Engineering topics
Publications and source records attributed to Apra, Edoardo.
The electronic properties, fragmentation by collision-induced dissociation and bond properties of gaseous closo -[B 6 X 6 ] 2− (X = Cl, Br, I) dianions are discussed and compared to their larger-sized [B 12 X 12 ] 2− analogues.
The reduction of carbon dioxide to oxalate has been studied by experimental Collisionally Induced Dissociation (CID) and vibrational characterization of the alkali metal oxalates, supplemented by theoretical electronic structure calculations. The critical step in the reductive process is the coordination of the heterocumulene CO2 to an alkali metal anion, forming a metal carbonite MCO2 ablt to subsequently add a second CO2 molecule. While the energetic demand for these reactions is generally low, we find that the degree of activation of CO2 in terms of charge transfer and transition state energies is the highest for lithium and systematically decreases down the group (M - Li - Cs).
Partitioned Global Address Space (PGAS) models are part of system software that are being designed to support communication runtime for exascale applications. Suitability of using MPI as a scalable PGAS communication subsystem has been shown as a viable option due to its standardization and higher performance. We used MPI two-sided semantics with a combination of automatic and user defined splitting of MPI communicators to achieve asynchronous progress. Our implementation can make use of multiple asynchronous progress ranks (PR) per node that can be mapped to the computing architecture of a node in a distributed cluster. We are able to show significant speed up of over 2.0X and scaling of communication bound computational chemistry application over 1024 nodes of state- of-the-art HPC clusters. Our results show that while running a communication bound application workload on a certain number of cluster nodes, a use of optimum number of ranks dedicated for communication may be used to achieve asynchronous communication progress and obtain highest performance.
Photoelectron spectroscopy and theoretical investigations have been performed to systematically probe the intrinsic electronic properties of [Mo6X14]2− (X = halogen). All three PE spectra of gaseous [Mo6X14]2− (X = Cl, Br, I) dianions, which were generated by electrospray ionization, exhibit multiple resolved peaks in the recorded binding energy range. Theoretical investigations on the orbital structure and charge distribution were performed to support interpretation of the observed spectra and were further extended onto [Mo6F14]2−, a dianion that was not available for the experimental study. The measured adiabatic (ADE) and vertical detachment energies (VDE) for X = Cl–I were well reproduced by density functional theory calculations (accuracy ∼0.1 eV). Corresponding ADE/VDE values for the dianions were found to be 1.48/2.13 (calc.) and 2.30/2.65, 2.30/2.62, and 2.20/2.42 eV (all expt.) for X = F, Cl, Br, and I, respectively, showing an interesting buckled trend of electron binding energy (EBE) along the halogen series, i.e., EBE (F) ≪ EBE (Cl) ∼ EBE (Br) > EBE (I). Molecular orbital analyses indicate different mixing of metal and halogen atomic orbitals, which is strongly dependent on the nature of X, and suggest that the most loosely bound electrons are detached mainly from the metal core for X = F and Cl, but from halide ligands for X = Br and I. The repulsive Coulomb barrier (RCB), estimated from the photon energy dependent spectra, decreases with increasing halogen size, from 1.8 eV for X = Cl to 1.6 eV for X = I. Electrostatic potential modeling confirms the experimental RCB values and predicts that the most favorable electron detaching pathway should lie via the face-bridging halide ligands.
Molecular re-orientation dynamics modulate the physical and chemical properties of molecules at interfaces. This is particularly the case for organic molecules interacting with metallic surfaces - structural motifs of current interest to ultrasensitive chemical/biological detection/imaging. In this context, surface-enhanced Raman scattering (SERS) can be used to gauge the orientation of molecules in the immediate vicinity of plasmonic metals. Herein, we analyze SERS spectra of two aromatic thiols (4-mercaptobenzonitrile and thiophenol) chemisorbed onto silver substrates using ab initio molecular dynamics (AIMD)-based Raman spectral simulations that account for the optical response of molecules in the bulk and oriented molecules at the surface. Through a comparison with prior works aimed at gauging the orientation of our two model systems on metallic substrates, we describe the advantages and discuss the limitations of our described models and approach to gauging the orientation of molecules on metals through time-domain simulations of their SERS signatures.
