Non-ergodic fragmentation upon collision-induced activation of cysteine-water cluster cations.

Cysteine-water cluster cations Cys(H2O)3,6+ and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collision-induced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies from DFT calculations showing that clusters do not only fragment exclusively by sequential emission of single water molecules but also by the release of small water clusters. Release of clustered water is observed also in the ADMP (atom centered density matrix propagation) molecular dynamics model of small Cys(H2O)3+ and Cys(H2O)3H+ clusters. For large clusters Cys(H2O)6+ and Cys(H2O)6H+ the less computationally demanding statistical Microcanonical Metropolis Monte-Carlo method (M3C) is used to model the experimental fragmentation patterns. We are able to detail the energy redistribution in clusters upon collision activation. In the present case, about two thirds of the collision energy redistribute via an ergodic process, while the remaining one third is transferred into a non-ergodic channel leading to ejection of a single water molecule from the cluster. In contrast to molecular fragmentation, which can be well described by statistical models, modelling of collision-induced activation of weakly bound clusters requires inclusion of non-ergodic processes.

A general approach to study molecular fragmentation and energy redistribution after an ionizing event.

We propose to combine quantum chemical calculations, statistical mechanical methods, and photoionization and particle collision experiments to unravel the redistribution of internal energy of the furan cation and its dissociation pathways. This approach successfully reproduces the relative intensity of the different fragments as a function of the internal energy of the system in photoelectron-photoion coincidence experiments and the different mass spectra obtained when ions ranging from Ar+ to Xe25+ or electrons are used in collision experiments. It provides deep insights into the redistribution of the internal energy in the ionized molecule and its influence on the dissociation pathways and resulting charged fragments. The present pilot study demonstrates the efficiency of a statistical exchange of excitation energy among various degrees of freedom of the molecule and proves that the proposed approach is mature to be extended to more complex systems.

SCC-DFTB Parameters for Fe-C Interactions.

We present an optimized density-functional tight-binding (DFTB) parameterization for iron-based complexes based on the popular trans3d set of parameters. The transferability of the original and optimized parameterizations is assessed using a set of 50 iron complexes, which include carbonyl, cyanide, polypyridine, and cyclometalated ligands. DFTB-optimized structures predicted using the trans3d parameters show a good agreement with both experimental crystal geometries and density functional theory (DFT)-optimized structures for Fe-N bond lengths. Conversely, Fe-C bond lengths are systematically overestimated. We improve the accuracy of Fe-C interactions by truncating the Fe-O repulsive potential and reparameterizing the Fe-C repulsive potential using a training set of six isolated iron complexes. The new trans3d*-LANLFeC parameter set can produce accurate Fe-C bond lengths in both geometry optimizations and molecular dynamics (MD) simulations, without significantly affecting the accuracy of Fe-N bond lengths. Moreover, the potential energy curves of Fe-C interactions are considerably improved. This improved parameterization may open the door to accurate MD simulations at the DFTB level of theory for large systems containing iron complexes, such as sensitizer-semiconductor assemblies in dye-sensitized solar cells, that are not easily accessible with DFT approaches because of the large number of atoms.

Unraveling the structural stability and the electronic structure of ThO2 clusters.

Unraveling the correlations between the geometry, the relative energy and the electronic structure of metal oxide nanostructures is crucial for a better control of their size, shape and properties. In this work, we investigated these correlations for stoichiometric thorium dioxide clusters ranging from ThO2 to Th8O16 using a chemically-driven geometry search algorithm in combination with state-of-the-art first principles calculations. This strategy allows us to homogeneously screen the potential energy surface of actinide oxide clusters for the first time. It is found that the presence of peroxo and superoxo groups tends to increase the total energy of the system by at least 3.5 eV and 7 eV, respectively. For the larger clusters, the presence of terminal oxygen atoms increases the energy by about 0.5 eV. Regarding the electronic structure, it is found that the HOMO-LUMO gap is larger in systems containing only bridging oxygen atoms (∼2-3.5 eV) than for systems containing oxo groups (∼1-3 eV), peroxo groups (∼0-2 eV), and superoxo groups (∼0-1 eV). Furthermore, while the LUMO is always dominated by thorium orbitals, the composition of the HOMO changes in the presence or the absence of oxo, peroxo and/or superoxo groups: in the presence of peroxo groups, it is dominated by thorium orbitals, in all other cases, it is dominated by oxygen orbitals, and is rather localized in the presence of terminal oxo or superoxo groups. These correlations are of great interest for synthesizing clusters with tailored properties, especially for applications in the field of nuclear energy and heterogeneous catalysis.

