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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.

Organic molecular thin-films are employed for manufacturing a wide variety of electronic devices, including memory devices 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, (C

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 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.

We report a thermodynamically feasible mechanism for producing H2 from NH3 using hBN as a catalyst.

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.

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 toward 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 that can simultaneously act as both a halogen and a hydrogen bond donor was paired with molecules that are effective acceptors for both of these interactions. The bimolecular networks that result from these pairings were studied by using scanning tunneling microscopy coupled with density functional 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.\ud \ud

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.

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.

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.

The coadsorption 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 ultrahigh vacuum to predominantly zwitterionic bidentate at hydrogen pressures above 0.1 Torr. This hydrogen-stabilized modifier geometry allows alternative mechanisms for proton transfer and the creation of enatioselective reaction environments. © 2018 American Chemical Society., Engineering and Physical Sciences Research Council M.S.I. Foundation Royal Society, The research leading to these results has received funding from the UK’s EPSRC through grants EP/G068593/1 and EP/ H015493/1. M.S. acknowledges the Royal Society for funding his fellowship and the HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), for use of the ARCHER UK National Supercomputing Service. The authors also thank the staff of ALS for their help during the experiments.

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).

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.

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 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.

6 págs.; 3 figs.; 2 tabs., This work presents an experimental picture of molecular ballistic diffusion on a surface, a process that is difficult to pinpoint because it generally occurs on 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 polyaromatic hydrocarbon (PAH) adsorbed on the basal plane of graphite. Pyrene, CH, 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 polyaromatic hydrocarbons adsorbed on graphite. © 2016 American Chemical Society, I.C.-A. is grateful to the Ramón Areces foundation for the funding of her postdoctoral research position. M.S. thanks the U.K.’s HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202); this work used the ARCHER U.K. National Supercomputing Service. E.B. acknowledges financial support by the graduate college of the Université de Grenoble (France) and A.T. thanks the FWF (Austrian Science Fund) for financial support within the project J3479-N20. S.M.-A. acknowledges the funding from the project FIS2014-52172- C2-1-P, from Ministerio de Economia y Competitividad (Spain).

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 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 be understood only 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.

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.

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.

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.

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.

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.

In this study, we use density functional theory (DFT) to investigate the surface co-adsorption of glycine with water on Cu{110}. Our results show that, under UHV conditions and for a wide range of temperatures, a pure glycine monolayer is more stable than either mixed gly–water phases or pure water (ice) monolayers, but for a high water pressure half-dissociated water layers can appear on the surface at low and medium temperatures.

Sulphide materials, in particular MoS(2), have recently received great attention from the surface science community due to their extraordinary catalytic properties. Interestingly, the chemical activity of iron pyrite (FeS(2)) (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 (NO(2)) on the FeS(2)(100) surface. Our results show that both those environmentally important NO(x) 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 NO(2) adsorption onto one of the non-equivalent Fe-Fe bridge sites of the (1 × 1)-FeS(2)(100) surface. From the calculated high barrier for NO and NO(2) direct dissociation on this surface, we can deduce that both nitrogen oxides species are adsorbed molecularly on pyrite surfaces.

Absorption spectra of silane in the region of the first overtone of the Si-H stretch vibration have been recorded in a seeded supersonic jet expansion by cavity ring-down spectroscopy as well as in a static gas cell at room temperature by photoacoustic spectroscopy. Spectral simplification due to strong rotational cooling in the jet expansion enables us to clearly resolve and assign the rovibrational transitions of the (2000) and (1100) bands of the three isotopologues, (28)SiH(4), (29)SiH(4), and (30)SiH(4), in their natural isotopic abundance. Interconversion between different nuclear spin species of SiH(4) is found to be absent during the jet expansion. Isotope shifts for (29)SiH(4) and (30)SiH(4) relative to (28)SiH(4) are measured and found to be suitable for selective vibrational excitation of any of three silane isotopologues by pulsed laser excitation in a jet expansion.

We have investigated methane (CH(4)) 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 ν(1) 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 ν(1) state and the calculated highest fractional vibrational energy content in this mode.

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 .

The quantum state-resolved reactivity S(0) of SiH(4) on Si(100)-2x1 has been measured for the first time for two vibrationally excited Si-H stretch local mode states (mid R:2000 and mid R:1100) as well the ground state S(0) as a function of translational energy E(n) and surface temperature T(s). We observe evidence for both direct and precursor-mediated chemisorption pathways. As expected, increasing E(n) (or T(s)) decreases S(0) for the precursor-mediated reaction and increases S(0) for the direct chemisorption. However, vibrational excitation of the incident SiH(4) increases S(0) for both the direct and the precursor-mediated pathway with a higher S(0) for the mid R:2000 state than for the mid R:1100 state, indicating a nonstatistical reaction mechanism.