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We report quantum calculations involving the dynamics of rotational energy-transfer processes, by collision with He atoms in interstellar environments, of the title molecular species which share the presence of the CN backbone and are considered of importance in those environments. The latter structural feature is taken to be especially relevant for prebiotic chemistry and for its possible role in the processing of the heterocyclic rings of RNA and DNA nucleobases in the interstellar space. We carry out ab initio calculations of their interaction potentials with He atoms and further obtain the state-to-state rotationally inelastic cross sections and rate coefficients over the relevant range of temperatures. The similarities and differences between such species and other similar partners which have been already detected are analyzed and discussed for their significance on internal state populations in interstellar space for the two title molecular radicals.

Non-covalent interactions between sulfur centers and aromatic rings play important roles in biological chemistry. We examined here the sulfur-arene interactions between the fused aromatic heterocycle benzofuran and two prototype sulfur divalent triatomics (sulfur dioxide and hydrogen sulfide). The weakly-bound adducts were generated in a supersonic jet expansion and characterized with broadband (chirped-pulsed) time-domain microwave spectroscopy. The rotational spectrum confirmed the detection of a single isomer for both heterodimers, consistent with the computational predictions for the global minima. The benzofuran⋯sulfur dioxide dimer exhibits a stacked structure with sulfur closer to benzofuran, while in benzofuran⋯hydrogen sulfide the two S-H bonds are oriented towards the bicycle. These binding topologies are similar to the corresponding benzene adducts, but offer increased interaction energies. The stabilizing interactions are described as S⋯π or S-H⋯π, respectively, using a combination of density-functional theory calculations (dispersion corrected B3LYP and B2PLYP), natural bond orbital theory, energy decomposition and electronic density analysis methods. The two heterodimers present a larger dispersion component, but nearly balanced by electrostatic contributions.

A new rationally designed fully rotationally restricted luciferin has been synthesised. This synthetic luciferin, based upon the structure of infraluciferin, has two intramolecular H-bonds to reduce degrees of freedom, an amine group to enhance ICT process, and an alkenyl group to increase π-conjugation. In the spectroscopic measurements and computational calculations, enamine luciferin showed more red-shifted absorption and fluorescence emission than LH 2 and iLH 2 . With PpyWT luciferase enamine luciferin gave bioluminescence at 564 nm which is similar to LH 2 at 561 nm. Further investigation by docking studies revealed that the emission wavelength of enamine luciferin might be attributed to the unwanted twisted structure caused by Asp531 within the enzyme. With mutant luciferase FlucRed, the major emission peak was shifted to 606 nm, a distinct shoulder above 700 nm, and 21% of its spectrum located in the nIR range.

The development of systems that can be switched between states with different thermal conductivities is one of the current challenges in materials science. Despite their enormous diversity and chemical richness, molecular materials have been only scarcely explored in this regard. Here, we report a reversible, light-triggered thermal conductivity switching of ≈30-40% in mesophases of pure 4,4'-dialkyloxy-3-methylazobenzene. By doping a liquid crystal matrix with the azobenzene molecules, reversible and bidirectional switching of the thermal conductivity can be achieved by UV/Vis-light irradiation. Given the enormous variety of photoactive molecules and chemically compatible liquid crystal mesophases, this approach opens unforeseen possibilities for developing effective thermal switches based on molecular materials., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Hard-sphere crystallization has been widely investigated over the last six decades by means of colloidal suspensions and numerical methods. However, some aspects of its nucleation behaviour are still under debate. Here, we provide a detailed computational characterisation of the polymorphic nucleation competition between the face-centered cubic (fcc) and the hexagonal-close packed (hcp) hard-sphere crystal phases. By means of several state-of-the-art simulation techniques, we evaluate the melting pressure, chemical potential difference, interfacial free energy and nucleation rate of these two polymorphs, as well as of a random stacking mixture of both crystals. Our results highlight that, despite the fact that both polymorphs have very similar stability, the interfacial free energy of the hcp phase could be marginally higher than that of the fcc solid, which in consequence, mildly decreases its propensity to nucleate from the liquid compared to the fcc phase. Moreover, we analyse the abundance of each polymorph in grown crystals from different types of inserted nuclei: fcc, hcp and stacking disordered fcc/hcp seeds, as well as from those spontaneously emerged from brute force simulations. We find that post-critical crystals fundamentally grow maintaining the polymorphic structure of the critical nucleus, at least until moderately large sizes, since the only crystallographic orientation that allows stacking close-packed disorder is the fcc (111) plane, or equivalently the hcp (0001) one. Taken together, our results contribute with one more piece to the intricate puzzle of colloidal hard-sphere crystallization.

