Does Silica Surface Catalyse Peptide Bond Formation? New Insights from First‐Principles Calculations

The role that silica surface could have played in prebiotic chemistry as a catalyst for peptide bond formation has been addressed at the B3LYP/6-31+G(d,p) level for a model reaction involving glycine and ammonia on a silica cluster mimicking an isolated terminal silanol group present at the silica surface. Hydrogen-bond complexation between glycine and the silanol is followed by the formation of the mixed surface anhydride Si(surf)-O-C(=O)-R, which has been suggested in the literature to activate the C=O bond towards nucleophilic attack by a second glycine molecule, here simulated by the simpler NH3 molecule. However, B3LYP/6-31+G(d,p) calculations show that formation of the surface mixed anhydride Si(surf)-O-C(=O)-R is disfavoured (delta(r)G298 approximately 6 kcal mol(-1)), and that the surface bond only moderately lowers the free-energy barrier of the nucleophilic attack responsible for peptide bond formation (deltaG298(double dagger) approximately 48 kcal mol(-1)) in comparison with the uncatalysed reaction (deltaG298(double dagger) approximately 52 kcal mol(-1)). A further decrease of the free-energy barrier of peptide bond formation (deltaG298(double dagger) approximately 41 kcal mol(-1)) is achieved by a single water molecule close to the reaction centre acting as a proton-transfer helper in the activated complex. A possible role of strained silica surface defects on the formation of the surface mixed anhydride Si(surf)-O-C(=O)-R has also been addressed.     

Intramolecular Hydrogen Bonds in Low‐Molecular‐Weight Polyethylene Glycol

We used static DFT calculations to analyze, in detail, the intramolecular hydrogen bonds formed in low‐molecular‐weight polyethylene glycol (PEG) with two to five repeat subunits. Both red‐shifted O?H???O and blue‐shifting C?H???O hydrogen bonds, which control the structural flexibility of PEG, were detected. To estimate the strength of these hydrogen bonds, the quantum theory of atoms in molecules was used. Car–Parrinello molecular dynamics simulations were used to mimic the structural rearrangements and hydrogen‐bond breaking/formation in the PEG molecule at 300 K. The time evolution of the H???O bond length and valence angles of the formed hydrogen bonds were fully analyzed. The characteristic hydrogen‐bonding patterns of low‐molecular‐weight PEG were described with an estimation of their lifetime. The theoretical results obtained, in particular the presence of weak C?H???O hydrogen bonds, could serve as an explanation of the PEG structural stability in the experimental investigation.     

Dynamical Dimension to the Hofmeister Series: Insights from First‐Principles Simulations

A systematic characterization of the competing kosmotropic and chaotropic effects of a series of divalent salts on the aqueous H‐bonding structure by means of first‐principles molecular dynamics simulations is presented. The structural properties are quantified by means of experimental and computed ¹H NMR chemical shifts, whereby the local environments of cations and anions can be discriminated. Complementary to the well‐established structural features, a dynamical aspect is added to the concept of kosmotropes and chaotropes. The H‐bond dynamics, quantified in terms of the H‐bonding autocorrelation functions, shows a good correlation with the structural kosmotropic and chaotropic modifications, which are commonly referred to as the Hofmeister series. The considerably enhanced (reduced) fluctuations of the H‐bonding network in the hydration shells around the anions (cations) are a complementary dynamical dimension to the concept of kosmotropic/chaotropic behavior of solvated ions.     

Transport Processes at α‐Quartz–Water Interfaces: Insights from First‐Principles Molecular Dynamics Simulations

Car–Parrinello molecular dynamics (CP–MD) simulations are performed at high temperature and pressure to investigate chemical interactions and transport processes at the α‐quartz–water interface. The model system initially consists of a periodically repeated quartz slab with O‐terminated and Si‐terminated (1000) surfaces sandwiching a film of liquid water. At a temperature of 1000 K and a pressure of 0.3 GPa, dissociation of H₂O molecules into H⁺ and OH^? is observed at the Si‐terminated surface. The OH^? fragments immediately bind chemically to the Si‐terminated surface while Grotthus‐type proton diffusion through the water film leads to protonation of the O‐terminated surface. Eventually, both surfaces are fully hydroxylated and no further chemical reactions are observed. Due to the confinement between the two hydroxylated quartz surfaces, water diffusion is reduced by about one third in comparison to bulk water. Diffusion properties of dissolved SiO₂ present as Si(OH)₄ in the water film are also studied. We do not observe strong interactions between the hydroxylated quartz surfaces and the Si(OH)₄ molecule as would have been indicated by a substantial lowering of the Si(OH)₄ diffusion coefficient along the surface. No spontaneous dissolution of quartz is observed. To study the mechanism of dissolution, constrained CP–MD simulations are done. The associated free energy profile is calculated by thermodynamic integration along the reaction coordinate. Dissolution is a stepwise process in which two Si? O bonds are successively broken. Each bond breaking between a silicon atom at the surface and an oxygen atom belonging to the quartz lattice is accompanied by the formation of a new Si? O bond between the silicon atom and a water molecule. The latter loses a proton in the process which eventually leads to protonation of the oxygen atom in the cleaved quartz Si? O bond. The final solute species is Si(OH)₄.     

