Stacking Contacts Research Articles

An experimental and DFT study of the packing and structure of dithenoylmethane monocarbonylphosphine Rhodium(I) complex [Rh((C4H3S)COCHCO(C4H3S))(CO)(PPh3)

[Rh((C4H3S)COCHCO(C4H3S))(CO)(PPh3)] crystals stack in one dimensional linear chains in the solid state, with slightly slipped π-stacking of the thienyl groups of one molecule and the β-diketonato backbone of a neighbouring molecule. The observed stacking is possible due to the near planar orientation of the two aromatic thienyl groups and the β-diketonato backbone. The experimentally observed stacking and close intermolecular contacts are in agreement with theoretical QTAIM calculated intermolecular bond paths and intermolecular hydrogen bonds between neighbouring molecules. NBO calculations revealed donor – acceptor NBO interactions between the lone pair on rhodium of one molecule and (i) the empty antibonding orbital on C-H of the nearest thienyl group of a neighbouring molecule, as well as with the (ii) the empty antibonding orbital on two carbons of the nearest thienyl group to rhodium on the neighbouring molecule.

Ca-Doped CuO Diffusion Barrier for High-Performance <italic>a</italic>-IGZO Transistors With Cu-Based Source/Drain Material

A thermally stable Ca-doped CuOx (CuCaOx) diffusion barrier to prevent the migration of Cu to amorphous InGaZnO ( ${a}$ -IGZO) was developed by reactive sputtering and subsequent annealing. Insertion of a 5-nm-thick CaCuOx between the Ca-doped Cu (CuCa) and a-IGZO channel films in the source/drain contact regions provided the resulting transistors with superior charge transport and lower trap density compared to the diffusion barrier-free CuCa/a-IGZO transistors. The fabricated a-IGZO transistors with the CuCa/CuCaOx stack contact exhibited a high mobility of 20.8 cm $^{\textsf {2}}/\textsf {V}\cdot \textsf {s}$ and an Ion/off ratio of 108. Simultaneously, very stable behavior against the external positive/negate gate bias stress was observed for the a-IGZO thin-film transistors with the CuCa/CuCaOx stack contact. This was attributed to suppression of Cu-related acceptor-like traps due to the conformal formation of CuCaOx film with excellent barrier properties.

Synthesis, X-ray crystal structure and DFT studies of two octahedral cobalt(II) complexes with N,N,N-tridentate triazine-type ligand

Two new Co(II) complexes, [CoL2]X2∙2H2O, with N,N,N-tridentate triazine type ligand (L) and X = Cl− (1) or NO3− (2) are synthesized and characterized using elemental analysis, FTIR spectra, and single-crystal X-ray diffraction. Complexes 1 and 2 are crystallized in the centrosymmetric space groups P-1 and C2/c, respectively. The Co atoms are surrounded by two neutral tridentate ligands coordinated via nitrogen atoms, thus forming a distorted octahedral coordination sphere. Hirshfeld topology analyses of the molecular packing revealed that the polar Cl⋯H, O⋯H and N⋯H contacts are the most important intermolecular interactions while the nonpolar C⋯H and C⋯C (π–π stacking) contacts are weak and insignificant, respectively. DFT calculations indicated that the high-spin state is energetically more favored than the low-spin case. The Co(II) center transfers its spin density to the ligand donor atoms via the spin delocalization mechanism. Based on the atoms in molecules (AIM) results, all Co–N interactions have a predominant covalent character. The strength of the Co–N interactions decreases in the order Co–N(hydrazone) > Co–N(triazine) > Co–N(amine). The metal anti-bonding natural orbitals involved in the Co–N interactions have high and s-orbital characters. Both complexes showed good thermal stability up to 276°C and 250°C for complexes 1 and 2, respectively.

Structural basis for guanidine sensing by the ykkC family of riboswitches.

Regulation of gene expression by cis-encoded riboswitches is a prevalent theme in bacteria. Of the hundreds of riboswitch families identified, the majority of them remain as orphans, without a clear ligand assignment. The ykkC orphan family was recently characterized as guanidine-sensing riboswitches. Herein we present a 2.3 Å crystal structure of the guanidine-bound ykkC riboswitch from Dickeya dadantii. The riboswitch folds into a boot-shaped structure, with a coaxially stacked P1/P2 stem forming the boot, and a 3′-P3 stem–loop forming the heel. Sophisticated base-pairing and cross-helix tertiary contacts give rise to the ligand-binding pocket between the boot and the heel. The guanidine is recognized in its positively charged guanidinium form, in its sp2 hybridization state, through a network of coplanar hydrogen bonds and by a cation–π stacking contact on top of a conserved guanosine residue. Disruption of these contacts resulted in severe guanidinium-binding defects. These results provide the structural basis for specific guanidine sensing by ykkC riboswitches and pave the way for a deeper understanding of guanidine detoxification—a previously unappreciated aspect of bacterial physiology.

