Intramolecular Non-bonded Interactions Research Articles

Structural conformations and electronic interactions of the natural product, oroxylin: a vibrational spectroscopic study

AbstractThe oroxylin, 5,7‐dihydroxy 6‐methoxy flavone is a potent natural product extracted from ‘Vitex peduncularis’. Density functional theory (DFT) at B3LYP/6‐311G(d,p) level has been used to compute energies of different conformers of oroxylin to find out their stability, the optimized geometry of the most stable conformer and its vibrational spectrum. The conformer ORLN‐1 with torsion angles 0, 180, 180 and 0 degrees, respectively, for H13O12C6C5, H14O10C4C5, H13O12C6C5 and H14O10C4C5 is found to be most stable. The optimized geometry reveals that the dihedral angle φ between phenyl ring B and the chrome part of the molecule in − 19.21° is due to the repulsive force due to steric interaction between the ortho‐hydrogen atom H29 of the B ring and H18 of the ring C (H29·H18 = 2.198 Å). A vibrational analysis based on the near‐infrared Fourier transform(NIR‐FT) Raman, Fourier transform‐infrared (FT‐IR) and the computed spectrum reveals that the methoxy group is influenced by the oxygen lone pair‐aryl pz orbital by back donation. Hence the stretching and bending vibrational modes of the methoxy group possess the lowest wavenumber from the normal values of methyl group. The carbonyl stretching vibrations have been lowered due to conjugation and hydrogen bonding in the molecules. The intramolecular H‐bonding and nonbonded intramolecular interactions shift the band position of O10H14 and O12H13 stretching modes, which is justified by DFT results. Copyright © 2008 John Wiley & Sons, Ltd.

A Density Functional Theory Calculation of the Electronic Properties of Several High-Spin and Low-Spin Iron(II) Pyrazolylborate Complexes

Density functional theory has been used to study the electronic spin-state properties of low-spin Fe[HB(pz)3]2, high-spin Fe[HB(3-Mepz)3]2, high-spin Fe[HB(3,5-Me 2pz)3]2, and high-spin Fe[HB(3,4,5-Me 3pz)3]2 complexes that exhibit very different iron(II) electronic spin-sate crossover behaviors with changing temperature and pressure. Excellent agreement is obtained between the experimentally observed Mössbauer-effect quadrupole splittings and isomer shifts of these complexes and those calculated with the B3LYP functional and various different basis sets for both the high-spin and low-spin states of iron(II). The calculations for Fe[HB(pz)3]2 that use the LANL2DZ, 6-31++G(d,p), and 6-311++G(d,p) basis sets for iron all lead to very similar electric field gradients and thus quadrupole splittings. The initial calculations, which were based upon the known X-ray structures, were followed by structural optimization, an optimization that led to small increases in the Fe-N bond distances. Optimization led to at most trivial changes in the intraligand bond distances and angles. The importance of the 3-methyl-H...H-3-methyl nonbonded intramolecular interligand interactions in controlling the minimum Fe-N bond distances and determining the iron(II) spin state both in Fe[HB(3-Mepz)3]2 and in the related methyl-substituted complexes has been identified.

Evidence for the contribution of sulfur–bromine intramolecular interactions to the self-rigidification of thiophene-based π-conjugated systems

Bithiophene associating 3,4-ethylenedioxythiophene and 3-bromothiophene, and the corresponding polymer exhibit self-rigidified structures of the conjugated backbones resulting from the association of S–Br and S–O non-bonded intramolecular interactions.

O⋯S vs. N⋯S intramolecular nonbonded interactions in neutral and radical cation salts of TTF-oxazoline derivatives: synthesis, theoretical investigations, crystalline structures, and physical properties

