Weak Intramolecular Interactions Research Articles

Weak intramolecular interaction effects on the torsional spectra of ethylene glycol, an astrophysical species.

An elaborate variational procedure of reduced dimensionality based on explicitly correlated coupled clusters calculations is applied to understand the far infrared spectrum of ethylene-glycol, an astrophysical species. This molecule can be classified in the double molecular symmetry group G8 and displays nine stable conformers, gauche and trans. In the gauche region, the effect of the potential energy surface anisotropy due to the formation of intramolecular hydrogen bonds is relevant. For the primary conformer, stabilized by a hydrogen bond, the ground vibrational state rotational constants are computed to be A0 = 15 369.57 MHz, B0 = 5579.87 MHz, and C0 = 4610.02 MHz corresponding to differences of 6.3 MHz, 7.2 MHz, and 3.5 MHz from the experimental parameters. Ethylene glycol displays very low torsional energy levels whose classification is not straightforward and requires a detailed analysis of the torsional wavefunctions. Tunneling splittings are significant and unpredictable due to the anisotropy of the potential energy surface PES. The ground vibrational state splits into 16 sublevels separated ∼142 cm(-1). The splitting of the "G1 sublevels" was calculated to be ∼0.26 cm(-1) in very good agreement with the experimental data (0.2 cm(-1) = 6.95 MHz). Transitions corresponding to the three internal rotation modes allow assignment of previously observed Q branches. Band patterns, calculated between 362.3 cm(-1) and 375.2 cm(-1), 504 cm(-1) and 517 cm(-1), and 223.3 cm(-1) and 224.1 cm(-1), that correspond to the tunnelling components of the v21 fundamental (v21 = OH-torsional mode), are assigned to the prominent experimental Q branches.

Theoretically predicted Fox-7 based new high energy density molecules

Computational investigation of CHNO based high energy density molecules (HEDM) are designed with FOX-7 (1, 1-dinitro 2, 2-diamino ethylene) skeleton. We report structures, stability and detonation properties of these new molecules. A systematic analysis is presented for the crystal density, activation energy for nitro to nitrite isomerisation and the C–NO2 bond dissociation energy of these molecules. The Atoms in molecules (AIM) calculations have been performed to interpret the intra-molecular weak H-bonding interactions and the stability of C–NO2 bonds. The structure optimization, frequency and bond dissociation energy calculations have been performed at B3LYP level of theory by using G03 quantum chemistry package. Some of the designed molecules are found to be more promising HEDM than FOX-7 molecule, and are proposed to be candidate for synthetic purpose.

Cis-trans isomerism in a square-planar platinum(II) complex bearing bulky fluorinated phosphane ligands.

Transition-metal complexes bearing fluorinated phosphane and thiolate ligands has been an area of study in recent years and the chemical context of the current work is related to the metal-assisted functionalization of fluorinated derivatives. The cis and trans isomers of the square-planar complex bis[(pentafluorophenyl)diphenylphosphane-κP]bis(2,3,5,6-tetrafluorobenzenethiolato-κS)platinum(II), [Pt(C6HF4S)2{P(C6H5)2(C6F5)}2], have been crystallized from a single chromatographic fraction and characterized by X-ray diffraction analysis. The stabilization of the cis isomer results from weak intramolecular π-stacking interactions and possibly from the formation of a C-F...Pt contact, characterized by an F...Pt separation of 2.957 (6) Å. The natural bond orbital analysis (NBO) for this isomer confirms that the corresponding F → Pt charge transfer accounts for 6.92 kcal mol(-1) in the isomer stabilization. Such interactions are not present in the centrosymmetric trans isomer.

Photo- and acid induced multicolor switches based on pyridine-containing perfluorodiarylethene derivatives

Two novel perfluorodiarylethenes which contains a 2-methylbenzo[b]furane and a modified pyridine moiety were synthesized. Such structure may induce F⋯N or S⋯N heteroatom contact which was newly observed. Experiments results showed that the photocyclization quantum yield exhibited a strong correlation with the two weak intramolecular interactions, which behaved solvent independency. Moreover, both novel pyridine-perfluorodiarylethenes exhibited an obvious acidichromism, and the absorption maxima of their closed-ring isomers showed a prominent bathochromic shift to the near-infrared region.