High-angle annular dark field scanning transmission electron microscopic (HAADF-STEM) study of Fe-rich 7 Å–14 Å interstratified minerals from a hydrothermal deposit

AbstractThe distribution of octahedral cations in the two component layers of a 7 Å–14 Å interstratified mineral with a bulk chemical composition (Fe4.122+Mg0.07Mn0.01Al1.69□0.11)(Si2.56Al1.44) O10(OH)8was investigated using high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM) in combination with the image simulations. In the 14 Å component layers, comparison between the observed and simulated images revealed that the M4 sites of the interlayer sheets were occupied preferentially by Al together with a small amount of Fe; the other M1, M2 and M3 sites were occupied by dominant Fe and residual Al in equal proportions. Two types of octahedral sheets with disordered and ordered cation distributions were recognized in the 7 Å component layers. The two types of sheets were similar to the octahedral sheet of the 2:1 layer and the interlayer sheet in the 14 Å layer above, respectively. Irregular vertical stacking and lateral contact of the different component layers in structure and chemistry characterized the interstratification, which may be caused by rapid precipitation and accretion of the component layers in hydrothermal environments.

Stereospecific interaction of optically active sulfur-bridged dinuclear Co(III)–Pt(II) complex with pseudo-enantiomeric Co(III)–M(II) (M: Pd or Pt) complex involving unequivalent π electronic system

Assemblies between the pseudo-enantiomers with different π electronic systems, [Pt(bpy){Co(d-pen)2}]+ (bpy=2,2′-bipyridine, pen=penicillaminate) and [M(phen){Co(l-pen)2}]+ (M=Pt or Pd, phen=1,10-phenanthroline), or [Pt(bpy){Co(l-pen)2}]+ and [M(phen){Co(d-pen)2}]+, have been examined from stereo- and spectrochemical aspects. As a result, a mixture of equimolar amounts of optically active sulfur-bridged dinuclear complex, [Pt(bpy){Co(d-pen)2}]Cl, and its pseudo-enantiomer, [M(phen){Co(l-pen)2}]Cl, in H2O crystallizes as [Pt(bpy){Co(d-pen)2}][M(phen){Co(l-pen)2}]Cl2·14H2O, in which two complex cations with imperfect enantiomorphisms form a 1:1 π–π stacked unit. In the crystal, such a 1:1 π–π stacked unit develops into a linear-chain through further π–π stacking contacts with adjacent 1:1 π–π stacked units.

Crystal structure of 4-{2-[4-(di-methyl-amino)-phen-yl]diazen-1-yl}-1-methyl-pyridinium iodide.

The mol­ecular geometry of the ionic title compound, C14H17N4 +·I− or DAZOP+·I−, is essentially featureless. Regarding the crystal structure, in addition to the obvious cation–anion Coulombic inter­actions, the packing is mostly directed by non-covalent inter­actions involving both ring systems, as well as the iodide anion. It consists of cationic mol­ecules aligned along [101] and disposed in an anti­parallel fashion while linked into π-bonded dimeric entities by a stacking contact involving symmetry-related phenyl rings, with a centroid–centroid distance of 3.468 (3) Å and a slippage of 0.951 Å. The dimers are, in addition, sustained by a number of C—H⋯I and I⋯π (I⋯centroid = 3.876 Å) inter­actions involving the anion. Finally, inter­dimeric contacts are of the C—H⋯I and C—H⋯π types.

Crystal structure of 4-[(E)-(4-fluoro-benzyl-idene)amino]-3-methyl-1H-1,2,4-triazole-5(4H)-thione.

The title compound, C10H9FN4S, crystallizes with two mol­ecules (A and B) in the asymmetric unit. The dihedral angle between the planes of the trizole and fluoro­benzene rings is 7.3 (3)° in mol­ecule A and 41.1 (3)° in mol­ecule B. Mol­ecule A features an intra­molecular C—H⋯S hydrogen bond, which closes an S(6) ring. In the crystal, A+B dimers linked by pairs of N—H⋯S hydrogen bonds occur, generating R 2 2(8) loops. Weak π–π stacking contacts [centroid–centroid separation = 3.739 (6) Å] are also observed.

Review of Graphene as a Solid State Diffusion Barrier.

