A molecular balance for measuring aliphatic CH-π interactions

A series of conformationally flexible bicyclic N-arylimides were employed as molecular balances to study the weak aliphatic CH-π interaction between alkyl and arene groups. The formation of intramolecular CH-π interactions in the folded conformers was characterized by X-ray crystallography. The strengths of the interactions were characterized in CDCl(3) by the changes in the folded/unfolded ratios, as measured by (1)H NMR. The CH-π interaction between a methyl group and an aromatic surface was ～1.0 kcal/mol and was easily disrupted or masked by conformational entropy and repulsive steric interactions.     

A theoretical exploration of unexpected amine···π interactions

Counterintuitive amine lone pair···π interactions are computationally revealed by MP2 and CCSD(T) methods, attractive lone pair···π interactions are observed when the lone pair of nitrogen points toward the π system. Symmetry adapted perturbation theory (SAPT) calculations and atoms in molecules (AIM) analyses were performed and the origin of the calculated attractive interaction between nitrogen lone pairs and π rings is discussed. Dispersion effects were revealed to play a crucial role in the attractive lone pair···π interaction.     

A concise review of nanoscopic aspects of bioleaching bacteria–mineral interactions

Bioleaching is a technology for the recovery of metals from minerals by means of microorganisms, which accelerate the oxidative dissolution of the mineral by regenerating ferric ions. Bioleaching processes take place at the interface of bacteria, sulfide mineral and leaching solution. The fundamental forces between a bioleaching bacterium and mineral surface are central to understanding the intricacies of interfacial phenomena, such as bacterial adhesion or detachment from minerals and the mineral dissolution. This review focuses on the current state of knowledge in the colloidal aspect of bacteria–mineral interactions, particularly for bioleaching bacteria. Special consideration is given to the microscopic structure of bacterial cells and the atomic force microscopy technique used in the quantification of fundamental interaction forces at nanoscale.     

A study of oxaliplatin–nucleobase interactions using ion trap electrospray mass spectrometry

Oxaliplatin is an important anti-cancer drug that has been approved for the treatment of colorectal cancer. It is known that oxaliplatin, like other Pt-based drugs, interacts with DNA to form cytotoxic Pt-DNA adducts that disrupt important biological processes such as DNA replication and protein synthesis. Linear ion trap electrospray ionisation mass spectrometry (ESI-MS) was employed to study the interaction of oxaliplatin with DNA nucleobases. It was shown that oxaliplatin formed adducts with all four DNA nucleobases when present individually and in combination in solution. Multiple-stage tandem mass spectrometry (MSⁿ) enabled the fragmentation pathways of each adduct to be established. In addition, proposed structures for each product ion were obtained from the MS data. When all four bases were present together with the drug at near-equal molar concentrations, adducts containing predominantly adenine and guanine were formed, confirming that the drug preferentially binds to these nucleobases. A large molar excess of drug was required to ensure the formation of cytosine and thymine adducts in the presence of adenine and guanine. Even with a large excess of oxaliplatin, only mono-adducts of these nucleobases were observed when all four nucleobases were present. Figure Schematic of a linear ion trap mass spectrometer being used to isolate the diadduct of guanine with oxaliplatin showing the characteristic isotope pattern due to ¹⁹⁴Pt, ¹⁹⁵Pt and ¹⁹⁶Pt.     

A new sequence based encoding for prediction of host–pathogen protein interactions

Pathogen–host interactions are very important to figure out the infection process at the molecular level, where pathogen proteins physically bind to human proteins to manipulate critical biological processes in the host cell. Data scarcity and data unavailability are two major problems for computational approaches in the prediction of pathogen–host interactions. Developing a computational method to predict pathogen–host interactions with high accuracy, based on protein sequences alone, is of great importance because it can eliminate these problems. In this study, we propose a novel and robust sequence based feature extraction method, named Location Based Encoding, to predict pathogen–host interactions with machine learning based algorithms. In this context, we use Bacillus Anthracis and Yersinia Pestis data sets as the pathogen organisms and human proteins as the host model to compare our method with sequence based protein encoding methods, which are widely used in the literature, namely amino acid composition, amino acid pair, and conjoint triad. We use these encoding methods with decision trees (Random Forest, j48), statistical (Bayesian Networks, Naive Bayes), and instance based (kNN) classifiers to predict pathogen–host interactions. We conduct different experiments to evaluate the effectiveness of our method. We obtain the best results among all the experiments with RF classifier in terms of F1, accuracy, MCC, and AUC.     

