Dr Marco Sacchi MRSC

Mass transport at surfaces determines the kinetics of processes such as heterogeneous catalysis and thin-film growth, with the diffusivity being controlled by excitation across a translational barrier. Here, we use neutron time-of-flight and spin-echo spec-troscopy to follow the nanoscopic motion of triphenylphosphine (P(C6H5)3 or PPh3) adsorbed on exfoliated graphite. Together with force-field molecular dynamics simulations, we show that the motion is similar to that of a molecular motor, i.e. PPh3 " rolls " over the surface with an almost negligible activation energy for rotations and motion of the phenyl groups and a comparably small activation energy for translation. The unique behaviour of PPh3 is due to its three-point binding with the surface: Together with van der Waals corrected density functional theory calculations, we illustrate that the adsorption energy of PPh3 increases considerably compared to molecules with flat adsorption geometry, yet the effective diffusion barrier for translational motion increases only slightly. We rationalise these results in terms of molecular symmetry, structure and contact angle, illustrating that the molecular degrees of freedom in larger molecules, i.e. rotations and conformational changes, are intimately connected with the diffusivity.

Much effort has been devoted to the investigation of the reactivity of glycine, the smallest amino acid, in different environments in the interstellar medium (ISM). While the formation paths are expected to follow a gas-solid mechanism, the full picture of glycine survival in the ISM remains yet unrevealed. In this work, we have adopted density functional theory under periodic boundary conditions to simulate mechanisms for the decarboxylation of glycine on a water-rich surface and on a glycine ice. We have performed calculations at the PBE-D3/USPP level, from which several adsorption modes of glycine on each surface were investigated and decomposition mechanisms into CO2 and CH3NH2 on the different interfaces were suggested. Most favourable adsorption sites of glycine have adsorption energies of -106.54 and -98.52 kJ mol(-1) on the water ice and glycine ice, respectively. Glycine decomposes into CO2 and CH3NH2 through a two-step mechanism on the water ice and four-step mechanism on the glycine surface, from which the barrier heights of the determinant steps were of 288.98 and 111.58 kJ mol(-1), respectively. At temperatures of 50 K, decomposition of glycine into CO2 and CH3NH2 is an exergonic reaction, pointing to a thermodynamically controlled reaction in specific interstellar regions, such as hot-cores. Compared with reported glycine gas-phase reaction, much lower barrier heights for glycine formation were found in the surface models studied here.

Porphyrin–nanocarbon systems were used to generate a photocatalyst for the control of rhodamine B and rhodamine 6G photodegradation. Carboxylic functionalized multi-walled carbon nanotubes (o-MWCNTs) were decorated by two different porphyrin moieties: 5-(4-aminophenyl)-10,15,20-(triphenyl)­porphyrin (a-TPP) with an amine linker and 5-(4-carboxyphenyl)-10,15,20-(triphenyl)­porphyrin (c-TPP) with a carboxyl linker to the o-MWCNT, respectively, with their photocatalyst performances investigated. The optical properties of the mixed nanocomposite materials were investigated to reveal the intrinsic energy levels and mechanisms of degradation. The charge-transfer states of the o-MWCNTs were directly correlated with the performance of the complexes as well as the affinity of the porphyrin moiety to the o-MWCNT anchor, thus extending our understanding of energy-transfer kinetics in porphyrin–CNT systems. Both a-TPP and c-TPP o-MWCNT complexes offered improved photocatalytic performance for both RhB and Rh6G compared to the reference o-MWCNTs and both porphyrins in isolated form. The photocatalytic performance improved with higher concentration of o-MWCNTs in the complexed sample, indicating the presence of greater numbers of −H/–OH groups necessary to more efficient photodegradation. The large presence of the −H/–OH group in the complexes was expected and was related to the functionalization of the o-MWCNTs needed for high porphyrin attachment. However, the photocatalytic efficiency was affected at higher o-MWCNT concentrations due to the decomposition of the porphyrins and changes to the size of the CNT agglomerates, thus reducing the surface area of the reactant. These findings demonstrate a system that displays solar-based degradation of rhodamine moieties that are on par, or an improvement to, state-of-the-art organic systems.

Proton transfer along the hydrogen bonds of DNA can lead to the creation of short-lived, but biologically relevant point mutations that can further lead to gene mutation and, potentially, cancer. In this work, the energy landscape of the canonical A–T and G–C base pairs (standard, amino–keto) to tautomeric A*–T* and G*–C* (non-standard, imino–enol) Watson–Crick DNA base pairs is modelled with density functional theory and machine-learning nudge-elastic band methods. We calculate the energy barriers and tunnelling rates of hydrogen transfer between and within each base monomer (A, T, G and C). We show that the role of tunnelling in A–T tautomerisation is statistically unlikely due to the presence of a small reverse reaction barrier. On the contrary, the thermal populations of the G*–C* point mutation could be non-trivial and propagate through the replisome. For the direct intramolecular transfer, the reaction is hindered by a substantial energy barrier. However, our calculations indicate that tautomeric bases in their monomeric form have remarkably long lifetimes.

The use of copper canisters in the Swedish KBS-3 concept for spent nuclear fuel disposal could result in the formation of copper-bearing uranyl phases should a canister suffer from defects or if the containment were to fail before reducing conditions are established in the repository. Most uranyl species would be expected to display higher solubility than the original uranium(IV) dioxide fuel, leading to enhanced release, though this would depend on the phase and prevailing groundwater conditions. Secondary alteration products may also be poorly crystalline or even amorphous, making characterisation difficult during the pre-closure period owing to the high radiation field close to the canister. Vandenbrandeite, (CuUO2(OH)4), is a rare mineral in nature but known to form by alteration of primary uraninite through interaction with oxidising groundwater containing dissolved copper Consequently, an attempt has been made to characterise two vandenbrandeite specimens of varying crystallinity by luminescence and multiple-laser Raman spectroscopy; techniques amenable to remote, robotic deployment and which have proved useful in discriminating other uranyl oxy-hydroxides, silicates and phosphates. The first reported luminescence emission and excitation spectra for vandenbrandeite revealed near-negligible luminescence, with a slightly enhanced signal for the specimen displaying poorer crystallinity. This observation agrees well with density functional theory calculations. The simulated projected density of state and band structure show an unlikely transition from the U f-orbitals to Cu d-orbitals, or O states, would be required for luminescence to be detectable; this probably improves for poorly crystalline specimens as the spatial overlap between the orbitals increases. Further, negligible differences in the number of peaks and peak positions were detected in the laser wavelength-dependent Raman spectra although again, variation in background noise and peak shape was observed based on the degree of crystallinity. Good agreement was obtained between experimental and simulated Raman spectra, particularly with the environmentally sensitive axial uranyl stretching modes, validating the crystal system derived in this study. The findings of this study suggest luminescence spectroscopy, when combined with Raman spectroscopy, may be able to both identify vandenbrandeite and distinguish between crystalline and amorphous forms based on their relative luminescence intensity.

