An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• –indole amide minor groove binders connected through alkyl or ethoxyethyl linkers were developed by Tecilla et al. [111]. The authors confirmed that these conjugates with tach units, either free or Zn(II)-complexed forms, bind strongly to the minor groove through electrostatic interactions with the

• , thereby reducing strength of electrostatic interactions between the ligands with DNA phosphate backbone [120]. Wilson et al. rationally designed benzimidazole derivatives by keeping pre-organized N-methylbenzimidazole (N-MeBI)-thiophene as central fragment (conjugates 55 and 56, Figure 10) in order to

Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study

• Ahmet Altun,
• Frank Neese and
• Giovanni Bistoni

Beilstein J. Org. Chem. 2018, 14, 919–929, doi:10.3762/bjoc.14.79

• between the DFT-SAPT and DLPNO-CCSD(T) total interaction energies decreases with increasing intermolecular distance. A comparison of electrostatic interactions estimated by LED and DFT-SAPT is shown in the central panel of Figure 5. At the equilibrium geometry, the sum of Eelstat and (the only provides a

• previous sections, the geometric preparation, weak pairs, and perturbative triples do not contribute significantly to the relative stabilities of the different conformers. In all cases, the largest LED terms are electronic preparation and electrostatic interactions at the HF level. This is not surprising

• , considering the strong dipole moments of water and HF and in light of the fact that the electrostatic interaction is well described at the HF level, as shown in the previous section. Interestingly, Eelstat and ΔEe show similar trends, thus highlighting the importance of classical electrostatic interactions in

An uracil-linked hydroxyflavone probe for the recognition of ATP

• Márton Bojtár,
• Péter Zoltán Janzsó-Berend,
• Dávid Mester,
• Dóra Hessz,
• Mihály Kállay,
• Miklós Kubinyi and
• István Bitter

Beilstein J. Org. Chem. 2018, 14, 747–755, doi:10.3762/bjoc.14.63

• a uracil nucleobase to the known 4’-dimethylamino-hydroxyflavone fluorophore. Results: The complexation of this scaffold with ATP is already known. The complex is held together by stacking and electrostatic interactions. To achieve multi-point recognition, we designed the uracil-appended version of

• , 4’-dimethylaminohydroxyflavone) was utilized by Pivovarenko and co-workers in ATP sensing in aqueous solution and in mitochondria [34][44]. DMHF was found to form 1:1 and 1:2 complexes with ATP. The two components were held together by π-stacking and by electrostatic interactions of the positively

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• make a close contact. However, based on their detailed comparative studies between stemless PNA and DNA beacons, the Boston Probes group argued that the quenching was more likely due to hydrophobic and electrostatic interactions between the fluorophore and the quencher. Nevertheless, different

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• surface through electrostatic interactions with the phosphate backbone. However, that is plausible only for highly positive-charged ligands (at least four net positive charges present). 3.3.4. Strong ICD (intensity of ICD band similar or stronger than the CD bands of DNA/RNA): Usually of positive sign

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

• Susanne Huhmann,
• Anne-Katrin Stegemann,
• Kristin Folmert,
• Damian Klemczak,
• Johann Moschner,
• Michelle Kube and
• Beate Koksch

Beilstein J. Org. Chem. 2017, 13, 2869–2882, doi:10.3762/bjoc.13.279

• strong, short C–F bonds and perturb the acidity and basicity of adjacent functional groups. Moreover, these changes may strongly influence hydrogen bonding and electrostatic interactions that are crucial for binding to receptors or, in context of protease stability, enzymes. Thus, when introduced in the

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• binding efficiencies towards pDNA can be easily explained considering that, due to its peculiar conformation, the closer disposition of the negatively charged phosphate groups enables an optimization of the electrostatic interactions with the cationic AmCD. It is also reasonable to assume that the

Binding abilities of a chiral calix[4]resorcinarene: a polarimetric investigation on a complex case of study

• Marco Russo and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2698–2709, doi:10.3762/bjoc.13.268

• observed of purely aliphatic cations; ii) non-specific electrostatic interactions, as accounted for by the lack of inclusion of anions. Furthermore, at least in the case of the p-nitroaniline derivatives, the aliphatic moiety of the guest interacts with the prolinylmethyl groups at the host rim, affecting

What contributes to an effective mannose recognition domain?