Conventional thin-film diffusion barriers consist of 3D bulk films with high chemical and thermal stability. The purpose of the barrier material is to prevent intermixing or penetration from the two materials that encase it. Adhesion to both top and bottom materials is critical to the success of the barrier. Here, the effectiveness of a single atomic layer of graphene as a solid-state diffusion barrier for common metal schemes used in microelectronics is reviewed, and specific examples are discussed. Initial studies of electrical contacts to graphene show a distinct separation in behavior between metallic groups that strongly or weakly bond to it. The two basic classes of metal reactions with graphene are either physisorbed metals, which bond weakly with graphene, or chemisorbed metals, which bond strongly to graphene. For graphene diffusion barrier testing on Si substrates, an effective barrier can be achieved through the formation of a carbide layer with metals that are chemisorbed. For physisorbed metals, the barrier failure mechanism is loss of adhesion at the metal–graphene interface. A graphene layer encased between two metal layers, in certain cases, can increase the binding energy of both films with graphene, however, certain combinations of metal films are detrimental to the bonding with graphene. While the prospects for graphene's future as a solid-state diffusion barrier are positive, there are open questions, and areas for future research are discussed. A better understanding of the mechanisms which influence graphene's ability to be an effective diffusion barrier in microelectronic applications is required, and additional experiments are needed on a broader range of metals, as well as common metal stack contact structures used in microelectronic applications. The role of defects in the graphene is also a key area, since they will probably influence the barrier properties.

Crystal structure of 2-meth-oxy-1-nitro-naphthalene.

The asymmetric unit of the title compound, C11H9NO3, contains two mol­ecules, A and B. In mol­ecule A, the dihedral angle between the planes of the naphthalene ring system (r.m.s. deviation = 0.003 Å) and the nitro group is 89.9 (2)°, and the C atom of the meth­oxy group deviates from the naphthyl plane by 0.022 (2) Å. Equivalent data for mol­ecule B are 0.008 Å, 65.9 (2)° and −0.198 (2) Å, respectively. In the crystal, mol­ecules are linked by weak C—H⋯O inter­actions, forming [100] chains of alternating A and B mol­ecules. Weak aromatic π–π stacking contacts, with a range of centroid–centroid distances from 3.5863 (9) to 3.8048 (9) Å, are also observed.

Crystal structure of (2-amino-7-methyl-4-oxidopteridine-6-carboxyl-ato-κ(3) O (4),N (5),O (6))aqua-(1,10-phenanthroline-κ(2) N,N')zinc trihydrate.

In the title compound, [Zn(C8H5N5O3)(C12H8N2)(H2O)]·3H2O, a tridentate 2-amino-7-methyl-4-oxidopteridine-6-carboxyl­ate ligand, a bidentate ancillary 1,10-phenanthroline (phen) ligand and a water mol­ecule complete a distorted octa­hedral coordination geometry around the ZnII atom. The pterin ligand forms two chelate rings. The phen and pterin ring systems are nearly perpendicular [dihedral angle = 85.16 (5)°]. Classical N—H⋯O, O—H⋯N and O—H⋯O hydrogen bonds and weak C—H⋯O hydrogen bonds link the complex mol­ecules and lattice water mol­ecules into a three-dimensional network. π–π stacking contacts are observed as well, with centroid-to-centroid distances of 3.5679 (14), 3.7004 (14), 3.6641 (15), 3.6974 (13) and 3.3412 (12) Å.

Molecular Dynamics Investigation of a Mechanism of Allosteric Signal Transmission in Ribosomes.

The ribosome is a molecular machine that synthesizes all cellular proteins via translation of genetic information encoded in polynucleotide chain of messenger RNA. Transition between different stages of the ribosome working cycle is strictly coordinated by changes in structure and mutual position both of subunits of the ribosome and its ligands. Therein, information regarding structural transformations is transmitted between functional centers of the ribosome through specific signals. Usually, functional centers of ribosomes are located at a distance reaching up to several tens of angstroms, and it is believed that such signals are transduced allosterically. In our study, we attempted to answer the question of how allosteric signal can be transmitted from one of the so-called sensory elements of ribosomal tunnel (RT) to the peptidyl transferase center (PTC). A segment of RT wall from the E. coli ribosome composed of nucleotide residues A2058, A2059, m(2)A2503, G2061, A2062, and C2063 of its 23S rRNA was examined by molecular dynamics simulations. It was found that a potential signal transduction pathway A2058-C2063 acted as a dynamic ensemble of interdependent conformational states, wherein cascade-like changes can occur. It was assumed that structural rearrangement in the A2058-C2063 RT segment results in reversible inactivation of PTC due to a strong stacking contact between functionally important U2585 residue of the PTC and nucleotide residue C2063. A potential role for the observed conformational transition in the A2058-C2063 segment for regulating ribosome activity is discussed.