Catalytic methane decomposition (CMD) is receiving much attention as a promising application for hydrogen production. Due to the high energy required for breaking the C-H bonds of methane, the choice of catalyst is crucial to the viability of this process. However, atomistic insights for the CMD mechanism on carbon-based materials are still limited. Here, we investigate the viability of CMD under reaction conditions on the zigzag (12-ZGNR) and armchair (AGRN) edges of graphene nanoribbons employing dispersion-corrected density functional theory (DFT). First, we investigated the desorption of H and H2 at 1200 K on the passivated 12-ZGNR and 12-AGNR edges. The diffusion of hydrogen atom on the passivated edges is the rate determinant step for the most favourable H2 desorption pathway, with a activation free energy of 4.17 eV and 3.45 eV on 12-ZGNR and 12-AGNR, respectively. The most favourable H2 desorption occurs on the 12-AGNR edges with a free energy barrier of 1.56 eV, reflecting the availability of bare carbon active sites on the catalytic application. The direct dissociative chemisorption of CH4 is the preferred pathway on the non-passivated 12-ZGNR edges, with an activation free energy of 0.56 eV. We also present the reaction steps for the complete catalytic dehydrogenation of methane on 12-ZGNR and 12-AGNR edges, proposing a mechanism in which the solid carbon formed on the edges act as new active sites. The active sites on the 12-AGNR edges show more propensity to be regenerated due lower free energy barrier of 2.71 eV for the H2 desorption from the newly grown active site. Comparison is made between the results obtained here and experimental and computational data available in the literature. We provide fundamental insights for the engineering of carbon-based catalysts for the CMD, showing that the bare carbon edges of graphene nanoribbons have performance comparable to commonly used metallic and bi-metallic catalysts for methane decomposition.

Electrochemical carbon dioxide (CO2) reduction reaction (CO2RR) is an attractive approach to deal with the emission of CO2 and to produce valuable fuels and chemicals in a carbon-neutral way. Many efforts have been devoted to boost the activity and selectivity of high-value multicarbon products (C2+) on Cu-based electrocatalysts. However, Cu-based CO2RR electrocatalysts suffer from poor catalytic stability mainly due to the structural degradation and loss of active species under CO2RR condition. To date, most reported Cu-based electrocatalysts present stabilities over dozens of hours, which limits the advance of Cu-based electrocatalysts for CO2RR. Herein, a porous chlorine-doped Cu electrocatalyst exhibits high C2+ Faradaic efficiency (FE) of 53.8 % at -1.00 V versus reversible hydrogen electrode (V-RHE). Importantly, the catalyst exhibited an outstanding catalytic stability in long-term electrocatalysis over 240 h. Experimental results show that the chlorine-induced stable cationic Cu-0/Cu+ species and the well-preserved structure with abundant active sites are critical to the high FE of C2+ in the long-term run of electrochemical CO2 reduction.

Proton transfer across hydrogen bonds in DNA can produce non-canonical nucleobase dimers and is a possible source of single-point mutations when these forms mismatch under replication. Previous computational studies have revealed this process to be energetically feasible for the guanine-cytosine (GC) base pair, but the tautomeric product (G * C *) is short-lived. In this work we reveal, for the first time, the direct effect of the replisome enzymes on proton transfer, rectifying the shortcomings of existing models. Multi-scale quantum mechanical/molecular dynamics (QM/MM) simulations reveal the effect of the bacterial PcrA Helicase on the double proton transfer in the GC base pair. It is shown that the local protein environment drastically increases the activation and reaction energies for the double proton transfer, modifying the tautomeric equilibrium. We propose a regime in which the proton transfer is dominated by tunnelling, taking place instantaneously and without atomic rearrangement of the local environment. In this paradigm, we can reconcile the metastable nature of the tautomer and show that ensemble averaging methods obscure detail in the reaction profile. Our results highlight the importance of explicit environmental models and suggest that asparagine N624 serves a secondary function of reducing spontaneous mutations in PcrA Helicase.

We report a thermodynamically feasible mechanism for producing H2 from NH3 using hBN as a catalyst. 2D catalysts have exceptional surface areas with unique thermal and electronic properties suited for catalysis. Metal-free, 2D catalysts, are highly desirable materials that can be more sustainable than the ubiquitously employed precious and transition metal-based catalysts. Here, using density functional theory (DFT) calculations, we demonstrate that metal-free hexagonal boron nitride (hBN) is a valid alternative to precious metal catalysts for producing H2 via reaction of ammonia with a boron and nitrogen divacancy (VBN). Our results show that the decomposition of ammonia proceeds on monolayer hBN with an activation energy barrier of 0.52 eV. Furthermore, the reaction of ammonia with epitaxially grown hBN on a Ru(0001) substrate was investigated, and we observed similar NH3 decomposition energy barriers (0.61 eV), but a much more facile H2 associative desorption barrier (0.69 eV vs 5.89 eV). H2 generation from the free standing monolayer would instead occur through a diffusion process with an energy barrier of 3.36 eV. A detailed analysis of the electron density and charge distribution along the reaction pathways was carried out to rationalise the substrate effects on the catalytic reaction.

Electrochemical carbon dioxide (CO2) reduction reaction (CO2RR) is an attractive approach to deal with the excessive emission of CO2 and to produce valuable fuels and chemicals in a carbon-neutral way. Many efforts have been devoted to boost the activity and selectivity of high-value multicarbon products (C2+) on Cu-based electrocatalysts. However, Cu-based CO2RR electrocatalysts suffer from poor catalytic stability mainly due to the structural degradation and loss of active species under CO2RR condition. To date, most reported Cu-based electrocatalysts present stabilities over dozens of hours, which limits the advance of Cu-based electrocatalysts for CO2RR. Here, a porous chlorine-doped Cu electrocatalyst is reported and exhibits high C2+ Faradaic efficiency (FE) of 53.8 % at-1.00 V versus reversible hydrogen electrode (VRHE). Importantly, the catalyst exhibited an outstanding catalytic stability in long-term electrocatalysis over 240 hours. Experimental results show that the chlorine-induced stable cationic Cu 0-Cu + species and the well-preserved structure with abundant active sites are found to be critical to maintain the high FE of C2+ in the long-term run of electrochemical CO2 reduction.

Understanding the rules of life is one of the most important scientific endeavours and has revolutionised both biology and biotechnology. Remarkable advances in observation techniques allow us to investigate a broad range of complex and dynamic biological processes in which living systems could exploit quantum behaviour to enhance and regulate biological functions. Recent evidence suggests that these non-trivial quantum mechanical effects may play a crucial role in maintaining the non-equilibrium state of biomolecular systems. Quantum biology is the study of such quantum aspects of living systems. In this review, we summarise the latest progress in quantum biology, including the areas of enzyme-catalysed reactions, photosynthesis, spin-dependent reactions, DNA, fluorescent proteins, and ion channels. Many of these results are expected to be fundamental building blocks towards understanding the rules of life.

Organic molecular thin-films are employed for manufacturing a wide variety of electronic devices, including memories and transistors. A precise description of the atomic-scale interactions in aromatic carbon systems is of paramount importance for the design of organic thin-films and carbon based nanomaterials. Here we investigate the binding and structure of pyrazine on graphite with neutron diffraction and spin-echo measurements. Diffraction data of the ordered phase of deuterated pyrazine, (C4D4N2), adsorbed on the graphite (0001) basal plane surface are compared to scattering simulations and complemented by van der Waals corrected density functional theory calculations. The lattice constant of pyrazine on graphite is found to be (6.06±0.02) Å. Compared to benzene (C6D6) adsorption on graphite the pyrazine superstructure appears to be much more thermodynamically stable, up to 320 K, and continues in a layer-by-layer growth. Both findings suggest a direct correlation between the intensity of van der Waals bonding and the stability of the self-assembled overlayer, because the nitrogen atoms in the six-membered ring of pyrazine increase the van der Waals bonding in comparison to benzene, which only contains carbon atoms.