• Christoph P. Sager,
• Deniz Eriş,
• Martin Smieško,
• Rachel Hevey and
• Beat Ernst

Beilstein J. Org. Chem. 2017, 13, 2584–2595, doi:10.3762/bjoc.13.255

• ). With the entropically driven sLex interaction, surface waters are displaced to the bulk and penalized by a positive enthalpy term resulting from a desolvation penalty that is not compensated by the newly formed electrostatic interactions (Figure 6) [67]. According to Dunitz [68], the entropy that can

• desolvation are often neglected. Because of the large number of hydroxy groups present in carbohydrate ligands, and the polar amino acid side chains of the lectin binding sites, desolvation generates an essential enthalpic penalty which can hardly be compensated for by the newly formed electrostatic

• interactions [60]. Cabani et al. calculated that the desolvation of an isolated hydroxy group causes an enthalpic penalty of ΔH = 35 kJ/mol, which is slightly reduced by a beneficial entropic term of ΔS = 10 kJ/mol due to the release of solvating water molecules into bulk [61]. As a result, the desolvation

p-tert-Butylthiacalix[4]arenes functionalized by N-(4’-nitrophenyl)acetamide and N,N-diethylacetamide fragments: synthesis and binding of anionic guests

• Alena A. Vavilova and
• Ivan I. Stoikov

Beilstein J. Org. Chem. 2017, 13, 1940–1949, doi:10.3762/bjoc.13.188

• anions are larger in size than cations and therefore have a smaller charge in relation to their radius. It means that the electrostatic interactions for anions binding are weaker than for cations. Anions have various shape and geometry, and the design of receptors that are complementary to a specific

Conformational impact of structural modifications in 2-fluorocyclohexanone

• Francisco A. Martins,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2017, 13, 1781–1787, doi:10.3762/bjoc.13.172

• and σC–H2ax → π*C=S interactions are more stabilizing than σC–H2ax → π*C=C, but they are also accompanied by strong steric and electrostatic interactions (see the high values for both Lewis and non-Lewis terms when Y = O and S compared to CH2). When the X = S and NHeq groups take place, the equatorial

• < S, since the repulsion with the Feq substituent increases in this order. The hypothesis based on steric and electrostatic interactions is supported by the increase of the axial population from Y = CH2 to S, despite the better electron-acceptor ability of the π*C=S in comparison to π*C=O and π*C=C

• the electronic delocalization energies, as well as the Lewis (steric and electrostatic interactions) and non-Lewis (electron delocalization) contributions through the NOSTAR keyword. Chemical shifts and spin–spin coupling constant calculations were also performed at the ωB97X-D/6-311+g(d,p) level. All

Chemical systems, chemical contiguity and the emergence of life

• Terrence P. Kee and
• Pierre-Alain Monnard

Beilstein J. Org. Chem. 2017, 13, 1551–1563, doi:10.3762/bjoc.13.155

• research groups have demonstrated their abilities to induce formation of evolved protocell systems. For instance, they have been shown to be capable of accumulating small molecules on their charged surfaces (electrostatic interactions) [49] or within pores and brines by thermophoresis and convection

2-Methyl-2,4-pentanediol (MPD) boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerization

• Julia Kinzel,
• Daniel F. Sauer,
• Marco Bocola,
• Marcus Arlt,
• Tayebeh Mirzaei Garakani,
• Andreas Thiel,
• Klaus Beckerle,
• Tino Polen,
• Jun Okuda and
• Ulrich Schwaneberg

Beilstein J. Org. Chem. 2017, 13, 1498–1506, doi:10.3762/bjoc.13.148

• distributed MPD molecules as cosolvent [52][53][54][55][56]. The MD calculations (75 ns each) were performed using the AMBER99 force field for the protein and GAFF for MPD cosolvent. The electrostatic interactions were calculated using a 8 Å cut-off and Particle Mesh Ewald [57] for long range electrostatics

Towards open-ended evolution in self-replicating molecular systems

• Herman Duim and
• Sijbren Otto

Beilstein J. Org. Chem. 2017, 13, 1189–1203, doi:10.3762/bjoc.13.118

• enhanced by electrostatic interactions between amino acids residing on the c and g positions of the α-helices. Ghadiri et al. showed that such coiled-coil peptides are capable of self-replication [35]. As depicted in Figure 7, helical polypeptides can act as a template for shorter peptide fragments by

Fluorescent carbon dots from mono- and polysaccharides: synthesis, properties and applications

