The structure of two isomeric stacked dimers of Watson-Crick 9-methyladenine-1-methylthymine pairs was fully optimized using an approximate density functional theory (DFT) method augmented with an empirical dispersion interaction. The results of the...
We have theoretically examined the intermolecular interactions in the cationic states of π-stacked dimers of 4nπ antiaromatic molecules. The ground state of face-to-face π-dimer models, consisting of cyclobutadienes (CBDs), was analyzed as a...
The oxidation of tetraselenatetracene (TSeT) by tetracyanoquinodimethane in the presence of dysprosium(III) tris(hexafluoroacetylacetonate), DyIII(hfac)3, produces black crystals of {TSeT1.5}●+[DyIII(hfac)4]− (1) salt, which combines cond...
The (4′→6′)-linked DNA homolog 2′,3′-dideoxy-β-D-glucopyranosyl nucleic acid (dideoxy-glucose nucleic acid or homo-DNA) exhibits stable self-pairing of the Watson–Crick and reverse-Hoogsteen types, but does not...
G-quadruplex (G4), an important secondary structure of nucleic acids, is polymorphic in structure. G4 monomers can associate with each other to form multimers, which show better application performance than monomers in some aspects. G4 dimers, the si...
F-type ATP synthases play a key role in oxidative and photophosphorylation processes generating adenosine triphosphate (ATP) for most biochemical reactions in living organisms. In contrast to the mitochondrial FOF1-ATP synthases, those of chloroplast...
A novel π-stacked polymer based on a pseudo–meta–linked [2.2]paracyclophane moieties was synthesized by Sonogashira-Hagihara coupling. The UV-vis absorption spectra of the synthesized polymer and model compounds revealed an extension o...
Azobenzene-containing molecules may associate with each other in systems such as self-assembled monolayers or micelles. The interaction between azobenzene units leads to a formation of exciton states in these molecular assemblies. Apart from local ex...
Non-covalent π-π stacking interactions often play a key role in the stability of the secondary and tertiary structures of peptides and proteins, respectively, and can be a means of ensuring the binding of ligands within protein and enzyme bindi...
N′-Phenylbenzohydrazides are valuable precursors for air- and moisture-stable Blatter radicals, with applications in magnetism and spintronics. This study presents the single-crystal X-ray structures of N′-(4-methyl-2-nitrophenyl)benzohyd...
The Neutral to Ionic phase Transition (NIT) that occurs in few mixed stack charge transfer cocrystals at high pressure or low temperature is a charge instability combined with a structural instability. The lattice contraction, which increases the 3D...
Packing motifs within structurally characterized cis-[M(bpy)2X2] (M = any metal, bpy = 2,2′-bipyridine, X = F, Cl, Br, I) coordination compounds have been investigated using data from the Cambridge Structural Database. Compounds fall into two c...
Dimerization free energies are fundamental quantities that describe the strength of interaction of different molecules. Obtaining accurate experimental values for small molecules and disentangling the conformations that contribute most to the binding...
Cyanine dyes have been widely applied in various biological systems owing to their specific photochemical properties. Assembly and disassembly process of cyanine dyes were constructed and regulated by special biomolecules. In this paper, dimeric cyan...
Knowledge of reliable geometries and associated intermolecular interaction energy (ΔE) values at key fragments of the potential energy surface (PES) in the gas phase is indispensable for the modeling of various properties of the pyrene dimer (P...
Theoretical results for the magnetic shielding of protonated and unprotonated nitrogens of eumelanin building blocks including monomers, dimers, and tetramers in gas phase and water are presented. The magnetic property in water was determined by carr...
Effects of the number of monomers (N) on the two-photon absorption (TPA) properties of π-stacked multimer models consisting of phenalenyl radicals were investigated theoretically. We conducted spectral simulations for the π-stacked N-mer models...
In this article, we used molecular dynamics (MD), one of the most common methods for simulations of membranes, to study the interaction of fluorescent membranotropic biological probe 10-N-nonyl acridine orange (NAO) with the bilayer, mimicking a plas...
A concept of piezo-responsive hydrogen-bonded π-π-stacked organic frameworks made from Knoevenagel-condensed vanillin–barbiturate conjugates was proposed. Replacement of the substituent at the ether oxygen atom of the vanillin moiety from...
Owing to the attractive potential applications of porphyrin assemblies in photocatalysis, sensors, and material science, studies presently concerning porphyrin aggregation are widely diffused. π–π stacking, H-bonding, metal coordination,...
The peptidyl transferase center (PTC) in the ribosome is composed of two symmetrically arranged tRNA-like units that contribute to peptide bond formation. We prepared units of the PTC components with putative tRNA-like structure and attempted to obta...
Noncovalent interactions play a significant role in a wide variety of biological processes and bio-inspired species. It is, therefore, important to have at hand suitable computational methods for their investigation. In this paper, we report on the c...
The titular compound was characterized for the first time using a full range of spectroscopic methods, including UV, IR, 1H, and 13C NMR spectra. In solution, all methods showed a keto–enol equilibrium strongly shifted to the enol form. The X-r...
The nucleophilic addition of 3-(4-cyanopyridin-2-yl)-1,1-dimethylurea (1) to cis-[Pt(CNXyl)2Cl2] (2) gave a new cyclometallated compound 3. It was characterized by NMR spectroscopy (1H, 13C, 195Pt) and high-resolution mass spectrometry, as well as cr...
Noncovalent interactions are key to the stability of lignin dimers, the primary components of bio-oil. However, their specific influence on the infrared spectra remains poorly understood. Using dispersion-corrected density-functional theory (APFD/6-3...
The production of single dimensional carbon structures has recently been made easier using carbon nanotubes. We consider here encapsulated coronene molecules, which are flat and circular-shaped polycyclic aromatic hydrocarbons, inside carbon nanotube...
