Attractive acceptor-acceptor interactions in self-complementary quadruple hydrogen bonds for molecular self-assembly.

Molecular self-assembly provides the means for creating large supramolecular structures, extending beyond the capability of standard chemical synthesis. To harness the power of self-assembly, it is necessary to understand its driving forces. A potent method is to exploit self-complementary hydrogen bonding, where a molecule interacts with its own copy by suitable positions of hydrogen-bond donor (D) and acceptor (A) groups. With four hydrogen bonds, there are two possible self complementary patterns: the DDAA/AADD and the DADA/ADAD motifs. Of these, the DDAA pattern is usually more stable. The traditional explanation assumes that the secondary interactions between equal groups, that is, between donors (D⋯D) or acceptors (A⋯A), are repulsive. DDAA arrays would then have two, and DADA arrays six repulsive interactions. Here, using high-end quantum chemical analysis, we show that contrary to the traditional explanation, the secondary A⋯A interactions are, in fact, attractive. We revise the model of secondary interactions accordingly.

Synthesis and In Vitro Evaluation of a Set of 6-Deoxy-6-thio-carboranyl d-Glucoconjugates Shed Light on the Substrate Specificity of the GLUT1 Transporter.

Glucose- and sodium-dependent glucose transporters (GLUTs and SGLTs) play vital roles in human biology. Of the 14 GLUTs and 12 SGLTs, the GLUT1 transporter has gained the most widespread recognition because GLUT1 is overexpressed in several cancers and is a clinically valid therapeutic target. We have been pursuing a GLUT1-targeting approach in boron neutron capture therapy (BNCT). Here, we report on surprising findings encountered with a set of 6-deoxy-6-thio-carboranyl d-glucoconjugates. In more detail, we show that even subtle structural changes in the carborane cluster, and the linker, may significantly reduce the delivery capacity of GLUT1-based boron carriers. In addition to providing new insights on the substrate specificity of this important transporter, we reach a fresh perspective on the boundaries within which a GLUT1-targeting approach in BNCT can be further refined.

Magnetically induced ring currents in naphthalene-fused heteroporphyrinoids.

The magnetically induced current density of an intriguing naphthalene-fused heteroporphyrin has been studied, using the quantum-chemical, gauge-including magnetically induced currents (GIMIC) method. The ring-current strengths and current-density pathways for the heteroporphyrin, its Pd complex, and the analogous quinoline-fused heteroporphyrin provide detailed information about their aromatic properties. The three porphyrinoids have similar current-density pathways and are almost as aromatic as free-base porphyrin. Notably, we show that the global ring current makes a branch at three specific points. Thus, the global current is composed of a total of eight pathways that include 22 π-electrons, with no contributions from 18-electron pathways.

Halogenation at the Phenylalanine Residue of Monomethyl Auristatin F Leads to a Favorable cis/trans Equilibrium and Retained Cytotoxicity.

Halogenation can be utilized for the purposes of labeling and molecular imaging, providing a means to, e.g., follow drug distribution in an organism through positron emission tomography (PET) or study the molecular recognition events unfolding by nuclear magnetic resonance (NMR) spectroscopy. For cancer therapeutics, where often highly toxic substances are employed, it is of importance to be able to track the distribution of the drugs and their metabolites in order to ensure minimal side effects. Labeling should ideally have a negligible disruptive effect on the efficacy of a given drug. Using a combination of NMR spectroscopy and cytotoxicity assays, we identify a site susceptible to halogenation in monomethyl auristatin F (MMAF), a widely used cytotoxic agent in the antibody-drug conjugate (ADC) family of cancer drugs, and study the effects of fluorination and chlorination on the physiological solution structure of the auristatins and their cytotoxicity. We find that the cytotoxicity of the parent drug is retained, while the conformational equilibrium is shifted significantly toward the biologically active trans isomer, simultaneously decreasing the concentration of the inactive and potentially disruptive cis isomer by up to 50%. Our results may serve as a base for the future assembly of a multifunctional toolkit for the assessment of linker technologies and exploring bystander effects from the warhead perspective in auristatin-derived ADCs.

Exploring the Biochemical Foundations of a Successful GLUT1-Targeting Strategy to BNCT: Chemical Synthesis and In Vitro Evaluation of the Entire Positional Isomer Library of ortho-Carboranylmethyl-Bearing Glucoconjugates.