• Stephen Hill and
• M. Carmen Galan

Beilstein J. Org. Chem. 2017, 13, 675–693, doi:10.3762/bjoc.13.67

• pHs, further supported the proposed electrostatic interactions between DOX and the CDs. Further studies showed initial efficacy of the DOX–CD adduct as a beneficial drug-delivery system, even in animal models. On the other hand, Zhao et al. described an alternative synthesis for N/P-doped CDs

Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications

• Srikala Pangannaya,
• Neethu Padinchare Purayil,
• Shweta Dabhi,
• Venu Mankad,
• Prafulla K. Jha,
• Satyam Shinde and
• Darshak R. Trivedi

Beilstein J. Org. Chem. 2017, 13, 222–238, doi:10.3762/bjoc.13.25

• receptors for anions have been developed based on various modes of interactions such as hydrogen bond and electrostatic interactions which rely on directionality and distance-dependent nature, respectively. Hydrogen bond formation is further tuned by the acidity of protons by virtue of the presence of

Cross-linked cyclodextrin-based material for treatment of metals and organic substances present in industrial discharge waters

• Élise Euvrard,
• Nadia Morin-Crini,
• Coline Druart,
• Justine Bugnet,
• Bernard Martel,
• Cesare Cosentino,
• Virginie Moutarlier and
• Grégorio Crini

Beilstein J. Org. Chem. 2016, 12, 1826–1838, doi:10.3762/bjoc.12.172

• groups and CD cavities, the adsorption mechanism involves four main interactions: ion exchange, electrostatic interactions and precipitation for metal removal, and inclusion complexes for organics removal. In industrial discharge waters, competition effects appeared, especially because of the presence of

• material was initially activated by NaHCO3. Discussion To explain the adsorption performance of polyBTCA-CD, a chemisorption mechanism involving several interactions can occur including ion exchange, electrostatic interactions, inclusion complexation and/or precipitation [3][12][13][14][15][16]. The

• sodium bicarbonate was necessary to enhance metal retention, as also reported by Ducoroy et al. [17], allowing for a removal efficiency for metals higher than 99% for Co2+, Ni2+ and Zn2+, through both electrostatic interactions and ion exchange. Indeed, during the process of polymer synthesis, the cross

Beta-hydroxyphosphonate ribonucleoside analogues derived from 4-substituted-1,2,3-triazoles as IMP/GMP mimics: synthesis and biological evaluation

• Tai Nguyen Van,
• Audrey Hospital,
• Corinne Lionne,
• Lars P. Jordheim,
• Charles Dumontet,
• Christian Périgaud,
• Laurent Chaloin and
• Suzanne Peyrottes

Beilstein J. Org. Chem. 2016, 12, 1476–1486, doi:10.3762/bjoc.12.144

• very close to that of IMP or to the previously characterized inhibitor, UA1776. This may be explained by the presence of a phosphonate chain in all compounds which binds to the protein by electrostatic interactions through the magnesium ion and thus largely contributing to the final score. As the

Stimuli-responsive HBPS-g-PDMAEMA and its application as nanocarrier in loading hydrophobic molecules

• Yongsheng Chen,
• Li Wang,
• Haojie Yu,
• Zain-Ul-Abdin,
• Ruoli Sun,
• Guanghui Jing,
• Rongbai Tong and
• Zheng Deng

Beilstein J. Org. Chem. 2016, 12, 939–949, doi:10.3762/bjoc.12.92

• aggregation behavior of HBPS-g-PDMAEMA The electrostatic interaction is a major factor to influence the behavior of PDMAEMA in aqueous solution. So in this work, the influence of ionic strength, which affects the electrostatic interactions, was studied. In this case, pH was not adjusted and deionized water

• aqueous solution with relatively low concentrations of NaCl, and there was no maximum point. This is because higher concentrations of NaCl lowered the repulsive electrostatic interactions between PDMAEMA chains. So, higher concentrations of NaCl led to smaller aggregation sizes. The change of size was

Supramolecular structures based on regioisomers of cinnamyl-α-cyclodextrins – new media for capillary separation techniques

• Gabor Benkovics,
• Ondrej Hodek,
• Martina Havlikova,
• Zuzana Bosakova,
• Pavel Coufal,
• Milo Malanga,
• Eva Fenyvesi,
• Andras Darcsi,
• Szabolcs Beni and
• Jindrich Jindrich

Beilstein J. Org. Chem. 2016, 12, 97–109, doi:10.3762/bjoc.12.11

• held together by non-covalent interactions, such as electrostatic interactions, coordination bonds, hydrogen bonds, hydrophobic interactions and host–guest interactions [1]. Their formation is spontaneous and reversible by self-assembly of the monomer units. Because of this special non-covalent