A new supramolecular Pb(II) complex [PbL(NO2)]n was synthesized from Pb(NO3)2, N’-(1-(pyridin-2-yl)ethylidene)isonicotinohydrazide (HL) and NaNO2. [PbL(NO2)]n is constructed from discrete [PbL(NO2)] units with an almost ideal N2O3 square pyrami...
We present a simulation study of supramolecular aggregates formed by three-arm azobenzene (Azo) stars with a benzene-1,3,5-tricarboxamide (BTA) core in water. Previous experimental works by other research groups demonstrate that such Azo stars assemb...
We study the scattering of polarized light by two equal corner stacked Au nanorods that exhibit strong electromagnetic coupling. In the far field, this plasmonic dimer manifests very prominent asymmetric scattering in the transverse direction. Calcul...
Background: Surgically induced nerve damage is a common but debilitating side effect. By developing tracers that specifically target the most abundant protein in peripheral myelin, namely myelin protein zero (P0), we intend to support fluorescence-gu...
A study was carried out on the possibility of orderly and spontaneous dimerization at room temperature of C60 cages in fullerene liquid crystal fullerene dyads (R-C60). For this purpose, dyads with a structural elements feature supporting π-stacking...
Neutral-ionic transitions (NITs) occur in organic charge-transfer (CT) crystals of planar
In the process of a systematic study of the bis-chelate oxime-amide ligands with different polymethylene spacers and their transition metal complexes, two new Ni(II) and Cu(II) complexes of the mhiea2poh ligand have been isolated, and their molecular...
This is the first study of the crystal structure of cardamonin (CA) confirmed using single-crystal XRD analysis. In the crystal lattice of CA, two symmetry independent molecules are linked by hydrogen bonds within the layers and by the π·&m...
The molecular structure and vibrational spectra of six 1,2,3-triazoles-containing molecules with possible anticancer activity were investigated. For two of them, the optimized geometry was determined in the monomer, cyclic dimer and stacking forms us...
Although the Neutral-Ionic transition in mixed stack charge-transfer crystals was discovered almost forty years ago, many features of this intriguing phase transition, as well as open questions, remain at the heart of today’s science. First of all, t...
The synthesis and crystal structure of 4,11-dimethyl-2,13-di-m-tolyltribenzo[b,e,g][1,4]dioxocine-7,8-dicarbonitrile are reported. X-ray diffraction analysis reveals a rigid dioxocine core with m-tolyl substituents adopting torsional angles of 25&nda...
In this paper we report the first observation, through X-ray diffraction, of noncovalent uracil–uracil (U–U) dimeric π-stacking interactions in carbon nanotube (CNT)–based supramolecular assemblies. The directionally oriented morphology determined us...
Three photobicyclized benzodithienoquinolizinium tetrafluoroborates (BPDTQBF4) were prepared and evaluated by UV–Vis and fluorescence spectral, electrochemical analysis, and by theoretical calculations as possible organic n-type semiconductors. Evalu...
The title compound, 5-(4,5-dimethylthio-1,3-dithiol-2-ylidene)-1,3-diaza-2,4,6-trithiapentalene (4,5-dimethylthio [1,2,5]thiadiazolotetrathiafulvalene, molecular formula C8H6N2S7) crystallizes in the P21/n space group with one molecule in the asymmet...
Two 1:1 charge-transfer organic complexes were formed using tetrathiafulvalene as a donor and a 9H-fluorenone derivative as acceptor: 4,5,7-trinitro-9H-fluoren-9-one-2-carboxylic acid (complex 1) or 4,5,7-trinitro-9H-fluoren-9-one-2-carboxylic acid m...
To develop a new spin-crossover functional material, a magnetic hybrid compound [Fe(qsal)2][Ni(mnt)2] was designed and synthesized (Hqsal = N-(8-quinolyl)salicylaldimine, mnt = maleonitriledithiolate). The temperature dependence of magnetic susceptib...
Most recently a renewed interest in several areas has arisen in factors governing the 1H NMR chemical shift (1H CS) of protons in aromatic systems. Therefore, it is important to describe how 1H CS values are affected by π-stacking intermolecular i...
We review the magneto-structural properties of electron–electron correlated quasi-one- dimensional (1D) molecular organics. These weakly localized quarter-filled metallic-like systems with pronounced spin 1/2 antiferromagnetic (AF) interactions...
The spectroscopic features of the multilayer honeycomb model of structured water are analyzed on theoretical grounds, by using high-level ab initio quantum-chemical methodologies, through model systems built by two fused hexagons of water molecules:...
The equilibrium and conical intersection geometries of the benzene dimer were computed in the framework of the conventional, linear-response time-dependent and spin-flipped time-dependent density functional theories (known as DFT, TDDFT and SF-TDDFT)...
Structures characterized by the trigonal coordination of the gallium center that interacts with electron rich carbon sites are described. These interactions may be classified as Ga···C triel bonds. Their properties are analyzed i...
Progesterone receptor membrane component 1 (PGRMC1) is highly expressed in various cancer cells and contributes to tumor progression. We have previously shown that PGRMC1 forms a unique heme-stacking functional dimer to enhance EGF receptor (EGFR) ac...
We present the magnetic properties of the metal-organic framework {[CoCxAPy]·2.15 H2O}n (Cx = bis(carboxypropyl)tetramethyldisiloxane; APy = 4,4`-azopyridine) (1) that builds up from the stacking of 2D coordination polymers. The 2D-coordination polym...
This paper reports a new packing type of α-cyclodextrin inclusion complexes, obtained here with succinic acid under low-temperature crystallization conditions. The structure of the 1:1 complex is characterized by heavy disorder of the guest, the solv...
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