Weak Intramolecular Interactions Research Articles

Nature of weak inter-and intramolecular interactions in crystals 8. Influence of intermolecular contacts on the strength of intramolecular O-H...N bonds in crystals of 3-(2-hydroxyphenyl)-1,2,4-triazoles

The nature and energy of the intramolecular H-bond in 3-(2-hydroxyphenyl)-1,2,4-triazoles was studied by X-ray diffraction and quantum chemical methods. In this system, the conjugation does not additionally contribute to the enhancement of the H-bond energy. The cooperative effects lead to a strengthening of the intramolecular H-bond.

Towards a better understanding of photo-excited spin alignment processes using silole diradicals

The synthesis of two nitroxide-based diradicals connected to a 2,3,4,5-tetraphenylsilole (TPS) unit, especially designed to present high spin photo-excited states, is reported. While the bisnitronylnitroxide (NN) silole-based diradical, TPSNN, is unstable and experiences a spontaneous fragmentation of its imidazolinic ring into a iso-butylammomium salt, the corresponding bisiminonitroxide (IN), TPSIN, is stable both in solution and in the solid state. This diradical crystallizes in the triclinic P-1 space group with a = 10.984(1), b = 11.474(1), c = 17.492(1) A, α = 81.10(1), β = 89.01(1), and γ = 65.71(2)°. Ground state magnetic properties of TPSIN have been investigated by means of SQUID and ESR measurements: the diradical displays weak intramolecular antiferromagnetic interactions (J/kB ≈ −1 K), in agreement with its topology and with the molecular packing observed in its crystal structure. In order to investigate the magnetic photo-excited states of TPSIN, time-resolved ESR experiments (TRESR) have been performed on this radical species. Despite the presence of both an appropriate topology for the diradical and a triplet photo-excited state for the TPS coupler, no TRESR signal was observed for this molecule within the timescale of the measurement. In addition to the work already published in this field, this result clearly indicates that besides the radical nature, the π-topological requirements and the need of photo-tunable spin-states for the coupler, the flexibility of the molecule also plays a crucial role in the achievement of photo-induced spin alignment processes.

Reversible modulus reinforcement of end-linked polydimethylsiloxane ionomer networks

We report the mechanical behavior and swelling properties of covalently end-linked networks of polydimethylsiloxane with tailored number of monomers between side carboxyl groups and number of carboxyl groups along the chain. Imperfect carboxyl networks are reinforced by neutralization of the carboxyl groups with gallium ions via conversion of pendent chains into elastically active strands due to formation of inter-molecular ionic cross-links. These networks swell in non-polar solvents to a similar degree as unmodified end-linked PDMS networks of comparable moduli. For unannealed samples, the modulus reinforcement is reversed by a polar THF:water solution that breaks the ionic cross-links. Neutralization with transition metal cations such as cobalt causes no initial reinforcement due to weak intra-molecular interactions. Reinforcement in annealed gallium, cobalt or carboxyl networks is not readily reversible.

Weak Intramolecular Interactions in Ethylene Glycol Identified by Vapor Phase OH−Stretching Overtone Spectroscopy

Vapor phase OH-stretching overtone spectra of ethylene glycol were recorded to investigate weak intramolecular hydrogen bonding. The spectra were recorded with conventional absorption spectroscopy and laser photoacoustic spectroscopy in the first to fourth OH-stretching overtone regions. The room-temperature spectra are dominated by two conformers that show weak intramolecular hydrogen bonding. A less abundant third conformer, with no sign of hydrogen bonding, is also observed. Vapor phase spectra of the ethylene-d(4) glycol isotopomer were also recorded and used to identify an interfering resonance between CH-stretching and OH-stretching states in the fourth overtone. Anharmonic oscillator local mode calculations of the OH-stretching transitions have provided an accurate simulation of the observed spectra. The local mode parameters were calculated with coupled cluster ab initio methods. The calculations facilitate assignment of the different conformers in the spectra and illustrate the effect of the intramolecular hydrogen bonding.