Nanocellulose–surfactant interactions

Biomass-derived nanomaterials, such as cellulose nanocrystals and nanofibrils, are attractive building blocks for the formulation of foams, emulsions, suspensions and multiphase systems. Depending on their surface chemistry, aspect ratio and crystallinity, nanocelluloses can control the rheology and stability of dispersions; they can also confer robust mechanical properties to composites. Synthetic modification of fibrillar cellulose is an option to achieve chemical compatibility in related systems, in the formation of composites, etc. However, this can also limit the environmental benefits gained from the use of the cellulosic component. Thus, an attractive mean to compatibilize and to further expand the applications of nanocelluloses is through the use of surfactants. The chemical toolbox of surfactants developed over the last 60 years allows for a large versatility while their environmental impact can also be minimized. Furthermore, relatively small amounts of surfactants are sufficient to significantly impact the interfacial forces, which has implications in material development, from the colloidal scale to the macro-scale. In this review we attempt to cover the literature pertaining to the combined uses of surfactants and nanocelluloses. We summarize reports on the incorporation with nanocellulose of nonionic, anionic, amphoteric and cationic surfactants. With the ever-expanding interest in the use of renewable materials in a vast range of applications, we hope to provide insights into the application of surfactants as a tool to tailor the compatibility and the surface chemistry of nanocelluloses.     

A simple chiral recognition system to investigate substituent effects on π-π interactions

We have used a simple molecular recognition system to study substituent effects in aromatic interactions. A series of substituted benzoylleucine diethyl amides with aromatic rings of varying electronic character were crystallized. All of the substituted dimers organized into homochiral dimers in the solid state but with pronounced differences in regard to the orientation of the aromatic rings with respect to each other. However, no homochiral dimerization was observed in the unsubstituted case.     

A calorimetric investigation into copper–arginine and copper–alanine solid state interactions

Complexes of formula CuCl₂ · 2arg and CuCl₂ · 4ala (arg = arginine; ala = alanine) were prepared at room temperature by a solid state route. The metal–amino acid solid state interactions were studied by i.r. spectroscopy and solution calorimetry. For both complexes, participation of the carboxylate group as well as nitrogen in coordination are inferred, based on the i.r. data. For the copper–arginine compound, the calculated thermochemical parameters are: _rH_m = –114.9 ± 1.42 and _fH_m = –1608.3 ± 11.6 kJ mol^–1. For copper–alanine compound, a complete set of thermochemical parameters were calculated: _rH_m = –18.0 ± 0.9; _fH_m = –2490.4 ± 4.3; _DH_m = 597.2 ± 17.7; _MH_m = 771.9 ± 18.7; _gH_m = 627.1 ± 22.3 and D (Cu–L) = 156.8 ± 5.7 kJ mol^–1. Based on _rH_m and dissolution enthalpy values, a stronger intermolecular solid state interaction can be inferred for the arginine complex, than for the alanine one complex, probably due to the formation of intermolecular hydrogen bonds in the former.     

A quantitative study of intrinsic non-covalent interactions within complexes of α-cyclodextrin and benzoate derivatives

A novel deconvolution method for energy-resolved reaction cross sections is applied to determine intrinsic gas-phase dissociation energies for non-covalent α-cyclodextrin host-guest complexes. M06-2X//M06-L/6-31+G(d,p) calculations reproduce the experimental results and enable us to quantify the contribution of intermolecular hydrogen bonding.     

Theoretical investigations on chalcogen-chalcogen interactions: what makes these nonbonded interactions bonding?

To understand the intermolecular interactions between chalcogen centers (O, S, Se, Te), quantum chemical calculations on pairs of model systems were carried out. For the oxygen derivatives, one of the components of the supermolecules consists of dimethyl ether, while the second component is either dimethyl ether (1) or ethynyl methyl ether (2) or methyl cyanate (3). The model calculations were also extended to the sulfur (4-6), selenium (7-9), and tellurium congeners (10-12). The MP2/SDB-cc-pVTZ, 6-311G level of theory was used to derive the geometrical parameters and the global energies of the model systems. A detailed analysis based on symmetry adapted perturbation theory (SAPT) reveals that induction and dispersion forces contribute to the bonding in each case. For 1-3 the electrostatic energy also contributes to the intermolecular bonding, but not for 4-12. The NBO analysis reveals that the interaction in the dimers 1-3 is mainly due to weak hydrogen bonding between methyl groups and chalcogen centers. Similar hydrogen bonding is also found in the case of 4 and to a lesser extent in 5 and 7. For the aggregates with heavier centers the chalcogen-chalcogen interaction dominates, and hydrogen bonding only plays a minor role. Electron-withdrawing groups on the chalcogen centers increase the interaction energy and reduce the intermolecular distance dramatically. The one-electron picture of an interaction between the lone pair of the donor and the chalcogen carbon sigma orbital allows a qualitatively correct reproduction of the observed trend.     