Colloidal particles have been extensively used to comprehend the main principles governing liquid-crystal nucleation. Multiple mechanisms and frameworks have been proposed, through either experiments or computational approaches, to rationalise the ubiquitous formation of colloidal crystals. In this work, we elucidate the nucleation scenario behind the crystallization of oppositely charged colloids. By performing molecular dynamics simulations of colloidal electrolytes in combination with the Seeding technique, we evaluate the fundamental factors, such as the nucleation rate, free energy barrier, surface tension and kinetic pre-factor, that determine the liquid-to-solid transition of several crystalline polymorphs. Our results show that at a high packing fraction, there is a cross-over between the nucleation of the CsCl structure and that of a substitutionally disordered fcc phase, despite the CuAu crystal being the most stable phase. We demonstrate that the crucial factor in determining which phase nucleates the fastest is the free energy cost of the cluster formation rather than their kinetic ability to grow from the liquid. While at a low packing fraction, the stable phase, CsCl, is the one that nucleates and subsequently grows, we show how at moderate and high packing fractions, a disordered fcc phase subsequently grows regardless of the nature of the nucleating phase, termed parasitic crystallization. Taken together, our results provide a panoramic perspective of the complex nucleation scenario of oppositely charged colloids at moderate temperature and rationalise the different thermodynamic and kinetic aspects behind it.

Thermal rate constants of nine-atom hydrogen abstraction reactions, X + C2H6 → HX + C2H5 (X ≡ H, Cl, F) with qualitatively different reaction paths, have been investigated using two kinetics approaches - variational transition state theory with multidimensional tunnelling (VTST/MT) and ring polymer molecular dynamics (RPMD) - and full dimensional analytical potential energy surfaces. For the H + C2H6 reaction, which proceeds through a noticeable barrier height of 11.62 kcal mol-1, kinetics approaches showed excellent agreement between them (with differences less than 30%) and with the experiment (with differences less than 60%) in the wide temperature range of 200-2000 K. For X = Cl and F, however, the situation is very different. The barrier height is either low or very low, 2.44 and 0.23 kcal mol-1, respectively, and the presence of van der Waals complexes in the entrance channel leads to a very flat topography and, consequently, imposes theoretical challenges. For the Cl(2P) reaction, VTST/MT underestimates the experimental rate constants (with differences less than 86%), and RPMD demonstrates better agreement (with differences less than 47%), although the temperature dependence is opposite to the experiment at low temperatures. Finally, for the F(2P) reaction, available experimental information shows discrepancies, both in the absolute values of the rate constants and also in the temperature dependence. Unfortunately, kinetics theories did not resolve this discrepancy. Different possible causes of these theory/experiment discrepancies were analyzed.