Nature of weak inter-and intramolecular interactions in crystals 6. Intramolecular O—H...O bond in enol forms of (phosphoryl)acylacetonitriles

The nature of the intramolecular O—H...O bond was studied and its energy was estimated by X-ray diffraction analysis and quantum-chemical calculations (B3LYP/6-311G**) of (diphenylphosphoryl)acylacetonitriles. The influence of the nature of the substituents at the double bond in the H-bonded ring and the crystal packing effects on the hydrogen bond were investigated.

Control of Photochemical, Photophysical, Electrochemical, and Photocatalytic Properties of Rhenium(I) Complexes Using Intramolecular Weak Interactions between Ligands

Intramolecular interactions between ligands have been successfully applied as a novel tool for controlling various properties of a series of cis,trans-[Re(dmb)(CO)(2)(PR(3))(PR'(3))](+)-type complexes (dmb = 4,4'-dimethyl-2,2'-bipyridine), in the ground state and in the excited state and in the one-electron reduced form. For rhenium complexes with two triarylphosphine ligands, P(p-XPh)(3), the dmb ligand was sandwiched by four aryl rings having CH(aryl)-pi(pyridine)-pi(aryl) interactions. On the other hand, complexes with one triarylphosphine ligand and one trialkylphosphite ligand, P(OR)(3), had pi-pi and CH-pi interactions between each pyridine ring in the dmb ligand and the aryl group in the P(p-XPh)(3). Various properties of these two series of rhenium complexes were compared with those of complexes having two trialkylphosphite ligands, which do not interact through space with the dmb ligand. Properties of the complexes associated mainly with the dmb ligand are strongly affected by the intramolecular interactions: (1) UV/vis absorptions to the pi-pi and (1)MLCT excited states were both red-shifted, but (2) emission from the (3)MLCT excited state was blue-shifted; (3) the lifetime of the (3)MLCT excited state was prolonged up to 3-fold; (4) the reduction potential in the ground state was positively shifted by 110 mV with pi-pi and CH-pi interactions and by 180-200 mV with the CH-pi-pi interactions. (5) In the excited states, the oxidation power of the complex was also enhanced by the intramolecular interactions. (6) In the corresponding one-electron-reduced species cis,trans-[Re(dmb(-.)(CO)(2)(PR(3))(PR'(3))], the intramolecular interactions are maintained and strongly affected their UV/vis spectra. (7) Photocatalysis for CO(2) reduction was significantly enhanced only by the CH-pi-pi interaction.

A novel intra-molecular protein–protein interaction code based on partial complementary coding of co-locating amino acids

Proteins are assumed to contain all the information necessary for unambiguous folding and specific interaction with each other. However, ab initio structure prediction is often not successful because the amino acid sequence itself is simply not sufficient to guide between endless folding possibilities. It seems to be logical to try to find the "missing" information in nucleic acids, in the redundant codon. Statistical analyses of approximately 35K amino acid co-locations in 80 different protein structures indicate the existence of a weak intra-molecular protein-protein interaction code. Co-locating amino acids are preferentially coded by codons which are complementary in reverse orientation to each other at the 1st and 3rd codon positions, but not necessarily at the 2nd. This code, called D-1 X 3/RC-3 X 1, limits the number of preferred amino acid pairs from 20 to 10.3+/-0.8 (SEM, n=20) and emphasizes the importance of "strictly" defined amino acids (those having less synonymous codons). The existence of this code does not by any means violate the known physicochemical rules of protein folding or interaction. It is suggested that the biological source of preferential (specific) amino acid co-locations is the partial complementarity of their codons. This special coding of co-locating amino acids is important to better understanding of some fundamental biochemical processes and observations such as: (a) protein folding; (b) specific and high affinity protein-protein interactions; (c) the role of the wobble bases; (d) the significance of the redundant genetic code; (e) the origin of specific protein-protein interactions. Furthermore it might be useful even in protein design.

