Impact of Deuteration and Temperature on Furan Ring Dynamics.

Despite significant progress in conformational analysis of cyclic molecules, the number of computational studies is still limited while most of that available in the literature data have been obtained long time ago with outdated methods. In present research, we have studied temperature driven conformational changes of the furan ring at three different temperatures. Additionally, the effect of deuteration on the ring dynamics is discussed; in addition, the aromaticity indices following the Bird and HOMA schemes are computed along all trajectories. Our ab initio molecular dynamic simulations revealed that deuteration has changed the furan ring dynamics and the obvious consequences; in addition, the shape and size of molecule are expected to be different.

Mechanochemical disulfide reduction reveals imprints of noncovalent sulfuroxygen chalcogen bonds in protein-inspired mimics in aqueous solution.

The surprisingly rich chemistry of mechanically activated cleavage of disulfide bonds has been uncovered only recently. Using a disulfide protein mimic together with Cleland's reagent (DTT) as the attacking nucleophile in aqueous solution, our isotensional ab initio simulations add another surprise to the list. They unveil that noncovalent chalcogen-chalcogen 1,5-type SO interactions involving the S-S bridge and γ-carbonyl O are controlling the mechanochemical reactivity of disulfides at very low forces, thus adding a third reactivity regime to the hitherto known ones. In stark contrast to what is found in aqueous solution, no such chalcogen bonding arrangements are observed in the gas phase, which supports the conclusion that water plays a crucial role in stabilizing preferred conformations that support noncovalent SO bonds. These findings open the door to investigate chalcogen bonding in the realm of proteins using single-molecule force spectroscopy.

About the Aromaticity of symm-Triaminotrinitrobenzene.

Aromaticity and structural features of the isolated symm-triaminotrinitrobenzene (TATB) were examined using the nonempirical ab initio quantum chemical method and molecular dynamics at the Car-Parrinello level. Different criteria of the aromaticity were combined with the study of conformational flexibility of molecule and analysis of the electron density distribution. It was found that the cooperative effect of the resonance-assisted hydrogen bonds results in the ultimate decreasing aromaticity of the benzene ring in TATB. Values of the HOMA index indicate that it could be classified as low-aromatic in equilibrium state at zero temperature but completely nonaromatic at room temperature. An extremely high flexibility of the molecule is also not typical for aromatic rings. The electron delocalization in H-bonded O═N-C═C-N-H quasi-aromatic rings was found to be greater than that in the benzene ring of TATB.

Unclicking the Click: Metal-Assisted Mechanochemical Cycloreversion of Triazoles Is Possible.

The mechanochemical cycloreversion of 1,2,3-triazole compounds, which serve as unusually stable building blocks in materials and biomolecular chemistry as a result of mild "click chemistry", remains puzzling. We show that the hitherto discussed straight-forward retro-click mechanism of the 1,4-disubstituted isomer, even if CuI catalyzed, can be ruled out in view of more favorable activation free energies of destructive pathways. In stark contrast, the 1,5-regioiomer can undergo cycloreversion under rather mild mechanochemical conditions owing to its favorable response to the external force in conjunction with standard RuII catalysis.

Unexpected mechanochemical complexity in the mechanistic scenarios of disulfide bond reduction in alkaline solution.

The reduction of disulfides has a broad importance in chemistry, biochemistry and materials science, particularly those methods that use mechanochemical activation. Here we show, using isotensional simulations, that strikingly different mechanisms govern disulfide cleavage depending on the external force. Desolvation and resolvation processes are found to be crucial, as they have a direct impact on activation free energies. The preferred pathway at moderate forces, a bimolecular SN2 attack of OH- at sulfur, competes with unimolecular C-S bond rupture at about 2 nN, and the latter even becomes barrierless at greater applied forces. Moreover, our study unveils a surprisingly rich reactivity scenario that also includes the transformation of concerted SN2 reactions into pure bond-breaking processes at specific forces. Given that these forces are easily reached in experiments, these insights will fundamentally change our understanding of mechanochemical activation in general, which is now expected to be considerably more intricate than previously thought.