Toward understanding tautomeric switching in 4-hydroxynaphthaldehyde and its dimers: A DFT and quantum topology study

The electronic structures and stabilities of all benzenoid (enol) and quinonoid (keto) forms of 4-hydroxynaphthaldehyde (ALD-14) have been investigated using density functional theory (DFT) with a range of functionals and basis sets. The anti-enol form represents the global minimum energy structure. Low rotation barriers of both the hydroxyl and the aldehyde groups characterize this form. Fourier analysis of the potential energy function for rotation indicate that the conformational preference of ALD-14 is determined by both the dipole–dipole repulsion and bond moments interactions. Further, three different ALD-14 dimer complexes are investigated, i.e. head-to-tail (HT), head-to-head (HH), and stacked (S) forms. The analysis of natural bond order, quantum topology features of the Laplacian of the electron density, binding energies and structural parameters of these dimers point to comparable stabilities of the HT and S-dimers, with a preference for a stacking contact. The origin of its stability can be traced to π-conjugative, H-bonding and dispersion interactions.

Stereospecific π–π stacking interactions between pseudo-enantiomeric sulfur-bridged dinuclear Co(III)–Pd(II) and Co(III)–Pt(II) complexes of optically active penicillaminates

The reactions of trans(N)-[Co(d-pen)2]− (pen=penicillaminate) with [MCl2(bpy)] (M=Pd or Pt, bpy=2,2′-bipyridine) and trans(N)-[Co(l-pen)2]− with [M′Cl2(bpy)] (M′=Pd or Pt) stereoselectively gave optically active S-bridged dinuclear complexes, [M(bpy){Co(d-pen)2}]+ and [M′(bpy){Co(l-pen)2}]+, respectively. Assemblies between these pseudo-enantiomers with different d8 metal centers, [M(bpy){Co(d-pen)}2]+ and [M′(bpy){Co(l-pen)}2]+ (M′≠M), have been examined from stereo- and spectrochemical aspects. As a result, a mixture of equimolar amounts of optically active sulfur-bridged dinuclear complex, [M(bpy){Co(d-pen)}2]Cl·3H2O, and its pseudo-enantiomer, [M′(bpy){Co(l-pen)}2]Cl·3H2O, in H2O crystallizes as [M(bpy){Co(d-pen)}2][M′(bpy){Co(l-pen)}2]Cl·14H2O, in which two complex cations with heterometallic square-planar units form a 1:1 π–π stacked unit. The 1:1 π–π stacked unit between pseudo-enantiomeric complex cations develops into a linear-chain with further π–π stacking contacts. These structural characteristics reflect their solid-state spectral behaviors.

6,7-Di-chloro-2,3-bis(pyridin-2-yl)quinox-aline.

The title compound, C18H10Cl2N4, synthesized by the condensation reaction between 4,5-di­chloro­benzene-1,2-di­amine and 1,2-di(pyridin-2-yl)ethane-1,2-dione in boiling acetic acid, has a nearly planar quinoxaline moiety [maximum deviation = 0.070 (1) Å] whose mean plane makes dihedral angles of 40.51 (2) and 39.29 (3)° with the pyridine rings. Within the unit cell, there are no classical hydrogen bonds. Molecules in the structure pack with π–π stacking contacts between the quinoxaline units and nearby pyridine rings with an intercentroid distance of 3.7676 (9) Å.

Monomer–Dimer Divergent Behavior toward DNA in a Half-Sandwich Ruthenium(II) Aqua Complex. Antiproliferative Biphasic Activity

The complex [(η6-p-cymene)Ru(OH2)(κ2-N,N-HL1)](OTf)2 (HL1 = 2-pyridin-2-yl-1H-benzimidazole), [2c](OTf)2, undergoes easy deprotonation of the N–H group at physiological pH, producing [(η6-p-cymene)Ru(OH2)(κ2-N,N-L1)]+, [2c′]+, prone to dimerization both in solution and in the solid state. X-ray measurements on [2c′]BF4 have shown that dimer units are formed in the solid state by a combination of π–π stacking contacts between the aromatic rings of [L1]− and hydrogen bonding involving the water molecules coordinated to the metal center and the deprotonated imidazolyl N atom. The T-jump kinetic curves of the 2D ↔ D2 equilibrium recorded in the microsecond time scale have allowed us to determine the parameters of the dimerization process. The dimer content diminishes as the ionic strength drops. The different kinetic and thermodynamic techniques have all shown that the monomer reacts with DNA, producing the bifunctional intercalated (through the benzimidazole ligand)-covalent (Ru/N7G) [(η6-p-cymene)Ru(κ2-N,N-L1)]/DNA complex. The cytotoxic activity of [2c′]+ was evaluated against human lung carcinoma cells (A549) by the MTT cell viability assay. Interestingly, the percentage of surviving cells as a function of the [2c′]+ content displayed biphasic behavior, interpreted as a result of the rise in the dimer content of [2c′]+. As only the monomer can react with DNA, a reasonable correlation between cytotoxic activity and formation of the [(η6-p-cymene)Ru(κ2-N,N-L1)]/DNA complex is established.