Boron neutron capture therapy (BNCT) is a noninvasive binary therapeutic modality applicable to the treatment of cancers. While BNCT offers a tumor-targeting selectivity that is difficult to match by other means, the last obstacles preventing the full harness of this potential come in the form of the suboptimal boron delivery strategies presently used in the clinics. To address these challenges, we have developed delivery agents that target the glucose transporter GLUT1. Here, we present the chemical synthesis of a number of ortho-carboranylmethyl-substituted glucoconjugates and the biological assessment of all positional isomers. Altogether, the study provides protocols for the synthesis and structural characterization of such glucoconjugates and insights into their essential properties, for example, cytotoxicity, GLUT1-affinity, metabolism, and boron delivery capacity. In addition to solidifying the biochemical foundations of a successful GLUT1-targeting approach to BNCT, we identify the most promising modification sites in d-glucose, which are critical in order to further develop this strategy toward clinical use.

Core-Satellite Gold Nanoparticle Complexes Grown by Inert Gas-Phase Condensation.

Spontaneous growth of complexes consisted of a number of individual nanoparticles in a controlled manner, particularly in demanding environments of gas-phase synthesis, is a fascinating opportunity for numerous potential applications. Here, we report the formation of such core-satellite gold nanoparticle structures grown by magnetron sputtering inert gas condensation. Combining high-resolution scanning transmission electron microscopy and computational simulations, we reveal the adhesive and screening role of H2O molecules in formation of stable complexes consisted of one nanoparticle surrounded by smaller satellites. A single layer of H2O molecules, condensed between large and small gold nanoparticles, stabilizes positioning of nanoparticles with respect to one another during milliseconds of the synthesis time. The lack of isolated small gold nanoparticles on the substrate is explained by Brownian motion that is significantly broader for small-size particles. It is inferred that H2O as an admixture in the inert gas condensation opens up possibilities of controlling the final configuration of the different noble metal nanoparticles.

Addressing the Biochemical Foundations of a Glucose-Based "Trojan Horse"-Strategy to Boron Neutron Capture Therapy: From Chemical Synthesis to In Vitro Assessment.

Boron neutron capture therapy (BNCT) for cancer is on the rise worldwide due to recent developments of in-hospital neutron accelerators which are expected to revolutionize patient treatments. There is an urgent need for improved boron delivery agents, and herein we have focused on studying the biochemical foundations upon which a successful GLUT1-targeting strategy to BNCT could be based. By combining synthesis and molecular modeling with affinity and cytotoxicity studies, we unravel the mechanisms behind the considerable potential of appropriately designed glucoconjugates as boron delivery agents for BNCT. In addition to addressing the biochemical premises of the approach in detail, we report on a hit glucoconjugate which displays good cytocompatibility, aqueous solubility, high transporter affinity, and, crucially, an exceptional boron delivery capacity in the in vitro assessment thereby pointing toward the significant potential embedded in this approach.

Dispersion forces drive water oxidation in molecular ruthenium catalysts.

Rational design of artificial water-splitting catalysts is central for developing new sustainable energy technology. However, the catalytic efficiency of the natural light-driven water-splitting enzyme, photosystem II, has been remarkably difficult to achieve artificially. Here we study the molecular mechanism of ruthenium-based molecular catalysts by integrating quantum chemical calculations with inorganic synthesis and functional studies. By employing correlated ab initio calculations, we show that the thermodynamic driving force for the catalysis is obtained by modulation of π-stacking dispersion interactions within the catalytically active dimer core, supporting recently suggested mechanistic principles of Ru-based water-splitting catalysts. The dioxygen bond forms in a semi-concerted radical coupling mechanism, similar to the suggested water-splitting mechanism in photosystem II. By rationally tuning the dispersion effects, we design a new catalyst with a low activation barrier for the water-splitting. The catalytic principles are probed by synthesis, structural, and electrochemical characterization of the new catalyst, supporting enhanced water-splitting activity under the examined conditions. Our combined findings show that modulation of dispersive interactions provides a rational catalyst design principle for controlling challenging chemistries.

Increasing the Potential of the Auristatin Cancer-Drug Family by Shifting the Conformational Equilibrium.

Monomethyl auristatin E and monomethyl auristatin F are widely used cytotoxic agents in antibody-drug conjugates (ADCs), a group of promising cancer drugs. The ADCs specifically target cancer cells, releasing the auristatins inside, which results in the prevention of mitosis. The auristatins suffer from a potentially serious flaw, however. In solution, the molecules exist in an equal mixture of two conformers, cis and trans. Only the trans-isomer is biologically active and the isomerization process, i.e., the conversion of cis to trans is slow. This significantly diminishes the efficiency of the drugs and their corresponding ADCs, and perhaps more importantly, raises concerns over drug safety. The potency of the auristatins would be enhanced by decreasing the amount of the biologically inactive isomer, either by stabilizing the trans-isomer or destabilizing the cis-isomer. Here, we follow the computer-aided design strategy of shifting the conformational equilibrium and employ high-level quantum chemical modeling to identify promising candidates for improved auristatins. Coupled cluster calculations predict that a simple halogenation in the norephedrine/phenylalanine residues shifts the isomer equilibrium almost completely toward the active trans-conformation, due to enhanced intramolecular interactions specific to the active isomer.

