Oligodeoxynucleotide Duplexes Containing (5′S)‐5′‐C‐Alkyl‐Modified 2′‐Deoxynucleosides: Can an Alkyl Zipper across the DNA Minor‐Groove Enhance Duplex Stability?

A series of oligonucleotides containing (5′S)‐5′‐C‐butyl‐ and (5′S)‐5′‐C‐isopentyl‐substituted 2′‐deoxyribonucleosides were designed, prepared, and characterized with the intention to explore alkyl‐zipper formation between opposing alkyl chains across the minor groove of oligonucleotide duplexes as a means to modulate DNA‐duplex stability. From four possible arrangements of the alkyl groups that differ in the density of packing of the alkyl chains across the minor groove, three (duplex types I – III , Fig. 2) could experimentally be realized and their duplex‐forming properties analyzed by UV‐melting curves, CD spectroscopy, and isothermal titration calorimetry (ITC), as well as by molecular modeling. The results show that all arrangements of alkyl residues within the minor groove of DNA are thermally destabilizing by 1.5–3°/modification in T_m. We found that, within the proposed duplexes with more loosely packed alkyl groups (type‐ III duplexes), accommodation of alkyl residues without extended distorsion of the helical parameters of B‐DNA is possible but does not lead to higher thermodynamic stability. The more densely packed and more unevenly distributed arrangement (type‐ II duplexes) seems to suffer from ecliptic positioning of opposite alkyl groups, which might account for a systematic negative contribution to stability due to steric interactions. The decreased stability in the type‐ III duplexes described here may be due either to missing hydrophobic interactions of the alkyl groups (not bulky enough to make close contacts), or to an overcompensation of favorable alkyl‐zipper formation presumably by loss of structured H₂O in the minor groove.     

Interplay between H‐Bonding and Alkyl‐Chain Ordering in Self‐Assembly of Monodendritic L‐Alanine Derivatives

This paper reports on the synthesis and self‐organizing properties of monodendrons consisting of L ‐alanine at the focal point and alkyl chains with different length at the periphery. The structures of thin films and monolayers are studied by temperature‐resolved grazing‐incidence X‐ray diffraction and scanning force microscopy. The interplay between H‐bonding and ordering of the alkyl chains results in a rich temperature‐dependent phase behavior. The monodendrons form H‐bonded stabilized clusters with the number of molecules depending on the length of the aliphatic chains and temperature. The clusters play the role of constitutive units in the subsequent self‐assembly. Short alkyl chains allow the material to form thermodynamically stable crystalline phases. The molecules with longer side groups exhibit additional transitions from the crystalline phase to thermotropic columnar hexagonal or columnar rectangular liquid‐crystalline phases. In monolayers deposited on highly ordered pyrolytic graphite, the materials show ordering similar to thin films. However, for the compound bearing hexadecyl chains the affinity of the alkyl groups to graphite dominates the self‐assembly and thereby allows epitaxial growth of a 2D lattice with flat‐on oriented molecules.     

Nanopatterned Superlattices in Self‐Assembled C2‐Symmetric Oligodimethylsiloxane‐Based Benzene‐1,3,5‐Tricarboxamides

The synthesis of C₃‐ and C₂‐symmetric benzene‐1,3,5‐tricarboxamides (BTAs) containing well‐defined oligodimethylsiloxane (oDMS) and/or alkyl side chains has been carried out. The influence of the bulkiness of the oDMS chains in the aggregation behavior of dilute solutions of the oDMS‐BTAs in methylcyclohexane was studied by temperature‐dependent UV spectroscopy. The formation of hierarchically self‐assembled aggregates was observed at different BTA concentrations, the tendency of aggregation increases by shortening or removing oDMS chains. Chiral BTAs were investigated with circular dichroism (CD) spectroscopy, showing a stronger tendency to aggregate than the achiral ones. Majority rules experiments show a linear behavior consistent with the existence of a high mismatch penalty energy. The most efficient oDMS‐BTAs organogelators have the ability to form stable organogels at 5 mg mL^?1 (0.75 wt %) in hexane. Solid‐state characterization techniques indicate the formation of an intermolecular threefold hydrogen bonding between adjacent molecules forming thermotropic liquid crystals, exhibiting a hexagonal columnar organization from room temperature to above 150 °C. A decrease of the clearing temperatures was observed when increasing the number and length of the oligodimethylsiloxane chains. In addition to the three‐fold hydrogen bonding that leads to columnar liquid crystalline phase, segregation between the oDMS and aliphatic chains takes place in the BTA functionalized with two alkyl and one oDMS chain leading to a superlattice within the hexagonal structure with potential applications in lithography.     

