The effect of hydrogen bonding on the π depletion and the π-π stacking interaction.

Non-covalent interactions such as hydrogen bonding and π-π stacking are essential types of interactions governing molecular self-assembly. The π-π stacking ability of aromatic rings depends on the electron density of the π orbitals, which is affected by the electron-withdrawing or electron-donating properties of the substituents. We have here studied the effect of hydrogen bonding on the strength of the π-π stacking interactions by calculating the binding energies at the explicitly correlated Møller-Plesset (MP2-F12) perturbation theory level using polarized triple- quality basis sets.

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.

Synthesis and 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).

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.

Halogenation at the Phenylalanine Residue of Monomethyl Auristatin F Leads to a Favorable / 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.

Exploring the Biochemical Foundations of a Successful GLUT1-Targeting Strategy to BNCT: Chemical Synthesis and Evaluation of the Entire Positional Isomer Library of -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.

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.

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 HO molecules in formation of stable complexes consisted of one nanoparticle surrounded by smaller satellites.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Interheme electron tunneling in cytochrome c oxidase.

Cytochrome c oxidase (CcO) is the terminal enzyme of the respiratory chain that catalyzes respiratory reduction of dioxygen (O(2)) to water in all eukaryotes and many aerobic bacteria. CcO, and its homologs among the heme-copper oxidases, has an active site composed of an oxygen-binding heme and a copper center in the vicinity, plus another heme group that donates electrons to this site. In most oxidoreduction enzymes, electron transfer (eT) takes place by quantum-mechanical electron tunneling.

Magnetizabilities at Self-Interaction-Corrected Density Functional Theory Level.

Using a recent high-quality ab initio coupled cluster benchmark set for magnetizabilities, we assess the performance of a set of density functionals, representing different levels of complexity, from the local density approximation (LDA), via generalized gradient approximations (GGA's) to kinetic energy density including meta-GGA's. The effect of self-interaction correction (SIC) is remarkable and, in most cases, leads to a significant error reduction, revealing the sensitivity of magnetizability toward a physically sound exchange-correlation potential.

WAu12(CO)12?

Calculations suggest that the previously predicted and experimentally observed cluster WAu(12) can be covered by twelve mu(1)-CO molecules. The symmetry remains I(h) and the binding energy per carbonyl is about 100 kJ mol(-1) up to the last one.

Fixing the chirality and trapping the transition state of helicene with atomic metal glue.

By combining the intriguing geometrical properties of two classes of well-established molecules, the metallocenes and the helicenes, we propose a hybrid class of structures-the metallohelicenes. In these, the outer most aryl groups of a specific helicene are glued together by a complexing metal atom. This effectively fixes the chirality of the parent helicene, which otherwise easily undergoes thermal racemization.