Hard-sphere model systems are well-suited in both experiment and simulations to investigate fundamental aspects of the crystallization of fluids. In experiments on colloidal models of hard-sphere fluids, the fluid is unavoidably in contact with the walls of the sample cell, where heterogeneous crystallization may take place. In this work we use simulations to investigate the competition between homogeneous and heterogeneous crystallization. We report simulations of wall-induced nucleation for different confining walls. Combining the results of these simulations with earlier studies of homogeneous crystallization allows us to assess the competition between homogeneous and heterogeneous nucleation as a function of the wall type, fluid density and the system size. On flat walls, heterogeneous nucleation will typically overwhelm homogeneous nucleation. Even for surfaces randomly coated with spheres with a diameter that was some three times larger than that of the fluid spheres - as has been used in some experiments - heterogeneous nucleation is likely to be dominant for volume fractions smaller than ∼0.535. Only for a disordered coating that has the same structure as the liquid did we find that nucleation was likely to occur in the bulk. Hence, such coatings might be used to suppress heterogeneous nucleation in experiments. Finally, we report the apparent homogeneous nucleation rate taking into account the formation of crystallites both in the bulk and at the walls. We find that the apparent overall nucleation rates coincide with those reported in "homogeneous nucleation" experiments. This suggests that heterogeneous nucleation at the walls could partly explain the large discrepancies found between experimental measurements and simulation estimates of the homogeneous nucleation rate.

Pure water can be substantially supercooled below the melting temperature. The pressures and temperatures where water is observed to freeze in supercooling experiments define the so-called homogeneous nucleation line. The slope of such a line changes from negative to positive as pressure increases. In our work, we use computer simulations with the TIP4P/Ice water model to investigate such a change of slope. The simulation prediction for the melting and the homogeneous nucleation lines is in reasonable agreement with the experiment. We find, in accordance with a previous hypothesis, that the aforementioned slope sign inversion can be explained by a change in the nucleating ice polymorph from ice Ih to ice III. Moreover, we underline the kinetic character of the homogeneous nucleation line by defining different lines for different values of the nucleation rate. We analyse in detail the factors that affect the competition between ices Ih and III in the framework of classical nucleation theory.

A theoretical study of the dynamics of the F( 2 P) + C 2 H 6 hydrogen abstraction reaction was presented using quasi-classical trajectories propagated on an ab initio fitted global potential energy surface, PES-2018. The results were compared with experimental information at a collision energy of 3.2 kcal mol -1 . We found a small fraction of available energy, 13%, deposited as C 2 H 5 internal energy, the largest fraction, 67%, being deposited as HF(v) vibration, where the HF(v,j) rotational distribution is colder when the vibrational level increases. These results reproduce the experimental evidence. In addition, the reaction cross section scarcely changes with energy, and the scattering distribution shifts from isotropic to forward when the HF(v) vibrational state increases. These last two findings await experimental confirmation. Finally, two important issues related to the title reaction were analysed: the role of an ethyl radical, and the theory/experiment controversy about the HF(v) bimodal vibrational distribution. We found that in spite of its low internal energy, the ethyl product does not act as a spectator of the reaction, and that the controversy can be explained by the net result of two opposite effects: strong couplings between vibrational modes, which are the rule and complicate dynamics analysis in polyatomic systems, and an artificial energy transfer from the ethyl radical to the HF molecule due to the classical nature of the quasi-classical trajectory calculations. As is seen, the ethyl radical actively participates in both effects.

Herein, we present a fabrication approach that produces homogeneous core-satellite SERS encoded particles with minimal interparticle gaps (<2-3 nm) and maximum particle loading, while positioning the encoding agents at the gaps. Integration of plasmonic building blocks of different sizes, shapes, compositions, surface chemistries or encoding agents is achieved in a modular fashion with minimal modification of the general synthetic protocol. These materials present an outstanding optical performance with homogeneous enhancement factors over 4 orders of magnitude as compared with classical SERS encoded particles, which allows their use as single particle labels., Competing Interests: The authors declare no competing interests., (This journal is © The Royal Society of Chemistry.)

In the study of non-reactive energy transfer between O 2 and N 2 molecules bearing different vibrationally excited states we have faced the problem of selecting a proper formulation of the interaction. To this end we have compared the values of the related observables computed either on a potential energy surface globally fitted to very large ab initio potential energy values [Varga et al., J. Chem. Phys., 2016, 144, 024310] or on two more traditional ones formulated as a combination of an intra- and inter-molecular model component of the interaction (and based on a different combined use of experimental and ab initio information) [Garcia et al., J. Phys. Chem. A, 2016, 120, 5208] in order to enforce an appropriate modelling of the long-range tail of the potential, crucial for the description of inelastic vibrational energy transfer. A detailed graphical analysis of the potential plus a quantitative analysis of the computed opacity functions, of the state-to-state rate coefficients, of the second virial coefficient and of the integral non-reactive cross section allowed us to conclude that the model formulation of the interaction has to be preferred for non-reactive studies of the O 2 + N 2 energy transfer processes in thermal and subthermal regimes.