Large-area single-crystal monolayers of two-dimensional (2D) materials such as graphene and hexagonal boron nitride (h-BN) can be grown by chemical vapour deposition (CVD). However, the high temperatures and fast timescales at which the conversion from a gas-phase precursor to the 2D material appear, make it extremely challenging to simultaneously follow the atomic arrangements. We utilise helium atom scattering to discover and control the growth of novel 2D h-BN nanoporous phases during the CVD process. We find that prior to the formation of h-BN from the gas-phase precursor, a metastable $(3\times3)$ structure is formed, and that excess deposition on the resulting 2D h-BN leads to the emergence of a $(3\times4)$ structure. We illustrate that these nanoporous structures are produced by partial dehydrogenation and polymerisation of the borazine precursor upon adsorption. These steps are largely unexplored during the synthesis of 2D materials and we unveil the rich phases during CVD growth. Our results provide significant foundations for 2D materials engineering in CVD, by adjusting or carefully controlling the growth conditions and thus exploiting these intermediate structures for the synthesis of covalent self-assembled 2D networks.

We have investigated methane (CH4) dissociative chemisorption on the Ni{100} surface by first-principles molecular dynamics (MD) simulations. Our results show that this reaction is mode-specific, with the ν1 state being the most strongly coupled to efficient energy flow into the reaction coordinate when the molecule reaches the transition state. By performing MD simulations for two different transition state (TS) structures we provide evidence of TS structure-specific energy redistribution in methane chemisorption. Our results are compared with recently reported state-resolved measurement of methane adsorption probability on nickel surfaces, and we find that a strong correlation exists between the highest vibrational efficacy measured on Ni{100} for the ν1 state and the calculated highest fractional vibrational energy content in this mode.

Amino acids adsorbed over single crystal metal surfaces have emerged as prototypical systems for exploring the properties that govern the development of long-range chirality in self-assembled monolayers (SAM) and supramolecular 2D networks. In this study, we characterise the self-assembly mechanism for glycine on the Cu(110) surface. This process occurs on a time scale that is too fast for most atomically resolved microscopic techniques, so the mechanism we propose here provides new insight for an important unexplored surface phenomenon.

We use helium spin-echo spectroscopy (HeSE) to investigate the dynamics of the diffusion of benzene adsorbed on Cu(111). The results of these measurements show that benzene moves on the surface through an activated jump-diffusion process between adsorption sites on a Bravais lattice. Density Functional Theory (DFT) calculations with van der Waals (vdW) corrections help us understand that the molecule diffuses by jumps through non-degenerate hollow sites. The results of the calculations shed light on the nature of the binding interaction between this prototypical aromatic molecule and the metallic surface. The highly accurate HeSE experimental data provide a quantitatively stringent benchmark for the vdW correction schemes applied to the DFT calculations and we compare the performances of several dispersion interactions schemes.

The formation of a halogen bonded self-assembled co-crystal physisorbed monolayer containing N⋯Br interactions is reported for the first time. The co-crystal monolayer is identified experimentally by synchrotron X-ray diffraction and the structure determined. Density functional theory (DFT) calculations are also employed to assess the magnitudes of the different interactions in the layer. Significantly, compared to other halogen bonds in physisorbed monolayers we have reported recently, the N⋯Br bond here is found to be non-linear. It is proposed that the increasing importance of the lateral hydrogen bond interactions, relative to the halogen bond strength, leads to the bending of the halogen bonds.

The interaction of water and surfaces, at molecular level, is of critical importance for understanding processes such as corrosion, friction, catalysis and mass transport. The significant literature on interactions with single crystal metal surfaces should not obscure unknowns in the unique behaviour of ice and the complex relationships between adsorption, diffusion and long-range inter-molecular interactions. Even less is known about the atomic-scale behaviour of water on novel, non-metallic interfaces, in particular on graphene and other 2D materials. In this manuscript, we review recent progress in the characterisation of water adsorption on 2D materials, with a focus on the nano-material graphene and graphitic nanostructures; materials which are of paramount importance for separation technologies, electrochemistry and catalysis, to name a few. The adsorption of water on graphene has also become one of the benchmark systems for modern computational methods, in particular dispersion-corrected density functional theory (DFT). We then review recent experimental and theoretical advances in studying the single-molecular motion of water at surfaces, with a special emphasis on scattering approaches as they allow an unparalleled window of observation to water surface motion, including diffusion, vibration and self-assembly.

The misincorporation of a noncomplementary DNA base in the polymerase active site is a critical source of replication errors that can lead to genetic mutations. In this work, we model the mechanism of wobble mispairing and the subsequent rate of misincorporation errors by coupling first principles quantum chemistry calculations to an open quantum systems master equation. This methodology allows us to accurately calculate the proton transfer between bases, allowing the misincorporation and formation of mutagenic tautomeric forms of DNA bases. Our calculated rates of genetic error formation are in excellent agreement with experimental observations in DNA. Furthermore, our quantum mechanics/molecular mechanics model predicts the existence of a short-lived "tunnelling ready " configuration along the wobble reaction pathway in the polymerase active site, dramatically increasing the rate of proton transfer by a hundredfold, demonstrating that quantum tunnelling plays a critical role in determining the transcription error frequency of the polymerase.

The adenine-thymine tautomer (A*-T*) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A*-T* while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A*-T* as the DNA strands unzip and the hydrogen bonds between the bases stretch. Molecular Dynamics simulations reveal the time scales and dynamics of DNA strand separation and the statistical ensemble of opening angles present in a biological environment. Our results demonstrate that the unwinding of DNA, an inherently out-of-equilibrium process facilitated by helicase, will change the energy landscape of the adenine-thymine tautomerization reaction. We propose that DNA strand separation allows the stable tautomeriza-tion of adenine-thymine, providing a feasible pathway for genetic point mutations via proton transfer between the A-T bases.

This supplementary information contains the files necessary to reproduce DFT calculations contained in the publication titled "Dehydrogenation of ammonia on free-standing and epitaxial hexagonal boron nitride", published in Physical Chemistry Chemical Physics (PCCP) (DOI: 10.1039/d2cp01392d). Please see the README for coordinate files and corresponding total energies of all structures in the article including geometry optimizations and transition states of the reaction mechanisms using the CASTEP program. This work made use of ARCHER2, the UK’s national high-performance computing service, via the UK’s HPC Materials Chemistry Consortium, which is funded by EPSRC (EP/R029431) and Eureka, the University of Surrey’s High-Performance Computing facility.

The dissociation of NO on metal-free graphene was studied using density functional theory (DFT). The effect of heteroatomic substitution of boron and nitrogen on the activity of the single vacancy was explored. While the doping did not affect the NO chemisorption barrier, it was found that the dissociation step was activated by B (down to 4 meV) but deactivated by N (up to 2.42 eV). In addition to the nature of the dopant, the location of the heteroatom with respect to the single vacancy site had an even stronger influence on the reactivity of graphene, reducing the barrier for dissociation fourfold.

Understanding the interplay between intrinsic molecular chirality and chirality of the bonding footprint is crucial in exploiting enantioselectivity at surfaces. As such, achiral glycine and chiral alanine are the most obvious candidates if one is to study this interplay on different surfaces. Here, we have investigated the adsorption of glycine on Cu{311} using reflection–absorption infrared spectroscopy, low-energy electron diffraction, temperature-programmed desorption, and first-principles density-functional theory. This combination of techniques has allowed us to accurately identify the molecular conformations present under different conditions and discuss the overlayer structure in the context of the possible bonding footprints. We have observed coverage-dependent local symmetry breaking, with three-point bonded glycinate moieties forming an achiral arrangement at low coverages, and chirality developing with the presence of two-point bonded moieties at high coverages. Comparison with previous work on the self-assembly of simple amino acids on Cu{311} and the structurally similar Cu{110} surface has allowed us to rationalize the different conditions necessary for the formation of ordered chiral overlayers.