Racemic and enantiopure ethylenedithio-tetrathiafulvalene-thiomethyl-oxazoline (EDT-TTF-(SMe)-OX) derivatives have been synthesized. Single-crystal X-ray diffraction analyses reveal the establishment of O⋯S nonbonded interactions, unprecedented in the TTF series, characterized by short S⋯O distances and linear O⋯SMe motifs. Theoretical calculations at the DFT/B3LYP level on a model molecule demonstrate that both possible planar s-trans (O⋯S interaction) and s-cis (N⋯S interaction) conformations are energy minima, separated by an extremely weak energy gap. The energy barrier corresponding to the equilibrium between the two forms has been also estimated from DFT calculations, as well as their relative stability in the radical cation state of the TTF. According to the latter, there is a slight tendency towards the enhancement of the N⋯S interactions. Following the predictions of the theoretical calculations, the coexistence of both O⋯S and N⋯S nonbonded interactions is observed in two mixed valence radical cation salts of the racemic TTF with the dianionic cluster Mo6Cl14, prepared upon electrocrystallization. Interestingly, the ratio TTF : dianion is finely tuned by the choice of the electrocrystallization solvent. Physical measurements such as electrical conductivity and thermoelectric power on single crystals combined with magnetic susceptibility data in one case and extended Huckel tight-binding calculations demonstrate and rationalize the semiconducting behavior of both mixed valence salts. This study demonstrates that intramolecular N⋯S and O⋯S interactions can efficiently modulate and direct in the TTF series the occurrence of original solid-state structures provided with physical properties.

Intramolecular Nonbonding Interactions between Selenium and Sulfur – Spectroscopic Evidence and Importance in Asymmetric Synthesis

AbstractChiral sulfur‐containing electrophilic selenium reagents can be employed to effect efficient asymmetric syntheses. Spectroscopic and chemical evidence demonstrate that the observed high selectivity of the asymmetric reactions is associated with a nonbonding selenium–sulfur interaction that is present in both the crystalline form and in solution. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)

Effect of the Phosphoryl Substituent in the Linear Nitrone on the Spin Trapping of Superoxide Radical and the Stability of the Superoxide Adduct: Combined Experimental and Theoretical Studies

A new phosphorylated linear nitrone N-(4-hydroxybenzyliene)-1-diethoxyphosphoryl-1-methylethylamine N-oxide (4-HOPPN) was synthesized, and its X-ray structure was determined. The spin trapping ability of various kinds of free radicals by 4-HOPPN was evaluated. Kinetic study of decay of the superoxide spin adduct (4-HOPPN-OOH) shows the half-life time of 8.8 min. On the basis of the X-ray structural coordinates, theoretical analyses using density functional theory (DFT) calculations at the B3LYP/6-31+G(d,p)//B3LYP/6-31G(d) level were performed on spin-trapping reactions of superoxide radical with 4-HOPPN and PBN and three possible decay routes for their corresponding superoxide adducts. The comparative calculations on the spin-trapping reactions with superoxide radical predicted that both spin traps share an identical reaction type and have comparable potency when spin trapping superoxide radical. Analysis of the optimized geometries of 4-HOPPN-OOH and PBN-OOH reveals that an introduction of the phosphoryl group can efficiently stabilize the spin adduct through the intramolecular H-bonds, the intramolecular nonbonding attractive interactions, as well as the bulky steric protection. Examination of the decomposition thermodynamics of 4-HOPPN-OOH and PBN-OOH further supports the stabilizing role of the phosphoryl group to a linear phosphorylated spin adduct.

Molecular Dynamics Simulation of Structure, Thermodynamic, and Dynamic Properties of Poly(dimethylsilamethylene), Poly(dimethylsilatrimethylene) and Their Alternating Copolymer

Molecular dynamics is used for the simulation of silicon-containing polymers with promising membrane material properties. An atomistic force field is developed for the description of bond bending, torsional angle variation, and nonbonded intra- and intermolecular interactions. Detailed ab initio quantum mechanics calculations on corresponding monomers that appeared recently in the literature are used for the parametrization of the bonded and nonbonded local intramolecular force field. For the intermolecular and nonbonded nonlocal intramolecular interactions, parameters are obtained from accurate force fields proposed in the literature for similar compounds. The force field is used subsequently for the calculation of thermodynamic, structure, and dynamic properties of two homopolymers, namely, poly(dimethylsilamethylene) and poly(dimethylsilatrimethylene), and their alternating copolymer. A wide range of temperatures and pressures is examined. Polymer systems of different molecular weights are simulated. Experimental data available for these polymers are very limited. In all cases, simulation results are in good agreement with these data. Furthermore, simulation results agree very well with empirical macroscopic correlations used widely for rubbery polymers for the properties under consideration.