We report a joint benchmark study on the electronic stability of closo-dodecaborate [B12H12]2- employing negative ion photoelectron spectroscopy and high level electronic structure methods. The photoelectron spectra of [B12H12]2-, measured at 266, 193 and 157 nm, yield the Adiabatic and Vertical Detachment Energies (ADE and VDE) of this dianion at 0.93 ± 0.05 eV and 1.15 ± 0.05 eV, respectively, along with a ~ 3 eV Repulsive Coulomb Barrier (RCB) against electron detachment. Theoretical calculations at various levels of electronic structure theory confirm the high stability of this dianion. The ADE and VDE values calculated at the CCSD(T)/aug-cc-PVQZ level are 0.92, and 1.16 eV, in excellent agreement with the experimental benchmark values. The comparison between the experimental and the theoretical values obtained at different levels of theory indicate that the PBE0 density functional represents a cost-effective method of sufficient accuracy to describe the molecular properties of this dianion and associated compounds. The theoretical RCB was modelled after the electrostatic potential (ESP) and point charge method (PCM) along three different detachment pathways, viz. along the B-H bond, perpendicular to a B-B bond, and normal to a B-B-B triangle. It was found that detachment of the electron along the B-H bond is preferred, as this pathway is associated with RCBs between 2.3 eV (PCM) and 3.3 eV (ESP), values that bracket the experimental estimate of ~ 3 eV.
Chemically binding argon (Ar) at room temperature has remained the privilege of the most reactive electrophiles, all of which are cationic (or even dicationic) in nature. Herein, we report a concept for the rational design of anionic superelectrophiles that comprise a strong electrophilic center firmly embedded in a negativelycharged framework of exceptional stability. To validate our concept, we synthesized the percyano-dodecoborate [B12(CN)12]2-, the electronically most stable dianion ever investigated experimentally. It serves as a precursor for the generation of the monoanion [B12(CN)11]-, which indeed spontaneously binds Ar at 298 K. Our mass spectrometric and spectroscopic studies are accompanied by high-level computational investigations including a bonding analysis of the exceptional B-Ar bond. The first detection and characterization of this highly reactive, structurally stable anionic superelectrophile starts a new chapter in the metal-free activation of particularly inert compounds and elements.
Anionic closo-borate anions [closo-BnXn]2- are part of the most famous textbook examples of polyhedral compounds. Substantial differences in their reactivity and interactions with other compounds depending on the substituent X and clustersize n have been recognized, which favors specific closo-borates for different applications in cancer treatment, chemical synthesis, and materials science. Surprisingly, a fundamental understanding of the molecular properties underlying these differences is lacking. Here, we report our study of electronic structure and reactivity of closo-borate anions [closo-BnXn]2- (X = Cl, Br, I, n = 10, 11, 12 in all combinations). We investigated the free dianions and the ion pairs [nBu4N]+[closo-BnXn]2- by gas phase anion photoelectron spectroscopy accompanied by theoretical investigations. Strong similarities in electronic structure for n = 10 and 11 were observed, while n = 12 clusters are different. A systematic picture of the development in electronic stability along the dimension X is derived. Collision induced dissociation shows that fragmentation of the free dianions is mainly dependent on the substituent X and gives access to a large variety of boron-rich molecular ions. Fragmentation of the ion pair depends strongly on n. The results reflect the high chemical stability of cluster with n = 10 and 12, while those with n = 11 are much easier prone to dissociation. We bridge our study to the condensed phase by performing comparative electrochemistry and reactivity studies on closo-borates in solution. The trends found at the molecular level are also reflected in the condensed-phase properties. We discuss how the gas phase values allow to evaluate the influence of the condensed phase on the electronic stability of closo-borates. A novel synthetic method via an oxidation/chlorination reaction yielding [closo-B10Cl10]2– from highly chlorinated {closo-B11} clusters is introduced, which underlines the intrinsically high reactivity of the {closo-B11} cage.