Synthesis and Structure Characterizations of Coordination Polymers Based on Silver(I) and Nitrogen Donors

Yellow crystals of the coordination polymers (CP) [Ag(qox)NO3], 1 [Ag(pyzca)], 2 were obtained by the reaction of AgNO3, quinoxaline (qox) or pyrazinecarboxylic acid (pyzcaH), respectively. The crystal structure of 1 displays 1D-extended chain of [Ag(qox)]n with NO3 coordinated to every Ag atom. The 1D-chains of 1 are interconnected by strong hydrogen bonds, π–π stacking and short contacts developing two dimensional sheets containing channels. Furthermore, the overall packing arrangement of 1 results 3D topology with corrugated network. The Ag atom in 2 acquires tetrahedral geometry while each pyzca ligand provides three donor sites connected to three Ag atoms. The structure of CP 2 displays 1D-extended helical chain of [Ag(pyzca)]n. The 3D-packing of the CP 2 creates nanometer pores. The luminescence properties of 1 and 2 were discussed.

Double pancake bonds: pushing the limits of strong π-π stacking interactions.

The concept of a double-bonded pancake bonding mechanism is introduced to explain the extremely short π–π stacking contacts in dimers of dithiatriazines. While ordinary single pancake bonds occur between radicals and already display significantly shorter interatomic distances in comparison to van der Waals (vdW) contacts, the double-bonded pancake dimer is based on diradicaloid or antiaromatic molecules and exhibits even shorter and stronger intermolecular bonds that breach into the range of extremely stretched single bonds in terms of bond distances and binding energies. These properties give rise to promising possibilities in the design of new materials with high electrical conductivity and for the field of spintronics. The analysis of the double pancake bond is based on cutting edge electron correlation theory combining multireference (nondynamical) effects and dispersion (dynamical) contributions in a balanced way providing accurate interaction energies and distributions of unpaired spins. It is also shown that the present examples do not stand isolated but that similar mechanisms operate in several analogous nonradical molecular systems to form double-bonded π-stacking pancake dimers. We report on the amazing properties of a new type of stacking interaction mechanism between π conjugated molecules in the form of a “double pancake bond” which breaks the record for short intermolecular distances and provides formidable strength for some π–π stacking interactions.

Crystal structure of 3-(3-oxo-2,3,4,4a,5,6-hexa-hydro-benzo[h]cinnolin-2-yl)propionic acid.

The asymmetric unit of the title compound, C15H16N2O3, contains two independent mol­ecules, which present a different conformation of the carb­oxy­lic acid side chain [C—C—C—OH torsion angles = 65.3 (7) and −170.1 (5)°]. In both mol­ecules, the di­hydro­pyridazinone ring adopts a geometry inter­mediate between a twisted-boat and a half-chair conformation, while the central six-membered ring is almost in a half-boat conformation. In the crystal, mol­ecules are linked by O—H⋯Ok (k = ketone) hydrogen bonds, generating [01-1] chains. Aromatic π–π stacking contacts between the benzene and the di­hydro­pyridazinone rings [centroid–centroid distance [3.879 (9) Å] are also observed.

Cocrystallization of C60 or C70 with the Bowl-Shaped Hydrocarbon Hexakis[(E)-3,3-dimethyl-1-butenyl]benzene To Form Chains of Clamshell Assemblies

The bowl-shaped hydrocarbon hexakis[(E)-3,3-dimethyl-1-butenyl]benzene (HB) has been cocrystallized with either C60 or C70 to form clamshell-like assemblies with the fullerenes residing within the concave surfaces of two HB molecules. The structures of these two crystals have been determined by single-crystal X-ray diffraction. The HB molecules exhibit back-to-back stacking and close contacts in both cocrystals. This trait is remarkably similar to the packing seen in cases in which fullerenes cocrystallize with MII(OEP), where OEP is the dianion of octaethylporphyrin and M is generally Ni or Co. The C60 structure features an ordered cage with a disordered solvent position, while the C70 structure exhibits two orientations of the cage, all other components being ordered.