Dissociation dynamics of the diamondoid adamantane upon photoionization by XUV femtosecond pulses.

This work presents a photodissociation study of the diamondoid adamantane using extreme ultraviolet femtosecond pulses. The fragmentation dynamics of the dication is unraveled by the use of advanced ion and electron spectroscopy giving access to the dissociation channels as well as their energetics. To get insight into the fragmentation dynamics, we use a theoretical approach combining potential energy surface determination, statistical fragmentation methods and molecular dynamics simulations. We demonstrate that the dissociation dynamics of adamantane dications takes place in a two-step process: barrierless cage opening followed by Coulomb repulsion-driven fragmentation.

Development of Density Functional Tight-Binding Parameters Using Relative Energy Fitting and Particle Swarm Optimization.

We provide a strategy to optimize density functional tight-binding (DFTB) parameterization for the calculation of the structures and properties of organic molecules consisting of hydrogen, carbon, nitrogen, and oxygen. We utilize an objective function based on similarity measurements and the Particle Swarm Optimization (PSO) method to find an optimal set of parameters. This objective function considers not only the common DFTB descriptors of binding energies and atomic forces but also incorporates relative energies of isomers into the fitting procedure for more chemistry-driven results. The quality in the description of the binding energies and atomic forces is measured based on the Ballester similarity index and relative energies through a similarity index induced by the Levenshtein edit distance to quantify the correct energetic order of isomers. Training and testing datasets were created to include all relevant chemical functional groups. The accuracy of this strategy is assessed, and its range of applicability is discussed by comparison against our previous parameterization [A. Krishnapriyan, et al., J. Chem. Theory Comput. 13, 6191 (2017)]. The improved performance of the new DFTB parameterization is validated with respect to the density functional theory large datasets QM-9 [R. Ramakrishnan, et al., Sci. Data 1, 140022 (2014)] and ANI-1 [J. S. Smith, et al., Sci. Data 4, 170193 (2017)], where excellent agreement is found between the structures and properties available in these datasets, and the ones obtained with DFTB.

Fully versus constrained statistical fragmentation of carbon clusters and their heteronuclear derivatives.

The Microcanonical Metropolis Monte Carlo (MMMC) method has been shown to describe reasonably well fragmentation of clusters composed of identical atomic species. However, this is not so clear in the case of heteronuclear clusters as some regions of phase space might be inaccessible due to the different mobility of the different atomic species, the existence of large isomerization barriers, or the quite different chemical nature of the possible intermediate species. In this paper, we introduce a constrained statistical model that extends the range of applicability of the MMMC method to such mixed clusters. The method is applied to describe fragmentation of isolated clusters with high, moderate, and no heteronuclear character, namely, CnHm, CnN, and Cn clusters for which experimental fragmentation branching ratios are available in the literature. We show that the constrained statistical model describes fairly well fragmentation of CnHm clusters in contrast with the poor description provided by the fully statistical model. The latter model, however, works pretty well for both Cn and CnN clusters, thus showing that the ultimate reason for this discrepancy is the inability of the MMMC method to selectively explore the whole phase space. This conclusion has driven us to predict the fragmentation patterns of the C4N cluster for which experiments are not yet available.

Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations.

