterns which are in astounding agreement with qualitative bonding models of organic chemists, such as the ‘double bond character of the CO? OR single bond’ or the ‘hyperconjugative n → σ* interactions between lone pairs on the O-atoms and neighbouring σ-bonds’ in ester groups (Fig. 8). The noncovalent, dipole/pole-type character of bonding between Na⁺ and the triolide carbonyl O-atoms in the crown-ester complex (the Na? O?C plane is roughly perpendicular to the O? C?O plane) is confirmed by the ELF calculation; other bonding features such as the C?N bond in the NaSCN complex 2 are also included in the discussion (Fig. 9).