Quantification of Intramolecular Nonbonding Interactions in Organochalcogens

Intramolecular nonbonding interactions between chalcogen atoms in a series of ortho substituted arylselenides (S/O...Se-Y, with Y = -Me, -CN, -Cl, and -F) are quantified using the coupled cluster CCSD(T)/cc-pVDZ level of theory. A homodesmic reaction method as well as an ortho-para approach are employed in evaluating the strength of intramolecular interactions. Comparison of the results obtained using the ab initio MP2 method and pure and hybrid density functional theories are performed with that of the coupled cluster values to assess the quality of different density functionals in evaluating the strength of nonbonding interactions. The interaction energies are found to be higher when the thioformyl group acts as the donor and the Se-F bond acts as the acceptor. In a given series with the same donor atom, the strength of the interaction follows the order Me < CN < Cl < F, exhibiting fairly high sensitivity to the group attached to selenium (Se-Y). Analysis of electron density at the S/O...Se bond critical point within the Atoms in Molecule framework shows a very good correlation with the computed intramolecular interaction energies.

Estimation and analysis of the rheological properties of a perfluoropolyether through molecular dynamics simulation

Equilibrium and non-equilibrium molecular dynamics simulations of a perfluoropolyether C 8F 18O 4 are reported using an atomistic interaction potential. The bulk rheological properties of the perfluoropolyether are investigated through molecular dynamics simulations as a function of both temperature and shear rate. The effect of molecular structure on viscosity is explored in detail. The rotational relaxation time is reported as a function of temperature. Structural properties, including the mean-square end-to-end chain length, the mean-square radius of gyration of chains, and the distribution functions of bond lengths, bond angles, and bond torsional angles are collected and analyzed as functions of shear rate. After an initial plateau, both mean-square end-to-end chain length and mean-square radius of gyration decrease monotonically with increasing shear rate. The behaviors of the rheological and structural properties are explained through an analysis of the individual contributions due to bond stretching, bond bending, and bond torsion, as well as both intramolecular and intermolecular non-bonded interactions. A further analysis is possible through a meticulous breakdown of each contribution into a specific type of mode; e.g., the total bond stretching is comprised of CC, CO, and CF bond stretching terms. In this way, one can relate the shear viscosity to the specific chemical structure of C 8F 18O 4.

Hypervalent organoantimony compounds 12-ethynyl-tetrahydrodibenz[c,f][1,5]azastibocines: Highly efficient new transmetallating agent for organic halides

Extremely efficient and high-speed ethynylation of acyl chlorides, aryl iodides and bromides was demonstrated by palladium-catalyzed cross-coupling reaction of N- t-butyl- Sb-ethynyl-5,6,7,12-tetrahydrodibenz[c,f][1,5]azastibocine under mild conditions. Optimization and generalization of the hypervalent antimony-mediated coupling reaction are presented in detail. Single-crystal X-ray analysis of the N-methyl-1,5-azastibocine revealed that the remarkable reactivity enhancement of the azastibocine was derived from elongation of the antimony–ethynyl carbon bond originated from Sb–N intramolecular non-bonding interaction.

Cation-π Interactions in Serotonin: Conformational, Electronic Distribution, and Energy Decomposition Analysis.

An adiabatic conformational analysis of serotonin (5-hydroxytryptamine, 5-HT) using quantum chemistry led to six stable conformers that can be either +gauche (Gp), -gauche (Gm), and anti (At) depending upon the value taken by ethylamine side chain and 5-hydroxyl group dihedral angles φ1, φ2, and φ4, respectively. Further vibrational frequency analysis of the GmGp, GmGm, and GmAt conformers with the 5-hydroxyl group in the anti position revealed an additional red-shifted N-H stretch mode band in GmGp and GmGm that is absent in GmAt. This band corresponds to the 5-HT side-chain N-H bond involved in an intramolecular nonbonded interaction with the 5-hydroxy indole ring. The influence of this nonbonded interaction on the electronic distribution was assessed by analysis of the spin-spin coupling constants of GmGp and GmGm that show a marked increase for C2-C3 and C8-C9 bonds in GmGm and GmGp, respectively, with a decrease of their double bond character and an increase of their length. The Atoms in Molecules (AIM), Natural Bond Orbital (NBO), and fluorescence and CD spectra (TDDFT method) analyses confirmed the existence in GmGp and GmGm of a through-space charge-transfer between the HOMO and the HOMO-1 π-orbital of the indole ring and the LUMO σ* N-H antibonding orbital of the ammonium group. The strength of the cation-π interaction was determined by calculating binding energies of the NH4(+)/5-hydroxyindole complexes extracted from stable conformers. The energy decomposition analysis indicated that cationic-π interactions in the GmGp and GmGm conformers are governed by the electrostatic term with significant contributions from polarization and charge transfer. The lower stability of the GmGm over the GmGp comes from a higher exchange repulsion and a weaker polarization contributions. Our results provide insight into the nature of intramolecular forces that influence the conformational properties of 5-HT.