Force-Induced Reversal of ß-Eliminations: Stressed Disulfide Bonds in Alkaline Solution.

Understanding the impact of tensile forces on disulfide bond cleavage is not only crucial to the breaking of cross-linkers in vulcanized materials such as strained rubber, but also to the regulation of protein activity by disulfide switches. By using ab initio simulations in the condensed phase, we investigated the response of disulfide cleavage by ß-elimination to mechanical stress. We reveal that the rate-determining first step of the thermal reaction, which is the abstraction of the ß-proton, is insensitive to external forces. However, forces larger than about 1 nN were found to reshape the free-energy landscape of the reaction so dramatically that a second channel is created, where the order of the reaction steps is reversed, turning ß-deprotonation into a barrier-free follow-up process to C-S cleavage. This transforms a slow and force-independent process with second-order kinetics into a unimolecular reaction that is greatly accelerated by mechanical forces.

The effect of tensile stress on the conformational free energy landscape of disulfide bonds.

Disulfide bridges are no longer considered to merely stabilize protein structure, but are increasingly recognized to play a functional role in many regulatory biomolecular processes. Recent studies have uncovered that the redox activity of native disulfides depends on their C-C-S-S dihedrals, χ2 and χ'2. Moreover, the interplay of chemical reactivity and mechanical stress of disulfide switches has been recently elucidated using force-clamp spectroscopy and computer simulation. The χ2 and χ'2 angles have been found to change from conformations that are open to nucleophilic attack to sterically hindered, so-called closed states upon exerting tensile stress. In view of the growing evidence of the importance of C-C-S-S dihedrals in tuning the reactivity of disulfides, here we present a systematic study of the conformational diversity of disulfides as a function of tensile stress. With the help of force-clamp metadynamics simulations, we show that tensile stress brings about a large stabilization of the closed conformers, thereby giving rise to drastic changes in the conformational free energy landscape of disulfides. Statistical analysis shows that native TDi, DO and interchain Ig protein disulfides prefer open conformations, whereas the intrachain disulfide bridges in Ig proteins favor closed conformations. Correlating mechanical stress with the distance between the two a-carbons of the disulfide moiety reveals that the strain of intrachain Ig protein disulfides corresponds to a mechanical activation of about 100 pN. Such mechanical activation leads to a severalfold increase of the rate of the elementary redox S(N)2 reaction step. All these findings constitute a step forward towards achieving a full understanding of functional disulfides.

The Janus-faced role of external forces in mechanochemical disulfide bond cleavage.

Recent force microscopy measurements on the mechanically activated cleavage of a protein disulfide bond through reaction with hydroxide ions revealed that for forces greater than 0.5 nN, the acceleration of the reaction rate is substantially reduced. Here, using ab initio simulations, we trace this 'reactivity switch' back to a dual role played by the mechanical force, which leads to antagonistic effects. On the one hand, the force performs work on the system, and thereby accelerates the reaction. On the other hand, the force also induces a conformational distortion that involves the S-S-C-C dihedral angle, which drives the disulfide into a conformation that is shielded against nucleophilic attack because of steric hindrance. The discovery of force-induced conformational changes that steer chemical reactivity provides a new key concept that is expected to be relevant beyond this specific case, for example in understanding how 'disulfide switches' regulate protein function and for the rational design of mechanoresponsive materials.

Entropy versus aromaticity in the conformational dynamics of aromatic rings.

Comparison of the results of Car-Parrinello molecular dynamics simulations of isolated benzene, pyrimidine and 1,2,4-triazine molecules reveals that the unusually low population of planar geometry of the benzene ring is caused by entropy effects despite its high aromaticity. The decrease in symmetry of the molecule results in smaller changes in entropy and Gibbs free energy due to out-of-plane deformations of the ring, leading to an increase in the population of planar geometry of the ring. This leads to differences in the topology of potential energy and Gibbs free energy surfaces.