Versatile Coordination Modes in Silver-Imidazolecarbaldehyde Oxime Complexes: Structural and Computational Analysis

Silver imidazolecarbaldehyde oxime complexes [Ag(1-methyl-1H-imidazole-2-carbaldehyde oxime)2][NO3] (1), [Ag(1-methyl-1H-imidazole-2-carbaldehyde oxime)2][ClO3] (2), [Ag(1H-5-methylimidazole-4-carbaldehyde oxime)]2[NO3]2 (3), [Ag(1H-imidazole-2-carbaldehyde oxime)]n[NO3]n (4), [Ag(1H-4-methylimidazole-5-carbaldehyde oxime)]n[ClO3]n (5), and [Ag(N-hydroxy-1-methyl-1H-imidazole-2-carboximidamide)2]2[CF3SO3]2 (6) were structurally and computationally analyzed. Weak intramolecular interactions were found to play the main role in determining the most favorable structure of the free ligands, therefore controlling the final coordination mode, and the nuclearity of the complexes. Further information on the nature of the intra- and intermolecular interactions were provided utilizing computational density functional theory calculations and topological charge density analysis according to the Quantum Theory of Atoms in Molecules. The efficient control of the structure of the complexes also results in a better control of the material properties.

Structure and magnetic properties of bis-o-benzosemiquinonato zinc complexes

New bis-o-benzosemiquinonato complexes of zinc (3,6-SQ)2Zn(Phen) (1), (3,6-SQ)2Zn(MePhen) (2), (3,6-SQ)2Zn(Dipy) (3) based on sterically hindered 3,6-di-tert-butyl-o-benzoquinone (3,6-Q) were synthesized. The crystal structures of compounds 1, 2 were investigated using X-ray diffraction. The coordination polyhedron of both complexes is distorted octahedron. The magnetic properties of solid bis-o-semiquinonates were found to be complicated by intermolecular interaction between diradical molecules. The combination of the magnetic susceptibilities measurements and quantum chemical calculations has established that the weak intramolecular ferromagnetic interaction between o-semiquinone radicals is accompanied by the comparable in magnitude intermolecular antiferromagnetic exchange.

Peptide-Graphene Interactions Enhance the Mechanical Properties of Silk Fibroin.

Studies reveal that biomolecules can form intriguing molecular structures with fascinating functionalities upon interaction with graphene. Then, interesting questions arise. How does silk fibroin interact with graphene? Does such interaction lead to an enhancement in its mechanical properties? In this study, using large-scale molecular dynamics simulations, we first examine the interaction of graphene with several typical peptide structures of silk fibroin extracted from different domains of silk fibroin, including pure amorphous (P1), pure crystalline (P2), a segment from N-terminal (P3), and a combined amorphous and crystalline segment (P4), aiming to reveal their structural modifications. Our study shows that graphene can have intriguing influences on the structures formed by the peptides with sequences representing different domains of silk fibroin. In general, for protein domains with stable structure and strong intramolecular interaction (e.g., β-sheets), graphene tends to compete with the intramolecular interactions and thus weaken the interchain interaction and reduce the contents of β-sheets. For the silk domains with random or less ordered secondary structures and weak intramolecular interactions, graphene tends to enhance the stability of peptide structures; in particular, it increases the contents of helical structures. Thereafter, tensile simulations were further performed on the representative peptides to investigate how such structure modifications affect their mechanical properties. It was found that the strength and resilience of the peptides are enhanced through their interaction with graphene. The present work reveals interesting insights into the interactions between silk peptides and graphene, and contributes in the efforts to enhance the mechanical properties of silk fibroin.

Direct C5‐Isomerization Approach to l‐Iduronic Acid Derivatives

AbstractInspired by the biosynthesis of heparan sulfate (HS), we present a direct epimerization approach to l‐iduronic acid synthons (IdoA) from the corresponding C5 epimers, d‐glucuronic acids (GlcA). With the best result, 95 % conversion was achieved. Weak intramolecular interactions dramatically affect the equilibrium constants of this thermodynamically governed process. Based on this approach, GlcA and IdoA donors required for the synthesis of fondaparinux were prepared in 14 steps, whereas over 20 steps were required previously.

Synthesis, crystal structure, conformational analysis, nonlinear optical property and computational study of novel pregnane derivatives

The molecular structure and detailed spectroscopic analysis of some novel newly synthesized pregnane derivatives have been performed using experimental techniques like 1H, 13C NMR, NOESY, FT-IR, UV–visible spectroscopy, mass spectrometry, crystallography, as well as theoretical calculations. The structure and stereochemistry of 3β-benzoyloxy 16α-methoxy pregn-5-ene-20-one (3) has been confirmed by single crystal X-ray diffraction, which crystallized in orthorhombic form having P212121 space group with unit cell parameters a=6.395(5)Å, b=19.872(17)Å, c=19.898(16)Å and Z=4. Quantum chemical calculations have been performed by density functional theory (DFT) using B3LYP functional and 6-31G (d,p) basis set. The electronic properties such as frontier orbitals and band gap energies have been calculated using time dependent density functional theory (TD-DFT). The strength and nature of weak intramolecular interactions have been studied by AIM approach. The vibrational wavenumbers have been calculated using DFT method and assigned with the help of potential energy distribution (PED). Global and local reactivity descriptors have been computed to predict reactivity and reactive sites in the molecule. First hyperpolarizability values have been calculated to describe the nonlinear optical (NLO) property of the synthesized compounds. Molecular electrostatic potential (MEP) analysis has also been carried out.