A Remarkably Simple Class of Imidazolium‐Based Lipids and Their Biological Properties

A series of imidazolium salts bearing two alkyl chains in the backbone of the imidazolium core were synthesized, resembling the structure of lipids. Their antibacterial activity and cytotoxicity were evaluated using Gram‐positive and Gram‐negative bacteria and eukaryotic cell lines including tumor cells. It is shown that the length of alkyl chains in the backbone is vital for the antibiofilm activities of these lipid‐mimicking components. In addition to their biological activity, their surface activity and their membrane interactions are shown by film balance and quartz crystal microbalance (QCM) measurements. The structure–activity relationship indicates that the distinctive chemical structure contributes considerably to the biological activities of this novel class of lipids.     

Polymer‐Assisted Solution‐Phase Synthesis and Neurite‐Outgrowth‐Promoting Activity of 15‐Deoxy‐Δ12,14‐PGJ2 Derivatives

An efficient solution‐phase synthesis of rac‐15‐deoxy‐Δ^12,14‐PGJ₂ (15dPGJ₂) derivatives that contain variable α and ω chains based on a polymer‐assisted strategy and their neurite‐outgrowth‐promoting activity are described. The strategy for the synthesis of PGJ₂ derivatives involves the use of a vinyl iodide bearing cyclopentenone as a key intermediate, which undergoes Suzuki–Miyaura coupling and subsequent Lewis acid catalyzed aldol condensation for incorporation of the ω and α chains, respectively. For easy access to the PGJ₂ derivatives, a polymer‐supported catalyst and scavengers were adapted for use in these four diverse steps, in which workup and purification can be performed by simple filtration of the solid‐supported reagents. By using this methodology, we succeeded in the synthesis of 16 PGJ₂ derivatives with four alkyl boranes and four aldehydes. The neurite‐outgrowth‐promoting activity of the 16 synthetic compounds in PC12 cells revealed that the side‐chains play a major role in modulating their biological activity. The carboxylic acid on the α chain improved the biological activity, although it was not absolutely required. Furthermore, a PGJ₂ derivative with a phenyl moiety on the ω chain was found to exhibit an activity comparable to that of natural 15dPGJ₂.     

Control of H‐ and J‐Type π Stacking by Peripheral Alkyl Chains and Self‐Sorting Phenomena in Perylene Bisimide Homo‐ and Heteroaggregates

The synthesis, self‐assembly, and gelation ability of a series of organogelators based on perylene bisimide (PBI) dyes containing amide groups at imide positions are reported. The synergetic effect of intermolecular hydrogen bonding among the amide functionalities and π–π stacking between the PBI units directs the formation of the self‐assembled structure in solution, which beyond a certain concentration results in gelation. Effects of different peripheral alkyl substituents on the self‐assembly were studied by solvent‐ and temperature‐dependent UV‐visible and circular dichroism (CD) spectroscopy. PBI derivatives containing linear alkyl side chains in the periphery formed H‐type π stacks and red gels, whereas by introducing branched alkyl chains the formation of J‐type π stacks and green gels could be achieved. Sterically demanding substituents, in particular, the 2‐ethylhexyl group completely suppressed the π stacking. Coaggregation studies with H‐ and J‐aggregating chromophores revealed the formation of solely H‐type π stacks containing both precursor molecules at a lower mole fraction of J‐aggregating chromophore. Beyond a critical composition of the two chromophores, mixed H‐aggregate and J‐aggregate were formed simultaneously, which points to a self‐sorting process. The versatility of the gelators is strongly dependent on the length and nature of the peripheral alkyl substituents. CD spectroscopic studies revealed a preferential helicity of the aggregates of PBI building blocks bearing chiral side chains. Even for achiral PBI derivatives, the utilization of chiral solvents such as (R)‐ or (S)‐limonene was effective in preferential population of one‐handed helical fibers. AFM studies revealed the formation of helical fibers from all the present PBI gelators, irrespective of the presence of chiral or achiral side chains. Furthermore, vortex flow was found to be effective in macroscopic orientation of the aggregates as evidenced from the origin of CD signals from aggregates of achiral PBI molecules.     