Using a full-dimensional analytical potential energy surface describing the OH/OD + GeH 4 hydrogen abstraction reactions (J. Espinosa-Garcia, C. Rangel and J. C. Corchado, Phys. Chem. Chem. Phys., 2016, 18, 16941), quasi-classical trajectory calculations were performed at 298 K to simulate the scarce experimental data at this temperature. This system presents wells in the entrance and exit channels, influencing product angular distribution, which is practically isotropic. Moreover, isotopic effects were not observed. It was found that the GeH 3 co-product presents little internal energy (11% of the total available energy), although not negligible, and that the water product receives the major part of the available energy, mainly in the newly formed OH bond, while the initial OH/OD reactant bond acts as a spectator mode. These results reproduce the experimental evidence, the larger discrepancy being in the water bending vibrational distribution, which is broader in the experiment. Several factors were analyzed to account for this discrepancy, and it was concluded that the zero-point energy violation per mode is the main, but not the only, cause.

An interaction between two atoms, bonded or non-bonded, consists of interatomic contributions: electrostatic energy, exchange energy and electronic correlation energy. Together with the intra-atomic energy of an atom, these contributions are the basic components of the Interacting Quantum Atom (IQA) energy decomposition scheme. Here, we investigate IQA's proper use in conjunction with an explicit implementation of the B3LYP functional. The recovery of the total molecular energy from the IQA components is emphasised, for the first time. A systematic study of three model systems of biological relevance, N-methylacetamide (NMA), the doubly capped tripeptide GlyGlyGly and an alloxan dimer, shows the stabilization effect of B3LYP on most of the interatomic exchange energies (V) compared to their Hartree-Fock values. Diagrams of exchange energies versus interatomic distance show the clustering of interactions, one cluster for each 1,n (n = 1 to 6 where the atoms are separated by n - 1 bonds). The positioning of some V values outside their expected cluster marks interesting interactions.

We report an analytical full-dimensional potential energy surface for the GeH4 + OH → GeH3 + H2O reaction based on ab initio calculations. It is a practically barrierless reaction with very high exothermicity and the presence of intermediate complexes in the entrance and exit channels, reproducing the experimental evidence. Using this surface, thermal rate constants for the GeH4 + OH/OD isotopic reactions were calculated using two approaches: variational transition state theory (VTST) and quasi-classical trajectory (QCT) calculations, in the temperature range 200-1000 K, and results were compared with the only experimental data at 298 K. Both methods showed similar values over the whole temperature range, with differences less than 30%; and the experimental data was reproduced at 298 K, with negative temperature dependence below 300 K, which is associated with the presence of an intermediate complex in the entrance channel. However, while the QCT approach reproduced the experimental kinetic isotope effect, the VTST approach underestimated it. We suggest that this difference is associated with the harmonic approximation used in the treatment of vibrational frequencies.

As water is involved in countless natural and industrial processes, its thermodynamic properties have been measured in a wide temperature and pressure range. Data on supercooled water are also available down to -73 °C and up to 400 MPa. In contrast, data at negative pressures are extremely scarce. Here we provide an experimental equation of state for water down to -120 MPa. In particular, we obtain the line of density maxima (LDM) of water down to a pressure six times more negative than previously available. As temperature increases from 4 up to 18 °C, the pressure PLDM(T) along the LDM decreases monotonically from 0 down to -120 MPa, while the slope dPLDM/dT becomes more negative. The experimental results are compared with molecular dynamic simulations of TIP4P/2005 water and a two-state model. We also discuss the possibility to observe extrema in compressibility and heat capacity at negative pressures, features that have remained elusive at positive pressures.