The dissociative adsorption of cyclopentadiene (C5H6) on Cu(111) yields a cyclopentadienyl (Cp) species with strongly anionic characteristics. The Cp potential energy surface and frictional coupling to the substrate are determined from measurements of dynamics of the molecule together with density functional calculations. The molecule is shown to occupy degenerate threefold adsorption sites and molecular motion is characterized by a low diffusional energy barrier of 40±3  meV with strong frictional dissipation. Repulsive dipole-dipole interactions are not detected despite charge transfer from substrate to adsorbate.

The state-resolved reaction probability of CH4 on Pt(110)−(1×2) was measured as a function of CH4 translational energy for four vibrational eigenstates comprising different amounts of C-H stretch and bend excitation. Mode-specific reactivity is observed both between states from different polyads and between isoenergetic states belonging to the same polyad of CH4. For the stretch/bend combination states, the vibrational efficacy of reaction activation is observed to be higher than for either pure C-H stretching or pure bending states, demonstrating a concerted role of stretch and bend excitation in C-H bond scission. This concerted role, reflected by the nonadditivity of the vibrational efficacies, is consistent with transition state structures found by ab initio calculations and indicates that current dynamical models of CH4 chemisorption neglect an important degree of freedom by including only C-H stretching motion.

Sulphide materials, in particular MoS2, have recently received great attention from the surface science community due to their extraordinary catalytic properties. Interestingly, the chemical activity of iron pyrite (FeS2) (the most common sulphide mineral on Earth), and in particular its potential for catalytic applications, has not been investigated so thoroughly. In this study, we use density functional theory (DFT) to investigate the surface interactions of fundamental atmospheric components such as oxygen and nitrogen, and we have explored the adsorption and dissociation of nitrogen monoxide (NO) and nitrogen dioxide (NO2) on the FeS2(100) surface. Our results show that both those environmentally important NOx species chemisorb on the surface Fe sites, while the S sites are basically unreactive for all the molecular species considered in this study and even prevent NO2 adsorption onto one of the non-equivalent Fe–Fe bridge sites of the (1 × 1)–FeS2(100) surface. From the calculated high barrier for NO and NO2 direct dissociation on this surface, we can deduce that both nitrogen oxides species are adsorbed molecularly on pyrite surfaces.

The chemisorption of CH4 on Pt{110}-(1 2) has been studied by vibrational analysis of the reaction pathway defined by the potential energy surface and, in time reversal, by first-principles molecular dynamics simulations of CH4 associative desorption, with the electronic structure treated explicitly using density functional theory. We find that the symmetric stretch vibration ν1 is strongly coupled to the reaction coordinate; our results therefore provide a firm theoretical basis for recently reported state-resolved reactivity measurements, which show that excitation of the ν1 normal mode is the most efficient way to enhance the reaction probability.

The reactivity of methane (CH 4 ) on Pt(110)-(1×2) Pt(110)-(1×2) has been studied by quantum state-resolved surface reactivity measurements. Ground state reaction probabilities, S 0 (v=0)≅S 0 (laser-off) S0(v=0)≅S0(laser-off) , as well as state-resolved reaction probabilities S 0 (2ν 3 ) S0(2ν3) , for CH 4 CH4 excited to the first overtone of the antisymmetric C–H stretch (2ν 3 ) (2ν3) have been measured at incident translational energies in the range of 4–64 kJ/mol. We observe S 0 (2ν 3 ) S0(2ν3) to be up to three orders of magnitude higher than S 0 (v=0) S0(v=0) , demonstrating significant vibrational activation of CH 4 CH4 dissociation on Pt(110)-(1×2) Pt(110)-(1×2) by 2ν 3 2ν3 excitation. Furthermore, we explored the azimuthal and polar incident angle dependence of S 0 (2ν 3 ) S0(2ν3) and S 0 (v=0) S0(v=0) for a fixed incident translational energy E t =32 kJ/mol Et=32 kJ/mol . For incidence perpendicular to the missing row direction on Pt(110)-(1×2) Pt(110)-(1×2) and polar angles θ>40° θ>40° , shadowing effects prevent the incident CH 4 CH4 molecules from impinging into the trough sites. Comparison of this polar angle dependence with reactivity data for incidence parallel to the missing rows yields state-resolved site specific reactivity information consistent with a Pt(110)-(1×2) Pt(110)-(1×2) reactivity that is dominated by top layer Pt atoms located at the ridge sites. A comparison of S 0 (v=0) S0(v=0) measured on Pt(110)-(1×2) Pt(110)-(1×2) and Pt(111) yields a lower average barrier for Pt(110)-(1×2) Pt(110)-(1×2) by 13.7±2.0 kJ/mol 13.7±2.0 kJ/mol .

Self-assembled monolayers containing conjugated π systems find application in organic electronics to functionalize and modify the electronic properties of metals and metal oxides. Isolated cyclopentadienyl is an aromatic molecular anion similar in size to benzene that, unlike benzene, adsorbs quite strongly even on coinage metal surfaces. In this study, the electronic structure, bonding, and minimum energy configuration of cyclopentadienyl (c-C5H5 or Cp) adsorbed on Cu{111} are calculated via first-principles density functional theory (DFT). The Cu{111} surface has been modeled within a (2√3 × 2√3)R30° cell, and the adsorbed Cp has been found to reside preferentially on the hollow sites, with a binding energy of 1.73 eV. Electronic population analysis reveals a net charge transfer of ∼1.1 electrons from the metal to the Cp, indicating that the adsorption is dominated by ionic bonding. The surface diffusion barrier between two adjacent hollow sites was calculated to be 55 meV, in good agreement with previously reported measurements by helium spin echo (HeSE) spectroscopy. It was found that lateral interactions do not significantly influence the binding energy and mobility of the adsorbate. The physical–chemical properties of this strongly bound but weakly mutually interacting molecular adsorbate suggest that Cp could become a model system for ionically adsorbed molecular adsorbates.

We have investigated the chemisorption of CH3D and CD3H on Pt{1 1 0}-(1 × 2) by performing first-principles molecular dynamics simulations of the recombinative desorption of CH3D (from adsorbed methyl and deuterium) and of CD3H (from adsorbed trideuteromethyl and hydrogen). Vibrational analysis of the symmetry adapted internal coordinates of the desorbing molecules shows that excitation of the single C–D (C–H) bond in the parent molecule is strongly correlated with energy excess in the reaction coordinate. The results of the molecular dynamics simulations are consistent with observed mode- and bond-specific reactivity measurements for chemisorption of methane and its isotopomers on platinum and nickel surfaces.

The motion of adsorbate molecules across surfaces is fundamental to self-assembly, material growth, and heterogeneous catalysis. Recent Scanning Tunneling Microscopy studies have demonstrated the electron-induced long-range surface-migration of ethylene, benzene, and related molecules, moving tens of Angstroms across Si(100). We present a model of the previously unexplained long-range recoil of chemisorbed ethylene across the surface of silicon. The molecular dynamics reveal two key elements for directed long-range migration: first ‘ballistic’ motion that causes the molecule to leave the ab initio slab of the surface traveling 3–8 Å above it out of range of its roughness, and thereafter skipping-stone ‘bounces’ that transport it further to the observed long distances. Using a previously tested Impulsive Two-State model, we predict comparable long-range recoil of atomic chlorine following electron-induced dissociation of chlorophenyl chemisorbed at Cu(110).

This work presents an experimental picture of molecular ballistic diffusion on a surface, a process which is difficult to pinpoint since it generally occurs at very short length scales. By combining neutron-time-of-flight data, with molecular dynamics simulations and density functional theory calculations, we provide a complete description of the ballistic translations and rotations of a poly-aromatic hydrocarbon (PAH) adsorbed on the basal plane of graphite. Pyrene, C16H10, adsorbed on graphite is a unique system where at relative surface coverages of about 10-20 %, its mean free path matches the experimentally accessible time/space scale of neutron time-of-flight spectroscopy (IN6 at the Institut Laue-Langevin). The comparison between the diffusive behavior of large and small PAHs such as pyrene and benzene adsorbed on graphite, brings a strong experimental indication that the interaction between molecules is the dominating mechanism in the surface diffusion of poly-aromatic hydrocarbons adsorbed on graphite.