Evaluation of Energy Gradients and Infrared Vibrational Spectra through Molecules-in-Molecules Fragment-Based Approach.

Molecules-in-Molecules (MIM) is a general hybrid fragment-based extrapolation approach for calculating accurate total energies of large molecules, similar in spirit to the popular ONIOM methodology. In this work, the MIM model is extended for the precise evaluation of the energy gradients and infrared (IR) vibrational spectra of large molecules. The overlapping subsystems in this work are constructed from nonoverlapping fragments using a number-based scheme, and the dangling bonds are saturated with link-hydrogen atoms. Independent fragment calculations are performed to evaluate the energies and its gradients. Subsequently, the link-atom energy gradient components are projected back onto the corresponding host and supporting atoms, through the Jacobian projection method, as in the ONIOM approach. After geometry optimization, the Jacobian link-atom projection method is also employed for the precise evaluation of the force constants and dipole derivatives of the full molecule. The performance of the MIM model is benchmarked on 25 small-to-large peptides, with inevitable weak long-range intramolecular interactions. Upon accounting these long-range interactions through a second layer, at an inexpensive low-level of theory (MIM2), the energy accuracy improve by 80%, compared to MIM with one layer (MIM1). The MIM2 IR frequencies and intensities have an ∼75% improvement, compared to the corresponding values at the MIM1 level of theory. A similar improvement is also observed for anion, cation, and radical systems constructed from the neutral benchmark molecules. The accuracy and performance of the benchmark systems validate the MIM model for exploring the vibrational infrared spectra of large molecules.

Syntheses, characterization, interaction with DNA, cytotoxic and apoptosis of two novel complexes of Zn(II) and Mn(II) with 2-methyl-1H-4,5-imidazoledicarboxylic acid

Two new complexes, Zn(L)2(H2O)2 (1) and Mn(L)2(H2O)2 (2) [L=2-Methyl-1H-4,5-imidazoledicarboxylic acid] were synthesized and characterized by elemental analysis, infrared spectroscopy, and single crystal X-ray diffraction. Intramolecular weak interactions, such as hydrogen-bond and intermolecular interactions were presented in the complexes. The activities of the complexes binding with DNA, and cytotoxic activities were studied. The binding of complexes with fish sperm DNA (FS-DNA) was investigated by fluorescence spectra. Gel electrophoresis assay demonstrated the ability of the complexes to cleave the pBR322 plasmid DNA. The cytotoxic activities of the complexes were tested against the KB cell line. Cytotoxic activity studies showed the two complexes exhibited significant cancer cell inhibitory rate. The most active compound was complex 1 with IC50 and CC50value of 36.5, 429, with the selectivity index (SI=11.75) among the tested compounds.

Triphenylacetic Acid Amides: Molecular Propellers with Induced Chirality

AbstractThe combination of electronic circular dichroism spectroscopy (ECD), X‐ray diffraction, and theoretical calculations permitted a detailed description of an unexpected chirality transfer in triphenylacetamides, which is achieved solely through weak intramolecular interactions. The observed phenomenon proceeds as a cascade process. The triphenylacetamide chromophore is sensitive to even small changes in the relative size of the substituent attached to the stereogenic center. Substitution at the stereogenic center influences helicity of the distal trityl chromophore but does not affect its propeller shape. Deformation of the propeller shape and consequent loss of its C3 symmetry results mainly from substitution of the amide hydrogen and is connected with an increase in steric hindrance. As an outcome of our studies, a model of optical activity of chiral triphenylacetamides is proposed. The performed X‐ray studies revealed that this novel class of chiral compounds is likely to be of additional value due to the porosity of the crystals.

Segmental isotope-labeling of the intrinsically disordered protein PQBP1

Polyglutamine tract-binding protein 1 (PQBP1) is an intrinsically disordered protein abundantly expressed in the brain. Mutations in the PQBP1 gene are causative for X-linked mental retardation disorders. Here, we investigated the structure of the C-terminal segment within the context of full-length PQBP1. We produced a segmentally isotope-labeled PQBP1 composed of a non-labeled segment (residues 1–219; N-segment) and a 13C/15N-labeled segment (residues 220–265; C-segment). Our results demonstrate that the segmental isotope-labeling combined with NMR spectroscopy is useful for detecting a very weak intra-molecular interaction in an intrinsically disordered protein.