From a kinetics standpoint, reactive molecular collisions are the building blocks of the mechanisms of chemical reactions. In contrast, a dynamics standpoint reveals molecular collisions to have their own internal mechanisms, which are not mere theoretical abstractions: through suitable preparation of the reactants internal and stereochemical states, features of the mechanisms of a reactive molecular collision can be made evident and used as "handles" to control the reaction outcome. Using time-independent quantum dynamical calculations, we demonstrate this for the Br + H2(v = 0-1, j = 2) → H + HBr reaction in the 1.0-1.6 eV range of total energies. Despite its pronounced effect on reactivity, which is in agreement with the predictions from Polanyi rules, reactant vibration is found to have little effect on the mechanism of this endoergic, late-barrier reaction. Analysis of the correlations between directional reaction properties shows that the collision stereochemistry strongly depends on the total energy, but not on how this energy is partitioned between reactant translation and vibration. The stereodynamical preferences implied by the collision mechanisms determine how and to what extent one can control the reaction. Regarding the overall reaction, the extent of control is found to be large near the reaction threshold but not when the total energy is high. Regarding state-to-state reactions, the effect of reactant stereochemistry on the product rotational state distribution is found to be nontrivial and energy dependent.

Computational methods for accurately calculating the binding affinity of a ligand for a protein play a pivotal role in rational drug design. We herein present a theoretical study of the binding of five different ligands to one of the proteins responsible for the human immunodeficiency virus type 1 (HIV-1) cycle replication; the HIV-1 reverse transcriptase (RT). Two types of approaches are used based on molecular dynamics (MD) simulations within hybrid QM/MM potentials: the alchemical free energy perturbation method, FEP, and the pathway method, in which the ligand is physically pulled away from the binding site, thus rendering a potential of mean force (PMF) for the binding process. Our comparative analysis stresses their advantages and disadvantages and, although the results are not in quantitative agreement, both methods are capable of distinguishing the most and the less potent inhibitors of HIV-1 RT activity on an RNase H site. The methods can then be used to select the proper scaffold to design new drugs. A deeper analysis of these inhibitors through molecular electrostatic potential (MEP) and calculation of the binding contribution of the individual residues shows that, in a rational design, apart from the strong interactions established with the two magnesium cations present in the RNase H site, it is important to take into account interactions with His539 and with those residues that are anchoring the metals; Asp443, Glu478, Asp498 and Asp549. The MEPs of the active site of the protein and the different ligands show a better complementarity in those inhibitors that present higher binding energies, but there are still possibilities of improving the favourable interactions and decreasing those that are repulsive in order to design compounds with higher inhibitory activity.

The development of an innovative computational strategy suited to provide an accurate quantum evaluation of the detailed properties of the N + N(2) exchange reaction has been undertaken by carrying out an extended theoretical study of such reaction. To this end exact and approximate quantum calculations (based on both time-independent and time-dependent techniques) of state-specific and state-to-state probabilities of the title reaction have been performed by considering values of the total angular momentum quantum number up to 20, values of total energy up to 2.3 eV and by making a combined use of both high throughput and high performance computing platforms. The comparison of the results obtained from calculations performed by taking into account the full Coriolis coupling of the allowed helicity states with those obtained when neglecting the Coriolis coupling or even a model energy shift treatment has allowed us to find out when a workflow managing the distribution of the jobs can replace exact treatments with approximate ones and for what type of properties this is possible.