Acetyl Group Migration across the Saccharide Units in Oligomannoside Model Compound.

Acetylated oligosaccharides are common in nature. While they are involved in several biochemical and biological processes, the role of the acetyl groups and the complexity of their migration has largely gone unnoticed. In this work, by combination of organic synthesis, NMR spectroscopy and quantum chemical modeling, we show that acetyl group migration is a much more complex phenomenon than previously known. By use of synthetic oligomannoside model compounds, we demonstrate, for the first time, that the migration of acetyl groups in oligosaccharides and polysaccharides may not be limited to transfer within a single monosaccharide moiety, but may also involve migration over a glycosidic bond between two different saccharide units. The observed phenomenon is not only interesting from the chemical point of view, but it also raises new questions about the potential biological role of acylated carbohydrates in nature.

Conformational Selection of Dimethylarginine Recognition by the Survival Motor Neuron Tudor Domain.

Tudor domains bind to dimethylarginine (DMA) residues, which are post-translational modifications that play a central role in gene regulation in eukaryotic cells. NMR spectroscopy and quantum calculations are combined to demonstrate that DMA recognition by Tudor domains involves conformational selection. The binding mechanism is confirmed by a mutation in the aromatic cage that perturbs the native recognition mode of the ligand. General mechanistic principles are delineated from the combined results, indicating that Tudor domains utilize cation-π interactions to achieve ligand recognition.

New insight on the structural features of the cytotoxic auristatins MMAE and MMAF revealed by combined NMR spectroscopy and quantum chemical modelling.

Antibody-drug conjugates (ADCs) are emerging as a promising class of selective drug delivery systems in the battle against cancer and other diseases. The auristatins monomethyl auristatin E (MMAE) and monomethyl auristatin F (MMAF) appear as the cytotoxic drug in almost half of the state-of-the-art ADCs on the market or in late stage clinical trials. Here, we present the first complete NMR spectroscopic characterisation of these challenging molecules, and investigate their structural properties by a combined NMR and quantum chemical modelling approach. We find that in solution, half of the drug molecules are locked in an inactive conformation, severely decreasing their efficiency, and potentially increasing the risk of side-effects. Furthermore, we identify sites susceptible to future modification, in order to potentially improve the performance of these drugs.

Terminal Electron-Proton Transfer Dynamics in the Quinone Reduction of Respiratory Complex I.

Complex I functions as a redox-driven proton pump in aerobic respiratory chains. By reducing quinone (Q), complex I employs the free energy released in the process to thermodynamically drive proton pumping across its membrane domain. The initial Q reduction step plays a central role in activating the proton pumping machinery. In order to probe the energetics, dynamics, and molecular mechanism for the proton-coupled electron transfer process linked to the Q reduction, we employ here multiscale quantum and classical molecular simulations. We identify that both ubiquinone (UQ) and menaquinone (MQ) can form stacking and hydrogen-bonded interactions with the conserved Q-binding-site residue His-38 and that conformational changes between these binding modes modulate the Q redox potentials and the rate of electron transfer (eT) from the terminal N2 iron-sulfur center. We further observe that, while the transient formation of semiquinone is not proton-coupled, the second eT process couples to a semiconcerted proton uptake from conserved tyrosine (Tyr-87) and histidine (His-38) residues within the active site. Our calculations indicate that both UQ and MQ have low redox potentials around -260 and -230 mV, respectively, in the Q-binding site, respectively, suggesting that release of the Q toward the membrane is coupled to an energy transduction step that could thermodynamically drive proton pumping in complex I.

Dynamic stark control of torsional motion by a pair of laser pulses.

The torsional motion of a molecule composed of two substituted benzene rings, linked by a single bond, is coherently controlled by a pair of strong (3×10^{13} W cm^{-2}), nonresonant (800 nm) 200-fs-long laser pulses-both linearly polarized perpendicular to the single-bond axis. If the second pulse is sent at the time when the two benzene rings rotate toward (away from) each other the amplitude of the torsion is strongly enhanced (reduced). The torsional motion persists for more than 150 ps corresponding to approximately 120 torsional oscillations. Our calculations show that the key to control is the strong transient modification of the natural torsional potential by the laser-induced dynamic Stark effect.

Intramolecular halogen-halogen bonds?