Anion-π interactions—interactions between benzo-crown ether metal cation complexes and counter ions

The loss of X^· radical from [M + Cu + X]⁺ ions (copper reduction) has been studied by the so called in-source fragmentation at higher cone voltage (M = crown ether molecule, X⁻ = counter ion, ClO₄⁻, NO₃⁻, Cl⁻). The loss of X^· has been found to be affected by the presence/lack of aromatic ring poor/rich in electrons. Namely, the loss of X^· occurs with lower efficiency for the [NO₂-B15C5 + Cu + X]⁺ ions than for the [B15C5 + Cu + X]⁺ ions, where NO₂-B15C5 = 3-nitro-benzo-15-crown-5, B15C5 = benzo-15-crown-5. A reasonable explanation is that Anion-π interactions prevent the loss of X^· from the [NO₂-B15C5 + Cu + X]⁺ ions. The presence of the electron-withdrawing NO₂ group causes the aromatic ring to be poor in electrons and thus its enhances its interactions with anions. For the ion containing the aromatic ring enriched in electrons, namely [NH₂-B15C5 + Cu + ClO₄]⁺ where NH₂-B15C5 = 3-amino-benzo-15-crown-5, the opposite situation has been observed. Because of Anion-π repulsion the loss of X^· radical proceeds more readily for [NH₂-B15C5 + Cu + X]⁺ than for [B15C5 + Cu + X]⁺. Iron reduction has also been found to be affected by Anion-π interactions. Namely, the loss of CH₃O^· radical from the ion [B15C5 + Fe + NO₃ + CH₃O]⁺ proceeds more readily than from [NO₂⁻B15C5 + Fe + NO₃ + CH₃O]⁺.     

A study of peptide—Peptide interactions using MALDI ion mobility o-TOF and ESI mass spectrometry

Matrix-assisted laser desorption ionization ion mobility coupled to orthogonal time-of-flight mass spectrometry (MALDI-IM-oTOF MS) is evaluated as a tool for studying non-covalent complex (NCX) formation between peptides. The NCX formed between dynorphin 1-7 and Mini Gastrin I is used as a model system for comparison to previous MALDI experiments (Woods, A. S.; Huestis, M. A. J. Am. Soc. Mass Spectrom. 2001, 12, 88-96). The dynorphin 1-7/Mini Gastrin I complex is stable after more than a ms drift time through the He filled mobility cell. Furthermore, the effects of solution pH on NCX ion signal intensity is measured both by MALDI-IM-MS analysis and by nanoelectrospray mass spectrometry. When compared to the previous MALDI study this work shows that all three techniques give similar results. In addition, fragmentation can be observed from of the non-covalent complex parent ion that occurs prior to TOF mass analysis but after mobility separation, thus providing NCX composition information.     

Research progress in cation-π interactions

Cation-π interaction is a potent intermolecular interaction between a cation and an aromatic system,which has been viewed as a new kind of binding force,as being compared with the classical interactions(e.g. hydrogen bonding,electrostatic and hydrophobic interactions). Cation-π interactions have been observed in a wide range of biological contexts. In this paper,we present an overview of the typical cation-π interactions in biological systems,the experimental and theoretical investigations on cation-π interactions,as well as the research results on cation-π interactions in our group.     

Functioning via host–guest interactions

Molecular recognition is essential for realizing functional supramolecular materials. Non-covalent host–guest interactions are an effective tool to introduce switching and functional properties into materials. This review focuses on the achievement of selective molecular adhesion, self-healing, toughness, and actuation properties. These functions have been achieved by reversible bond formation with cyclodextrins (CDs). Self-healing materials with host–guest interactions involving CDs have been used to achieve redox-responsive healing properties and healing efficiency. Furthermore, the materials, which undergo self-healing by chemical and physical mechanisms, exhibit rapid and efficient self-healing properties under semi-dry conditions. To prepare a supramolecular actuator using host–guest complexes, two approaches have been introduced. The first is the functionalization of a supramolecular gel actuator by changing the cross-linking density, and the second is the functionalization of a topological gel actuator by changing distances between the cross-linking points. Both actuators exhibit contractive bending behavior. This review summarizes advancements within the past ten years in supramolecular materials that function via the chemical mechanism of host–guest interactions and the physical mechanism of the sliding motion of ring molecules.     