We present a complete exploration of the different fragmentation mechanisms of furan (C4H4O) operating at low and high energies. Three different theoretical approaches are combined to determine the structure of all possible reaction intermediates, many of them not described in previous studies, and a large number of pathways involving three types of fundamental elementary mechanisms: isomerization, fragmentation, and H/H2 loss processes (this last one was not yet explored). Our results are compared with the existing experimental and theoretical investigations for furan fragmentation. At low energies the first processes to appear are isomerization, which always implies the breaking of one C-O bond and one or several hydrogen transfers; at intermediate energies the fragmentation of the molecular skeleton becomes the most relevant mechanism; and H/H2 loss is the dominant processes at high energy. However, the three mechanisms are active in very wide energy ranges and, therefore, at most energies there is a competition among them.

M3C: A Computational Approach To Describe Statistical Fragmentation of Excited Molecules and Clusters.

The Microcanonical Metropolis Monte Carlo method, based on a random sampling of the density of states, is revisited for the study of molecular fragmentation in the gas phase (isolated molecules, atomic and molecular clusters, complex biomolecules, etc.). A random walk or uniform random sampling in the configurational space (atomic positions) and a uniform random sampling of the relative orientation, vibrational energy, and chemical composition of the fragments is used to estimate the density of states of the system, which is continuously updated as the random sampling populates individual states. The validity and usefulness of the method is demonstrated by applying it to evaluate the caloric curve of a weakly bound rare gas cluster (Ar13), to interpret the fragmentation of highly excited small neutral and singly positively charged carbon clusters (Cn, n = 5,7,9 and Cn+, n = 4,5) and to simulate the mass spectrum of the acetylene molecule (C2H2).

Structure, Ionization, and Fragmentation of Neutral and Positively Charged Hydrogenated Carbon Clusters: C(n)H(m)(q+) (n = 1-5, m = 1-4, q = 0-3).

In this work we present a systematic theoretical study of neutral and positively charged hydrogenated carbon clusters (C(n)H(m)(q+) with n = 1­5, m = 1­4, and q = 0­3). A large number of isomers and spin states (1490 in total) was investigated. For all of them, we optimized the geometry and computed the vibrational frequencies at the B3LYP/6-311++G(3df,2dp) level of theory; more accurate values of the electronic energy were obtained at the CCSD(T)/6-311++G(3df,2dp) level over the geometry previously obtained. From these simulations we evaluated several properties such as relative energies between isomers, adiabatic and vertical ionization potentials, and dissociation energies of several fragmentation channels. A new analysis technique is proposed to evaluate a large number of fragmentation channels in a wide energy range.

Communication: unraveling the (4)He droplet-mediated soft-landing from ab initio-assisted and time-resolved density functional simulations: Au@(4)He300/TiO2(110).

An ab-initio-based methodological scheme for He-surface interactions and zero-temperature time-dependent density functional theory for superfluid (4)He droplets motion are combined to follow the short-time collision dynamics of the Au@(4)He300 system with the TiO2(110) surface. This composite approach demonstrates the (4)He droplet-assisted sticking of the metal species to the surface at low landing energy (below 0.15 eV/atom), thus providing the first theoretical evidence of the experimentally observed (4)He droplet-mediated soft-landing deposition of metal nanoparticles on solid surfaces [Mozhayskiy et al., J. Chem. Phys. 127, 094701 (2007) and Loginov et al., J. Phys. Chem. A 115, 7199 (2011)].

Including nuclear quantum effects into highly correlated electronic structure calculations of weakly bound systems.

An interface between the APMO code and the electronic structure package MOLPRO is presented. The any particle molecular orbital APMO code [González et al., Int. J. Quantum Chem. 108, 1742 (2008)] implements the model where electrons and light nuclei are treated simultaneously at Hartree-Fock or second-order Möller-Plesset levels of theory. The APMO-MOLPRO interface allows to include high-level electronic correlation as implemented in the MOLPRO package and to describe nuclear quantum effects at Hartree-Fock level of theory with the APMO code. Different model systems illustrate the implementation: (4)He2 dimer as a protype of a weakly bound van der Waals system; isotopomers of [He-H-He](+) molecule as an example of a hydrogen bonded system; and molecular hydrogen to compare with very accurate non-Born-Oppenheimer calculations. The possible improvements and future developments are outlined.