On the Intramolecular Hydrogen Bond in Solution: Car-Parrinello and Path Integral Molecular Dynamics Perspective.

The issue of the symmetry of short, low-barrier hydrogen bonds in solution is addressed here with advanced ab initio simulations of a hydrogen maleate anion in different environments, starting with the isolated anion, going through two crystal structures (sodium and potassium salts), then to an aqueous solution, and finally in the presence of counterions. By Car-Parrinello and path integral molecular dynamics simulations, it is demonstrated that the position of the proton in the intramolecular hydrogen bond of an aqueous hydrogen maleate anion is entirely related to the solvation pattern around the oxygen atoms of the intramolecular hydrogen bond. In particular, this anion has an asymmetric hydrogen bond, with the proton always located on the oxygen atom that is less solvated, owing to the instantaneous solvation environment. Simulations of water solutions of hydrogen maleate ion with two different counterions, K(+) and Na(+), surprisingly show that the intramolecular hydrogen-bond potential in the case of the Na(+) salt is always asymmetric, regardless of the hydrogen bonds to water, whereas for the K(+) salt, the potential for H motion depends on the location of the K(+). It is proposed that repulsion by the larger and more hydrated K(+) is weaker than that by Na(+) and competitive with solvation by water.

Proton-transfer dynamics in the (HCO3-)2 dimer of KHCO3 from Car-Parrinello and path-integrals molecular dynamics calculations.

The proton motion in the (HCO(3)(-))(2) dimer of KHCO(3) at 298 K has been studied with Car-Parrinello molecular dynamics (CPMD) and path-integrals molecular dynamics (PIMD) simulations. According to earlier neutron diffraction studies at 298 K hydrogen is disordered and occupies two positions with an occupancy ratio of 0.804/0.196. A simulation with only one unit cell is not sufficient to reproduce the disorder of the protons found in the experiments. The CPMD results with four cells, 0.783/0.217, are in close agreement with experiment. The motion of the two protons along the O...O bridge is highly correlated inside one dimer, but strongly uncoupled between different dimers. The present results support a mechanism for the disorder which involves proton transfer from donor to acceptor and not orientational disordering of the entire dimer. The question of simultaneous or successive proton transfer in the two hydrogen bonds in the dimer remains unanswered. During the simulation situations with almost simultaneous proton transfer with a time gap of around 1 fs were observed, as well as successive processes where first one proton is transferred and then the second one with a time gap of around 20 fs. The calculated vibrational spectrum is in good agreement with the experimental IR spectrum, but a slightly different assignment of the bands is indicated by the present simulations.

Proton Transfer Dynamics in Crystalline Maleic Acid from Molecular Dynamics Calculations.

The crystal structure of maleic acid, the cis conformer of HOOC-CH═CH-COOH has been investigated by Car-Parrinello molecular dynamics (CPMD) and path integral molecular dynamics (PIMD) simulations. The interesting feature of this compound, compared to the trans conformer, fumaric acid, is that both intra- and intermolecular hydrogen bonds are present. CPMD simulations at 100 K indicate that the energy barrier height for proton transfer is too high for thermal jumps over the barrier in both the intra- and intermolecular hydrogen bonds. Dynamics at 295 K reveal that the occupancy ratio of the proton distribution in both the intra- and intermolecular hydrogen bonds is 0.96/0.04. The time lag between the proton transfers in the intra- and intermolecular hydrogen bonds is in the range of 2-9 fs. This is slightly shorter than the time lag obtained previously for fumaric acid, where only intermolecular hydrogen bonds are present. It is also interesting to notice that in most cases the proton transfer process starts in the intramolecular hydrogen bond and subsequently follows in the intermolecular hydrogen bond. Vibrational spectra of the investigated system and its deuterated analogs HOOC-CH═CH-COOD and DOOC-CH═CH-COOD have been calculated and compared with experimental data.