Does urea denature hydrophobic interactions?

It is generally accepted that clusters of hydrophobic moieties in water fall apart when urea is added in substantial amounts. We performed atomistic molecular dynamics simulations of hydrophobic solute pairs and found evidence that urea molecules act as "glue" bridging these pairs thereby holding them together. The picture is quite general as it applies to aliphatic-aliphatic as well as aromatic-aromatic interactions. The implications of this finding on the role of urea as a protein denaturant are discussed.     

Putting anion-π interactions into perspective

Supramolecular chemistry is a field of scientific exploration that probes the relationship between molecular structure and function. It is the chemistry of the noncovalent bond, which forms the basis of highly specific recognition, transport, and regulation events that actuate biological processes. The classic design principles of supramolecular chemistry include strong, directional interactions like hydrogen bonding, halogen bonding, and cation-π complexation, as well as less directional forces like ion pairing, π-π, solvophobic, and van der Waals potentials. In recent years, the anion-π interaction (an attractive force between an electron-deficient aromatic π system and an anion) has been recognized as a hitherto unexplored noncovalent bond, the nature of which has been interpreted through both experimental and theoretical investigations. The design of selective anion receptors and channels based on this interaction represent important advances in the field of supramolecular chemistry. The objectives of this Review are 1) to discuss current thinking on the nature of this interaction, 2) to survey key experimental work in which anion-π bonding is demonstrated, and 3) to provide insights into the directional nature of anion-π contact in X-ray crystal structures.     

DNA-cation interactions: quo vadis?

The interactions between double helical DNA and cations, specifically mono- and divalent metal ions, have recently received increased attention. Molecular dynamics simulations, solution NMR, and X-ray crystallography have all shed light on the coordination of ions in the major and minor grooves of DNA. Metal ion interactions may play key roles in the control of DNA conformation and topology, but despite progress in locating the ions and determining their precise binding modes, it remains difficult to figure out just how important ions really are. What have we learned and what remains to be done?     

A calorimetric study of plant–plant and plant–soil interactions of extracts from Ixorhea tschudiana

The effect of the CHCl₃ and MeOH extracts from aerial parts from the Northwestern Argentina endemic species Ixorhea tschudiana Fenzl. on germination of the dicot tomato and the monoct onion and on soil microbial activity was studied by calorimetric and calorespirometric experiments. The CHCl₃ extract inhibited seedling growth of tomato which increased with increasing concentrations. Seeds imbibed with 250 mg dm^?3 extract germinated 24 h later than control and those imbibed with 100 and 500 mg dm^?3 extract. This was reflected in the calculated low specific seedling growth rate (p_SGΔH_B) as determined from calorespirometric experiments. On the other hand, seedlings obtained in 500 mg dm^?3 extract showed shorter and thicker hairy roots than control with significantly higher p_SGΔH_B. Probably, the extract induces inhibition of water uptake by seedling roots. Germination was reduced 50% in onion seeds imbibed with 500 mg dm^?3 CHCl₃ extract which apparently is due to higher rate of imbibition during the first stages as determined for calorimetry. On the other hand, 83 and 250 mg kg^?1 of the MeOH and CHCl₃ extract seem to selectively inhibit the growth of certain microorganisms and to enhance the activity of soil actinomycetes. Two actinobacteria were isolated from soil treated with these concentrations of both extracts: Kocuria sp. and Kocuria rosea; this latter species is known as a keratinolytic agent and seems to degrade complex carbon compounds of the soil and those incorporated by the MeOH extract. Both Kocuria specie seem to be beneficial for the soil converting substrate into biomass and thus I. tschudiana could be used as a soil phytoremediator.     

Is a radical bridge a route to strong exchange interactions in lanthanide complexes? A computational examination

The origin of very strong antiferromagnetic exchange in N(2)(3-) bridged complex, [{[(Me(3)Si)(2)N](2)Gd(THF)}(2)(μ-η(2):η(2)-N(2))](-) (1) has been probed using density functional theory (DFT) combined with molecular orbital (MO) and natural bond orbital (NBO) analysis. The analysis helps us to propose a generic mechanism of coupling for a {2p-4f} class of compounds.