Non-equilibrium chemical phenomena are known to play an important role in single molecule microscopy and spectroscopy. Herein, we explore these effects through ab initio molecular dynamics (AIMD)-based Raman spectral simulations. We target an isolated aromatic thiol (thiobenzonitrile, TBN) as a prototypical molecular system. We first show that the essential features contained in the ensemble-averaged Raman spectrum of TBN can be reproduced by averaging over 18 short AIMD trajectories spanning a total simulation time of ~60 ps. This involved more than 90,000 polarizability calculations at the B3LYP/def2-TZVP level of theory. We then illustrate that the short trajectories (~3.3 ps total simulation time), where the accessible phase space is not fully sampled, provide a basis set for understanding key features that are often observed in measurements targeting single molecules. Our results suggest that a complete understanding of single molecule Raman scattering needs to account for molecular conformational flexibility and non-equilibrium chemical phenomena. These effects are well-captured using the described AIMD-based single molecule Raman spectral simulations.
Ions are promising building blocks for tunable self-organizing materials with advanced technological applications. However, because of strong Coulomb attraction with counterions, the intrinsic properties of ions are difficult to exploit for preparation of bulk materials. Here, we report the precisely-controlled preparation of macroscopic surface layers by soft landing of mass selected complex anions which determine the self organization of the layers with their molecular properties. The family of halogenated dodecaborates [B12X12]2- (X = F, Cl, Br, I), in which the internal charge distribution between core and shell regions of the molecular ions systematically vary, was deposited on different self assembled monolayer surfaces (SAMs) on gold at high coverage. Layers of anions were found to be stabilized by accumulation of neutral molecules. Different phases, self-organization mechanisms and optical properties were observed to depend upon the internal charge distribution of the deposited anions, the underlying surface and the coadsorbed molecules. This demonstrates rational control of the properties of anion based layers.
The NorthWest Chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers[6, 28, 49]. It contains an umbrella of modules that today includes Self Consistent Field (SCF), second order Mller-Plesset perturbation theory (MP2), Coupled Cluster, multi-conguration selfconsistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics, Car-Parrinello molecular dynamics, classical molecular dynamics (MD), QM/MM, AIMD/MM, GIAO NMR, COSMO, COSMO-SMD, and RISM solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities[ 22]. Moreover new capabilities continue to be added with each new release.
Here, several research groups have observed magnetism in monolayer-protected gold-cluster samples, but the results were often contradictory and thus a clear understanding of this phenomenon is still missing. We used Au 25 (SCH 2 CH 2 Ph) 18 0 , which is a paramagnetic cluster that can be prepared with atomic precision and whose structure is known precisely. Previous magnetometry studies only detected paramagnetism. We used samples representing a range of crystallographic orders and studied their magnetic behaviors by electron paramagnetic resonance (EPR). As a film, Au 25 (SCH 2 CH 2 Ph) 18 0 displays paramagnetic behavior but, at low temperature, ferromagnetic interactions are detectable. One or few single crystals undergo physical reorientation with the applied field and display ferromagnetism, as detected through hysteresis experiments. A large collection of microcrystals is magnetic even at room temperature and shows distinct paramagnetic, superparamagnetic, and ferromagnetic behaviors. Simulation of the EPR spectra shows that both spin-orbit coupling and crystal distortion are important to determine the observed magnetic behaviors. DFT calculations carried out on single cluster and periodic models predict values of spin6orbit coupling and crystal6splitting effects in agreement with the EPR derived quantities. Magnetism in gold nanoclusters is thus demonstrated to be the outcome of a very delicate balance of factors. To obtain reproducible results, the samples must be (i) controlled for composition and thus be monodispersed with atomic precision, (ii) of known charge state, and (iii) well defined also in terms of crystallinity and experimental conditions. This study highlights the efficacy of EPR spectroscopy to provide a molecular understanding of these phenomena
Simulating the spectroscopic properties of short-lived thermal and photochemical reaction intermediates and products is a challenging task, as these species often feature atypical molecular and electronic structures. The complex environments in which such species typically reside in practice add further complexity to the problem. Herein, we tackle this problem in silico using ab initio molecular dynamics (AIMD) simulations, employing iso-CHBr3, namely H(Br)C-Br-Br, as a prototypical system. This species was chosen because it features both a non-conventional C-Br-Br bonding pattern, as well as a strong dependence of its spectral features on the local environment in which it resides, as illustrated in recent experimental reports. The spectroscopic properties of iso-CHBr3 were measured by several groups that captured this transient intermediate in the photochemistry of CHBr3 in the gas phase, in rare gas matrices at 5K, and in solution under ambient laboratory conditions. We simulate the UV-Vis and IR spectra of iso-CHBr3 in all three media, including a Ne cluster (64 atoms) and a methylcyclohexane cage (14 solvent molecules) representative of the matrix isolated and solvated species. We exclusively perform fully quantum mechanical static and dynamic simulations. By comparing our condensed phase simulations to their experimental analogues, we stress the importance of (i) conformational sampling, even at cryogenic temperatures, and (ii) using a fully quantum mechanical description of both solute and bath to properly account for the experimental observables.