General Synthesis and Physicochemical Characterisation of a Series of Peptide‐Mimic Lysine‐Based Amino‐Functionalised Lipids

A series of novel malonic acid diamides (second generation) with two long hydrophobic alkyl chains and an alkaline polar head group was synthesised and characterised as a new class of amino‐functionalised lipids. These peptide‐mimic lipids are suitable for polynucleotide transfer. The lipids bear a novel backbone consisting of a lysine unit and a malonic acid unit. Six different head‐group structures, which vary in size and number of amino groups that can be protonated, were attached to the backbone structure. Furthermore, different alkyl chains were used to build the lipophilic part (namely tetradecyl, hexadecyl, and oleyl). Phase transitions of the new compounds in aqueous dispersions at pH 10 were analysed and discussed in terms of head group and alkyl chain variations. The shape and size of the formed aggregates of selected lipid dispersions were investigated by dynamic light scattering and transmission electron microscopy.     

Novel Ladder π‐Conjugated Materials—Sila‐Pentathienoacenes: Synthesis,Structure, and Electronic Properties

A novel series of ladder π‐conjugated materials—sila‐pentathienoacenes ( Si‐PTA ) are synthesized and characterized. Crystal structures of the compounds show that the length of alkyl chains substituting on the thiophene ring has a significant influence on molecular packing. A densely packed structure with an interfacial distance of about 3.66 Å between the adjacent molecules is observed for the compound with shorter alkyl chains. However, a large interfacial distance (7.99 Å) is obtained for another compound because of the insertion of long alkyl chains between two planes. The investigation of the optical and electrochemical properties shows that the silylene bridge incorporated into the pentathienoacene framework exerts a clear effect on the electronic properties by the σ*–π* conjugation. Although only a slight enhancement is observed for the HOMO levels, with respect to that of pentathienoacene, the LUMO levels are significantly lowered. The observed electronic properties are consistent with the theoretical calculations.     

Synthesis of Novel 2‐Amino‐(2‐thioxo‐3‐alkyl‐4‐methyl‐3H‐thiazol‐5‐yl)‐[1,3,4]thiadiazole Derivatives and Their Growth Stimulant Activity

On the base of synthesized 2‐amino and 2‐ethylamino‐(2‐thioxo‐3‐alkyl‐4‐methyl‐3H‐thiazol‐5‐yl)‐[1,3,4]thiadiazoles, their alkyl, acetyl, and alkylacetylamino derivatives are obtained. The alkylation of 2‐ethylamino derivatives can occur at both exo and endo nitrogen atoms of amidine group, and the acetylation takes place exclusively at the exocyclic nitrogen atom. At acetylation of 2‐amino‐[1,3,4]thiadiazoles, only exo substitution is observed. At the further alkylation of these products, a mixture of exo‐ and endo‐substituted forms is obtained. At preliminary screening, the synthesized compounds have shown expressed growth stimulant properties. The activity of the most active derivatives was in the range of 65–100%, compared with that of heteroauxin.     