Probing Polyoxometalate–Protein Interactions Using Molecular Dynamics Simulations

The molecular interactions between the Ce^IV‐substituted Keggin anion [PW₁₁O₃₉Ce(OH₂)₄]^3? ( CeK ) and hen egg‐white lysozyme (HEWL) were investigated by molecular dynamics simulations. The analysis of CeK was compared with the Ce^IV‐substituted Keggin dimer [(PW₁₁O₃₉)₂Ce]^10? ( CeK₂ ) and the Zr^IV‐substituted Lindqvist anion [W₅O₁₈Zr(OH₂)(OH)]^3? ( ZrL ) to understand how POM features such as shape, size, charge, or type of incorporated metal ion influence the POM???protein interactions. Simulations revealed two regions of the protein in which the CeK anion interacts strongly: cationic sites formed by Arg21 and by Arg45 and Arg68. The POMs chiefly interact with the side chains of the positively charged (arginines, lysines) and the polar uncharged residues (tyrosines, serines, aspargines) via electrostatic attraction and hydrogen bonding with the oxygen atoms of the POM framework. The CeK anion shows higher protein affinity than the CeK₂ and ZrL anions, because it is less hydrophilic and it has the right size and shape for establishing interactions with several residues simultaneously. The larger, more negatively charged CeK₂ anion has a high solvent‐accessible surface, which is sub‐optimal for the interaction, while the smaller ZrL anion is highly hydrophilic and cannot efficiently interact with several residues simultaneously.     

Coadsorbate‐Induced Reversal of Solid–Liquid Interface Dynamics

Coadsorbed anions are well‐known to influence surface reactivity and dynamics at solid–liquid interfaces. Here we demonstrate that the chemical nature of these spectator species can entirely determine the microscopic dynamic behavior. Quantitative in situ video‐STM data on the surface diffusion of adsorbed sulfur atoms on Cu(100) electrodes in aqueous solution covered by bromide and chloride spectators, respectively, reveal in both cases a strong exponential potential dependence, but with opposite sign. This reversal is highly surprising in view of the isostructural adsorbate arrangement in the two systems. Detailed DFT studies suggest an anion‐induced difference in the sulfur diffusion mechanism, specifically an exchange diffusion on the Br‐covered surface. Experimental evidence for the latter is provided by the observation of Cu vacancy formation in the Br system, which can be rationalized by a side reaction of the sulfur exchange diffusion.     

Exploring the Molecular Structure of Imidazolium–Silica‐Based Nanoparticle Networks by Combining Solid‐State NMR Spectroscopy and First‐Principles Calculations

A DFT‐based molecular model for imidazolium–silica‐based nanoparticle networks (INNs) is presented. The INNs were synthesized and characterized by using small‐angle X‐ray scattering (SAXS), NMR spectroscopy, and theoretical ab initio calculations. ¹¹B and ³¹P HETCOR CP MAS experiments were recorded. Calculated ¹⁹F NMR spectroscopy results, combined with the calculated anion–imidazolium (IM) distances, predicted the IM chain density in the INN, which was also confirmed from thermogravimetric analysis/mass spectrometry results. The presence of water molecules trapped between the nanoparticles is also suggested. First considerations on possible π–π stacking between the IM rings are presented. The predicted electronic properties confirm the photoluminescence emissions in the correct spectral domain.     

Color Polymorphism: Understanding the Diverse Solid‐State Packing and Color in Dimethyl‐3,6‐dichloro‐2,5‐dihydroxyterephthalate

Dimethyl‐3,6‐dichloro‐2,5‐dihydroxyterephthalate (MCHT) is known to exist in three differently packed crystals having three different colors, namely yellow (Y), light yellow (LY), and white (W). Apart from the difference in their color, the molecules in the crystals also differ in their intramolecular O?H???O and O?H???Cl hydrogen bonds. Time‐dependent DFT calculations reveal the role of the various types of hydrogen bonds in controlling the color of the polymorphs. Mechanistic pathways that lead to such transformations in the crystal are elucidated by solid‐state dispersion‐corrected DFT studies. Relative stabilities of the various polymorphs rationalize the experimentally observed transformations between them. Calculations reveal that the minimum‐energy pathway for the conversion of the Y form to a W form is through stepwise disrotatory motion of the two ?OH groups through a hybrid intermediate having one intramolecular O?H???O and one O?H???Cl bond. The LY form is shown to exist on the higher‐energy pathway involving a concerted Y→W transformation.     