Syntheses, crystal structures and magnetic properties of three new molecular solids based on bis(maleonitriledithiolate)copper(II) anion and 2-substituted benzyl triphenylphosphonium

Syntheses, crystal structures and magnetic properties of three molecular solids, [2RBzTPP]2[Cu(mnt)2] (mnt2−=maleonitriledithiolate; [2RBzTPP]+=1-(2′-R-benzyl)triphenylphosphonium, R=F(1), Cl(2) and Br(3)) are investigated. All three molecular metals crystallize in the triclinic space group P-1. The change of the molecular topology of the counteraction when the o-substituted group in the benzyl ring has changed from F to Cl and Br, results in the difference in the dihedral angles, the stacking mode and the weak interactions of the cations and anions of 1, 2 and 3. The effect of weak intramolecular interactions such as CH⋯X(X=F, Cl, Br), CH⋯S, CH⋯N, CH⋯Cu, CH⋯π hydrogen bonds and the short X⋯X interactions generates a 3D network structure. The magnetic susceptibilities of these molecular metals measured in the temperature range 2.0–300K show that the overall magnetic behaviors of 1–3 correspond to a paramagnetic system with a very weak ferromagnetic coupling interaction with θ=0.013K for 1, 0.019K for 2 and 0.025K for 3.

Characterization of polylactides with different stereoregularity using electrospray ionization ion mobility mass spectrometry.

We investigated the effect of stereoregularity on the gas-phase conformations of linear and cyclic polylactides (PLA) using electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) combined with molecular dynamics simulations. IM-MS analysis of PLA ions shows intriguing difference between the collision cross section (ΩD) value of poly-L-lactide (PLLA) and poly-LD-lactide (PLDLA) ions with respect to their chain architecture and stereoregularity. In the singly sodiated linear PLA (l-PLA∙Na(+)) case, both l-PLLA and l-PLDLA up to 11mer have very similar ΩD values, but the ΩD values of l-PLLA are greater than that of l-PLDLA ions for larger ions. In the case of cyclic PLA (c-PLA), c-PLLA∙Na(+) is more compact than c-PLDLA∙Na(+) for short PLA ions. However, c-PLLA exhibits larger ΩD value than c-PLDLA for PLA ions longer than 13mer. The origin of difference in the ΩD values was investigated using theoretical investigation of PLAs in the gas phase. The gas-phase conformation of PLA ions is influenced by Na(+)-oxygen coordination and the weak intramolecular hydrogen bond interaction, which are more effectively formed in more flexible chains. Therefore, the less flexible PLLA has a larger ΩD value than PLDLA. However, for short c-PLA, concomitant maximization of both Na(+)-oxygen coordination and hydrogen bond interaction is difficult due to the constricted chain freedom, which makes the ΩD value of PLAs in this range show a different trend compared with other PLA ions. Our study facilitates the understanding of correlation between stereoregularity of PLAs and their structure, providing potential utility of IM-MS to characterize stereoisomers of polymers.

Fundamental relation between molecular geometry and real-space topology. Combined AIM, ELI-D, and ASF analysis of hapticities and intramolecular hydrogen-hydrogen bonds in zincocene-related compounds.

Despite numerous advanced and widely distributed bonding theories such as MO, VB, NBO, AIM, and ELF/ELI-D, complex modes of bonding such as M-Cp*((R)) interactions (hapticities) in asymmetrical metallocenes or weak intramolecular interactions (e.g., hydrogen-hydrogen (H···H) bonds) still remain a challenge for these theories in terms of defining whether or not an atom-atom interaction line (a "chemical bond") should be drawn. In this work the intramolecular Zn-C(Cp*(R)) (R = Me, -(CH2)2NMe2, and -(CH2)3NMe2) and H···H connectivity of a systematic set of 12 zincocene-related compounds is analyzed in terms of AIM and ELI-D topology combined with the recently introduced aspherical stockholder fragment (ASF) surfaces. This computational analysis unravels a distinct dependency of the AIM and ELI-D topology against the molecular geometry for both types of interactions, which confirms and extends earlier findings on smaller sets of compounds. According to these results the complete real-space topology including strong, medium, and weak interactions of very large compounds such as proteins may be reliably predicted by sole inspection of accurately determined molecular geometries, which would on the one hand afford new applications (e.g., accurate estimation of numbers, types, and strengths of intra- and intermolecular interactions) and on the other hand have deep implications on the significance of the method.