Amino acids are some of the simplest biological molecules, yet they nevertheless manifest the ability to construct an incredibly complex variety of structures in which a delicate balance of intermolecular chemical forces drives the dynamics of self-recognition and assembly. Understanding the mechanism by which chiral structures are naturally synthesized is also extremely relevant to pharmaceutical and biochemical industries, in which enantioselectivity and enantiospecificity are vital factors in producing biologically compatible drugs. In this context, the adsorption of simple, naturally occurring amino acids on single crystal surfaces has become the playground for studying chiral self-assembly at the atomic scale and investigating pathways to enantioselective catalytic synthesis using a bottom-up approach. In particular, in the last two decades, several groups have dedicated a concerted effort to understand the formation of chiral self-assembled supramolecular networks of alanine, glycine and proline on Cu{110}, Cu{100}1 and Cu{111} surfaces. In the past, with few exceptions,1 the vast majority of the atomistic studies on supramolecular assembly of amino acids on metal surfaces have been conducted under UHV conditions. It is therefore one of the main challenges ahead of the surface-science community to attempt to bridge the gap between experiments conducted under “dry” vacuum conditions (in which the amino acids adsorb in the absence of a solvent and a co-adsorbate) and the more biologically and pharmaceutically relevant “wet” studies. In fact, when water is present in the system, a competition exists between the formation of hydrogen bonds between an amino acid with another and between an amino acid and the water shell immediately surrounding it. The interaction between amino acids and water is also particularly relevant to corrosion protection, since amino acids have recently become a natural and ecologically compatible alternative to traditional amine-based corrosion inhibitors. In this work we study the co-adsorption of water with glycine, the simplest naturally occurring amino acid, using first-principles density functional theory. Although in the past some authors have tried to account for the solvation of amino acids in the gas-phase, few studies have treated the solvation and interaction between adsorbed glycine and water molecules quantum mechanically.

The monolayer crystal structure of phenazine adsorbed on graphite is determined by a combination of synchrotron X-ray diffraction and DFT calculations. The molecules adopt a rectangular unit cell with lattice parameters a = 13.55 Å and b = 10.55 Å, which contains 2 molecules. The plane group of the unit cell is p2gg, and each molecule is essentially flat to the plane of the surface, with only a small amount of out-of-plane tilt. Density functional theory (DFT) calculations find a minimum energy structure with a unit cell which agrees within 7.5% with that deduced by diffraction. DFT including dispersion force corrections (DFT+D) calculations help to identify the nature of the intermolecular bonding. The overlayer interactions are principally van der Waals, with a smaller contribution from weak C-H···N hydrogen bonds. This behaviour is compared with that of 4,4′-bipyridyl.

Chirality can manifest itself in diverse ways when a molecule adsorbs on a metal surface. A clear understanding of the interplay between molecular chirality, “footprint chirality”, and chirality in the long-range self-organization is crucial if metal surfaces are to be exploited for enantioselective heterogeneous catalysis or enantio-discriminating sensors. We have investigated the self-organization of l-alanine adsorbed as alaninate on Cu{311}, using reflection–absorption infrared spectroscopy in conjunction with first-principles calculations to determine bonding configurations, and low-energy electron diffraction and scanning tunnelling microscopy to elucidate structural features. Three ordered structures are seen. One has a symmetric lattice and 3-point adsorbate bonding (the “symmetric lattice” or SL phase); the others, occurring at higher coverage, have chiral lattices and also involve 2-point bonding (the “chiral lattice” or CL phase). Possible models for these structures are discussed, together with the roles of footprint chirality and of long-range chirality in the self-organization. These results set the forms of chirality seen in alaninate overlayers on Cu{110} and {100} surfaces into a wider context. The common underlying principles should help in establishing a general framework for understanding the behavior of chiral adsorbates on low-symmetry metal surfaces.

We have used low-temperature STM, together with DFT calculations incorporating the effects of dispersion forces, to study from a structural point of view the interaction of NO2 with Au{111} surfaces. NO2 adsorbs molecularly on Au{111} at 80 K, initially as small, disordered clusters at the elbows of the type-x reconstruction lines of the clean-surface herringbone reconstruction, and then as larger, ordered islands on the fcc regions. Within the islands, the NO2 molecules define a (√3 × 2)rect. superlattice, for which we evaluate structural models. By around 0.25 ML coverage, the herringbone reconstruction has been lifted, accompanied by the formation of Au nanoclusters, and the islands have coalesced. At this stage, essentially the whole surface is covered with an overlayer consisting predominantly of domains of the (√3 × 2)rect. structure, but also containing less well-ordered regions. With further exposure, the degree of disorder in the overlayer increases; saturation occurs close to 0.43 ML.

Self-assembled monolayers of sulfur-containing heterocycles and linear oligomers containing thiophene groups have been widely employed in organic electronic applications. Here, we investigate the dynamics of isolated thiophene molecules on Cu(111) by combining helium spin-echo (HeSE) spectroscopy with density functional theory calculations. We show that the thiophene/Cu(111) system displays a rich array of aperiodic dynamical phenomena that include jump diffusion between adjacent atop sites over a 59–62 meV barrier and activated rotation around a sulfur–copper anchor, two processes that have been observed previously for related systems. In addition, we present experimental evidence for a new, weakly activated process, the flapping of the molecular ring. Repulsive inter-adsorbate interactions and an exceptionally high friction coefficient of 5 ± 2 ps–1 are also observed. These experiments demonstrate the versatility of the HeSE technique, and the quantitative information extracted in a detailed analysis provides an ideal benchmark for state-of-the-art theoretical techniques including nonlocal adsorbate–substrate interactions.

Classical diffusion—quantum barrier: On Cu(111), pyrrole diffuses in channels, hopping between adjacent bridge sites over a barrier above hollow sites. The motion of the center of mass can be described classically; however, the activation barrier arises from the quantum character of internal vibrational modes that are largely unexcited during the motion. The unique helium spin‐echo experiment is indicated by the green sphere and arrows.

We present a combined experimental and theoretical study of the self-diffusion of ammonia on exfoliated graphite. Using neutron time-of- flight spectroscopy we are able to resolve the ultrafast diffusion process of adsorbed ammonia, NH3, on graphite. Together with van der Waals corrected density functional theory calculations we show that the diffusion of NH3 follows a hopping motion on a weakly corrugated potential energy surface with an activation energy of about 4 meV which is particularly low for this type of diffusive motion. The hopping motion includes further a significant number of long jumps and the diffusion constant of ammonia adsorbed on graphite is determined with D = 3.9.10-8 m2/s at 94K.

The microscopic motion of water is a central question, but gaining experimental information about the interfacial dynamics of water for instance in catalysis, biophysics and nanotribology is extremely challenging due to its ultrafast dynamics, and the complex interplay of intermolecular and molecule-surface interactions. Here we present the first experimental and computational study of the nanoscale-nanosecond motion of water at the surface of a topological insulator (TI, Bi2Te3). In addition to the technological relevance and scientific interest on the interfacial behaviour of water, understanding the interaction of TI surfaces with molecules is a key to design and manufacturing for future applications. However the surface chemistry of these materials has hitherto been hardly addressed and exploratory work on the motion of molecules on TI surfaces has been so far solely based on computational studies. By analysing the scattering lineshape from helium spinecho spectroscopy and comparing the results with van der Waals-corrected density functional theory calculations we are able to obtain a general insight into the diffusion and mobility of water on a topological insulator surface. Instead of the expected Brownian motion, we find strong evidence of a complex diffusion mechanism which follows an activated hopping motion on a corrugated potential energy surface and shows signatures of correlated motion with unusual repulsive interactions between the individual water molecules. From the experimental lineshape broadening we determine the diffusion coefficient, the diffusion energy and the pre-exponential factor.