Towards the rational design of palladium- N-heterocyclic carbene catalysts by a combined experimental and computational approach

A combined experimental and computational approach towards the development of Pd–NHC catalysts is described. A range of benzimidazolylidinium ligands incorporating electron-rich and electron-poor substituents were prepared and evaluated in the Suzuki reaction. The most electron-rich ligand showed the highest catalytic activity. Based on this information, the first alkyl–alkyl Negishi cross-coupling reaction protocol was developed. Evaluation of N, N′-diaryl-(4,5-dihydro)imidazolylilidinium ligands showed a strong dependence on the steric topography around the metal centre. A computational study of the most active ligand in the Negishi reaction, its Pd(0) and PdCl 2-complexes and related structures were modelled at the B3LYP/DZVP and HF/3-21G levels of theory. The potential energy hypersurfaces flattened with increase in ligand size. Binding energies were computed for carbene/Pd(0) adducts (in the range ∼31–40 kcal mol −1), roughly double that for PH 3 (∼16 kcal mol −1). Weak intramolecular interactions were found using AIM analyses.

Hydrogen Bonding and Cooperativity in Isolated and Hydrated Sugars: Mannose, Galactose, Glucose, and Lactose

The conformation of phenyl-substituted monosaccharides (mannose, galactose, and glucose) and their singly hydrated complexes has been investigated in the gas phase by means of a combination of mass selected, conformer specific ultraviolet and infrared double resonance hole burning spectroscopy experiments, and ab initio quantum chemistry calculations. In each case, the water molecule inserts into the carbohydrate at a position where it can replace a weak intramolecular interaction by two stronger intermolecular hydrogen bonds. The insertion can produce significant changes in the conformational preferences of the carbohydrates, and there is a clear preference for structures where cooperative effects enhance the stability of the monosaccharide conformers to which the water molecule chooses to bind. The conclusions drawn from the study of monosaccharide-water complexes are extended to the disaccharide lactose and discussed in the light of the underlying mechanisms that may be involved in the binding of carbohydrate assemblies to proteins and the involvement, or not, of key structural water molecules.

Synthesis, structure and magnetism of a linear Cu–Cl–Cu entity found in [(Cu( tachH)( tach)) 2(μ-Cl)] 5+

Coordination of cis, trans-1,3,5-triaminocyclohexane ( tach) to copper(II) at pH 11 in the presence of chloride ions results in the formation of a μ 2-chloro-linked dimer of Cu( tach) 2 units, which was characterized by single-crystal X-ray analysis, UV/Vis and IR spectroscopy, elemental analysis and magnetic measurements. Within the Cu( tach) 2 halves, the structurally rigid, chelating tach ligands are oriented syn to each other and each ligand binds to the copper center via two amino groups, forming a near-square planar coordination environment. Under the present reaction conditions, half of the tach ligands are protonated at the pendant, non-coordinated amino group. The Cu( tach) 2 halves are joined in a D 2h -symmetric fashion. This complex is of special interest as only few Cu II dimers based on a single linear Cu–Cl–Cu motif are known. For the first time a magnetochemical analysis of such a species is provided that characterizes the weak antiferromagnetic intramolecular interactions between the two s = 1/2 Cu II centers.

The Role of Intramolecular Hydrogen Bonds vs. Other Weak Interactions on the Conformation of Hyponitrous Acid and Its Mono- and Dithio-Derivatives

High level ab initio and density functional theory calculations have been carried out to investigate the relative stability of the different conformers of hyponitrous acid and its mono- and dithio-derivatives. Geometries and vibrational frequencies were obtained at the B3LYP/6-311+G(d,p) level and final energies through B3LYP/6-311++G(3df,2pd) single point calculations. The reliability of this theoretical scheme has been assessed by comparing these DFT results with those obtained at the G3 level of theory, for some suitable cases. The cis conformers of hyponitrous acid and its mono- and dithio-derivatives are systematically more stable than the trans ones because in the cis conformation a dative interaction between the nitrogen-lone pairs and the σNX^* antibonding orbital is significantly favored. Quite interestingly, in general, the conformers presenting an intramolecular hydrogen bond (IHB) are not the global minima of the corresponding potential energy surfaces and only for hyponitrous acid the conformer with a OH ⋅s O IHB is slightly more stable than the cis conformer without IHB. The low stability of the tautomers with IHB is closely related with another weak intramolecular interaction which involves the lone-pairs of the chalcogen atoms and the πNN* antibondig orbital, and which is significantly perturbed when the IHB is formed.