Intramolecular Interactions between Chalcogen Atoms: Organoseleniums Derived from 1-Bromo-4-tert-butyl-2,6-di(formyl)benzene

[structure: see text] The synthesis and characterization of a series of low-valent organoselenium compounds derived from 1-bromo-4-tert-butyl-2,6-di(formyl)benzene (22) is described. The synthesis of diselenide 25 was achieved by the lithiation route whereas bis(4-tert-butyl-2,6-di(formyl)phenyl) diselenide (26) was synthesized by treating 22 with disodium diselenide. A series of monoselenides (27, 28, and 29) was obtained by facile nucleophilic substitution of bromine in 22, using the corresponding selenolates as nucleophiles. The halogenation reactions of bis(4-tert-butyl-2,6-di(formyl)phenyl) diselenide (26) did not afford the corresponding selenenyl halides but resulted in the isolation of an unexpected cyclic selenenate ester 34 as a product. The selenide 32 was synthesized by the treatment of dimethoxymethyl diselenide with trilithiated 2-bromo-5-tert-butyl-N,N'-di(phenyl)isophthalamide. The existence of potential Se...O intramolecular nonbonding interactions was examined by IR, (1)H, and (77)Se NMR spectroscopy, X-ray crystallography, and computational studies. The X-ray crystal structures of 26 and 27, having two ortho formyl groups, reveal the absence of any Se...O interactions. However, the Se...O interactions were observed in the selenenate ester 34 where one of the formyl groups has been utilized for the selenenate ring formation. The crystal structures of 26 and 27 exhibited intermolecular short-range C-H...Se interactions (hydrogen bonding). Although there are four heteroatoms in carbamoyl moieties ortho to selenium capable of forming a five-membered ring on intramolecular coordination, no such intramolecular Se...X (X = N, O) interaction was observed in the crystal structure of 32. The density functional theory calculations at the B3LYP/6-31G* level predicted that for all the diformyl systems (47a-c, 48a-c), the anti,anti conformer (when both formyl oxygen atoms point away from the selenium) is more stable. This preference was found to be reversed in the monoformyl-substituted systems (50a,b, 51a,b), where the syn conformer (when formyl oxygen is near the selenium) is energetically more favorable than the anti conformer.

Preparation, Solid-State Characterization, and Computational Study of a Crown Ether Attached to a Squaramide

[structure: see text] Crystals of a disecondary squaramide covalently linked to a crown ether presents a great variety of inter- and intramolecular nonbonded interactions including C-H/pi contacts, C-H...O and N-H...O hydrogen bonds, and pi-pi stacking between squaramide rings. Latter interaction, the stacking between squaramide rings, can be considered as an experimental evidence for the proposed aromaticity of squaramide when it is forming hydrogen bonds, either as acceptor or donor.

Tests of the MP2 Model and Various DFT Models in Predicting the Structures and B−N Bond Dissociation Energies of Amine−Boranes (X3C)mH3-mB−N(CH3)nH3-n (X = H, F; m = 0−3; n = 0−3): Poor Performance of the B3LYP Approach for Dative B−N Bonds

Computational studies of amine−boranes (X3C)mH3-mB−N(CH3)nH3-n (X = H, F; m = 0−3; n = 0−3) show that the B3LYP model performs poorly in predicting the structures and B−N bond dissociation energies of such species. A survey of several models shows that the MP2 approach gives the best agreement, but is too computationally intensive for general use. Among several hybrid and pure DFT approaches, the MPW1K model gives the best agreement with experiment and/or with the MP2 model. Scans of the potential surface for rotation around the B−N bond in several molecules and examinations of other amine−boranes suggest that the difficulty with the B3LYP method does not arise from its inability to incorporate nonbonded intramolecular interactions, but from an inherent inability to model the dative bond. The MPW1K approach evidently does this better because it was designed to model “incompletely bound” transition states, which mimic datively bonded systems.