This work describes the combined use of synchrotron X-ray diffraction and density functional theory (DFT) calculations to understand the cocrystal formation or phase separation in 2D monolayers capable of halogen bonding. The solid monolayer structure of 1,4-diiodobenzene (DIB) has been determined by X-ray synchrotron diffraction. The mixing behavior of DIB with 4,4′-bipyridyl (BPY) has also been studied and interestingly is found to phase-separate rather than form a cocrystal, as observed in the bulk. DFT calculations are used to establish the underlying origin of this interesting behavior. The DFT calculations are demonstrated to agree well with the recently proposed monolayer structure for the cocrystal of BPY and 1,4-diiodotetrafluorobenzene (DITFB) (the perfluorinated analogue of DIB), where halogen bonding has also been identified by diffraction. Here we have calculated an estimate of the halogen bond strength by DFT calculations for the DITFB/BPY cocrystal monolayer, which is found to be ∼20 kJ/mol. Computationally, we find that the nonfluorinated DIB and BPY are not expected to form a halogen-bonded cocrystal in a 2D layer; for this pair of species, phase separation of the components is calculated to be lower energy, in good agreement with the diffraction results.

We investigate the adsorption of pyridine on Cu(110) in ultra-high vacuum with a combination of work function measurements and femtosecond infrared-visible sum and difference frequency generation (SFG/DFG). A monolayer of pyridine substantially reduces the work function by 2.9 eV due to the large pyridine dipole. We perform density functional theory (DFT) calculations that provide us with a dipole moment change upon adsorption in very good agreement with the experimental results. The pyridine dipole strongly enhances the sum frequency response of the surface electrons, but surprisingly reduces the surface difference frequency signal. We propose a model based on the static electric field-induced nonlinear optical response generated by the collective electric field of the adsorbate layer. The pyridine dipole switches direction from the ground to the excited electronic state, as charge moves from nitrogen to the ring. SFG can then be enhanced by the electric field of adsorbed pyridine in its ground electronic state, while the 2.33 eV incident photon in DFG excites electrons into the pyridine LUMO, which reverses the electric field in the adsorbate layer and reduces the nonlinear optical response. The model is verified by 2.33 eV pump – SFG probe spectroscopy, where the pump pulse is found to reduce the surface electron response on a subpicosecond timescale. This demonstrates the potential to manipulate the work function in organic electronic devices by photon-induced dipole moment reversal.

The microscopic motion of water is a central question, but gaining experimental information about the interfacial dynamics of water in fields such as catalysis, biophysics and nanotribology is challenging due to its ultrafast motion, and the complex interplay of inter-molecular and molecule-surface interactions. Here we present an experimental and computational study of the nanoscale-nanosecond motion of water at the surface of a topological insulator (TI), Bi2Te3. Understanding the chemistry and motion of molecules on TI surfaces, while considered a key to design and manufacturing for future applications, has hitherto been hardly addressed experimentally. By combining helium spin-echo spectroscopy and density functional theory calculations, we are able to obtain a general insight into the diffusion of water on Bi2Te3. Instead of Brownian motion, we find an activated jump diffusion mechanism. Signatures of correlated motion suggest unusual repulsive interactions between the water molecules. From the lineshape broadening we determine the diffusion coefficient, the diffusion energy and the pre-exponential factor.

Mass-transport at a surface is a key factor in heterogeneous catalysis. The rate is determined by excitation across a translational barrier and depends on the energy landscape and the coupling to the thermal bath of the surface. Here we use helium spin-echo spectroscopy (HeSE) to track the microscopic motion of benzene adsorbed on Cu(001) at low coverage (θ ∼ 0.07 ML). Specifically, our combined experimental and computational data determine both the absolute rate and mechanism of the molecular motion. The observed rate is significantly higher by a factor of 3.0±0.1 than is possible in a conventional, point-particle model and can only be understood by including additional molecular (rotational) coordinates. We argue that the effect can be described as an entropic contribution that enhances the population of molecules in the transition state. The process is generally relevant to molecular systems and illustrates the importance of the pre-exponential factor alongside the activation barrier in studies of surface kinetics.

The co-adsorption of hydrogen with a simple chiral modifier, alanine, on Ni{111} was studied using Density Functional Theory in combination with ambient-pressure X-ray photoelectron spectroscopy and X-ray absorption spectroscopy at temperatures of 300~K and above, which are representative of chiral hydrogenation reactions. Depending on the hydrogen pressure, the surface enables protons to "pop on and off" the modifier molecules, thus significantly altering the adsorption geometry and chemical nature of alanine from anionic tridentate in ultra-high vacuum to predominantly zwitterionic bidentate at hydrogen pressures above 0.1 Torr. This hydrogen-stabilised modifier geometry allows alternative mechanisms for proton transfer and the creation of enatioselective reaction environments.

The doping of graphitic and nanocarbon structures with nonmetal atoms allows for the tuning of surface electronic properties and the generation of new active sites, which can then be exploited for several catalytic applications. In this work, we investigate the direct conversion of methane into H2 and C2Hx over Klein-type zigzag graphene edges doped with nitrogen, boron, phosphorus and silicon. We combine Density Functional Theory (DFT) and microkinetic modeling to systematically investigate the reaction network and determine the most efficient edge decoration. Among the four edge-decorated nanocarbons (EDNCs) inves-tigated, N-EDNC presented an outstanding performance for H2 production at temperatures over 900 K, followed by P-EDNC, Si-EDNC and B-EDNC. The DFT and microkinetic analysis of the enhanced desorption rate of atomic hydrogen reveal the presence of an Eley-Rideal mechanism, in which P-EDNC showed higher activity for H2 production in this scenario. Coke deposition resistance in the temperature range between 900 and 1500 K was evaluated, and we compared the selectivity toward H2 and C2H4 production. The N-EDNC and P-EDNC active sites showed strong resistance to carbon poisoning, whereas Si-EDNC showed higher propensity to regenerate its active sites at temperatures over 1100 K. This work shows that decorated EDNCs are promising metal-free catalysts for methane conversion into H2 and short-length alkenes.

Although hydrogen bonds have long been established as a highly effective intermolecular interaction for controlling the formation of self-assembled monolayers, the potential utility of the closely related halogen bonds has only recently emerged. The synergistic use of both halogen and hydrogen bonds provides a unique, multitiered strategy towards controlling the morphology of self-assembled structures. However, the interplay between these two interactions within monolayer systems has been little studied. Here, we have systematically investigated this interplay in self-assembled monolayers formed at the solid-liquid interface, with a specific attention on determining the structural relevance of the two interactions in the formation of 2D supramolecular structures. A single molecule which can simultaneously act as both a halogen and hydrogen bond donor was paired with molecules which are effective acceptors for both of these interactions. The bimolecular networks that result from these pairings were studied using scanning tunnelling microscopy coupled with density function theory calculations. Additional measurements on similar networks formed by using structural analogues in which halogen bonding interactions are no longer possible give significant insight into the structure-determining role of these interactions. We find that in some monolayer systems the halogen bonds serve no significant structure-determining role and the assembly is dominated by hydrogen bonding; however, in other systems, effective cooperation between the two interactions is observed. This study gives clear insight into the synergistic and competitive balance between halogen and hydrogen bonds in self-assembled monolayers. This information is expected to be of considerable value for the future design of monolayer systems using both halogen and hydrogen bonds.