Revisiting the crystallization of poly(2‐alkyl‐2‐oxazoline)s

Poly(2‐alkyl‐2‐oxazoline)s (PAOx) exhibit different crystallization behavior depending on the length of the alkyl side chain. PAOx having methyl, ethyl, or propyl side chains do not show any bulk crystallization. Crystallization in the heating cycle, that is, cold crystallization, is observed for PAOx with butyl and pentyl side chains. For PAOx with longer alkyl side chains crystallization occurs in the cooling cycle. The different crystallization behavior is attributed to the different polymer chain mobility in line with the glass transition temperature (T_g) dependency on alkyl side chain length. The decrease in chain mobility with decreasing alkyl side chain length hinders the relaxation of the polymer backbone to the thermodynamic equilibrium crystalline structure. Double melting behavior is observed for PButOx and PiPropOx which is explained by the melt‐recrystallization mechanism. Isothermal crystallization experiments of PButOx between 60 and 90 °C and PiPropOx between 90 and 150 °C show that PAOx can crystallize in bulk when enough time is given. The decrease of T_g and the corresponding increase in chain mobility at T > T_g with increasing alkyl side chain length can be attributed to an increasing distance between the polymer backbones and thus decreasing average strength of amide dipole interactions. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 721–729     

Association of hydrophobically α,ω‐end‐capped poly(2‐methyl‐2‐oxazoline) in water

The α,ω‐end‐capped poly(2‐methyl‐2‐oxazoline) (C_n‐POXZ‐C_n) have been synthesized by a one‐pot process using cationic ring‐opening polymerization with an appropriate initiator and terminating agent. The polymers bearing different alkyl groups C₁₂ and C₁₈ have molecular weight in the range of 2.4 × 10³ to 14 × 10³ with a small polydispersity index. The solution behavior of the free chains has been analyzed in a nonselective solvent, dichloromethane, by small‐angle neutron scattering and dynamic light scattering. These amphiphilic polymers associate in water to form flower‐like micellar structures. Critical micelle concentrations, investigated by fluorescence technique, are in the range of 0.03–0.5 g L^?1 and are dependent on the hydrophilic/lipophilic balance. The structural properties of the aggregates have also been investigated by viscometry. Intrinsic viscosities of these polymers are in the same range as that of the precursors poly(2‐methyl‐2‐oxazoline) (POXZ) and mono‐functionalized polymers. Large viscosity increase corresponding to intermicellar bridging was observed in the vicinity of the micelle overlap concentration. Addition of hydroxypropyl β‐cyclodextrin (HβCD) has dissociated the aggregates and the intrinsic viscosities of the HβCD‐end‐capped chains have become comparable with the ones of POXZ precursor chains. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 2477–2485, 2010     

Synthesis and Pharmacological Evaluation of a Novel Series of 2‐((2‐Aryl thiazol‐4‐yl)methyl)‐5‐(alkyl/alkylnitrile thio)‐1,3,4‐oxadiazole Derivatives as Possible Antifungal Agents

In the present investigation, a novel series of 2‐[(2‐arylthiazol‐4‐yl)methyl]‐5‐(alkyl/alkylnitrile thio)‐1,3,4‐oxadiazole derivatives were synthesized by cyclo‐condensation of 2‐(2‐substituted thiazol‐4‐yl)aceto hydrazide with carbon disulfide followed by S‐alkylation with alkyl halide in dry acetone. All the newly synthesized compounds were characterized by spectral (IR, ¹H NMR, ¹³C NMR, mass, and elemental analysis) methods. The title compounds were screened for in vitro antifungal activity and most of the synthesized compounds show moderate to good antifungal activity.     