Multinuclear Fe(III) Complexes with Polydentate Ligands of the Family of Dicarboxyimidazoles: Nuclearity- and Topology-Controlled Syntheses and Magneto-Structural Correlations

Two polydentate ligands of the family of dicarboxyimidazoles, H(2)MeDCBI (= 4,5-dicarboxy-1-methyl-1H-imidazole) and H(3)DCBI (= 4,5-dicarboxyimidazole), have been used in reactions with the [Fe(3,5-(t)()Bu(2)salpn)](+) species {3,5-(t)Bu(2)salpn = the dianion of 1,3-bis-[(3,5-di-tert-butylsalicylidene)amino]propane} to synthesize selectively complexes of different nuclearities. Four complexes have been synthesized: the mononuclear complex [Fe(3,5-(t)Bu(2)salpn)(HMeDCBI)] (1), the two binuclear but topologically different complexes [Fe(3,5-(t)Bu(2)salpn)(MeDCBI)Fe(3,5-(t)Bu(2)salpn)] (2) and {[Fe(3,5-(t)Bu(2)salpn)](2)(HDCBI)} (3), and the trinuclear complex {[Fe(3,5-(t)Bu(2)salpn)](2)(DCBI)Fe(3,5-(t)Bu(2)salpn)} (4). The structures of these complexes have been determined by X-ray crystallography. Variable-temperature direct-current magnetic susceptibility measurements were conducted for all compounds to obtain information about their electronic structure and to investigate the extent of magnetic communication among the Fe(III) centers. The results of these measurements allowed us to correlate the different structural motifs with the possible magnetic interactions that arise in multinuclear complexes of dicarboxyimidazoles. For 1, the room-temperature chi(M)T value reveals an S = (5)/(2) ground state. The data for the binuclear but topologically different complexes 2 and 3, and the trinuclear complex 4 suggest that weak intramolecular antiferromagnetic interactions are present, with interaction parameters ranging from -3.6 to -5.1 cm(-1). Differences in the extent of the magnetic communication between the metal centers through the two different interaction pathways of the ligands MeDCBI and DCBI (either through the imidazole ring or through the carboxylate groups) have been observed in complexes 2-4 that can be explained by the structural differences observed in the crystal structures of these compounds (the separation of the metal centers and the coplanarity of the metal ion orbitals with the pi system of the ligands). Cyclic voltammetry measurements for the mononuclear compound 1 show an irreversible reduction wave that is attributed to Fe(3+) + e(-) --> Fe(2+). The electrochemical behavior of the multinuclear complexes 2-4 is more complicated; however, it indicates that there is a degree of electronic communication between the Fe(III) centers.

Crystal Structure and Magnetic Exchange Interaction in a Binuclear Copper(II) Schiff Base Complex with a Bridging m-Phenylenediamine Ligand

Condensation of 2-hydroxy-3-methoxybenzaldehyde with m-phenylenediamine (1,3-diaminobenzene) (m-pda) gives the ligand [N,N′-bis(2-hydroxy-3-methoxybenzylidene)-1,3-diaminobenzene] which reacts with cupric acetate to give the complex [Cu2(L-m-pda)2]·2H2O, [L = 2-hydroxy-3- methoxybenzaldehyde)]. The molecular structure of the complex [Cu2(L-m-pda)2]·2H2O has been determined by single-crystal X-ray analysis. (C44H40Cu2N4O8)·2H2O, triclinic, space group P1̄. Two [Cu(L-m-pda)] fragments, related by an inversion center, are connected by m-phenylene groups to form a binuclear unit. The coordination geometry around each copper(II) can be described as a distorted tetrahedron formed by the N2O2 donor set of the Schiff base ligands. The intramolecular Cu···Cu separation is 7.401(6) Å. The magnetic susceptibility of the complex in the 5 - 301 K temperature range can be rationalized by the parameters J = −0.4 cm−1 and g = 2.17. This indicates a weak intramolecular antiferromagnetic interaction. Extended Hückel molecular orbital (EHMO) calculations have been performed in order to gain insight into the molecular orbitals that participate in the super-exchange pathway.