One of the most important topics in molecular biology is the genetic stability of DNA. One threat to this stability is proton transfer along the hydrogen bonds of DNA that could lead to tautomerisation, hence creating point mutations. We present a theoretical analysis of the hydrogen bonds between the Guanine-Cytosine (G-C) nucleotide, which includes an accurate model of the structure of the base pairs, the quantum dynamics of the hydrogen bond proton, and the influence of the decoher-ent and dissipative cellular environment. We determine that the quantum tunnelling contribution to the proton transfer rate is several orders of magnitude larger than the classical over-the-barrier hopping. Due to the significance of the quantum tunnelling even at biological temperatures, we find that the canonical and tautomeric forms of G-C inter-convert over timescales far shorter than biological ones and hence thermal equilibrium is rapidly reached. Furthermore, we find a large tautomeric occupation probability of 1.73 × 10 −4 , suggesting that such proton transfer may well play a far more important role in DNA mutation than has hitherto been suggested. Our results could have far-reaching consequences for current models of genetic mutations.

By adopting structural conformations with sub-nanometer precision, nature creates highly concentrated pigment-protein arrays to capture solar energy with high-efficiency. Synthetic analogues of such systems exhibit concentration dependent fluorescence quenching when approaching pigment concentrations of that seen in biological systems. Here we report on systems of acid functionalised multi-walled carbon nanotubes (o-MWCNT) and aminophenyl tetraporphyrins that create a novel synthetic pigment-scaffold complex. The complex does not follow the trend of typical fluorescence quenching. Our steady-state and time-resolved data suggest an optimal concentration that offers a luminescence enhancement compared to the expected standard Stern-Volmer quenching relationship. The quenching is modified by controlling 1 the pigment-distance via agglomerate size to near the upper limit for Dex-ter transfer of 10Å10˚10Å as confirmed by dynamic light scattering measurements and chromophore-chromophore nearest neighbour calculations. Our results highlight a potential synthetic complex with facile synthesis to investigate resonant electron transfer processes that do not follow traditional luminescence self-quenching relationships.

The interfacial behaviour of water remains a central question to fields as diverse as protein folding, friction and ice formation 1,2. While the structural and dynamical properties of water at interfaces differ strongly from those in the bulk, major gaps in our knowledge at the molecular level still prevent us from understanding these ubiquitous chemical processes. Information concerning the microscopic motion of water comes mostly from computational simulation 3,4 but the dynamics of molecules, on the atomic scale, is largely unexplored by experiment. Here we present experimental results combined with ab initio calculations to provide a detailed insight into the behaviour of water monomers on a graphene surface. We show that motion occurs by activated hopping on the graphene lattice. The dynamics of water diffusion displays remarkably strong signatures of cooperative behaviour due to repulsive forces between the monomers. The repulsive forces enhance the monomer lifetime (tm ≈ 3 s at TS = 125 K) in a free-gas phase that precedes the nucleation of ice islands and, in turn, provides the opportunity for our experiments to be performed. Our results give a unique molecular perspective on a kinetic barrier to ice nucleation on a crystalline surface, providing new understanding of the processes involved in ice formation. I ce often forms easily on solid surfaces and to understand why 1 that happens, the molecular basis of the water-surface inter-2 action needs to be studied 2,5. The structure, dynamics and 3 chemical properties of water at interfaces differ from those of bulk 4 water and ice 6–8. The early stages of ice nucleation involve ex-5 ceedingly small time and length scales 9 and while ice nucleation 6 and phase transitions are well understood macroscopically, unrav-7 elling the microscopic details presents one of the great challenges 8 in physical sciences with important implications from the chem-9 istry of the Earth's atmosphere 10 to physicochemical processes oc-10 curring on cosmic dust grains 11. 11 It is the motion of water molecules at surfaces, that controls 12 these fundamental phenomena in physics, chemistry and biology 13 as well as a diverse range of technological processes 1,2,12. Wet-14 ting, hydrophobicity and ice nucleation are all very widely studied 15 on the macroscopic scale, using routine methods such as contact 16 angle measurements 13–15. However, more precise measurements, 17 with a molecular level of detail, are much scarcer, despite the fact 18 that an understanding could open up new opportunities for the 19 design of advanced materials, by exploiting our ability to tune 20 surfaces at the nanoscale 16. For example, ice nucleation on sur-21 faces is alone of huge technological relevance to fields as diverse 22 as wind power 13,17 , aviation 14,18 and telecommunications 13. 23 Water is fundamentally challenging to study with atomic reso-24 lution. It is difficult to achieve sufficient contrast and resolution 25 with imaging techniques 19 , particularly in order to understand 26 the position of the H atoms and thus the molecular orientation. 27 Electron based techniques such as LEED also scatter weakly from 28 hydrogen and present a severe risk of damage, in the form of wa-29 ter dissociation 20,21. Some structural studies of water have been 30 possible experimentally, but are usually restricted to flat metal 31 surfaces 20–25 or a few ionic crystals, such as NaCl 19,26. These 32 studies have revealed the role of short range attractive forces. 33 Dynamics and low coverage measurements, which could exam-34 ine the nature of water interactions more generally, are further 35 complicated by fast diffusion rates and the short lifetimes of wa-36 ter monomers. Insight has therefore been mostly limited to that 37 possible with numerical simulations 3,4 , often without any direct 38 experimental validation to support them. 39 In this paper we report the serendipitous discovery of a regime 40 where freely mobile water can be studied on a Ni(111) supported 41 graphene surface. We use the helium spin-echo (HeSE) technique, 42 illustrated in Figure 1a, to measure surface correlations in the 43 water monomer motion (see Methods). HeSE uses wavepacket 44 splitting and recombination to give temporal sensitivity over pi-45 cosecond timescales, resulting in data of the form shown in the 46 inset of Figure 1a. The use of these very low energy He atoms 47 completely excludes any possibility of damage or dissociation of 48 the water. As we describe below, by analysing the dephasing rates 49 in the correlation measurements to obtain the signatures shown 50 in Figure 1b, we are able to establish that, contrary to expecta-51 tions, strong repulsive interactions exist between adsorbed water 52 molecules. We attribute these forces to dipolar interactions, aris-53 ing from structural hindrance of water reorientation by the ad-54 sorption geometry. The repulsion leads to a kinetic barrier that 55 inhibits the nucleation of solid ice, while extending the surface 56 lifetime of water monomers and simultaneously making our mea-57 surements possible. 58 Results 59 In order to identify the range of conditions where individual wa-60 ter molecules are mobile, we carried out extensive adsorption 61 and desorption measurements on the graphene/Ni(111) surface. 62 The substrate was prepared in ultra-high vacuum (UHV) condi-63 tions and graphene was grown using established methods 27 (see 64 Methods and Sample preparation in the supplementary informa-65 tion (SI)). Growing a thick film of water at 100 K results in a 66 1

Molecular simulations can measure strain in bond lengths, angles, torsion, and non-bonded interactions. High strain energy indicates a reactive and unstable molecule. Method 4-turn amylose and saturated FA models (C8-C22) were built using MOE2020.09 software. Molecular dynamics were simulated in water, with complexes containing 1 or 2 FAs per amylose helix. Results Conclusion The lower the energy, the more stable the molecule. • Double FA complexes are less stable than single FA complexes. • Trend: The stability increases from C8 and decreases from C14. • C10 single FA complexes have the lowest energy so are most likely to be stable, meaning they are a feasible candidate for practical use.