Oxidation of 7,8‐diaminotheophylline with lead tetraacetate and reaction of the oxidation product, 6‐cyanoimino‐5‐diazo‐1,3‐dimethylpyrimidine‐2,4‐dione with alcohols or amines

Oxidation of 7,8‐diaminotheophylline (1) with lead tetraacetate in refluxing toluene gave a mixture of 3‐amino‐5,7‐dimethylpyrimido[4,5‐e][1,2,4]triazine‐6,8‐dione ( 2 ) and 6‐cyanoimino‐5‐diazo‐1,3‐dimethylpyrimidine‐2,4‐dione ( 4 ). The latter was transformed to 2 by the reaction with 1‐propanethiol in quantitative yield. The reaction of 4 with methanol, ethanol and 1‐propanol in the presence of rhodium ( II ) acetate gave 5‐alkoxy‐6‐(2‐alkyl‐3‐isoureido)‐1,3‐dimethylpyrimidine‐2,4‐diones ( 7a‐c ). A similar reaction of 4 with alkylamines such as n‐propylamine, n‐butylamine, isobutylamine and n‐hexylamine gave a mixture of 7‐alkyl‐8‐aminotheophyllines ( 8a‐d ) and (5‐alkylamino‐1,3‐dimethyl‐2,4‐dioxopyrimidin‐6‐yl)cyanamides ( 9a‐d ).     

Isocyanide‐based three‐component synthesis of functionalized 5‐alkylimino‐2,5‐dihydrofuran‐3,4‐dicarboxylate and their conversion to substituted furanones

The zwitterionic 1:1 intermediates formed from alkyl isocyanides and acetylenic esters are trapped by alkyl bromides to form 5‐alkylimino‐2,5‐dihydrofuran‐3,4‐dicarboxylate in relatively good yields at room temperature under solventless conditions. Hydrolysis of these compounds by HCl (5%) produced substituted furanones. J. Heterocyclic Chem., (2011).     

Synthesis of alkyl 6‐methyl‐4‐(2‐pyridyl)‐1,2,3,4‐tetrahydro‐2H‐pyrimidine‐2‐one‐5‐carboxylates for evaluation as calcium channel antagonists

The Bigenelli acid catalyzed condensation of 2‐pyridylcarboxaldehyde ( 1 ), urea ( 2 ) and an alkyl acetoacetate ( 3 ) afforded the respective alkyl (Me, Et, i‐Pr, i‐Bu, t‐Bu) 6‐methyl‐4‐(2‐pyridyl)‐1,2,3,4‐tetrahydro‐2H‐pyrimidine‐2‐one‐5‐carboxylates ( 4a‐e ). The most potent calcium channel antagonist ethyl 6‐methyl‐4‐(2‐pyridyl)‐1,2,3,4‐tetrahydro‐2H‐pyrimidine‐2‐one‐5‐carboxylate ( 4b , IC₅₀ = 1.67 × 10^?5 M) wasa much weaker calcium channel antagonist than the reference drug nifedipine (Adalat®, IC₅₀ = 1.40 × 10^?8 M) on guinea pig ileal longitudinal smooth muscle (GPILSM). The alkyl 6‐methyl‐4‐(2‐pyridyl)‐1,2,3,4‐tetrahydro‐2H‐pyrimidine‐2‐one‐5‐carboxylates did not show any inotropic effect on heart since no increase, or decrease, in the contractile force of guinea pig left atrium was observed. These structure activity studies show that the alkyl 6‐methyl‐4‐(2‐pyridyl)‐1,2,3,4‐tetrahydro‐2H‐pyrimidine‐2‐one‐5‐carboxylates ( 4a‐e ) are partial bioisosteres of nifedipine with respect to calcium channel antagonist activity on guinea pig ileal longitudinal smooth muscle (GPILSM).     

4‐Aryl‐3,5‐bis(arylethynyl)aryl‐4H‐1,2,4‐triazoles: Multitasking Skeleton as a Self‐Assembling Unit

The synthesis of a series of 4‐aryl‐3,5‐bis(arylethynyl)aryl‐4H‐1,2,4‐triazoles derivatives is reported and the influence exerted by peripheral substitution on the morphology of the aggregates generated from these 1,2,4‐triazoles is investigated by SEM imaging. The presence of paraffinic side chains results in long fibrillar supramolecular structures, but unsubstituted triazoles self‐assemble into thinner ribbons and needle‐like aggregates. The crystals obtained from methoxy‐substituted triazoles have been utilised to elaborate a model that helps to justify aggregation of the investigated 1,2,4‐triazoles, in which the operation of arrays of C?H???π non‐covalent interactions plays a significant role. The results presented herein demonstrate the ability of simple molecules to behave as multitasking scaffolds with different properties, depending on peripheral substitution. Thus, although 1,2,4‐triazoles without long paraffinic side chains exhibit optical waveguiding behaviour, triazoles endowed with peripheral paraffinic side chains exhibit hexagonal columnar mesomorphism.     