Tetra-μ-acetato-κ8O:O′-bis[(N1,N2-di-p-anisylformamidine-κN2)ruthenium(II)](Ru—Ru): an example of an axial bis-adduct of {Ru2}4+tetracarboxylate with N-donor ligands

The title compound, [Ru2(C2H3O2)4(C15H16N2O2)2], lies on a crystallographic inversion center and exhibits an Ru-Ru bond length of 2.2847 (8) A. There are weak intramolecular hydrogen-bonding interactions between the N1,N2-di-p-anisylformamidine (HDAniF) ligands and the bridging acetate ligands. The molecule is one of the few examples of a crystallographically characterized axial bis-adduct of a {Ru2}4+ complex with two N-donor ligands.

Conformational and Structural Analysis of 6‐(4‐Methoxy‐phenyl)‐1,5,7a‐triphenyl‐tetrahydro‐imidazo[1,5‐b][1,2,4]oxadiazol‐2‐one

The cis stereochemistry of 6‐(4‐methoxy‐phenyl)‐1,5,7a‐triphenyl‐tetrahydro‐imidazo[1,5‐b][1,2,4]oxadiazol‐2‐one was studied by use of a PM3 semi‐empirical quantum mechanical model, and x‐ray crystallographic analysis. It crystallizes in the monoclinic space group P2 1 /n with a = 10.812(1) Å, b = 16.464(2) Å, c = 13.379(1) Å, α = 90.00°, β = 98.39(1)°, γ = 90.00°, V = 2356.07(4) Å3, Z = 4, D calc = 1.3067 g cm−3, F(0 0 0) = 976.41, and μ = 0.086 mm−1. The structure was solved by direct methods and refined to R = 0.066 for 1257 independent reflections [I > 4σ (I)]. The results from x‐ray diffraction were seen to be generally consistent with the results from previously reported spectroscopic investigations, beside theoretical calculations, except for conformations of five‐membered fused heterocycles. Two inter‐ and intramolecular weak interactions in addition to carbon atoms (C1 and C3) with different chiralities were found in the structure. The conformational study was performed by randomly scanning the potential energy surface belonging to the title compound with respect to selected torsion angles.

Copper(II)-assisted hydrolysis of 2,4,6-tris(2-pyrimidyl)-1,3,5-triazine (tpymt): syntheses, crystal structures and magnetic properties of [Cu(bpcam)(H 2O) 2]ClO 4 · 3H 2O, [Cu(bpcam)(H 2O) 2][Cu(bpcam)(H 2O)(SO 4)] · 2H 2O and [Cu 2(bpcam) 2(H 2O) 2(SO 4)] · H 2O [bpcam = bis(2-pyrimidylcarbonyl)amidate

The reaction of the 2,4,6-tris(2-pyrimidyl)-1,3,5-triazine (tpymt) ligand with copper(II) perchlorate or sulfate in aqueous solution affords complexes [Cu(bpcam)(H 2O) 2]ClO 4 · 3H 2O ( 1), [Cu(bpcam)(H 2O) 2][Cu(bpcam)(H 2O)(SO 4)] · 2H 2O ( 2) and [Cu 2(bpcam) 2(H 2O) 2(SO 4)] · H 2O ( 3) [bpcam = bis(2-pyrimidylcarbonyl)amidate], whose structures have been determined by single-crystal X-ray diffraction studies. Copper(II) promotes the hydrolysis of tpymt in mild conditions yielding the bpcam group which is present in the structures of 1– 3 as a tridentate ligand. The structure of 1 consists of mononuclear [Cu(bpcam)(H 2O) 2] + cations, uncoordinated perchlorate anions and water of crystallization. The structure of 2 is made up of [Cu(bpcam)(H 2O) 2] + cations, [Cu(bpcam)(H 2O)(SO 4)] − anions and lattice water whereas that of 3 contains the neutral dinuclear complex [Cu 2(bpcam) 2(H 2O) 2(SO 4)] and lattice water. While the sulfate group act as a terminal monodentate ligand in 2, it adopts a bis-monodentate bridging mode in 3. The copper atom coordination sphere in 1– 3 is distorted square pyramidal, with three bpcam nitrogen atoms ( 1– 3) and a water molecule ( 1 and 2) or a sulfate oxygen ( 2 and 3) building the basal plane and another water molecule ( 1– 3) in the apical position. The values of the shortest intermolecular copper–copper separation in 1 and 2 are 5.705 and 6.604 Å, respectively, whereas that through bridging sulfato in 3 is 5.494 Å. Variable-temperature magnetic susceptibility measurements show a Curie law behaviour for 2 whereas a weak intramolecular antiferromagnetic interaction [ J = −7.0 cm −1, the Hamiltonian being defined as H ^ = - J S ^ 1 · S ^ 2 ] occurs in 3. The potential use for metal assembling of the stable mononuclear [Cu(bpcam)] + unit is discussed in the light of the results obtained with the related [Cu(bpca)] + complex [bpca = bis(2-pyridylcarbonyl)amidate].