Supramolecular polymer assembly in aqueous solution arising from cyclodextrin host–guest complexation

• Jie Wang,
• Zhiqiang Qiu,
• Yiming Wang,
• Li Li,
• Xuhong Guo,
• Duc-Truc Pham,
• Stephen F. Lincoln and
• Robert K. Prud’homme

Beilstein J. Org. Chem. 2016, 12, 50–72, doi:10.3762/bjoc.12.7

• associative forces including hydrogen bonding, coordinate bonding, electrostatic interactions and hydrophobic interactions is ubiquitous in nature. This is exemplified by the use of DNA and RNA complementarity [1][2] and polypeptide helix formation [3][4] to produce three-dimensional structures and materials

Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin

• Waratchada Sangpheak,
• Jintawee Kicuntod,
• Roswitha Schuster,
• Thanyada Rungrotmongkol,
• Peter Wolschann,
• Nawee Kungwan,
• Helmut Viernstein,
• Monika Mueller and
• Piamsook Pongsawasdi

Beilstein J. Org. Chem. 2015, 11, 2763–2773, doi:10.3762/bjoc.11.297

• was truncated within a 12 Å cutoff distance. The particle-mesh of Ewald’s method [64] was used for adequate treatment of the long-range electrostatic interactions with 12 Å cutoff. All bond lengths involving hydrogen atoms were constrained by SHAKE [32]. The coordinates were recorded every 500 steps

Size-controlled and redox-responsive supramolecular nanoparticles

• Raquel Mejia-Ariza,
• Gavin A. Kronig and
• Jurriaan Huskens

Beilstein J. Org. Chem. 2015, 11, 2388–2399, doi:10.3762/bjoc.11.260

• role in controlling the aggregate growth. The attractive supramolecular and repulsive electrostatic interactions constitute a balance of forces in this system at low ionic strengths. At higher ionic strengths, the increased charge screening led to a loss of electrostatic repulsion and therefore to

• . Davis et al. showed the formation of SNPs using attractive electrostatic interactions between positively charged β-cyclodextrin (CD)-containing polymers and negatively charged siRNA at the core [8]. Neutral adamantyl-grafted poly(ethylene glycol) (Ad-PEG) was incorporated at the surface to stabilize

• repulsive electrostatic interactions using a multicomponent system based on a linear, negatively charged polymer. The force balance used in the latter approach was only observed with negatively charged polymers at low ionic strengths, and it is not known whether this balance occurs also for positively

Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

• Chompoonut Rungnim,
• Sarunya Phunpee,
• Manaschai Kunaseth,
• Supawadee Namuangruk,
• Kanin Rungsardthong,
• Thanyada Rungrotmongkol and
• Uracha Ruktanonchai

Beilstein J. Org. Chem. 2015, 11, 2306–2317, doi:10.3762/bjoc.11.251

• on a modified linear response to treat electrostatic interactions with an empirical term treating the dispersion interactions. In this work, the ΔGsolv was considered as polar and non-polar solvation terms. The polar solvation term is evaluated from the Poisson–Boltzmann (PB) solvation method which

• ) was a preferable arrangement. On the other hand, in complex I, the secondary rim is wide enough to support two functional groups of the C-ring. Even though α-MGS has three hydroxy groups, no hydrogen bonding between guest and host molecules was detected. Thus, electrostatic interactions may not be the

• higher than for electrostatic interactions (ΔEele). Through summation of the solvation free energy (ΔGsolv) and the entropy term (TΔS), the predicted binding free energies (ΔGbind) of the inclusion complexes I and II are similar with values of –8.86 ± 3.25 and –9.06 ± 2.87 kcal/mol, respectively. Thus

Efficient synthesis of π-conjugated molecules incorporating fluorinated phenylene units through palladium-catalyzed iterative C(sp²)–H bond arylations

• Fatiha Abdelmalek,
• Fazia Derridj,
• Safia Djebbar,
• Jean-François Soulé and
• Henri Doucet

Beilstein J. Org. Chem. 2015, 11, 2012–2020, doi:10.3762/bjoc.11.218

• dramatically influence both chemical properties and reactivities owing to its electronegativity, size, lipophilicity, and electrostatic interactions. For example, introduction of fluorine into natural products can result in beneficial biological properties [6]. On the other hand, fluorinated π-conjugated