In this dataset, we have included computational inputs and outputs related to the paper titled “Theoretical Insights Into the Methane Catalytic Decomposition on Graphene Nanoribbon Edges”, published in Frontiers in Chemistry (doi: 10.3389/fchem.2023.1172687). The dataset comprises geometry optimizations of the catalysts employed, namely H-passivated and H-free 12-ZGNR and 12-AGNR. It also includes local minimum energy points and transition states of the reaction mechanisms, starting from the physisorption of methane and leading to the formation of solid carbon and hydrogen. Additionally, the dataset contains input/output files for molecular dynamics simulations investigating the stability of 12-AGNR and 12-ZGNR, as well as the physisorption of methane on the edges. All files are associated with the CASTEP program, with input files generally having the .in extension and output files having the .castep extension.

Hachimoji DNA is a synthetic nucleic acid extension of DNA, formed by an additional four bases, Z, P, S, and B, that can encode information and sustain Darwinian evolution. In this paper, we aim to look into the properties of hachimoji DNA and investigate the probability of proton transfer between the bases, resulting in base mismatch under replication. First, we present a proton transfer mechanism for hachimoji DNA, analogous to the one presented by Löwdin years prior. Then, we use density functional theory to calculate proton transfer rates, tunnelling factors and the kinetic isotope effect in hachimoji DNA. We determined that the reaction barriers are sufficiently low that proton transfer is likely to occur even at biological temperatures. Furthermore, the rates of proton transfer of hachimoji DNA are much faster than in Watson–Crick DNA due to the barrier for Z–P and S–B being 30% lower than in G–C and A–T. Suggesting that proton transfer occurs more frequently in hachimoji DNA than canonical DNA, potentially leading to a higher mutation rate. Hachimoji DNA is a synthetic nucleic acid extension of DNA formed by an additional four bases that can encode information. We examine the possibility of proton transfer between the hachimoji bases, which can result in base mismatch under replication.

A homologous series of halogen bonding monolayers based on terminally iodinated perfluoroalkanes and 4,4′-bipyridine have been observed on a graphitic surface and noninvasively probed using powder X-ray diffraction. An excellent agreement is observed between the X-ray structures and density functional theory calculations with dispersion force corrections. Theoretical analysis of the binding energies of the structures indicate that these halogen bonds are strong (25 kJ mol–1), indicating that the layers are highly stable. The monolayer structures are found to be distinct from any plane of the corresponding bulk structures, with limited evidence of partitioning of hydrocarbon and perfluoro tectons. The interchain interactions are found to be slightly stronger than those in related aromatic systems, with important implications for 2D crystal engineering.

We examine the mechanism of pyrolysis and charring of large (> 10,000 atom) phenol-formaldehyde resin structures produced using pseudo-reaction curing techniques with formaldehyde/phenol ratios of 1.0, 1.5 and 2.0. We utilise Reactive Molecular Dynamics (RMD) with a hydrocarbon oxidation parameter set to simulate the high-temperature thermal decomposition of these resins at 1500, 2500 and 3500 K. Our results demonstrate that the periodic removal of volatile pyrolysis gasses from the simulation box allows us to achieve near complete carbonisation after only 2 ns of simulation time. The RMD simulations show that ring openings play a significantly larger role in thermal decomposition than has previously been reported. We also identify the major phases of phenolic pyrolysis and elucidate some of the possible mechanisms of fragment formation and graphitisation from the RMD trajectories and compute the thermal and mechanical properties of the final pyrolysed structures. [GRAPHICS] .

The adsorption of sodium on Ru(0001) is studied using 3He spin-echo spectroscopy (HeSE), molecular dynamics simulations (MD) and density functional theory (DFT). In the multi-layer regime, an analysis of helium reflectivity, gives an electron-phonon coupling constant of λ = 0.64 ± 0.06. At sub-monolayer coverage, DFT calculations show that the preferred adsorption site changes from hollow site to top site as the supercell increases and the effective coverage, θ, is reduced from 0.25 to 0.0625 adsorbates per substrate atom. Energy barriers and adsorption geometries taken from DFT are used in molecular dynamics calculations to generate simulated data sets for comparison with measurements. We introduce a new Bayesian method of analysis that compares measurement and model directly, without assuming analytic lineshapes. The value of adsorbate-substrate energy exchange rate (friction) in the MD simulation is the sole variable parameter. Experimental data at a coverage θ = 0.028 compares well with the low-coverage DFT result, giving an effective activation barrier Eeff = 46 ± 4 meV with a friction γ = 0.3 ps-1. Better fits to the data can be achieved by including additional variable parameters, but in all cases, the mechanism of diffusion is predominantly on a Bravais lattice, suggesting a single adsorption site in the unit cell, despite the close packed geometry.

The adenine-thymine tautomer (A*-T*) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A*-T* while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A*-T* as the DNA strands unzip and the hydrogen bonds between the bases stretch. Molecular Dynamics simulations reveal the timescales and dynamics of DNA strand separation and the statistical ensemble of opening angles present in a biological environment. Our results demonstrate that the unwinding of DNA, an inherently out-of-equilibrium process facilitated by helicase, will change the energy landscape of the adenine-thymine tautomerisation reaction. We propose that DNA strand separation allows the stable tautomerisation of adenine-thymine, providing a feasible pathway for genetic point mutations via proton transfer between the A-T bases.

The doping of graphitic and nanocarbon structures with non-metal atoms allows for the tuning of surface electronic properties and the generation of new active sites, which can then be exploited for several catalytic applications. In this work, we investigate the direct conversion of methane into H2 and C2Hx over Klein-type zigzag graphene edges doped with nitrogen, boron, phosphorous and silicon. We combine Density Functional Theory (DFT) and microkinetic modelling to systematically investigate the reaction network and determine the most efficient edge decoration. Among the four edge-decorated nanocarbons (EDNCs) investigated, N-EDNC presented an outstanding performance for H2 production at temperatures over 900 K, followed by P-EDNC, Si-EDNC and B-EDNC. The DFT and microkinetic analysis of the enhanced desorption rate of atomic hydrogen reveal the presence of an Eley-Rideal mechanism, in which P-EDNC showed higher activity for H2 production in this scenario. Coke deposition resistance in the temperature range between 900 K and 1500 K was evaluated and we compared the selectivity towards H2 and C2H4 production. The N-EDNC and P-EDNC active sites showed strong resistance to carbon poisoning, whereas Si-EDNC showed the higher propensity to regenerate its active sites at temperatures over 1100 K. This work shows that decorated EDNCs are promising metal-free catalysts for methane conversion into H2 and short-length alkenes.

Proton transfer between DNA bases can lead to mutagenic tautomers, but as their lifetimes are thought to be much shorter than DNA separation times their role during the DNA replication cycle is often overlooked. Here, the authors model the separation of the DNA base pair guanine-cytosine using density functional theory and find increased stability of the tautomer when the DNA strands unzip as they enter a helicase enzyme, effectively trapping the tautomer population. Proton transfer between the DNA bases can lead to mutagenic Guanine-Cytosine tautomers. Over the past several decades, a heated debate has emerged over the biological impact of tautomeric forms. Here, we determine that the energy required for generating tautomers radically changes during the separation of double-stranded DNA. Density Functional Theory calculations indicate that the double proton transfer in Guanine-Cytosine follows a sequential, step-like mechanism where the reaction barrier increases quasi-linearly with strand separation. These results point to increased stability of the tautomer when the DNA strands unzip as they enter the helicase, effectively trapping the tautomer population. In addition, molecular dynamics simulations indicate that the relevant strand separation time is two orders of magnitude quicker than previously thought. Our results demonstrate that the unwinding of DNA by the helicase could simultaneously slow the formation but significantly enhance the stability of tautomeric base pairs and provide a feasible pathway for spontaneous DNA mutations.