By analysing the properties of the electron density in the structurally simple perhalogenated ethanes, X3C-CY3 (X, Y = F, Cl), a previously overlooked non-covalent attraction between halogens attached to opposite carbon atoms is found. Quantum chemical calculations extrapolated towards the full solution of the Schrödinger equation reveal the complex nature of the interaction. When at least one of the halogens is a chlorine, the strength of the interaction is comparable to that of hydrogen bonds. Further analysis shows that the bond character is quite different from standard non-covalent halogen bonds and hydrogen bonds; no bond critical points are found between the halogens, and the σ-holes of the halogens are not utilised for bonding. Thus, the nature of the intramolecular halogen···halogen bonding studied here appears to be of an unusually strong van der Waals type.

Ab initio, density functional theory, and semi-empirical calculations.

This chapter introduces the theory and applications of commonly used methods of electronic structure calculation, with particular emphasis on methods applicable for modelling biomolecular systems. This chapter is sectioned as follows. We start by presenting ab initio methods, followed by a treatment of density functional theory (DFT) and some recent advances in semi-empirical methods. Treatment of excited states as well as basis sets are also presented.

Chemical bonding in supermolecular flowers.

We report here a systematic study on the ability of molecular cages to bind (transition) metals. Starting from the superferrocenophane we investigate the incorporation of first-row transition metal (Sc-Zn) and alkaline-earth metal (Mg, Ca) double cations into these supermetallocenophane (super[5]phane) cages, and compare them with the corresponding metallocenes (Inorg. Chim. Acta, 2007, 360, 179). Moreover, we also investigate the binding of neutral and double-cationic metals inside supermetallocyclophane (super[6]phane) cages. The heterolytic and homolytic associations show preferences for different metals, and new metal-containing cages are proposed that should be viable candidates for synthesis.

Density functional study on UV/VIS spectra of copper-protein active sites: the effect of mutations.

UV/VIS Electron excitation spectra have been computed for large, realistic model systems of the blue copper protein family. Fully quantum-chemical calculations at the density-functional theory level employing polarized triple-ζ basis sets have been performed on systems of over 120 atoms, without symmetry. Different mutants, with the ligating methionine of the wild type Cu center exchanged for histidine (M121H) and glutamine (M121Q), have been investigated in order to obtain insight about how the influence of the exact surrounding milieu of the Cu-atom affects the computed spectrum. With sufficiently large model sizes, inclusion of the environment by using continuum solvation models do not change the spectra significantly. More direct and rigorous treatments are needed to reliably assess the effect of the surrounding protein on the electronic structure of the active sites.

Control and femtosecond time-resolved imaging of torsion in a chiral molecule.

We study how the combination of long and short laser pulses can be used to induce torsion in an axially chiral biphenyl derivative (3,5-difluoro-3',5'-dibromo-4'-cyanobiphenyl). A long, with respect to the molecular rotational periods, elliptically polarized laser pulse produces 3D alignment of the molecules, and a linearly polarized short pulse initiates torsion about the stereogenic axis. The torsional motion is monitored in real-time by measuring the dihedral angle using femtosecond time-resolved Coulomb explosion imaging. Within the first 4 picoseconds (ps), torsion occurs with a period of 1.25 ps and an amplitude of 3° in excellent agreement with theoretical calculations. At larger times, the quantum states of the molecules describing the torsional motion dephase and an almost isotropic distribution of the dihedral angle is measured. We demonstrate an original application of covariance analysis of two-dimensional ion images to reveal strong correlations between specific ejected ionic fragments from Coulomb explosion. This technique strengthens our interpretation of the experimental data.

Subtle effects control the polymerisation mechanism in α-diimine iron catalysts.

α-diimine iron complexes have been suggested to catalyse polymerisation via two distinct pathways, depending on the spin state of the iron complex. Here, we study a typical complex of this family, (R'')[N,N]FeCl(2), with [N,N] = Cy-N=CR''-CR''=N-Cy (Cy = cyclohexyl, R'' = PhF (para-fluorophenyl), PhOMe (para-methoxyphenyl), PhNMe(2) (para-dimethylaminophenyl). With R'' = PhF, PhOMe, polymerisation proceeds as a catalytic chain transfer (CCT) mechanism, with R'' = PhNMe(2), the polymerisation follows an atom transfer radical polymerisation (ATRP) pathway. Contrary to previous suggestions, we show that the spin-states of the complexes involved are not affected by the R'' group. Instead, the different behaviour arises from a subtle interplay between the electron-withdrawing or donating character of the reasonably distant phenyl substituent and the iron centre, and small but crucial differences in the reorganisation energies affected during the reactions.