Time‐Dependent Density Functional Theory Molecular Dynamics Simulations of Liquid Water Radiolysis

The early stages of the Coulomb explosion of a doubly ionized water molecule immersed in liquid water are investigated with time‐dependent density functional theory molecular dynamics (TD–DFT MD) simulations. Our aim is to verify that the double ionization of one target water molecule leads to the formation of atomic oxygen as a direct consequence of the Coulomb explosion of the molecule. To that end, we used TD–DFT MD simulations in which effective molecular orbitals are propagated in time. These molecular orbitals are constructed as a unitary transformation of maximally localized Wannier orbitals, and the ionization process was obtained by removing two electrons from the molecular orbitals with symmetry 1B₁, 3A₁, 1B₂ and 2A₁ in turn. We show that the doubly charged H₂O²⁺ molecule explodes into its three atomic fragments in less than 4 fs, which leads to the formation of one isolated oxygen atom whatever the ionized molecular orbital. This process is followed by the ultrafast transfer of an electron to the ionized molecule in the first femtosecond. A faster dissociation pattern can be observed when the electrons are removed from the molecular orbitals of the innermost shell. A Bader analysis of the charges carried by the molecules during the dissociation trajectories is also reported.     

A First‐Principles Study on the Interaction between Alkyl Radicals and Graphene

The interaction between alkyl radicals and graphene was studied by means of dispersion‐corrected density functional theory. The results indicate that isolated alkyl radicals are not likely to be attached onto perfect graphene. It was found that the covalent binding energies are low, and because of the large entropic contribution, Δ${G{{{\ominus}\hfill \atop 298\hfill}}}$ is positive for methyl, ethyl, isopropyl, and tert‐butyl radicals. Although the alkylation may proceed by moderate heating, the desorption barriers are low. For the removal of the methyl and tert‐butyl radicals covalently bonded to graphene, 15.3 and 2.4 kcal mol^?1 are needed, respectively. When alkyl radicals are agglomerated, the binding energies are increased. For the addition in the ortho position and on opposite sides of the sheet, the graphene–CH₃ binding energy is increased by 20 kcal mol^?1, whereas for the para addition on the same side of the sheet, the increment is 9.4 kcal mol^?1. In both cases, the agglomeration turns the Δ${G{{{\ominus}\hfill \atop 298\hfill}}}$ <0. For the ethyl radical, the ortho addition on opposite sides of the sheet has a negative Δ${G{{{\ominus}\hfill \atop 298\hfill}}}$ , whereas for isopropyl and tert‐butyl radicals the reactions are endergonic. The attachment of the four alkyl radicals under consideration onto the zigzag edges is exergonic. The noncovalent adsorption energies computed for ethyl, isopropyl, and tert‐butyl radicals are significantly larger than the graphene–alkyl‐radical covalent binding energies. Thus, physisorption is favored over chemisorption. As for the Δ${G{{{\ominus}\hfill \atop 298\hfill}}}$ for the adsorption of isolated alkyl radicals, only the tert‐butyl radical is likely to be exergonic. For the phenalenyl radical we were not able to locate a local minimum for the chemisorbed structure since it moves to the physisorbed structure. An important conclusion of this work is that the consideration of entropic effects is essential to investigate the interaction between graphene and free radicals.     

Solvent‐Dependent Structure of the I3− Ion Derived from Photoelectron Spectroscopy and Ab Initio Molecular Dynamics Simulations

Ab initio molecular dynamics (MD) simulations of the solvation of LiI₃ in four different solvents (water, methanol, ethanol, and acetonitrile) are employed to investigate the molecular and electronic structure of the I₃^? ion in relation to X‐ray photoelectron spectroscopy (XPS). Simulations show that hydrogen‐bond rearrangement in the solvation shell is coupled to intramolecular bond‐length asymmetry in the I₃^? ion. By a combination of charge analysis and I 4 d core‐level XPS measurements, the mechanism of the solvent‐induced distortions has been studied, and it has been concluded that charge localization mediates intermolecular interactions and intramolecular distortion. The approach involving a synergistic combination of theory and experiment probes the solvent‐dependent structure of the I₃^? ion, and the geometric structure has been correlated with the electronic structure.     