Over the last forty years many computer simulations of water have been performed using rigid non-polarizable models. Since these models describe water interactions in an approximate way it is evident that they cannot reproduce all of the properties of water. By now many properties for these kinds of models have been determined and it seems useful to compile some of these results and provide a critical view of the successes and failures. In this paper a test is proposed in which 17 properties of water, from the vapour and liquid to the solid phases, are taken into account to evaluate the performance of a water model. A certain number of points between zero (bad agreement) and ten (good agreement) are given for the predictions of each model and property. We applied the test to five rigid non-polarizable models, TIP3P, TIP5P, TIP4P, SPC/E and TIP4P/2005, obtaining an average score of 2.7, 3.7, 4.7, 5.1, and 7.2 respectively. Thus although no model reproduces all properties, some models perform better than others. It is clear that there are limitations for rigid non-polarizable models. Neglecting polarizability prevents an accurate description of virial coefficients, vapour pressures, critical pressure and dielectric constant. Neglecting nuclear quantum effects prevents an accurate description of the structure, the properties of water below 120 K and the heat capacity. It is likely that for rigid non-polarizable models it may not be possible to increase the score in the test proposed here beyond 7.6. To get closer to experiment, incorporating polarization and nuclear quantum effects is absolutely required even though a substantial increase in computer time should be expected. The test proposed here, being quantitative and selecting properties from all phases of water can be useful in the future to identify progress in the modelling of water.

The β-sheet structure associated with chlorinated aromatics (d(Cl···Cl)≈ 4.0 Å) has been implemented to drive formation of π-stacked structures of dithiadiazolyl radicals. Both title compounds exhibit an increase in paramagnetism above 150 K but solid-state EPR studies indicate that the origin of the paramagnetism in these two systems is different.

An extended comparison of the reactive properties of the N + N(2) exchange reaction calculated on a non-collinear dominant potential energy surface using both a centrifugal sudden and a J-shift quantum method is reported. The choice of carrying out such an investigation for N + N(2) is motivated by the fact that the best available (and currently used for spacecraft re-entry simulations) computed set of kinetic data has been worked out using the low level J-shift approximation though based on exact quantum zero total angular momentum probabilities. The fact that our investigation is carried out for a heavy system and a potential energy surface free of wells in the strong interaction region minimizes the occurrence of tunnel, resonance and interference effects which would make the rationalization of the result difficult and the centrifugal sudden treatment less accurate. The study has provided evidence of two important limits of the J-shift approximation: the wrong determination of the maximum value of the total angular momentum quantum number J contributing to reactivity and the lack of deformation of the partial reactive probability dependence on energy at fixed J value. Accordingly, it has been found that the J-shift state-specific cross sections underestimate the corresponding CS values when the initial diatomic rotational energy is low while the situation reverses when the initial diatomic rotational energy is high.

A new global potential energy surface for the N + N2 exchange reaction has been built from ab initio data. To overcome the difficulty of carrying out ab initio calculations for a large set of geometries the alternative strategy of fitting the minimum energy paths of the surface and their angular dependence using a modified LAGROBO functional form has been adopted. In this way we have been able to reproduce all the main features of the potential using a fairly small set of ab initio values.

The electrochemical behaviour of pipemidic acid (8-ethyl-5,8-dihydro-5-oxo-2-(1-piperazinyl)-pyrido[2,3-d]pyrimidine-6- carboxylic acid), a well known antimicrobial agent used for urinary infections, was investigated by linear-sweep, differential-pulse and square-wave voltammetry at a hanging mercury drop electrode. Two reduction processes were observed in Britton-Robinson buffers at acid pH, whereas only one or two processes were observed in alkaline solutions, dependent on the pH of the buffer employed. Adsorptive effects were used to accumulate the drug on to the electrode. The adsorbed species were measured voltammetrically by using a cathodic process appearing at -0.76 V in 0.1 M HCIO4. Linear calibration graphs were obtained in the range 2.5 x 10(-9)-2.0 x 10(-7) M. A simple procedure of extraction was employed for the determination of the drug in urine samples.

A spectrofluorimetric method for the determination of ultratrace amounts of lead and cadmium is described based on the sequential extraction of the ternary ion-association complexes formed between the cation, a cryptand as the ligand and eosin as a counter ion. A linear working range from the detection limit (0.5 ng ml(-1) to 250 ng ml(-1) of lead and to 1 50 ng ml(-1) of cadmium was obtained. The relative standard deviation was 2-4%. The proposed method has been applied successfully to the determination of lead and cadmium in zinc metals and soft drinks.