Solvent states and spectroscopy of doped helium clusters as a quantum-chemistry-like problem.

The Full-Configuration-Interaction Nuclear-Orbital (FCI-NO) approach [J. Chem. Phys., 2009, 131, 19401], as the implementation of the quantum-chemistry ansatz, is overviewed and applied to (He)N-Cl2(X) clusters (N≤ 4). The ground and excited states of both fermionic (3)He and bosonic (4)He [see also, J. Phys. Chem. Lett., 2012, 2, 2145] clusters are studied. It is shown that the FCI-NO approach allows us to overcome three main difficulties: (1) the Fermi-Dirac (Bose-Einstein) nuclear statistics; (2) the wide (highly anharmonic) amplitudes of the He-dopant and He-He motions; and (3) both the weakly attractive (long-range) and the strongly repulsive (short-range) interaction between the helium atoms. Special emphasis is placed on the dependence of the cluster properties on the number of helium atoms, and on the comparison between the two helium isotopes. In particular, we analyze the analogies between quantum rings comprising electrons and (3)He atoms. The synthetic vibro-rotational Raman spectra of Cl2(X) immersed in ((3,4)He)N clusters (N≤ 4) are discussed as a function of the cluster size and the nuclear statistics. It is shown that the Coriolis couplings play a key role in modifying the spectral dopant profile in (3)He. Finally, we point out possible directions for future research using the quantum-chemistry ansatz.

Helium mediated deposition: modeling the He-TiO2(110)-(1×1) interaction potential and application to the collision of a helium droplet from density functional calculations.

This paper is the first of a two-part series dealing with quantum-mechanical (density-functional-based) studies of helium-mediated deposition of catalytic species on the rutile TiO(2)(110)-(1×1) surface. The interaction of helium with the TiO(2)(110)-(1×1) surface is first evaluated using the Perdew-Burke-Ernzerhof functional at a numerical grid dense enough to build an analytical three-dimensional potential energy surface. Three (two prototype) potential models for the He-surface interaction in helium scattering calculations are analyzed to build the analytical potential energy surface: (1) the hard-corrugated-wall potential model; (2) the corrugated-Morse potential model; and (3) the three-dimensional Morse potential model. Different model potentials are then used to study the dynamics upon collision of a (4)He(300) cluster with the TiO(2)(110) surface at zero temperature within the framework of a time-dependent density-functional approach for the quantum fluid [D. Mateo, D. Jin, M. Barranco, and M. Pi, J. Chem. Phys. 134, 044507 (2011)] and classical dynamics calculations. The laterally averaged density functional theory-based potential with an added long-range dispersion interaction term is further applied. At variance with classical dynamics calculations, showing helium droplet splashing out of the surface at impact, the time evolution of the macroscopic helium wave-function predicts that the helium droplet spreads on the rutile surface and leads to the formation of a thin film above the substrate. This work thus provides a basis for simulating helium mediated deposition of metallic clusters embedded within helium nanodroplets.

Quantum solvent states and rovibrational spectra of small doped (3)He clusters through the full-configuration-interaction nuclear orbital approach: The ((3)He)(N)-Cl(2)(X) case (N

A full-configuration-interaction nuclear orbital treatment has been recently developed as a benchmark quantum-chemistry-like method to study small doped (3)He clusters [M. P. de Lara-Castells et al., J. Chem. Phys. 125, 221101 (2006)]. Our objective in this paper is to extend our previous study on ((3)He)(N)-Cl(2)(B) clusters, using an enhanced implementation that allows employing very large one-particle basis sets [M. P. de Lara-Castells et al., J. Chem. Phys. 131, 194101 (2009)], and apply the method to the ((3)He)(N)-Cl(2)(X) case, using both a semiempirical T-shaped and an ab initio He-dopant potential with minima at both T-shaped and linear conformations. Calculations of the ground and low-lying excited solvent states stress the key role played by the anisotropy of the He-dopant interaction in determining the global energies and the structuring of the (3)He atoms around the dopant. Whereas (3)He atoms are localized in a broad belt around the molecular axis in ground-state N-sized complexes with N=1-3, irrespective of using the T-shaped or the ab initio He-dopant potential function, the dopant species becomes fully coated by just four (3)He atoms when the He-dopant potential also has a minimum at linear configurations. However, excited solvent states with a central ring-type clustering of the host molecule are found to be very close in energy with the ground state by using the ab initio potential function. A microscopic analysis of this behavior is provided. Additional simulations of the molecular rovibrational Raman spectra, also including excited solvent states, provide further insights into the importance of proper modeling the anisotropy of the He-dopant interaction in these weakly bound systems and of taking into account the low-lying excitations.