Lithium clusters Lin (n=1-20) have been investigated with density functional theory (DFT) and coupled—cluster (CC) methods. The global-minimum structures are located via an improved basin---hopping algorithm and the lowest energy Lin isomers are confirmed with DFT geometry optimizations, CCSD(T) energy calculations, and by comparing simulated and experimental polarizabilities. The tetrahedral Li4 structure is found to be the basic building block of lithium clusters Lin (n=6-20). Simulated polarizabilities, including thermal effects at room temperature, are in good agreement with measured isotropic polarizabilities.
Methods based on quantum mechanics equations have been developed since the 1930's with the purpose of accurately studying the electronic structure of molecules. However, it is only during the last two decades that intense development of new computational algorithms has opened the possibility of performing accurate simulations of challenging molecular processes with high-order many-body methods. A wealth of evidence indicates that the proper inclusion of instantaneous interactions between electrons (or the so-called electron correlation effects) is indispensable for the accurate characterization of chemical reactivity, molecular properties, and interactions of light with matter. The availability of reliable methods for benchmarking of medium-size molecular systems provides also a unique chance to propagate high-level accuracy across spatial scales through the multiscale methodologies. Some of these methods have potential to utilize computational resources in an effi*cient way since they are characterized by high numerical complexity and appropriate level of data granularity, which can be effi*ciently distributed over multi-processor architectures. The broad spectrum of coupled cluster (CC) methods falls into this class of methodologies. Several recent CC implementations clearly demonstrated the scalability of CC formalisms on architectures composed of hundreds thousand computational cores. In this context NWChem provides a collection of Tensor Contraction Engine (TCE) generated parallel implementations of various coupled cluster methods capable of taking advantage of many thousand of cores on leadership class parallel architectures.
This paper presents the implementation and performance of the highly accurate CCSD(T) quantum chemistry method on the Intel Xeon Phi coprocessor within the context of the NWChem computational chemistry package. The widespread use of highly correlated methods in electronic structure calculations is contingent upon the interplay between advances in theory and the possibility of utilizing the ever-growing computer power of emerging heterogeneous architectures. We discuss the design decisions of our implementation as well as the optimizations applied to the compute kernels and data transfers between host and coprocessor. We show the feasibility of adopting the Intel Many Integrated Core Architecture and the Intel Xeon Phi coprocessor for developing efficient computational chemistry modeling tools. Remarkable scalability is demonstrated by benchmarks. Our solution scales up to a total of 62560 cores with the concurrent utilization of Intel Xeon processors and Intel Xeon Phi coprocessors.
In this paper we discuss the application of novel parallel implementation of the coupled cluster (CC) and equation-of-motion coupled cluster methods (EOMCC) in calculations of excitation energies of triplet states in beta-carotene. Calculated excitation energies are compared with experimental data, where available. We also provide a detailed description of the new parallel algorithms for iterative CC and EOMCC models involving single and doubles excitations.
Attaining performance in the evaluation of two-electron repulsion integrals and constructing the Fock matrix is of considerable importance to the computational chemistry community. Due to its numerical complexity improving the performance behavior across a variety of leading supercomputing platforms is an increasing challenge due to the significant diversity in high-performance computing architectures. In this paper, we present our successful tuning methodology for these important numerical methods on the Cray XE6, the Cray XC30, the IBM BG/Q, as well as the Intel Xeon Phi. Our optimization schemes leverage key architectural features including vectorization and simultaneous multithreading, and results in speedups of up to 2.5x compared with the original implementation.