1,5-Type nonbonded O⋯S and S⋯S interactions in (acylimino) and (thioacylimino)benzothiazoline systems. Crystal structures and theoretical calculations

Intramolecular nonbonded interactions have been observed in the crystalline structures of 6-ethoxy-2-trifluoroacetyliminobenzothiazoline ( 4 ) (S⋯O close contact) and 6-ethoxy-2-trifluorothioacetyliminobenzothiazoline ( 5 ) (S⋯S close contact). Density functional B3LYP/6-311G ∗∗ calculations were performed for all conformers and tautomers of 4 and 5 in order to explain the preference for the S⋯O and S⋯S close contact structures. The calculations agree with the observed crystallographic structures only when solvent effects are included via a continuum model, thus showing the importance of the solvent effects to establish the correct relative energies.

Influence of Both Steric Effects and Te···N Intramolecular Nonbonded Interactions on the Stabilization of Organotellurium Compounds Incorporating [2-[1-(3,5-Dimethylphenyl)-2- naphthyl]-4,5-dihydro-4,4-dimethyloxazole

A series of novel low-valent organotellurium compounds incorporating [2-[1-(3,5-dimethylphenyl)-2-naphthyl]-4,5-dihydro-4,4-dimethyloxazole] (1) stabilized by Te···N nonbonded interactions have been synthesized. The synthesis has been achieved by the ortholithium route. The lithium arenetellurolate 3 was obtained by direct metalation of 1 with 1.6 M of n-BuLi in hexane followed by the insertion of tellurium into the Li−C bond. Oxidation of 3 then afforded the desired ditelluride 4. The reaction of 4 with a stoichiometric amount of sulfuryl chloride yielded stable tellurenyl(II) chloride 5, whereas the addition of an excess sulfuryl chloride led to the formation of tellurium(IV) trichloride 6. The stable bromo compound 7 was obtained by the controlled bromination of 4 with bromine. No tellurium tribromide formation was observed when the ditelluride was treated with an excess of bromine. Compound 4 underwent facile reaction with a stoichiometric amount of iodine to give a stable mono iodo compound (8). The ...

Conformational analysis of sulfur-containing 6-deoxy-l-hexose derivatives by molecular modeling and NMR spectroscopy. A theoretical study and experimental evidence of intramolecular nonbonded interactions between sulfur and oxygen.

6-Deoxy-l-mannose diphenyldithioacetal (1) unexpectedly gave the rearranged products phenyl 3,4-di-O-acetyl-2-S-phenyl-1,2-dithio-6-deoxy-beta-l-glucopyranoside (9) and 3,4-di-O-acetyl-2,5-anhydro-6-deoxy-l-glucose diphenyldithioacetal (10) upon treatment with acetyl chloride, while 6-deoxy-l-mannose ethylenedithioacetal (3) yielded (4aR,6S,7S,8R,8aS)-7,8-diacetyloxy-6-methylhexahydro-4aH-[1,4]dithiino[2,3b]pyran (11), whose structure was further confirmed by X-ray diffraction, and 3,4-di-O-acetyl-2,5-anhydro-l-rhamnose ethylenedithioacetal (12). The geometry of the four rearranged products as well as that of 1-thio-6-deoxy-l-mannopyranosides 5 and 7 and their acetyl derivatives 6 and 8 was studied by density functional theory (B3LYP/6-31G) molecular models, in combination with a Karplus-type analysis of the NMR vicinal coupling constants, revealing that the six-membered ring of pyranosides 5-9 and 11 exists in a slightly distorted chair conformation (6-13% distortion) and that the conformational behavior of the 2,5-anhydro-6-deoxy-l-glucose dithioacetals 10 and 12 is strongly influenced by the presence of stabilizing intramolecular nonbonded sulfur-oxygen 1,4- and 1,5-interactions. Compounds 9-12 were formed by a molecular rearrangement via sulfonium ion intermediates followed by stereoselective intramolecular cyclizations as formulated by the quantum chemical calculations performed in the present study.