A First‐Principles Study of Lithium Adsorption on a Graphene–Fullerene Nanohybrid System

The mechanism of Li adsorption on a graphene–fullerene (graphene–C₆₀) hybrid system has been investigated using density functional theory (DFT). The adsorption energy for Li atoms on the graphene–C₆₀ hybrid system (?2.285 eV) is found to be higher than that on bare graphene (?1.375 eV), indicating that the Li adsorption on the former system is more stable than on the latter. This is attributed to the high affinity of Li atoms to C₆₀ and the charge redistribution that occurs after graphene is mixed with C₆₀. The electronic properties of the graphene–C₆₀ system such as band structure, density of states, and charge distribution have been characterized as a function of the number of Li atoms adsorbed in comparison to those of the pure graphene and C₆₀. Li adsorption is found to preferentially occur on the C₆₀ side due to the high adsorption energy of Li on C₆₀, which imparts a metallic character to the C₆₀ in the graphene–C₆₀ hybrid system.     

First‐Row Transition‐Metal–Diborane and –Borylene Complexes

A combined experimental and quantum chemical study of Group 7 borane, trimetallic triply bridged borylene and boride complexes has been undertaken. Treatment of [{Cp*CoCl}₂] (Cp*=1,2,3,4,5‐pentamethylcyclopentadienyl) with LiBH₄ ? thf at ?78 °C, followed by room‐temperature reaction with three equivalents of [Mn₂(CO)₁₀] yielded a manganese hexahydridodiborate compound [{(OC)₄Mn}(η⁶‐B₂H₆){Mn(CO)₃}₂(μ‐H)] ( 1 ) and a triply bridged borylene complex [(μ₃‐BH)(Cp*Co)₂(μ‐CO)(μ‐H)₂MnH(CO)₃] ( 2 ). In a similar fashion, [Re₂(CO)₁₀] generated [(μ₃‐BH)(Cp*Co)₂(μ‐CO)(μ‐H)₂ReH(CO)₃] ( 3 ) and [(μ₃‐BH)(Cp*Co)₂(μ‐CO)₂(μ‐H)Co(CO)₃] ( 4 ) in modest yields. In contrast, [Ru₃(CO)₁₂] under similar reaction conditions yielded a heterometallic semi‐interstitial boride cluster [(Cp*Co)(μ‐H)₃Ru₃(CO)₉B] ( 5 ). The solid‐state X‐ray structure of compound 1 shows a significantly shorter boron–boron bond length. The detailed spectroscopic data of 1 and the unusual structural and bonding features have been described. All the complexes have been characterized by using ¹H, ¹¹B, ¹³C NMR spectroscopy, mass spectrometry, and X‐ray diffraction analysis. The DFT computations were used to shed light on the bonding and electronic structures of these new compounds. The study reveals a dominant B?H?Mn, a weak B?B?Mn interaction, and an enhanced B?B bonding in 1 .     

The Influence of Defects on Mo‐Doped TiO2 by First‐Principles Studies

TiO₂ doped with transition metals shows improved photocatalytic efficiency. Herein the electronic and optical properties of Mo‐doped TiO₂ with defects are investigated by DFT calculations. For both rutile and anatase phases of TiO₂, the bandgap decreases continuously with increasing Mo doping level. The 4d electrons of Mo introduce localized states into the forbidden band of TiO₂, and this shifts the absorption edge into the visible‐light region and enhances the photocatalytic activity. Since defects are universally distributed in TiO₂ or doped TiO₂, the effect of oxygen deficiency due to oxygen vacancies or interstitial Mo atoms is systemically studied. Oxygen vacancies associated with the Mo dopant atoms or interstitial Mo will reduce the spin polarization and magnetic moment of Mo‐doped TiO₂. Moreover, oxygen deficiency has a negative impact on the improved photocatalytic activity of Mo‐doped TiO₂. The current results indicate that substitutional Mo, interstitial Mo, and oxygen vacancy have different impacts on the electronic/optical properties of TiO₂ and are suited to different applications.     

Understanding the Supramolecular Self‐Assembly of the Fullerene Derivative PCBM on Gold Surfaces

We report a DFT study on the self‐assembly of the fullerene derivative PCBM on the Au(111) surface. Recent STM experiments (Angew. Chem. 2007 , 119, 8020–8023^[1]) show a coverage‐dependent transition of the adsorption and self‐assembly of PCBM on this surface. To understand the origin of this observation, we compute the geometries and relative energies of ten PCBM dimers and four tetramers. The calculations show that the self‐assembly of PCBM at high coverage is mainly controlled by hydrogen bonding between the PCBM tails. Due to the large size of the fullerene cage, the hydrogen bonds are formed far away from the surface; hence they are very similar to those found in the gas phase. This picture successfully explains the observed site‐insensitive adsorption at high coverage and the 2D arrangement of PCBM on the surface.