Synthesis of novel N‐alkyl/aryl‐N′‐(4‐arylthiazol‐2‐yl)‐N″‐xylosyl guanidines

The reaction of 2,3,4‐tri‐O‐acetyl‐β‐D‐xylopyranosyl isothiocyanate ( 1 ) and 2‐amino‐4‐arylthiazoles ( 2 ) gave xylosylthioureas 3 . These thiourea derivatives reacted with alkyl/aryl amine in the presence of HgCl₂ to give a new series of N‐alkyl/aryl‐N″‐(4‐arylthiazol‐2‐yl)‐N″‐xylosyl guanidines 4 . Some of the synthesized guanidines were screened for their biological activity. © 2007 Wiley Periodicals, Inc. Heteroatom Chem 18:688–694, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20379     

Synthesis and Herbicidal Activity of 2‐Alkyl(aryl)‐4‐amino‐3‐[alkyl(alkoxy)carbonyl]‐5‐cyano‐6‐[(3‐trifluoromethyl)phenoxy]‐pyridines

To find novel bleaching herbicide lead compounds, a series of novel 2‐alkyl(aryl)‐4‐amino‐3‐[alkyl(alkoxy)carbonyl]‐5‐cyano‐6‐[(3‐trifluoromethyl)phenoxy]‐pyridines was designed and synthesized by the multistep reactions. N,S‐acetal 1 reacted with 2 to obtain multisubstituted pyridines 3 in the presence of zinc nitrate as the catalyst. The target compounds 5a , 5b , 5c , 5d , 5e , 5f , 5g , 5h , 5i , 5j , 5k , 5l were formed by the oxidation of 3 , followed by the substitution with 3‐(trifluoromethyl)phenol in the presence of potassium carbonate. Their structures were confirmed by IR, ¹H NMR, EI‐MS, and elemental analyses. The preliminary bioassays indicated that some of them displayed moderate herbicidal activity against dicotyledonous weed Brassica campestris L at the concentration of 100 mg/L.     

Synthesis and photophysical properties of 2,5,8,11‐tetrakis(5‐hexylthiophen‐2‐yl)tetrathieno[2,3‐a:3′,2′‐c:2′′,3′′‐f:3′′′,2′′′‐h]naphthalene

The title compound, C₅₈H₆₄S₈, has been prepared by Pd‐catalysed direct C—H arylation of tetrathienonaphthalene (TTN) with 5‐hexyl‐2‐iodothiophene and recrystallized by slow evaporation from dichloromethane. The crystal structure shows a completely planar geometry of the TTN core, crystallizing in the monoclinic space group P2₁/c. The structure consists of slipped π‐stacks and the interfacial distance between the mean planes of the TTN cores is 3.456 (5) Å, which is slightly larger than that of the comparable derivative of tetrathienoanthracene (TTA) with 2‐hexylthiophene groups. The packing in the two structures is greatly influenced by both the aromatic core of the structure and the alkyl side chains.     

Synthesis of indole‐4‐carboxaldehydes and 4‐acetylindole from N‐alkyl‐5‐aminoisoquinolinium salts

N‐Alkyl‐5‐aminoisoquinolinium salts ( 8a‐d ) are converted into indole‐4‐carboxaldehydes ( 1a‐c ) on heating in a two phase alkyl acetate‐water system containing an excess of a 2:1 sodium bisulfite‐sodium sulfite mixture. 4‐Acetylindole 1e is prepared in the same way from 1‐methyl‐2‐cyanomethylisoquinolinium bromide 8f .