Synthesis and characterization of ferrocene-perylenetetracarboxylic diimide–fullerene triad

Novel ferrocene-perylenetetracarboxylic diimide–fullerene hybrid has been synthesized and characterized. UV/vis spectroscopic and cyclic voltammetric results indicate that ferrocene-contained hybrid show weak intramolecular charge transfer interaction in their ground states. The preliminary studies have shown that electron transfer from the ferrocene unit to the perylenetetracarboxylic diimide in dyad FcP takes place, while electron transfer from the ferrocene to the perylenetetracarboxylic diimide and electron transfer from the perylenetetracarboxylic diimide unit to the fullerene are proposal process in the case of FcPF.

(4-Fluorobenzoyl)(1H-1,2,4-triazol-1-yl)methyl morpholine-4-carbodithioate

In the title compound, C15H15FN4O2S2, the morpholine ring adopts a chair conformation. The dihedral angle between the benzene and triazole rings is 77.1 (7)°. There are some weak intermolecular and intramolecular interactions in the crystal structure, providing stabilization.

Crystal structure and magnetic properties of a heteronuclear, gadolinium–zinc carboxylate complex

A novel heteronuclear complex, [Gd2Zn2L10(bipy)(H2O)2]2 (HL = α-methylacrylic acid, bipy = 4,4′-bipyridine), was synthesized and characterized. Its structure, determined by X-ray diffraction, reveals a discrete octanuclear molecule, in which two ZnII ions are linked by a bipy molecule and GdIII ions, and GdIII and ZnII ions are bridged by bidentate α-methylacrylato groups. The complex crystallizes in space group P with Z = 1, a = 13.4504(6), b = 14.9697(5), c = 16.4374(5) Å, α = 64.212(3), β = 89.727(2), γ = 86.241(1)°. The structure was refined to R = 0.0303 for 8925 observed reflections. The temperature dependence of the magnetic susceptibility of the complex shows that a weak intramolecular ferromagnetic interaction exists as well as an intermolecular antiferromagnetic interaction.

Weak intramolecular interactions as controlling factors in the diastereoselective formation of 3-phosphinoxido- and 3-phosphono-1,2,3,6-tetrahydrophosphinine 1-oxides

A series of 3-phosphinoxido-and 3-phosphono-1,2,3,6-tetrahydrophosphinine oxides was synthesized by the diastereoselective addition of diphenylphosphine oxide and dialkyl phosphites to the α,β-double-bond of 1,2-dihydrophosphinine oxides. Further refunctionalizations led to a 3-P(O)(OH) 2 derivative and to a disulfide. The conformation of the products was evaluated using the B3LYP/6-31+G ∗//B3LYP/3-21G ∗ method, validated by calculation for a simple tetrahydrophosphinine oxide with a known stereostructure. The preferred conformers of the 3-P(X)Z 2-tetrahydrophosphinine derivatives were among the twist-boat forms containing the exocyclic P-function in the axial position due to three kinds of favorable intramolecular interactions. Only the 3-P(O)(OH) 2 derivative was found to adopt a half-chair conformation as a consequence of intramolecular H-bonding.