Three molecular metals containing bis(maleonitriledithiolate)nickel(III) anion and 2-substituted benzyl triphenylphosphonium: Syntheses, crystal structures and magnetic properties

Three new molecular metals, [2RBzTPP][Ni(mnt)2] (mnt2−=maleonitriledithiolate; [2RBzTPP]+=1-(2′-R-benzyl)triphenylphosphonium, R=F(1), Br(2), NO2(3)) have been synthesized and characterized by elemental analyses, IR, UV, single crystal X-ray diffraction and magnetic measurements. The single-crystal structure analysis indicates that 1 crystallizes in the triclinic space group P−1, while both 2 and 3 crystallizes in the monoclinic space group P21/n. The Ni(III) ions of 1, 2, and 3 form a 1D non-uniform magnetic chain within a [Ni(mnt)2]− anions column through Ni⋯Ni, Ni⋯S or S⋯S interactions. The effect of weak intramolecular interactions such as CH⋯N, CH⋯F, CH⋯Br, CH⋯π or CH⋯O hydrogen bonds in these molecular solids 1, 2 or 3 generate a 3D network structure. Magnetic measurements have shown that 1 exhibits a characteristic of spin-gap (Δ/kb=249.5K) around 128K, while 2 and 3 showed a very strong antiferromagnetic coupling feature with J=−875.6 and −820.3cm−1 when the temperature is lowered.

Insight into the role of fluorinated dendrimers in ruthenium(II) catalyst for asymmetric transfer hydrogenation: The stabilizing effects from experimental and DFT approach

A series of fluorinated dendritic chiral ligands have been designed and synthesized. These fluorinated dendrimers are capable of forming a well-defined semi-rigid structure, which was revealed to play a vital role in the ruthenium(II) bifunctional catalyst for asymmetric transfer hydrogenation of prochiral ketone substrates. In contrast to the classical non-fluorinated dendrimer carrier, both NMR and DFT study exhibit that the introduction of fluorine atoms leads to considerable intramolecular weak interactions such as π–π stacking and hydrogen bonding interactions, which make the dendritic backbone exist with a semi-rigid structure in the catalyst. This influences the performance of the catalytic center in terms of the stability and reusability. This concept was employed as a strategy to design a new Ru(II)-complex catalyst Ru-G-2′-F, which demonstrated obviously improved recycling ability up to fifteen times. Significantly enhanced activity, high enantioselectivity and outstanding recycling ability have also been achieved even at high reaction temperature with Ru-G-2-F.

Isolable atropisomers of 2-aryl indoline derivatives: determination of rotational barrier by density functional theory approach

The rotational process of 2-aryl ring in 1-acyl-2-aryl-3,3-dimethylindolines was determined by density functional theory (DFT) at B3LYP/6-31G(d) level. The calculated barrier height for the rotational process of [2-(2-hydroxynaphthalen-1-yl)-3,3-dimethylindolin-1-yl]phenylmethanone (1) was ca. 30 kcal/mol, comparable to the previously reported experimental values of 26–28 kcal/mol for the corresponding derivatives. The Hartree–Fock (HF) calculation overestimated the barrier. The DFT-calculated rotational barrier height provided valuable information for knowing whether the conformers were isolable or not. The transition structure analyses showed that the presence of 2,6-substituents on the aryl ring is essential for the isolation of the conformers at room temperature. Based on the DFT-calculated geometries, the rotational process and the intramolecular weak interactions in the restricted rotation were analyzed.

Carbohydrates in the gas phase: conformational preference ofd-ribose and 2-deoxy-d-ribose

A full exploration of the conformational landscape of D-ribose and 2-deoxy-D-ribose monosaccharides in the gas phase has been performed using DFT methods (B3LYP and M06-2X). Open-chain, furanose and pyranose configurations have been examined. Up to 954 and 668 stable structures have been obtained for D-ribose and 2-deoxy-D-ribose. Among these structures, up to 35 and 22 have relative energies smaller than 5 kJ mol−1 with respect to the absolute minimum of each molecule, respectively. For D-ribose, pyranose in α- and β-forms is the most populated according to both functionals, the β-diastereoisomer being the most populated. For 2-deoxy-D-ribose, the α-pyranose form is in majority. The β/α relationship of pyranose forms presents different results for both functionals: for M06-2X it increases in D-ribose and decreases in 2-deoxy-D-ribose at 0 K with respect to the room temperature results, the opposite case occurring in B3LYP. Intramolecular weak interactions have been characterized using the AIM and NBO methodologies.