Binuclear and Starburst Organoplatinum(II) Complexes of 2,2‘-Dipyridylamino Derivative Ligands: Structures, Fluxionality, and Luminescence

New binuclear and starburst trinuclear organoplatinum complexes based on 2,2‘-dipyridylamino (dpa) derivative ligands, Pt2Ph4(bab), bab = 1,4-bis(2,2‘-dipyridylamino)benzene, 1, Pt2Ph4(babp), babp = 4,4‘-bis(2,2‘-dipyridylamino)biphenyl, 2, Pt3Ph6(tab), tab = 1,3,5-tris(2,2‘-dipyridylamino)benzene, 3, Pt3Ph6(tat), tat = 2,4,6-tris(2,2‘-dipyridylamino)-1,3,5-triazine, 4, Pt3Ph6(tapb), tapb = 1,3,5-tris[p-(2,2‘-dipyridylamino)phenyl]benzene, 5, Pt3Ph6(tapt), tapt = 2,4,6-tris[p-(2,2‘-dipyridylamino)phenyl]-1,3,5-triazine, 6, Pt3Ph6(tabpb), tabpb = 1,3,5-tris{4‘-[4‘ ‘-(2,2‘-dipyridylamino)]biphenyl}benzene, 7, and Pt3Ph6(tabpt), tabpt = 1,3,5-tris{4‘-[4‘ ‘-(2,2‘-dipyridylamino)]biphenyl}benzene, 8, were synthesized by the reaction of [PtPh2(SMe2)]n with the corresponding chelate ligand. The structures of complexes 1−5 and 8 were determined by single-crystal X-ray diffraction. All eight complexes have phosphorescent emissions in the blue/green region at 77 K, attributed to ligand-centered π → π* transitions. Ligand-based fluorescent emission was also detected for complexes 5, 6, and 8. Complexes 1−8 display versatile structures in the solid state. Complex 4 was found to be fluxional in solution. The key factors that influence the structures of the complexes in solution and the solid state are the degree of conjugation of the amino nitrogen lone pair electrons of the dpa unit with the central aromatic linker and intramolecular nonbonding interactions.

Synthesis, crystal structure, and ESR study of a novel phosphorylated lipophilic spin trap.

In this article, the synthesis of a novel alpha-phosphorus-containing spin trap DEPPEPO [2-(diethoxyphosphoryl)-2-phenethyl-3,4-dihydro-2H-pyrrole-1-oxide] and the evaluation of its ability to spin-trap radicals, especially superoxide and hydroxyl radicals, are described. Single crystal X-ray structure analysis reveals that there exist a lot of intramolecular nonbonded attractive interactions in the molecule. The phenethyl group is located away from the diethoxyphosphoryl group and the nitronyl plane, and only one face of the nitronyl plane is sterically hindered by the oxygen attached to the phosphorus with a double bond. The latter feature is responsible for the stereoselection of the free radical additions on the nitronyl moiety. The ability of DEPPEPO to trap the active superoxide anion radical generated in the HX/XO system and the stability of their spin adduct were investigated with that for DEPMPO. The half-life of DEPPEPO is about 13.4 min, and as a result, the DEPPEPO seems to be a promising lipophilic spin trap, perhaps in both in vitro and in vivo ESR investigation. Because DEPPEPO is a solid compound, it is quite easy to purify by recrystallization and to store the compound even at room temperature. In addition, an obvious increase in lipophilicity for DEPPEPO was found as a contribution of 2-substituted phenethyl.

Heavy-Row Atom Effects on the Strength of the Weak Nonbonded Interactions between Divalent Selenium and Halogen Atoms

Abstract The 77Se NMR chemical shifts observed for 2-selenobenzyl halide derivatives and the density functional theoretical calculation revealed that the strength of intramolecular nonbonded interactions between a divalent selenium and halogen atoms decreases in the order, Se···F&amp;gt;Se···Cl≥Se···Br.