Apmo: un prograaa computacional para el estudiode efectos cuánticos nucleares mediante la teoría del orbital molecular electrónico y no electrónico / Apmo: a comuter program based on the electronic and non-electronic molecular orbital theory for studies of nuclear quantum effetts / Apmo: umprogramaa computacional para o estudo dos efeito quânticos nuclleares por meio do teoria do orbital molecular eletrônico e não - elerôônico

Con el fin de estudiar teóricamente fenómenos en donde los núcleos atómicos presentan comportamiento cuántico, hemos desarrollado el paquete computacional APMO (Any-Particle Molecular Orbital). Éste implementa el método de orbitales moleculares nucleares y electrónicos (OMNE) a un nivel de teoría Hartree- Fock (HF), en el que tanto núcleos como electrones se representan como funciones de onda. Para comprobar la correcta implementación del método se realizaron cálculos de estructura electrónica regular y núcleo- electrónica de las moléculas H2 y LiH. Las componentes de energía calculadas siguen las tendencias y están en el mismo orden de magnitud de cálculos similares reportados en la literatura. A diferencia de otros paquetes que implementan el método OMNE, el nuestro fue diseñado para estudiar sistemas con cualquier número de especies cuánticas.

With the aim of studying phenomena where atomic nuclei have a quantal behavior, we have developed the APMO (Any-Particle Molecular Orbital) software package. This implements the nuclear and electronic molecular orbital approach (NEMO) at a Hartree-Fock level of theory, where both nuclei and electrons are represented as wave functions. To verify the correct implementation of the method, a number of electronic and nuclear-electronic calculations were carried out on H2 and LiH molecules. The calculated energy components follow the trends and are of the same order of magnitude of similar calculations reported in the literature. In contrast to other packages that implement the NEMO approach, ours is designed to allow for studying systems with any number of quantum particles.

Com a finalidade de estudar teoricamente fenômenos cujos núcleos atômicos apresentam comportamento quântico, desenvolvemos o pacote computacional APMO (Any-Particle Molecular Orbital). Este implementa o método de orbitais moleculares nucleares e eletrônicos (OMNE) no nível da teoria Hartree-Fock (HF), onde tanto núcleos como elétrons se apresentam como funções de onda. Para comprovar a utilização correta do método, se realizaram cálculos da estrutura eletrônica regular e do núcleo eletrônico das moléculas H_2 y LiH. Os componentes de energia calculados seguem as tendências e estão na mesma ordem de magnitude de cálculos similares reportados na literatura. Diferentemente de outros pacotes que utilizam o método OMNE, o nosso foi desenhado para estudar sistemas de qualquer número de espécies quânticas.

Graph theoretical similarity approach to compare molecular electrostatic potentials.

In this work we introduce a graph theoretical method to compare MEPs, which is independent of molecular alignment. It is based on the edit distance of weighted rooted trees, which encode the geometrical and topological information of Negative Molecular Isopotential Surfaces. A meaningful chemical classification of a set of 46 molecules with different functional groups was achieved. Structure--activity relationships for the corticosteroid binding affinity (CBG) of 31 steroids by means of hierarchical clustering resulted in a clear partitioning in high, intermediate, and low activity groups, whereas the results from quantitative structure--activity relationships, obtained from a partial least-squares analysis, showed comparable or better cross-validated correlation coefficients than the ones reported for previous methods based solely in the MEP.